Query gi|254780424|ref|YP_003064837.1| transcriptional regulator protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 144
No_of_seqs 111 out of 3925
Neff 8.2
Searched_HMMs 39220
Date Sun May 29 16:15:01 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780424.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09706 transcriptional repre 99.8 3.8E-20 9.7E-25 149.2 14.0 123 14-142 5-127 (135)
2 PRK09943 DNA-binding transcrip 99.7 1.6E-16 4E-21 126.1 8.2 68 12-79 5-72 (185)
3 PHA01976 helix-turn-helix prot 99.7 4.4E-16 1.1E-20 123.2 8.0 64 14-77 2-65 (67)
4 PRK13890 conjugal transfer pro 99.4 8.2E-13 2.1E-17 102.3 6.8 62 16-77 7-68 (119)
5 TIGR03070 couple_hipB transcri 99.4 1.1E-12 2.7E-17 101.6 6.6 57 14-70 2-58 (58)
6 smart00530 HTH_XRE Helix-turn- 99.4 1.5E-12 3.8E-17 100.6 6.2 56 18-73 1-56 (56)
7 pfam01381 HTH_3 Helix-turn-hel 99.4 1.4E-12 3.6E-17 100.7 6.1 55 19-73 1-55 (55)
8 PRK08154 anaerobic benzoate ca 99.4 2.5E-11 6.3E-16 92.8 12.4 74 5-78 19-92 (304)
9 COG1476 Predicted transcriptio 99.3 1.1E-11 2.9E-16 95.0 6.9 60 18-77 5-64 (68)
10 cd00093 HTH_XRE Helix-turn-hel 99.2 2E-11 5.1E-16 93.4 6.3 58 16-73 1-58 (58)
11 PRK09726 DNA-binding transcrip 99.2 5.2E-11 1.3E-15 90.7 8.2 68 1-70 1-68 (88)
12 COG3620 Predicted transcriptio 98.9 3.9E-09 1E-13 78.7 6.3 55 7-67 4-58 (187)
13 PRK06424 transcription factor; 98.8 1.1E-08 2.8E-13 75.9 6.3 57 14-70 84-140 (144)
14 PRK08359 transcription factor; 98.8 1.5E-08 3.7E-13 75.0 6.2 58 14-71 83-140 (175)
15 PRK04140 hypothetical protein; 98.8 1.7E-08 4.2E-13 74.7 6.5 57 16-72 127-183 (319)
16 COG1813 Predicted transcriptio 98.8 1.2E-08 3.1E-13 75.6 5.8 67 14-80 79-145 (165)
17 PRK13355 bifunctional HTH-doma 98.6 2.5E-07 6.3E-12 67.2 7.5 67 14-80 5-76 (518)
18 COG2944 Predicted transcriptio 98.5 2.2E-07 5.7E-12 67.4 5.7 46 15-60 45-90 (104)
19 TIGR02612 mob_myst_A mobile my 98.4 8.2E-07 2.1E-11 63.8 7.0 112 18-131 29-144 (150)
20 COG1395 Predicted transcriptio 98.4 7.5E-07 1.9E-11 64.1 6.0 56 16-71 127-182 (313)
21 TIGR02607 antidote_HigA addict 98.3 5.9E-07 1.5E-11 64.7 4.4 64 13-76 5-69 (81)
22 COG3093 VapI Plasmid maintenan 98.3 2.4E-06 6.1E-11 60.9 6.9 64 13-76 8-72 (104)
23 COG1396 HipB Predicted transcr 98.3 3.8E-06 9.7E-11 59.6 7.6 64 15-78 2-66 (120)
24 COG1709 Predicted transcriptio 98.2 1.2E-06 3.2E-11 62.7 3.5 53 14-66 27-80 (241)
25 PRK10072 putative transcriptio 98.2 3.8E-06 9.8E-11 59.5 5.6 47 17-63 36-82 (96)
26 KOG3398 consensus 98.1 4.4E-06 1.1E-10 59.2 5.0 66 7-72 66-131 (135)
27 COG1426 Predicted transcriptio 98.1 8E-06 2E-10 57.5 5.9 68 14-81 3-76 (284)
28 pfam07022 Phage_CI_repr Bacter 98.0 2.5E-05 6.4E-10 54.3 6.9 61 19-80 3-64 (65)
29 TIGR00270 TIGR00270 conserved 98.0 1.2E-05 3.2E-10 56.3 4.8 62 15-76 84-145 (169)
30 PRK10856 hypothetical protein; 97.9 4E-05 1E-09 53.0 6.7 65 14-78 14-84 (332)
31 COG3655 Predicted transcriptio 97.9 3.4E-05 8.6E-10 53.5 5.8 65 15-79 3-68 (73)
32 COG5499 Predicted transcriptio 97.8 6.1E-05 1.6E-09 51.8 6.5 64 5-74 56-119 (120)
33 TIGR02684 dnstrm_HI1420 probab 97.3 0.00024 6.2E-09 48.0 4.1 51 18-70 38-88 (91)
34 COG2522 Predicted transcriptio 96.8 0.002 5.1E-08 42.1 4.6 35 19-54 15-49 (119)
35 pfam08667 BetR BetR domain. Th 96.7 0.011 2.9E-07 37.3 7.7 64 13-76 4-71 (146)
36 COG4800 Predicted transcriptio 96.3 0.011 2.9E-07 37.3 5.9 52 14-66 16-67 (170)
37 PRK02866 cyanate hydratase; Va 96.2 0.034 8.6E-07 34.3 7.8 60 14-73 5-64 (147)
38 TIGR02846 spore_sigmaK RNA pol 96.2 0.002 5E-08 42.2 1.4 26 25-50 193-218 (228)
39 smart00352 POU Found in Pit-Oc 96.1 0.014 3.5E-07 36.8 5.4 54 8-63 4-64 (75)
40 TIGR02980 SigBFG RNA polymeras 95.8 0.0056 1.4E-07 39.3 2.3 49 13-77 80-128 (229)
41 PRK10014 DNA-binding transcrip 95.6 0.017 4.4E-07 36.1 4.3 49 25-73 4-55 (342)
42 COG3636 Predicted transcriptio 95.6 0.037 9.4E-07 34.0 5.9 55 15-71 39-93 (100)
43 PRK09492 treR trehalose repres 95.6 0.019 4.8E-07 35.9 4.3 49 25-73 2-53 (315)
44 pfam00157 Pou Pou domain - N-t 95.5 0.036 9.2E-07 34.1 5.5 53 8-62 4-63 (75)
45 PHA00542 putative Cro-like pro 95.5 0.034 8.6E-07 34.3 5.3 48 18-65 22-70 (82)
46 PRK03975 tfx putative transcri 95.2 0.017 4.4E-07 36.1 2.9 49 21-70 14-64 (139)
47 PRK09526 lacI lac repressor; R 95.1 0.034 8.8E-07 34.2 4.3 49 25-73 3-54 (342)
48 KOG3802 consensus 94.9 0.064 1.6E-06 32.5 5.3 59 7-67 202-267 (398)
49 COG3423 Nlp Predicted transcri 94.8 0.092 2.4E-06 31.5 5.9 57 18-77 12-68 (82)
50 pfam00356 LacI Bacterial regul 94.7 0.06 1.5E-06 32.7 4.7 40 29-68 1-43 (46)
51 PRK11303 DNA-binding transcrip 94.7 0.062 1.6E-06 32.6 4.6 46 28-73 1-52 (330)
52 PRK10401 DNA-binding transcrip 94.7 0.064 1.6E-06 32.5 4.7 46 28-73 2-50 (346)
53 PRK08099 nicotinamide-nucleoti 94.6 0.13 3.4E-06 30.5 6.2 56 17-72 5-61 (411)
54 smart00354 HTH_LACI helix_turn 94.4 0.078 2E-06 32.0 4.7 45 29-73 2-49 (70)
55 COG5606 Uncharacterized conser 94.4 0.052 1.3E-06 33.1 3.7 59 13-71 27-86 (91)
56 COG2390 DeoR Transcriptional r 94.4 0.11 2.9E-06 30.9 5.5 60 14-73 13-85 (321)
57 PRK10727 DNA-binding transcrip 94.4 0.078 2E-06 31.9 4.6 45 29-73 3-50 (342)
58 PRK11041 DNA-binding transcrip 94.3 0.084 2.1E-06 31.7 4.6 46 28-73 10-58 (341)
59 PRK10344 DNA-binding transcrip 94.1 0.16 4.2E-06 29.9 5.8 65 8-76 3-67 (90)
60 PRK10703 DNA-binding transcrip 94.1 0.095 2.4E-06 31.4 4.6 45 29-73 3-50 (335)
61 PRK10339 DNA-binding transcrip 94.0 0.1 2.7E-06 31.1 4.7 42 29-70 3-49 (327)
62 COG1609 PurR Transcriptional r 94.0 0.1 2.5E-06 31.3 4.5 46 28-73 1-49 (333)
63 pfam08965 DUF1870 Domain of un 93.9 0.13 3.4E-06 30.4 5.1 48 18-65 4-53 (117)
64 TIGR00721 tfx DNA-binding prot 93.8 0.039 9.8E-07 33.9 2.1 48 25-72 19-68 (142)
65 TIGR01321 TrpR trp operon repr 93.7 0.083 2.1E-06 31.8 3.6 34 14-47 41-76 (95)
66 COG1356 tfx Transcriptional re 93.6 0.038 9.8E-07 33.9 1.9 51 24-74 20-72 (143)
67 COG4197 Uncharacterized protei 93.5 0.06 1.5E-06 32.7 2.7 46 29-74 14-61 (96)
68 pfam07037 DUF1323 Putative tra 93.4 0.084 2.2E-06 31.7 3.3 23 28-50 1-23 (122)
69 TIGR02885 spore_sigF RNA polym 93.4 0.024 6.1E-07 35.2 0.5 39 14-52 94-139 (231)
70 TIGR02959 SigZ RNA polymerase 93.3 0.024 6.2E-07 35.2 0.4 33 22-54 111-144 (170)
71 TIGR01950 SoxR redox-sensitive 93.0 0.15 3.8E-06 30.2 4.1 47 28-74 2-64 (142)
72 PRK08558 adenine phosphoribosy 92.9 0.28 7E-06 28.4 5.3 54 22-75 17-73 (238)
73 pfam04814 HNF-1_N Hepatocyte n 92.6 0.35 9E-06 27.7 5.6 46 14-59 115-160 (177)
74 PRK10423 transcriptional repre 92.6 0.2 5E-06 29.4 4.2 43 31-73 2-47 (327)
75 KOG1168 consensus 92.5 0.087 2.2E-06 31.6 2.3 44 8-51 214-267 (385)
76 COG1191 FliA DNA-directed RNA 92.5 0.18 4.5E-06 29.7 3.9 57 13-74 84-144 (247)
77 pfam01371 Trp_repressor Trp re 92.5 0.18 4.6E-06 29.6 3.9 37 14-50 34-72 (88)
78 pfam02001 DUF134 Protein of un 92.1 0.1 2.6E-06 31.1 2.4 42 18-66 41-84 (100)
79 PRK07773 replicative DNA helic 91.9 0.25 6.3E-06 28.7 4.1 56 12-70 709-764 (868)
80 PRK11179 DNA-binding transcrip 91.8 0.41 1.1E-05 27.3 5.2 41 1-45 1-41 (153)
81 cd01392 HTH_LacI Helix-turn-he 91.8 0.22 5.5E-06 29.1 3.6 40 31-70 1-43 (52)
82 cd00569 HTH_Hin_like Helix-tur 91.6 0.27 6.8E-06 28.5 4.0 30 18-47 10-41 (42)
83 PHA00675 hypothetical protein 91.6 0.35 9E-06 27.7 4.6 47 4-54 20-69 (78)
84 COG1513 CynS Cyanate lyase [In 91.6 1.2 3E-05 24.4 7.4 68 8-76 3-70 (151)
85 COG2973 TrpR Trp operon repres 91.5 0.57 1.5E-05 26.4 5.6 52 14-65 45-98 (103)
86 pfam05339 DUF739 Protein of un 91.3 0.72 1.8E-05 25.8 5.9 57 17-73 6-62 (69)
87 COG2842 Uncharacterized ATPase 91.3 0.36 9.2E-06 27.7 4.3 57 14-71 6-63 (297)
88 TIGR02835 spore_sigmaE RNA pol 91.2 0.15 3.8E-06 30.2 2.3 24 27-50 198-221 (234)
89 PRK12529 RNA polymerase sigma 91.1 0.24 6E-06 28.8 3.3 51 14-67 22-80 (178)
90 PRK01381 Trp operon repressor; 90.9 0.25 6.4E-06 28.7 3.2 52 14-65 40-93 (99)
91 pfam04545 Sigma70_r4 Sigma-70, 90.5 0.29 7.3E-06 28.3 3.2 34 17-50 10-43 (50)
92 PRK04217 hypothetical protein; 90.4 0.2 5.1E-06 29.3 2.4 42 18-66 47-90 (110)
93 PRK11169 leucine-responsive tr 89.9 0.87 2.2E-05 25.2 5.3 45 1-45 1-46 (164)
94 PRK07408 RNA polymerase sigma 89.4 0.49 1.2E-05 26.8 3.8 19 29-47 131-149 (256)
95 pfam05269 Phage_CII Bacterioph 89.4 0.27 7E-06 28.4 2.4 41 27-69 23-63 (91)
96 PRK07122 RNA polymerase sigma 89.0 0.54 1.4E-05 26.6 3.7 18 29-46 144-161 (263)
97 COG1342 Predicted DNA-binding 88.9 0.37 9.5E-06 27.6 2.8 42 18-66 38-81 (99)
98 PRK08301 sporulation sigma fac 88.9 0.5 1.3E-05 26.8 3.5 11 25-35 79-89 (239)
99 cd04762 HTH_MerR-trunc Helix-T 88.7 0.33 8.3E-06 28.0 2.4 23 28-50 1-23 (49)
100 PRK05572 sporulation sigma fac 88.7 0.55 1.4E-05 26.5 3.6 18 29-46 134-151 (251)
101 PRK12427 flagellar biosynthesi 88.6 0.55 1.4E-05 26.5 3.5 31 17-47 103-135 (229)
102 PRK08583 RNA polymerase sigma 88.6 0.59 1.5E-05 26.3 3.7 19 29-47 134-152 (257)
103 TIGR02147 Fsuc_second hypothet 88.5 0.28 7.2E-06 28.3 2.0 52 22-73 20-78 (281)
104 PRK06288 RNA polymerase sigma 88.3 0.59 1.5E-05 26.3 3.5 20 28-47 131-150 (261)
105 cd04766 HTH_HspR Helix-Turn-He 88.1 1.5 3.9E-05 23.7 5.5 27 28-54 2-29 (91)
106 TIGR00673 cynS cyanate hydrata 88.0 2 5.2E-05 22.8 6.1 63 14-76 13-75 (156)
107 TIGR02937 sigma70-ECF RNA poly 88.0 0.77 2E-05 25.6 3.9 33 17-49 120-152 (162)
108 PRK08215 sporulation sigma fac 87.9 0.69 1.8E-05 25.9 3.7 16 29-44 141-156 (257)
109 PRK12528 RNA polymerase sigma 87.5 0.9 2.3E-05 25.1 4.0 49 14-66 19-71 (167)
110 PRK12525 RNA polymerase sigma 87.3 0.67 1.7E-05 26.0 3.3 52 14-69 18-73 (168)
111 PRK12523 RNA polymerase sigma 87.1 1 2.6E-05 24.8 4.1 52 13-68 18-73 (172)
112 cd04781 HTH_MerR-like_sg6 Heli 86.9 1.8 4.7E-05 23.2 5.4 46 28-73 1-62 (120)
113 pfam08535 KorB KorB domain. Th 86.6 0.49 1.2E-05 26.8 2.3 30 25-54 1-30 (93)
114 PRK07670 RNA polymerase sigma 86.3 0.81 2.1E-05 25.4 3.3 20 28-47 122-141 (250)
115 PRK06986 fliA flagellar biosyn 86.0 0.87 2.2E-05 25.2 3.3 20 29-48 113-132 (234)
116 smart00419 HTH_CRP helix_turn_ 85.9 0.6 1.5E-05 26.3 2.4 24 25-48 6-29 (48)
117 PRK05911 RNA polymerase sigma 85.9 0.86 2.2E-05 25.2 3.3 30 21-50 118-149 (257)
118 pfam01047 MarR MarR family. Th 85.3 0.92 2.3E-05 25.1 3.2 31 18-48 8-38 (59)
119 COG2512 Predicted membrane-ass 85.1 0.86 2.2E-05 25.3 2.9 32 17-48 199-231 (258)
120 COG1974 LexA SOS-response tran 84.9 0.8 2E-05 25.5 2.7 55 20-75 5-59 (201)
121 cd01108 HTH_CueR Helix-Turn-He 84.7 2.6 6.6E-05 22.2 5.2 46 28-73 1-63 (127)
122 cd04768 HTH_BmrR-like Helix-Tu 84.7 3 7.7E-05 21.8 5.6 46 28-73 1-63 (96)
123 COG1737 RpiR Transcriptional r 84.6 3.3 8.4E-05 21.5 8.1 60 10-69 18-79 (281)
124 PRK11512 DNA-binding transcrip 84.5 1.1 2.8E-05 24.6 3.2 28 19-46 46-73 (144)
125 pfam04967 HTH_10 HTH DNA bindi 84.2 0.84 2.1E-05 25.3 2.6 24 26-49 22-45 (53)
126 PRK03573 transcriptional regul 84.2 1.1 2.9E-05 24.5 3.2 28 20-47 38-66 (144)
127 PRK06930 positive control sigm 84.1 1.6 4E-05 23.6 3.9 18 40-58 40-58 (170)
128 pfam02084 Bindin Bindin. 84.1 3.5 8.9E-05 21.4 5.7 70 45-124 90-159 (239)
129 PRK09954 hypothetical protein; 83.7 1.3 3.3E-05 24.1 3.3 29 19-47 9-37 (362)
130 cd04782 HTH_BltR Helix-Turn-He 83.6 3.6 9.2E-05 21.3 5.6 47 28-74 1-64 (97)
131 TIGR02405 trehalos_R_Ecol treh 83.6 0.36 9.3E-06 27.7 0.5 42 27-68 1-42 (311)
132 TIGR02999 Sig-70_X6 RNA polyme 83.5 1.2 3E-05 24.4 3.1 30 17-46 151-180 (194)
133 COG0789 SoxR Predicted transcr 83.2 2.4 6.2E-05 22.4 4.6 46 28-73 1-63 (124)
134 COG3415 Transposase and inacti 83.1 1 2.6E-05 24.8 2.6 29 22-50 16-44 (138)
135 cd00092 HTH_CRP helix_turn_hel 83.1 2.3 5.9E-05 22.5 4.4 25 24-48 22-46 (67)
136 pfam08279 HTH_11 HTH domain. T 82.9 1.4 3.7E-05 23.8 3.3 31 18-48 5-36 (55)
137 pfam07638 Sigma70_ECF ECF sigm 82.8 1.8 4.7E-05 23.1 3.8 12 39-50 53-64 (185)
138 PRK07037 extracytoplasmic-func 82.7 2.1 5.2E-05 22.8 4.1 15 57-73 64-78 (183)
139 TIGR02997 Sig70-cyanoRpoD RNA 82.5 2.9 7.3E-05 21.9 4.7 41 13-73 190-230 (336)
140 cd04774 HTH_YfmP Helix-Turn-He 82.5 4 0.0001 21.0 5.6 22 28-49 1-22 (96)
141 PRK07500 rpoH2 RNA polymerase 82.4 1.1 2.7E-05 24.6 2.5 20 30-49 151-170 (289)
142 cd06171 Sigma70_r4 Sigma70, re 82.2 2.2 5.7E-05 22.6 4.1 33 17-49 16-48 (55)
143 smart00347 HTH_MARR helix_turn 82.0 1.7 4.3E-05 23.4 3.4 33 17-49 14-46 (101)
144 PHA01083 hypothetical protein 81.7 3.7 9.4E-05 21.2 5.1 60 17-76 3-64 (153)
145 PRK09744 DNA-binding transcrip 81.7 1 2.6E-05 24.8 2.1 43 29-73 12-57 (75)
146 pfam01710 Transposase_14 Trans 81.4 4.4 0.00011 20.7 7.2 32 17-49 9-40 (120)
147 pfam04552 Sigma54_DBD Sigma-54 81.2 0.85 2.2E-05 25.3 1.6 44 25-77 47-91 (160)
148 cd01110 HTH_SoxR Helix-Turn-He 81.2 4.3 0.00011 20.8 5.2 47 27-73 1-63 (139)
149 PRK11753 cAMP-regulatory prote 80.3 1.3 3.4E-05 24.1 2.4 20 28-47 169-188 (211)
150 COG1522 Lrp Transcriptional re 80.3 3.2 8.1E-05 21.6 4.3 37 7-46 5-41 (154)
151 PRK10227 DNA-binding transcrip 80.3 3.7 9.4E-05 21.2 4.6 46 28-73 1-63 (135)
152 PRK09651 RNA polymerase sigma 80.0 3 7.7E-05 21.8 4.1 53 13-69 18-74 (172)
153 PRK11302 DNA-binding transcrip 79.9 5 0.00013 20.4 6.4 56 13-68 19-76 (284)
154 PRK12527 RNA polymerase sigma 79.9 3 7.5E-05 21.8 4.0 33 31-64 19-54 (159)
155 pfam07471 Phage_Nu1 Phage DNA 79.8 1.5 3.9E-05 23.7 2.5 24 26-49 1-24 (164)
156 PRK05932 RNA polymerase factor 79.7 1.2 3.1E-05 24.3 2.0 42 26-76 348-390 (461)
157 PRK11161 fumarate/nitrate redu 79.7 1.5 3.7E-05 23.8 2.4 22 27-48 184-205 (235)
158 pfam01527 Transposase_8 Transp 79.5 1.6 4E-05 23.6 2.6 27 24-50 20-46 (75)
159 TIGR02850 spore_sigG RNA polym 79.3 1.6 4.2E-05 23.5 2.6 59 10-74 91-154 (254)
160 pfam02376 CUT CUT domain. The 79.2 4.7 0.00012 20.5 4.9 37 13-49 6-43 (81)
161 PRK12469 RNA polymerase factor 78.9 1.2 3.1E-05 24.3 1.8 43 25-76 361-404 (475)
162 PRK05657 RNA polymerase sigma 78.7 2.8 7E-05 22.0 3.6 24 27-50 192-215 (328)
163 PRK09391 fixK transcriptional 78.4 1.8 4.5E-05 23.2 2.5 23 25-47 171-193 (224)
164 PRK05803 sporulation sigma fac 78.2 2.8 7.1E-05 22.0 3.5 10 26-35 71-80 (228)
165 PRK13752 putative transcriptio 78.0 5.6 0.00014 20.0 5.1 49 25-73 5-70 (144)
166 TIGR01764 excise DNA binding d 78.0 1.4 3.5E-05 24.0 1.9 27 28-54 2-28 (49)
167 pfam05930 Phage_AlpA Prophage 78.0 2.3 5.9E-05 22.5 3.0 32 28-59 4-35 (51)
168 TIGR01817 nifA Nif-specific re 77.7 2.7 7E-05 22.0 3.3 37 7-46 526-562 (574)
169 pfam08281 Sigma70_r4_2 Sigma-7 77.6 3.5 9E-05 21.3 3.9 31 17-47 16-46 (54)
170 cd01104 HTH_MlrA-CarA Helix-Tu 77.5 2.5 6.3E-05 22.3 3.1 22 28-49 1-22 (68)
171 TIGR02417 fruct_sucro_rep D-fr 77.3 1.3 3.4E-05 24.1 1.6 46 29-74 1-52 (335)
172 pfam07750 GcrA GcrA cell cycle 77.2 2 5E-05 23.0 2.5 32 17-48 6-41 (162)
173 PRK13918 CRP/FNR family transc 77.1 1.9 4.9E-05 23.0 2.4 23 26-48 144-166 (201)
174 pfam01418 HTH_6 Helix-turn-hel 77.1 3.8 9.7E-05 21.1 3.9 59 10-68 16-76 (106)
175 PRK11337 DNA-binding transcrip 77.1 6 0.00015 19.9 6.5 46 22-67 42-88 (293)
176 pfam10668 Phage_terminase Phag 77.1 1.4 3.5E-05 23.9 1.7 25 26-50 21-45 (60)
177 smart00344 HTH_ASNC helix_turn 77.0 3 7.7E-05 21.8 3.4 35 9-46 2-36 (108)
178 PRK09480 slmA nucleoid occlusi 76.9 6.1 0.00016 19.8 5.0 61 15-75 15-78 (194)
179 pfam04645 DUF603 Protein of un 76.8 2.9 7.4E-05 21.9 3.2 39 17-57 10-53 (181)
180 TIGR00491 aIF-2 translation in 76.4 0.74 1.9E-05 25.7 0.1 48 15-68 415-462 (1145)
181 PRK06596 RNA polymerase factor 76.1 2.2 5.6E-05 22.6 2.5 31 19-49 139-173 (284)
182 TIGR02985 Sig70_bacteroi1 RNA 76.1 3.2 8.1E-05 21.6 3.3 41 30-73 24-68 (167)
183 pfam05225 HTH_psq helix-turn-h 75.6 6.3 0.00016 19.7 4.7 38 15-53 5-42 (45)
184 pfam09048 Cro Cro. Members of 75.6 3.6 9.2E-05 21.3 3.5 36 19-56 5-40 (58)
185 COG1654 BirA Biotin operon rep 75.1 3.9 9.8E-05 21.1 3.5 29 19-47 9-39 (79)
186 cd04767 HTH_HspR-like_MBC Heli 74.5 7 0.00018 19.4 5.6 46 28-73 2-63 (120)
187 PRK09646 RNA polymerase sigma 74.5 7 0.00018 19.4 6.1 50 12-64 37-91 (194)
188 cd04761 HTH_MerR-SF Helix-Turn 74.3 2.5 6.4E-05 22.3 2.4 23 28-50 1-23 (49)
189 pfam02796 HTH_7 Helix-turn-hel 74.2 3.7 9.4E-05 21.2 3.2 32 18-50 13-44 (45)
190 PRK09775 hypothetical protein; 74.0 3.6 9.3E-05 21.2 3.2 31 18-48 3-33 (443)
191 pfam02954 HTH_8 Bacterial regu 74.0 5.1 0.00013 20.3 3.9 30 17-46 8-37 (42)
192 pfam04760 IF2_N Translation in 73.8 7.3 0.00019 19.3 4.7 44 26-69 2-52 (52)
193 cd01105 HTH_GlnR-like Helix-Tu 73.6 3.8 9.8E-05 21.1 3.2 23 28-50 2-24 (88)
194 cd04773 HTH_TioE_rpt2 Second H 73.5 2.8 7.1E-05 22.0 2.5 46 28-73 1-63 (108)
195 pfam04218 CENP-B_N CENP-B N-te 73.3 3 7.7E-05 21.8 2.6 36 17-52 11-47 (53)
196 smart00422 HTH_MERR helix_turn 73.1 2.9 7.3E-05 21.9 2.4 24 28-51 1-24 (70)
197 cd04780 HTH_MerR-like_sg5 Heli 73.0 2.9 7.3E-05 21.9 2.4 24 28-51 1-24 (95)
198 COG5484 Uncharacterized conser 72.8 2.5 6.5E-05 22.2 2.1 31 23-53 15-45 (279)
199 cd01107 HTH_BmrR Helix-Turn-He 72.8 3 7.6E-05 21.8 2.5 46 28-73 1-64 (108)
200 PRK09514 zntR zinc-responsive 72.7 7.7 0.0002 19.2 4.8 46 28-73 2-64 (140)
201 PHA01082 putative transcriptio 72.5 7.8 0.0002 19.1 6.0 48 25-72 28-78 (133)
202 COG3413 Predicted DNA binding 72.4 3.1 7.9E-05 21.7 2.5 17 54-70 176-192 (215)
203 TIGR02941 Sigma_B RNA polymera 72.2 1.8 4.5E-05 23.3 1.2 49 13-77 106-154 (256)
204 cd04763 HTH_MlrA-like Helix-Tu 72.0 3.7 9.3E-05 21.2 2.8 22 28-49 1-22 (68)
205 PRK13182 racA polar chromosome 71.9 8.1 0.00021 19.0 8.6 35 28-62 1-46 (178)
206 cd06170 LuxR_C_like C-terminal 71.7 3.7 9.4E-05 21.2 2.7 28 23-50 11-38 (57)
207 cd04790 HTH_Cfa-like_unk Helix 71.5 4.6 0.00012 20.6 3.2 47 28-74 2-65 (172)
208 PRK09392 ftrB transcriptional 71.4 3.4 8.7E-05 21.4 2.5 21 27-47 173-193 (236)
209 pfam00376 MerR MerR family reg 71.1 3.2 8.3E-05 21.6 2.3 25 29-53 1-25 (38)
210 cd01111 HTH_MerD Helix-Turn-He 71.0 8.4 0.00022 18.9 5.1 46 28-73 1-63 (107)
211 PRK12516 RNA polymerase sigma 70.9 4 0.0001 21.0 2.8 33 14-49 22-54 (190)
212 PRK05472 redox-sensing transcr 70.8 8.5 0.00022 18.9 5.2 72 1-72 1-85 (211)
213 PRK09834 DNA-binding transcrip 70.6 8.6 0.00022 18.9 4.6 30 19-48 17-47 (264)
214 PRK09637 RNA polymerase sigma 70.1 6.1 0.00016 19.8 3.6 56 13-73 9-68 (181)
215 cd04787 HTH_HMRTR_unk Helix-Tu 69.8 3.8 9.6E-05 21.2 2.4 46 28-73 1-63 (133)
216 cd04789 HTH_Cfa Helix-Turn-Hel 69.7 3.7 9.4E-05 21.2 2.4 47 28-74 2-64 (102)
217 PRK13919 putative RNA polymera 69.6 8.2 0.00021 19.0 4.1 58 11-73 29-91 (187)
218 PRK11924 RNA polymerase sigma 69.5 7.8 0.0002 19.1 4.0 18 31-49 37-54 (180)
219 COG1595 RpoE DNA-directed RNA 69.2 5.5 0.00014 20.1 3.2 59 11-73 21-82 (182)
220 COG1318 Predicted transcriptio 69.2 5.7 0.00015 20.0 3.3 32 22-53 56-87 (182)
221 pfam00196 GerE Bacterial regul 69.2 4.5 0.00011 20.7 2.7 26 24-49 15-40 (58)
222 cd04785 HTH_CadR-PbrR-like Hel 69.0 4 0.0001 21.0 2.5 46 28-73 1-63 (126)
223 smart00421 HTH_LUXR helix_turn 69.0 4.5 0.00011 20.7 2.7 27 23-49 14-40 (58)
224 cd04770 HTH_HMRTR Helix-Turn-H 68.9 4 0.0001 21.0 2.4 46 28-73 1-63 (123)
225 cd04764 HTH_MlrA-like_sg1 Heli 68.8 4.1 0.0001 20.9 2.4 23 28-50 1-23 (67)
226 COG1508 RpoN DNA-directed RNA 68.5 4.1 0.0001 20.9 2.4 41 28-76 331-371 (444)
227 PRK11557 putative DNA-binding 68.5 7.9 0.0002 19.1 3.9 55 12-66 18-74 (282)
228 PRK11922 RNA polymerase sigma 68.5 7.2 0.00018 19.4 3.7 35 12-49 37-71 (231)
229 PRK12539 RNA polymerase sigma 68.4 8.5 0.00022 18.9 4.0 17 101-118 123-139 (184)
230 PRK12524 RNA polymerase sigma 68.1 9 0.00023 18.7 4.1 33 13-48 34-66 (196)
231 cd04783 HTH_MerR1 Helix-Turn-H 68.1 4.3 0.00011 20.8 2.4 46 28-73 1-63 (126)
232 PRK05602 RNA polymerase sigma 67.7 9.2 0.00023 18.7 4.1 58 11-73 26-88 (186)
233 PRK12532 RNA polymerase sigma 67.2 7.7 0.0002 19.2 3.6 49 14-64 14-66 (195)
234 smart00342 HTH_ARAC helix_turn 67.2 7.1 0.00018 19.4 3.4 37 28-64 2-38 (84)
235 cd00592 HTH_MerR-like Helix-Tu 67.1 4.7 0.00012 20.6 2.5 46 28-73 1-62 (100)
236 PRK09639 RNA polymerase sigma 67.0 9.5 0.00024 18.6 4.0 50 12-64 10-61 (166)
237 PRK12526 RNA polymerase sigma 67.0 7.8 0.0002 19.1 3.6 42 29-73 60-106 (206)
238 PRK12546 RNA polymerase sigma 66.9 5.4 0.00014 20.2 2.8 13 102-114 106-118 (188)
239 PRK09641 RNA polymerase sigma 66.7 9.4 0.00024 18.6 4.0 58 11-73 24-85 (187)
240 pfam11268 DUF3071 Protein of u 66.6 6 0.00015 19.9 3.0 50 18-70 59-108 (169)
241 PRK10046 dpiA two-component re 66.6 5.1 0.00013 20.3 2.6 10 28-37 134-143 (225)
242 PRK09638 RNA polymerase sigma 66.4 10 0.00026 18.4 4.1 58 11-73 25-86 (177)
243 PRK12519 RNA polymerase sigma 66.4 9.7 0.00025 18.5 4.0 34 30-64 52-89 (194)
244 cd04786 HTH_MerR-like_sg7 Heli 66.4 4.9 0.00013 20.4 2.5 47 28-74 1-64 (131)
245 pfam07900 DUF1670 Protein of u 66.4 10 0.00027 18.3 4.5 52 15-66 92-150 (220)
246 PRK09647 RNA polymerase sigma 66.2 7 0.00018 19.4 3.2 15 11-25 53-67 (222)
247 PHA00361 cI Repressor 66.2 3.2 8.3E-05 21.6 1.5 19 61-79 1-19 (165)
248 cd01106 HTH_TipAL-Mta Helix-Tu 66.2 5 0.00013 20.3 2.5 46 28-73 1-63 (103)
249 PRK12547 RNA polymerase sigma 66.1 11 0.00027 18.3 4.1 12 102-113 105-116 (164)
250 PRK12531 RNA polymerase sigma 65.9 8.6 0.00022 18.9 3.6 41 30-73 50-95 (194)
251 PRK12537 RNA polymerase sigma 65.8 10 0.00027 18.3 4.0 57 12-73 30-91 (184)
252 PRK09652 RNA polymerase sigma 65.7 11 0.00027 18.3 4.0 35 11-48 25-59 (192)
253 PRK12543 RNA polymerase sigma 65.6 10 0.00026 18.4 4.0 18 31-49 43-60 (190)
254 COG2826 Tra8 Transposase and i 65.6 5.3 0.00013 20.2 2.5 34 15-49 10-45 (318)
255 PRK12541 RNA polymerase sigma 65.6 8.7 0.00022 18.8 3.6 16 56-73 56-71 (161)
256 pfam09339 HTH_IclR IclR helix- 65.5 5.6 0.00014 20.0 2.6 31 19-49 9-40 (52)
257 cd01109 HTH_YyaN Helix-Turn-He 65.1 5.3 0.00014 20.2 2.4 46 28-73 1-63 (113)
258 PRK12517 RNA polymerase sigma 64.6 9.4 0.00024 18.6 3.6 11 103-113 122-132 (188)
259 TIGR03001 Sig-70_gmx1 RNA poly 64.5 4.1 0.0001 20.9 1.7 48 26-73 181-229 (249)
260 PRK12536 RNA polymerase sigma 64.4 6.5 0.00017 19.6 2.8 59 11-73 24-86 (178)
261 cd01282 HTH_MerR-like_sg3 Heli 64.4 5.6 0.00014 20.1 2.4 46 28-73 1-62 (112)
262 PRK12514 RNA polymerase sigma 64.2 11 0.00029 18.1 4.0 57 12-73 26-87 (179)
263 PRK09644 RNA polymerase sigma 64.2 11 0.00027 18.2 3.9 15 57-73 53-67 (165)
264 PRK07405 RNA polymerase sigma 64.1 5.5 0.00014 20.1 2.4 39 13-51 162-209 (318)
265 PRK09047 RNA polymerase factor 64.1 7.8 0.0002 19.1 3.1 12 103-114 100-111 (161)
266 PRK10783 mltD membrane-bound l 63.9 11 0.00029 18.1 3.9 25 25-49 349-373 (449)
267 PRK09645 RNA polymerase sigma 63.8 11 0.00029 18.1 3.9 52 11-65 13-69 (171)
268 PRK12542 RNA polymerase sigma 63.7 11 0.00028 18.2 3.8 18 31-49 33-50 (185)
269 TIGR02899 spore_safA spore coa 63.6 4 0.0001 21.0 1.6 23 55-77 3-25 (44)
270 PRK12511 RNA polymerase sigma 63.5 5.2 0.00013 20.3 2.1 41 30-73 27-71 (182)
271 PRK12534 RNA polymerase sigma 63.5 10 0.00026 18.4 3.6 41 30-73 48-93 (187)
272 cd04777 HTH_MerR-like_sg1 Heli 63.5 12 0.0003 18.0 5.4 28 28-55 1-29 (107)
273 COG3311 AlpA Predicted transcr 63.5 7.3 0.00019 19.3 2.9 32 28-59 14-45 (70)
274 pfam00440 TetR_N Bacterial reg 63.4 5.9 0.00015 19.9 2.4 35 17-51 6-40 (47)
275 TIGR02989 Sig-70_gvs1 RNA poly 62.8 12 0.00031 17.9 3.9 31 17-47 121-151 (163)
276 PRK12518 RNA polymerase sigma 62.7 12 0.00031 17.9 4.1 42 29-73 32-77 (175)
277 cd04775 HTH_Cfa-like Helix-Tur 62.6 12 0.00031 17.9 5.3 47 28-74 2-64 (102)
278 TIGR01529 argR_whole arginine 62.5 8 0.0002 19.1 2.9 36 17-52 5-47 (155)
279 PRK12515 RNA polymerase sigma 62.1 13 0.00032 17.8 4.1 36 12-50 29-64 (189)
280 PRK12540 RNA polymerase sigma 61.7 7.7 0.0002 19.1 2.8 11 103-113 105-115 (181)
281 COG2761 FrnE Predicted dithiol 61.5 13 0.00033 17.7 7.7 64 4-75 96-159 (225)
282 PRK05949 RNA polymerase sigma 61.1 6.9 0.00017 19.5 2.4 42 13-54 171-221 (327)
283 cd04776 HTH_GnyR Helix-Turn-He 61.0 6.9 0.00018 19.5 2.4 46 28-73 1-61 (118)
284 smart00420 HTH_DEOR helix_turn 60.7 7.9 0.0002 19.1 2.7 28 19-46 6-33 (53)
285 TIGR02812 fadR_gamma fatty aci 60.5 2.8 7.2E-05 21.9 0.4 23 31-64 34-56 (275)
286 TIGR03454 partition_RepB plasm 60.5 7.2 0.00018 19.3 2.4 50 24-73 174-224 (325)
287 PRK09863 putative frv operon r 60.5 9 0.00023 18.7 2.9 28 21-48 86-113 (585)
288 PRK12544 RNA polymerase sigma 60.2 8.5 0.00022 18.9 2.8 20 8-27 22-41 (207)
289 TIGR00160 MGSA methylglyoxal s 60.1 5.5 0.00014 20.1 1.8 20 53-72 90-109 (143)
290 PRK09649 RNA polymerase sigma 60.0 8.7 0.00022 18.8 2.8 26 44-73 65-90 (185)
291 smart00346 HTH_ICLR helix_turn 59.9 8.2 0.00021 19.0 2.6 25 25-49 18-42 (91)
292 cd04788 HTH_NolA-AlbR Helix-Tu 59.7 7.6 0.00019 19.2 2.4 46 28-73 1-63 (96)
293 smart00418 HTH_ARSR helix_turn 59.7 9.8 0.00025 18.5 3.0 27 20-47 4-30 (66)
294 cd04784 HTH_CadR-PbrR Helix-Tu 59.7 7.7 0.0002 19.2 2.5 46 28-73 1-63 (127)
295 PRK12535 RNA polymerase sigma 59.5 9.1 0.00023 18.7 2.8 12 102-113 125-136 (195)
296 PRK11923 algU RNA polymerase s 59.0 14 0.00035 17.5 3.7 35 12-49 27-61 (193)
297 pfam09571 RE_XcyI XcyI restric 58.9 3.7 9.3E-05 21.2 0.7 63 18-80 76-141 (318)
298 PRK10572 DNA-binding transcrip 58.7 14 0.00037 17.4 3.7 45 11-55 181-227 (290)
299 PRK13749 transcriptional regul 58.5 14 0.00037 17.4 5.0 48 26-73 2-66 (121)
300 PRK12530 RNA polymerase sigma 58.4 14 0.00036 17.5 3.6 57 11-73 15-76 (191)
301 PRK12512 RNA polymerase sigma 58.3 15 0.00037 17.4 4.1 13 102-114 124-136 (184)
302 TIGR02395 rpoN_sigma RNA polym 58.2 2 5E-05 23.0 -0.8 46 23-77 361-407 (477)
303 PRK12538 RNA polymerase sigma 57.9 15 0.00038 17.3 4.1 51 11-65 69-125 (233)
304 PRK12513 RNA polymerase sigma 57.8 15 0.00038 17.3 4.1 32 14-48 35-66 (194)
305 PRK06811 RNA polymerase factor 57.7 15 0.00038 17.3 4.0 51 20-73 31-87 (185)
306 pfam10654 DUF2481 Protein of u 57.4 12 0.0003 18.0 3.1 24 25-48 78-101 (126)
307 PRK07921 RNA polymerase sigma 57.2 8.6 0.00022 18.9 2.4 24 27-50 185-208 (320)
308 cd04772 HTH_TioE_rpt1 First He 57.1 8.1 0.00021 19.0 2.2 27 28-54 1-27 (99)
309 COG2452 Predicted site-specifi 57.1 9.4 0.00024 18.6 2.5 25 27-51 1-25 (193)
310 PRK10163 DNA-binding transcrip 57.0 9.7 0.00025 18.5 2.6 30 19-48 31-61 (271)
311 TIGR02293 TIGR02293 conserved 57.0 10 0.00026 18.4 2.7 56 25-81 35-96 (138)
312 cd01279 HTH_HspR-like Helix-Tu 56.9 8.6 0.00022 18.9 2.3 22 28-49 2-23 (98)
313 COG1414 IclR Transcriptional r 56.4 13 0.00033 17.7 3.2 26 24-49 16-41 (246)
314 PRK07406 RNA polymerase sigma 56.4 13 0.00033 17.7 3.2 40 13-52 228-276 (385)
315 COG3888 Predicted transcriptio 56.2 11 0.00029 18.1 2.8 31 17-47 8-40 (321)
316 COG3355 Predicted transcriptio 55.9 16 0.00041 17.1 4.3 24 24-47 39-62 (126)
317 cd04765 HTH_MlrA-like_sg2 Heli 55.8 9.7 0.00025 18.5 2.4 27 28-54 1-29 (99)
318 pfam08822 DUF1804 Protein of u 55.7 16 0.00041 17.1 4.7 42 7-50 1-42 (165)
319 pfam06056 Terminase_5 Putative 55.1 7.4 0.00019 19.3 1.7 28 25-52 11-38 (58)
320 PRK07598 RNA polymerase sigma 54.8 10 0.00026 18.4 2.4 37 13-49 250-295 (410)
321 TIGR02233 Myxo_sigma_rel Myxoc 54.7 7.9 0.0002 19.1 1.8 49 25-73 38-87 (106)
322 PRK13705 plasmid-partitioning 54.5 17 0.00043 17.0 4.4 56 15-70 17-98 (388)
323 COG4189 Predicted transcriptio 54.4 14 0.00035 17.6 3.0 28 19-46 29-56 (308)
324 PRK11511 DNA-binding transcrip 54.4 11 0.00029 18.1 2.6 31 25-55 23-53 (127)
325 pfam04297 UPF0122 Putative hel 54.3 9.3 0.00024 18.6 2.1 24 24-47 30-53 (101)
326 PRK11569 transcriptional repre 54.1 12 0.00029 18.0 2.6 23 25-47 41-63 (274)
327 PRK11050 manganese transport r 53.8 14 0.00036 17.5 3.0 26 22-47 48-74 (155)
328 TIGR00014 arsC arsenate reduct 53.7 17 0.00044 16.9 4.1 43 36-78 8-61 (114)
329 pfam00325 Crp Bacterial regula 53.7 12 0.0003 18.0 2.6 22 27-48 2-23 (32)
330 COG1339 Transcriptional regula 53.7 7.6 0.00019 19.2 1.6 26 22-48 15-40 (214)
331 cd00090 HTH_ARSR Arsenical Res 53.5 17 0.00045 16.9 4.6 36 8-47 5-40 (78)
332 PRK00118 putative DNA-binding 53.3 10 0.00026 18.4 2.2 26 22-47 28-53 (105)
333 PRK12522 RNA polymerase sigma 53.2 18 0.00045 16.9 3.6 35 11-48 9-43 (173)
334 COG1349 GlpR Transcriptional r 53.0 12 0.00031 17.9 2.6 30 17-46 9-38 (253)
335 cd04779 HTH_MerR-like_sg4 Heli 53.0 12 0.00029 18.0 2.4 46 28-73 1-62 (134)
336 COG2963 Transposase and inacti 52.9 18 0.00046 16.8 3.5 33 17-49 14-47 (116)
337 pfam01726 LexA_DNA_bind LexA D 52.8 18 0.00046 16.8 4.5 35 13-47 9-46 (65)
338 pfam01022 HTH_5 Bacterial regu 52.7 16 0.00042 17.1 3.2 29 19-48 8-36 (47)
339 pfam08220 HTH_DeoR DeoR-like h 52.4 13 0.00034 17.6 2.7 28 19-46 6-33 (57)
340 PRK09415 RNA polymerase factor 51.6 19 0.00048 16.7 3.9 56 13-73 24-83 (177)
341 PRK09648 RNA polymerase sigma 51.5 19 0.00048 16.7 3.6 53 11-64 28-87 (187)
342 pfam09572 RE_XamI XamI restric 51.5 16 0.00041 17.1 3.0 49 18-66 18-74 (251)
343 PRK09643 RNA polymerase sigma 51.4 19 0.00048 16.7 3.6 58 11-73 33-94 (197)
344 COG1497 Predicted transcriptio 51.4 11 0.00028 18.2 2.1 25 25-49 23-47 (260)
345 COG1309 AcrR Transcriptional r 51.1 13 0.00033 17.7 2.5 42 23-64 28-69 (201)
346 PRK12533 RNA polymerase sigma 50.3 16 0.0004 17.2 2.8 18 44-64 63-80 (217)
347 PRK00215 LexA repressor; Valid 50.2 20 0.0005 16.5 4.0 35 13-47 7-44 (204)
348 pfam04539 Sigma70_r3 Sigma-70 49.6 20 0.00051 16.5 4.5 41 14-54 5-47 (78)
349 PRK05066 arginine repressor; P 49.3 20 0.00052 16.5 3.8 32 17-48 12-50 (156)
350 COG4565 CitB Response regulato 49.1 20 0.00052 16.4 3.8 47 18-68 120-169 (224)
351 PRK12681 cysB transcriptional 48.9 21 0.00052 16.4 3.8 29 18-46 5-35 (324)
352 PRK12545 RNA polymerase sigma 48.2 21 0.00054 16.4 3.5 39 31-73 32-75 (201)
353 TIGR03453 partition_RepA plasm 48.2 21 0.00054 16.3 5.0 55 14-68 10-86 (387)
354 PRK09210 RNA polymerase sigma 48.1 14 0.00036 17.5 2.3 21 29-49 235-255 (368)
355 PRK10681 DNA-binding transcrip 47.4 16 0.00042 17.1 2.5 30 17-46 11-40 (252)
356 PRK05901 RNA polymerase sigma 47.2 15 0.00038 17.3 2.3 29 22-50 255-285 (398)
357 pfam06322 Phage_NinH Phage Nin 46.8 16 0.0004 17.2 2.3 27 26-52 15-41 (64)
358 PRK09642 RNA polymerase sigma 46.7 22 0.00057 16.2 3.6 15 57-73 47-61 (160)
359 COG0856 Orotate phosphoribosyl 46.5 22 0.00057 16.2 5.8 39 17-55 6-50 (203)
360 pfam05732 RepL Firmicute plasm 46.5 14 0.00035 17.6 2.0 52 26-79 74-126 (165)
361 PRK09990 DNA-binding transcrip 46.4 17 0.00043 17.0 2.5 45 2-48 1-56 (251)
362 PRK10906 DNA-binding transcrip 46.3 18 0.00045 16.8 2.6 28 19-46 11-38 (252)
363 PRK00767 transcriptional regul 46.1 23 0.00058 16.1 7.1 50 25-74 27-76 (197)
364 PRK09802 DNA-binding transcrip 45.9 18 0.00046 16.8 2.6 28 19-46 23-50 (269)
365 PRK10411 DNA-binding transcrip 45.9 18 0.00047 16.7 2.6 28 19-46 10-37 (240)
366 PRK10820 DNA-binding transcrip 45.7 23 0.00059 16.1 3.8 14 60-73 427-440 (513)
367 pfam00392 GntR Bacterial regul 45.6 14 0.00036 17.5 1.9 18 29-46 26-43 (64)
368 PRK11886 biotin--protein ligas 45.5 21 0.00054 16.3 2.9 30 18-47 9-38 (319)
369 COG1438 ArgR Arginine represso 45.5 23 0.00059 16.1 3.8 33 17-49 9-47 (150)
370 smart00345 HTH_GNTR helix_turn 45.2 16 0.0004 17.2 2.1 33 14-46 4-39 (60)
371 PHA02519 plasmid partition pro 45.1 21 0.00053 16.4 2.7 56 15-70 17-98 (387)
372 PRK09409 insertion element IS2 44.8 23 0.00058 16.2 2.9 26 24-49 8-33 (301)
373 COG2378 Predicted transcriptio 44.7 24 0.00061 16.0 3.4 34 14-47 9-42 (311)
374 PRK10668 DNA-binding transcrip 44.6 18 0.00045 16.8 2.3 44 26-73 30-73 (216)
375 cd04769 HTH_MerR2 Helix-Turn-H 43.8 25 0.00063 15.9 8.9 46 28-73 1-62 (116)
376 PRK09413 insertion sequence 2 43.5 20 0.00052 16.5 2.5 34 17-50 17-52 (121)
377 PRK13509 transcriptional repre 43.5 22 0.00055 16.3 2.6 29 19-47 11-39 (251)
378 cd07377 WHTH_GntR Winged helix 42.7 18 0.00047 16.8 2.2 32 15-46 10-44 (66)
379 PRK10402 DNA-binding transcrip 42.3 20 0.00052 16.5 2.3 15 59-73 159-173 (213)
380 TIGR02534 mucon_cyclo muconate 41.9 20 0.0005 16.5 2.2 43 42-84 88-134 (369)
381 COG1510 Predicted transcriptio 41.7 15 0.00039 17.3 1.6 35 14-48 27-62 (177)
382 pfam07506 RepB RepB plasmid pa 41.7 27 0.00068 15.7 2.9 25 24-48 18-42 (185)
383 TIGR02983 SigE-fam_strep RNA p 41.6 9.6 0.00024 18.6 0.6 23 23-45 125-147 (165)
384 PRK10141 DNA-binding transcrip 41.3 27 0.00069 15.7 3.2 31 18-48 16-49 (106)
385 PRK12679 cbl transcriptional r 40.9 27 0.0007 15.6 3.8 30 17-46 4-35 (316)
386 pfam07453 NUMOD1 NUMOD1 domain 40.6 14 0.00037 17.4 1.4 19 29-47 18-36 (37)
387 PRK10434 srlR DNA-bindng trans 40.5 25 0.00063 15.9 2.6 28 19-46 11-38 (256)
388 PRK03837 transcriptional regul 40.2 16 0.00041 17.1 1.5 34 15-48 23-63 (243)
389 TIGR03541 reg_near_HchA LuxR f 40.2 28 0.0007 15.6 2.7 12 17-28 22-33 (232)
390 PRK10219 DNA-binding transcrip 40.1 28 0.00072 15.6 4.9 35 17-51 9-45 (107)
391 PRK13503 transcriptional activ 39.8 25 0.00063 15.9 2.5 23 27-49 187-209 (278)
392 PRK09975 DNA-binding transcrip 39.7 24 0.00061 16.0 2.4 29 25-53 29-57 (213)
393 pfam00165 HTH_AraC Bacterial r 39.7 25 0.00065 15.8 2.5 27 25-51 6-33 (43)
394 pfam06971 Put_DNA-bind_N Putat 39.7 29 0.00073 15.5 3.9 40 7-46 2-46 (49)
395 PRK04280 arginine repressor; P 39.6 29 0.00073 15.5 3.8 31 17-47 8-44 (149)
396 PRK11525 dinD DNA-damage-induc 39.3 29 0.00074 15.5 5.0 42 28-76 22-63 (279)
397 PRK10365 transcriptional regul 39.2 29 0.00074 15.5 3.9 27 54-80 146-173 (441)
398 pfam06323 Phage_antiter_Q Phag 39.0 20 0.00051 16.5 1.9 16 33-48 17-32 (230)
399 PRK04984 fatty acid metabolism 38.9 26 0.00067 15.8 2.5 45 1-45 1-49 (239)
400 pfam01325 Fe_dep_repress Iron 38.8 29 0.00075 15.4 2.8 21 27-47 20-40 (58)
401 COG2739 Uncharacterized protei 38.7 23 0.0006 16.1 2.2 22 25-46 31-52 (105)
402 pfam05848 CtsR Firmicute trans 38.5 25 0.00063 15.9 2.3 42 9-51 2-48 (151)
403 TIGR02047 CadR-PbrR Cd(II)/Pb( 38.5 14 0.00035 17.6 1.0 45 29-73 2-63 (127)
404 cd00086 homeodomain Homeodomai 38.0 23 0.00059 16.1 2.1 23 51-73 22-44 (59)
405 PRK13502 transcriptional activ 37.6 31 0.00078 15.3 3.6 21 27-47 192-212 (282)
406 pfam02042 RWP-RK RWP-RK domain 37.5 31 0.00079 15.3 3.7 36 19-69 7-42 (52)
407 TIGR02960 SigX5 RNA polymerase 37.5 28 0.00072 15.5 2.5 30 21-50 153-182 (329)
408 smart00497 IENR1 Intron encode 37.4 18 0.00045 16.8 1.4 24 29-52 19-42 (53)
409 TIGR02043 ZntR Zn(II)-responsi 37.4 31 0.00079 15.3 2.7 58 30-87 4-81 (132)
410 PRK12680 transcriptional regul 37.1 31 0.0008 15.3 3.7 30 18-47 5-36 (327)
411 pfam03333 PapB Adhesin biosynt 36.9 24 0.0006 16.0 2.0 30 17-46 41-72 (91)
412 PRK10371 DNA-binding transcrip 36.8 31 0.0008 15.3 2.6 25 26-50 206-230 (302)
413 TIGR03338 phnR_burk phosphonat 36.7 22 0.00056 16.2 1.8 40 4-44 6-51 (212)
414 TIGR00738 rrf2_super rrf2 fami 36.6 26 0.00068 15.7 2.2 22 28-49 26-47 (133)
415 PRK08241 RNA polymerase factor 36.4 32 0.00082 15.2 2.9 23 22-44 167-189 (341)
416 PRK11891 aspartate carbamoyltr 36.3 29 0.00073 15.5 2.3 35 17-51 7-41 (430)
417 PRK10100 DNA-binding transcrip 36.0 33 0.00083 15.2 2.7 10 46-55 123-132 (216)
418 TIGR02297 HpaA 4-hydroxyphenyl 35.9 33 0.00083 15.1 2.7 42 18-59 198-239 (292)
419 KOG2252 consensus 35.8 33 0.00084 15.1 5.9 57 13-70 329-391 (558)
420 pfam01316 Arg_repressor Argini 35.7 33 0.00084 15.1 3.2 32 17-48 8-45 (70)
421 cd06571 Bac_DnaA_C C-terminal 35.6 33 0.00084 15.1 2.8 24 57-80 3-26 (90)
422 PRK11534 DNA-binding transcrip 35.5 24 0.00062 16.0 1.9 23 26-48 29-55 (224)
423 TIGR02318 phosphono_phnM phosp 35.4 33 0.00085 15.1 4.6 55 15-71 182-238 (391)
424 TIGR03384 betaine_BetI transcr 35.4 33 0.00085 15.1 6.8 46 25-70 26-71 (189)
425 pfam06970 RepA_N Replication i 35.3 27 0.00068 15.7 2.1 20 28-47 53-72 (76)
426 PRK09685 DNA-binding transcrip 35.3 33 0.00085 15.1 2.6 42 25-66 213-259 (303)
427 PRK13866 plasmid partitioning 35.2 32 0.00083 15.2 2.5 57 17-73 168-226 (336)
428 pfam00046 Homeobox Homeobox do 34.5 26 0.00067 15.8 1.9 23 51-73 22-44 (57)
429 pfam01476 LysM LysM domain. Th 34.2 20 0.00051 16.5 1.3 21 56-76 6-26 (43)
430 smart00257 LysM Lysin motif. 34.0 20 0.0005 16.6 1.2 24 55-78 6-29 (44)
431 PRK10421 DNA-binding transcrip 33.6 28 0.00071 15.6 1.9 35 14-48 6-51 (253)
432 smart00389 HOX Homeodomain. DN 33.6 30 0.00076 15.4 2.0 22 52-73 23-44 (56)
433 cd00118 LysM Lysin domain, fou 33.5 18 0.00047 16.8 1.0 23 56-78 8-30 (46)
434 PRK13869 plasmid-partitioning 33.4 36 0.00091 14.9 5.0 54 15-68 26-101 (405)
435 TIGR03613 RutR pyrimidine util 32.8 37 0.00093 14.8 7.4 51 23-73 24-74 (202)
436 COG2207 AraC AraC-type DNA-bin 32.7 37 0.00094 14.8 3.0 36 15-51 25-60 (127)
437 TIGR02018 his_ut_repres histid 32.5 25 0.00065 15.8 1.6 18 31-48 29-46 (234)
438 PRK11414 putative DNA-binding 32.0 27 0.00069 15.6 1.7 35 14-48 15-59 (221)
439 pfam12116 SpoIIID Stage III sp 31.4 39 0.00098 14.7 3.3 23 24-46 16-38 (82)
440 COG1321 TroR Mn-dependent tran 31.3 39 0.00099 14.7 3.4 33 16-48 12-45 (154)
441 PRK11361 acetoacetate metaboli 31.1 39 0.00099 14.6 3.9 28 53-80 149-177 (457)
442 PRK04435 hypothetical protein; 31.0 22 0.00056 16.2 1.0 30 23-52 29-58 (146)
443 COG1725 Predicted transcriptio 30.9 35 0.00088 15.0 2.0 18 29-46 37-54 (125)
444 pfam05344 DUF746 Domain of Unk 30.5 40 0.001 14.6 2.4 27 24-50 10-36 (65)
445 KOG0774 consensus 30.0 18 0.00047 16.8 0.5 21 31-51 222-242 (334)
446 PRK12423 LexA repressor; Provi 29.8 41 0.001 14.5 3.5 35 13-47 9-46 (202)
447 COG5424 Pyrroloquinoline quino 29.8 41 0.001 14.5 5.6 37 42-78 79-116 (242)
448 PRK04424 fatty acid biosynthes 29.4 10 0.00025 18.4 -0.9 53 21-75 15-75 (185)
449 COG1802 GntR Transcriptional r 29.2 32 0.00083 15.2 1.6 35 14-48 24-64 (230)
450 PRK02277 orotate phosphoribosy 29.2 42 0.0011 14.4 2.5 32 15-47 7-38 (201)
451 pfam10078 DUF2316 Uncharacteri 29.1 42 0.0011 14.4 4.9 50 16-66 12-61 (89)
452 TIGR02392 rpoH_proteo alternat 28.8 43 0.0011 14.4 2.3 21 33-53 149-169 (279)
453 PRK10870 transcriptional repre 28.6 43 0.0011 14.4 2.2 25 104-129 137-161 (176)
454 PRK05306 infB translation init 28.5 43 0.0011 14.4 3.4 53 20-72 263-322 (839)
455 PRK11523 DNA-binding transcrip 28.3 44 0.0011 14.3 4.8 45 3-48 2-57 (258)
456 pfam05043 Mga Mga helix-turn-h 28.2 44 0.0011 14.3 3.1 45 18-70 21-65 (87)
457 pfam00126 HTH_1 Bacterial regu 28.2 44 0.0011 14.3 2.3 31 29-70 15-45 (60)
458 PRK05022 anaerobic nitric oxid 28.0 44 0.0011 14.3 4.1 34 10-49 365-398 (510)
459 COG3720 HemS Putative heme deg 27.9 44 0.0011 14.3 4.7 36 16-51 10-46 (349)
460 PRK13756 tetracycline represso 27.8 34 0.00086 15.0 1.5 40 15-54 10-51 (205)
461 smart00529 HTH_DTXR Helix-turn 27.8 35 0.00088 15.0 1.6 17 31-47 3-19 (96)
462 TIGR02479 FliA_WhiG RNA polyme 27.6 45 0.0011 14.3 2.2 50 15-64 85-136 (227)
463 TIGR03337 phnR transcriptional 27.5 45 0.0011 14.3 2.2 18 29-46 27-44 (231)
464 PRK09636 RNA polymerase sigma 27.3 45 0.0012 14.2 3.1 26 22-47 122-147 (289)
465 KOG0775 consensus 27.2 30 0.00075 15.4 1.2 22 31-52 207-228 (304)
466 PRK10225 DNA-binding transcrip 27.0 41 0.0011 14.5 1.9 34 15-48 14-58 (257)
467 cd04778 HTH_MerR-like_sg2 Heli 26.9 46 0.0012 14.2 2.2 20 18-37 46-67 (219)
468 COG2771 CsgD DNA-binding HTH d 26.9 46 0.0012 14.2 4.1 33 18-50 10-42 (65)
469 cd04334 ProRS-INS INS is an am 26.7 34 0.00088 15.0 1.4 25 51-75 30-54 (160)
470 pfam08280 HTH_Mga M protein tr 26.6 43 0.0011 14.4 1.9 27 25-51 17-43 (59)
471 PRK11202 DNA-binding transcrip 26.5 36 0.00092 14.9 1.5 31 24-54 29-59 (203)
472 TIGR02044 CueR Cu(I)-responsiv 25.9 44 0.0011 14.3 1.9 45 29-73 2-63 (127)
473 PRK03341 arginine repressor; P 25.8 48 0.0012 14.1 3.4 30 17-46 18-53 (168)
474 COG4977 Transcriptional regula 25.6 49 0.0012 14.0 3.0 34 14-47 221-256 (328)
475 COG1405 SUA7 Transcription ini 25.1 47 0.0012 14.1 1.9 19 28-46 158-176 (285)
476 PRK03902 manganese transport t 25.1 50 0.0013 14.0 3.0 25 23-47 17-42 (142)
477 pfam05121 GvpK Gas vesicle pro 25.0 50 0.0013 14.0 4.7 45 28-73 20-76 (89)
478 PRK13501 transcriptional activ 24.9 50 0.0013 14.0 2.6 21 27-47 192-212 (290)
479 pfam11300 DUF3102 Protein of u 24.7 50 0.0013 13.9 3.2 42 13-67 26-70 (130)
480 COG4367 Uncharacterized protei 24.3 51 0.0013 13.9 5.4 56 9-66 4-60 (97)
481 PRK00441 argR arginine repress 24.2 52 0.0013 13.9 3.6 30 17-46 7-42 (149)
482 PRK12682 transcriptional regul 24.1 52 0.0013 13.9 3.9 30 17-46 4-35 (309)
483 pfam12368 DUF3650 Protein of u 24.1 52 0.0013 13.9 1.9 14 24-37 12-25 (28)
484 pfam07600 DUF1564 Protein of u 24.1 52 0.0013 13.9 2.1 21 55-75 92-112 (167)
485 pfam06413 Neugrin Neugrin. Thi 23.9 52 0.0013 13.8 4.3 45 17-61 17-63 (225)
486 COG4753 Response regulator con 23.7 53 0.0013 13.8 2.5 21 27-47 388-408 (475)
487 TIGR02329 propionate_PrpR prop 23.6 53 0.0014 13.8 3.0 31 19-49 627-657 (658)
488 PRK13558 bacterio-opsin activa 23.5 53 0.0014 13.8 2.1 21 26-46 638-658 (674)
489 PRK01905 DNA-binding protein F 23.1 54 0.0014 13.7 3.5 28 19-46 42-69 (77)
490 pfam03932 CutC CutC family. Co 23.1 46 0.0012 14.2 1.5 26 45-70 28-53 (202)
491 PRK06347 autolysin; Reviewed 23.1 54 0.0014 13.7 3.4 50 25-74 486-574 (593)
492 PRK09764 DNA-binding transcrip 23.1 54 0.0014 13.7 2.2 18 29-46 31-48 (239)
493 PRK12684 transcriptional regul 22.5 56 0.0014 13.7 3.8 30 17-46 4-35 (313)
494 PRK05574 holA DNA polymerase I 22.5 56 0.0014 13.7 4.6 66 1-66 240-310 (336)
495 PRK11552 putative DNA-binding 22.2 56 0.0014 13.6 4.6 109 29-141 34-142 (224)
496 PRK13832 plasmid partitioning 22.0 57 0.0015 13.6 4.8 36 9-47 103-138 (518)
497 PRK01770 sec-independent trans 22.0 46 0.0012 14.2 1.3 39 1-40 19-57 (171)
498 pfam01978 TrmB Sugar-specific 22.0 57 0.0015 13.6 2.5 21 27-47 22-42 (68)
499 COG2964 Uncharacterized protei 21.9 57 0.0015 13.6 2.0 17 31-47 195-211 (220)
500 PRK12683 transcriptional regul 21.6 58 0.0015 13.5 3.9 30 17-46 4-35 (308)
No 1
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=99.85 E-value=3.8e-20 Score=149.25 Aligned_cols=123 Identities=15% Similarity=0.255 Sum_probs=94.1
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf 99999999999819979999998724699999985289883589999999754999999506774431111101454211
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMD 93 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~~~~~~~~~~~~~~~~~ 93 (144)
.||+||+++|+++||||.+||+.+|||.++|++||+|.+.|+.+.|.+||++|||+++|||.|..............+
T Consensus 5 tiG~Ri~~~R~~~glTQ~eLA~~~Gvs~~tVs~wE~g~~~P~~~~L~~LA~~L~vs~~wLL~G~~d~~~~~~~~~~~~-- 82 (135)
T PRK09706 5 TLGQRIRYRRKQLKLSQRALAKAVGVSHVSISQWERDETEPAGKNLFALAQALQCSPTWLLFGDEDKQPTPPVPLEQP-- 82 (135)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCCCCCCCCCCCCC--
T ss_conf 099999999998599999999996988999999982898889999999999989099998488877899864333365--
Q ss_pred HHCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2038678999999872899999999999999999999997539998732
Q gi|254780424|r 94 FISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMV 142 (144)
Q Consensus 94 ~~~~~e~~~l~~~~~~l~~~~~r~~i~~l~~~l~~~e~~~~~~~ee~l~ 142 (144)
...+++...++..|..+|+.+.. + +++.+....+......+|++-
T Consensus 83 ~~L~~~q~~LLeLf~~LP~sEq~-~---~l~el~~r~~~~~~l~~Ell~ 127 (135)
T PRK09706 83 VELSEDQKELLELFDALPESEQE-A---QLSEMRARVENFNKLFEELLK 127 (135)
T ss_pred CCCCHHHHHHHHHHHHCCHHHHH-H---HHHHHHHHHHHHHHHHHHHHH
T ss_conf 55899999999999978899999-9---999999999999999999999
No 2
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.68 E-value=1.6e-16 Score=126.07 Aligned_cols=68 Identities=26% Similarity=0.339 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCCC
Q ss_conf 99999999999998199799999987246999999852898835899999997549999995067744
Q gi|254780424|r 12 DINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPT 79 (144)
Q Consensus 12 d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~~~ 79 (144)
+..||+|||++|+++|||+++||++.|||.++||++|+|..+||+.+|++||++|+|++.+||.....
T Consensus 5 ~~~iG~rIr~lR~~~glTL~eLA~~sGvS~s~LSqIErg~~~PSl~tL~kIa~aL~v~l~~lf~~~~~ 72 (185)
T PRK09943 5 GLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEK 72 (185)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCC
T ss_conf 32488999999998599899999887969999999987999999999999999849999998277455
No 3
>PHA01976 helix-turn-helix protein
Probab=99.65 E-value=4.4e-16 Score=123.22 Aligned_cols=64 Identities=11% Similarity=0.169 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCC
Q ss_conf 9999999999981997999999872469999998528988358999999975499999950677
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVS 77 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~ 77 (144)
..|.||+++|+++||||+|||+++||++++|++||+|.+.|++++|.+||++|||+++||++..
T Consensus 2 ~F~~RL~~lR~~~g~sQ~eLA~~lGVs~~~is~wE~g~~~P~~d~L~~la~~~~VS~D~LlGr~ 65 (67)
T PHA01976 2 SFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGRC 65 (67)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCC
T ss_conf 7899999999986999999999949989999999878989998999999999797899992678
No 4
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=99.39 E-value=8.2e-13 Score=102.28 Aligned_cols=62 Identities=13% Similarity=0.251 Sum_probs=59.0
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCC
Q ss_conf 99999999981997999999872469999998528988358999999975499999950677
Q gi|254780424|r 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVS 77 (144)
Q Consensus 16 G~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~ 77 (144)
=.+|+.+|.++||||.|||++.|||.+++|.+|+|+.+||+.+|.+||++|+||..+|++..
T Consensus 7 ftNv~RLr~ErGmT~~eLAe~AGIS~s~LSqIE~Gk~NPSL~tLe~IA~AL~VPL~~Lle~~ 68 (119)
T PRK13890 7 FTNVLRLLDERHMTKKELSDRSGVSISFLSDLTTGKANPSLKVMEDIAQALETPLPLLLEST 68 (119)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHC
T ss_conf 88799999985997999998829889999999779989879999999999879779987623
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=99.38 E-value=1.1e-12 Score=101.57 Aligned_cols=57 Identities=26% Similarity=0.480 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf 999999999998199799999987246999999852898835899999997549999
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~ 70 (144)
.||..||+.|+++||||.+||+.+|||+++|+++|+|+.+|+++++.+||.+||+++
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
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=99.35 E-value=1.5e-12 Score=100.64 Aligned_cols=56 Identities=23% Similarity=0.406 Sum_probs=54.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 99999998199799999987246999999852898835899999997549999995
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
+||++|+++||||++||+.+|||.++|++||+|...|+.+.+.+||++||+++++|
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 7
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=99.35 E-value=1.4e-12 Score=100.73 Aligned_cols=55 Identities=29% Similarity=0.437 Sum_probs=53.6
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 9999998199799999987246999999852898835899999997549999995
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
||++|+..||||++||+.+|||+++|++||+|.+.|+.+.+.+||++||||++||
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 8
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=99.35 E-value=2.5e-11 Score=92.78 Aligned_cols=74 Identities=22% Similarity=0.351 Sum_probs=67.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCC
Q ss_conf 66899899999999999999819979999998724699999985289883589999999754999999506774
Q gi|254780424|r 5 KKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSP 78 (144)
Q Consensus 5 ~~~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~~ 78 (144)
....||.=.++|+|+|.+|..+|||+++||+..|||..++.++|.|..+||+..|.+||.+|++|+.+|+....
T Consensus 19 ~~~~~~~l~~lg~rvr~~R~~rg~sr~~la~~sgvS~r~la~lE~G~gN~si~~L~~iA~Al~~~l~~l~~~~~ 92 (304)
T PRK08154 19 AAEEDPFLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCPLADLLGDED 92 (304)
T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCC
T ss_conf 44336699999999999999759989999987299899999882588885199999999995998999817888
No 9
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.27 E-value=1.1e-11 Score=95.00 Aligned_cols=60 Identities=25% Similarity=0.381 Sum_probs=57.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCC
Q ss_conf 999999981997999999872469999998528988358999999975499999950677
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVS 77 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~ 77 (144)
++|++|...||||++||+.+|||++||..||+|+.+||+..-.+||..|+.+++++|-..
T Consensus 5 k~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~iedIF~~~ 64 (68)
T COG1476 5 KLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQLE 64 (68)
T ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 999999982858999999919579999999917988309999999999399799998652
No 10
>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=99.23 E-value=2e-11 Score=93.40 Aligned_cols=58 Identities=24% Similarity=0.435 Sum_probs=56.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 9999999998199799999987246999999852898835899999997549999995
Q gi|254780424|r 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 16 G~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
|++||.+|+.+|+||.+||+.+|+|.+++++||+|...|+.+.+.+||++|++++++|
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 11
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=99.22 E-value=5.2e-11 Score=90.74 Aligned_cols=68 Identities=22% Similarity=0.374 Sum_probs=64.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf 9987668998999999999999998199799999987246999999852898835899999997549999
Q gi|254780424|r 1 MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70 (144)
Q Consensus 1 ~~~~~~~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~ 70 (144)
||+-.|...|- .+|..||..|+.+||||.++|+++|+.+++||++|+|-..+++++|++|+.+||+.+
T Consensus 1 ~~~~~ki~sp~--qLa~~Lr~~Rk~~gLsQ~~lA~~vGi~Q~TiS~~E~~p~~~~leTLFkiL~aL~Lel 68 (88)
T PRK09726 1 MMSFQKIYSPT--QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSM 68 (88)
T ss_pred CCCCCCCCCHH--HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEE
T ss_conf 98752028999--999999999998598799999981974999999975998786999999999678768
No 12
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=98.89 E-value=3.9e-09 Score=78.68 Aligned_cols=55 Identities=31% Similarity=0.489 Sum_probs=50.1
Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCC
Q ss_conf 8998999999999999998199799999987246999999852898835899999997549
Q gi|254780424|r 7 IPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLE 67 (144)
Q Consensus 7 ~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~ 67 (144)
+|+|- -||..|+++|+||++||++.|||+++|.++|.|+..|+++++.+|-++|-
T Consensus 4 ~P~pe------dlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~ 58 (187)
T COG3620 4 LPTPE------DLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALE 58 (187)
T ss_pred CCCHH------HHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 79879------99999987597789999870864888999863887930899999999999
No 13
>PRK06424 transcription factor; Provisional
Probab=98.81 E-value=1.1e-08 Score=75.88 Aligned_cols=57 Identities=16% Similarity=0.157 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf 999999999998199799999987246999999852898835899999997549999
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~ 70 (144)
--|++||..|+.+||||++||.+++++.+.|.++|+|...|+.+...+|-++|||.+
T Consensus 84 Dy~~~Ir~ARE~~GlsqeeLA~ki~ek~svI~kiE~G~l~P~~~~~kKLEk~L~I~L 140 (144)
T PRK06424 84 DYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITL 140 (144)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCEE
T ss_conf 799999999998499999999996544999999983898999899999999849676
No 14
>PRK08359 transcription factor; Validated
Probab=98.78 E-value=1.5e-08 Score=75.03 Aligned_cols=58 Identities=12% Similarity=0.233 Sum_probs=55.4
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHH
Q ss_conf 9999999999981997999999872469999998528988358999999975499999
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPIS 71 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~ 71 (144)
--|++||..|..+||||+|||.+++++.+.|.++|+|...|+.+...+|-++|||.+-
T Consensus 83 DY~~~Ir~ARE~~GlSqeeLA~ki~ek~nvI~kiE~G~l~P~~~~akKLEk~L~IkL~ 140 (175)
T PRK08359 83 DYAERVYEAIRKSGLSYEELSHKVGLSVNDLRRIAHGEYTPTIEEARKLERFFKIKLI 140 (175)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCEEEE
T ss_conf 6999999999985999999999972229999999838879998999999998490688
No 15
>PRK04140 hypothetical protein; Provisional
Probab=98.78 E-value=1.7e-08 Score=74.69 Aligned_cols=57 Identities=28% Similarity=0.459 Sum_probs=54.6
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHH
Q ss_conf 999999999819979999998724699999985289883589999999754999999
Q gi|254780424|r 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISF 72 (144)
Q Consensus 16 G~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~ 72 (144)
|+.||+.|+++|||..+||+.+|||+.++++||+|...+|+++..+|.+.||.++-.
T Consensus 127 g~~Lr~~Re~~g~SlG~LA~~LGVSRrtv~~YE~g~~~~sievA~kLeeif~~~i~~ 183 (319)
T PRK04140 127 GDLLRELREKLGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDEPLTK 183 (319)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCC
T ss_conf 799999999819888899998498699999997068866499999999983873235
No 16
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=98.78 E-value=1.2e-08 Score=75.56 Aligned_cols=67 Identities=22% Similarity=0.255 Sum_probs=61.1
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCC
Q ss_conf 9999999999981997999999872469999998528988358999999975499999950677443
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTV 80 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~~~~ 80 (144)
-.|++||..|+.+||||++||++++++.+.|.+||+|...|+.....+|.++|+|...+.....+..
T Consensus 79 dY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~~~~~~~~ 145 (165)
T COG1813 79 DYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEKVDEEEEG 145 (165)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCEEEEECCCCCCC
T ss_conf 7999999999982888999999965469999999841367558899999998585522003555446
No 17
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=98.58 E-value=2.5e-07 Score=67.18 Aligned_cols=67 Identities=13% Similarity=0.199 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHH-----HHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCC
Q ss_conf 999999999998199799999987-----2469999998528988358999999975499999950677443
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECL-----GITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTV 80 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~l-----Gvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~~~~ 80 (144)
..++||++++..+||+|.+|+... .+++|.+|+|++|++.|..+.+.-+|..|+|+.+||+++..+.
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (518)
T PRK13355 5 TQAERLVQLMNSRGLKQEDLVHAAEARGVKVGKSHISQYVRGKTGPRSDKLPFLASELGVSEGWLLGGESES 76 (518)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCC
T ss_conf 089999999987699689999999981755047888777338864421179999999688978860799765
No 18
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=98.51 E-value=2.2e-07 Score=67.44 Aligned_cols=46 Identities=28% Similarity=0.480 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHH
Q ss_conf 9999999999819979999998724699999985289883589999
Q gi|254780424|r 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQ 60 (144)
Q Consensus 15 iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~ 60 (144)
=|..|+++|+..||||.+||..+|||.+++++||+|...|+..-+.
T Consensus 45 s~~eIk~iRe~~~lSq~vFA~~L~vs~~Tv~~WEqGr~kPsg~Alk 90 (104)
T COG2944 45 SPTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAALK 90 (104)
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHH
T ss_conf 8899999999828889999999888799999998178589979999
No 19
>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=98.43 E-value=8.2e-07 Score=63.83 Aligned_cols=112 Identities=19% Similarity=0.185 Sum_probs=71.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC--CCCCCHHHHHHHHHHCCCCHHHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 999999981997999999872469999998528--988358999999975499999950677443111110145421120
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKG--VNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFI 95 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G--~~~ps~~~L~~iA~~l~v~~~~l~~~~~~~~~~~~~~~~~~~~~~ 95 (144)
=||.+|+++|||-.+||.++||.++.|..+|+. .-.+++.+|-+-|++||+..-|-|=- +.....+...........
T Consensus 29 WvR~~R~ALGms~~QLA~RlGV~p~Rv~~~E~~E~~G~VTL~tlr~aAEAl~C~FVYafVP-~~sLE~t~~~QArKvA~~ 107 (150)
T TIGR02612 29 WVRAIRKALGMSGAQLAARLGVTPQRVEAIEKSELSGAVTLKTLRKAAEALDCTFVYAFVP-KTSLEATVRAQARKVAKE 107 (150)
T ss_pred CHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEECCC-CCCHHHHHHHHHHHHHHH
T ss_conf 1688987725157887665289737799988887555355888999999859844340188-602789999999999999
Q ss_pred C-CHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 3-86789999998-728999999999999999999999
Q gi|254780424|r 96 S-TPDGLQLNRYF-IQIDDVKVRQKIIELVRSIVSSEK 131 (144)
Q Consensus 96 ~-~~e~~~l~~~~-~~l~~~~~r~~i~~l~~~l~~~e~ 131 (144)
. .+-.. .+..= =.+++......+.++++.|.....
T Consensus 108 ~~~r~~H-tM~LE~Qa~~~~~~e~~v~~~~~ELLr~~~ 144 (150)
T TIGR02612 108 ILKRVAH-TMELESQATSKEELEAEVEALTEELLREMP 144 (150)
T ss_pred HHHHHHH-HHHHHHCCCCHHHHHHHHHHHHHHHHHHCH
T ss_conf 9861775-376562158827899999999998875210
No 20
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=98.39 E-value=7.5e-07 Score=64.10 Aligned_cols=56 Identities=29% Similarity=0.504 Sum_probs=53.7
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHH
Q ss_conf 99999999981997999999872469999998528988358999999975499999
Q gi|254780424|r 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPIS 71 (144)
Q Consensus 16 G~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~ 71 (144)
|+.||+.|.+.|+|...||..+|||+.+|++||+|...||+++..++-+.||.++-
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 21
>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=98.33 E-value=5.9e-07 Score=64.73 Aligned_cols=64 Identities=17% Similarity=0.310 Sum_probs=57.0
Q ss_pred HHHHHHH-HHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCC
Q ss_conf 9999999-999998199799999987246999999852898835899999997549999995067
Q gi|254780424|r 13 INVGKRI-RLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 13 ~~iG~rI-r~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~ 76 (144)
+|-|+-| .++=..+|+|+.+||+.+|||+++||++-+|+..+|.++-.+||++||.++++-++-
T Consensus 5 ~HPGE~L~eEfL~PLg~s~~~LA~~LgVsr~~~sriv~~~~~iT~dmALRL~~~lG~sp~~WLnl 69 (81)
T TIGR02607 5 AHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPEFWLNL 69 (81)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf 78841328775210470689999870999788888874489988889999999738987689987
No 22
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=98.30 E-value=2.4e-06 Score=60.87 Aligned_cols=64 Identities=20% Similarity=0.389 Sum_probs=58.6
Q ss_pred HHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCC
Q ss_conf 99999999999981-99799999987246999999852898835899999997549999995067
Q gi|254780424|r 13 INVGKRIRLRRMIL-GMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 13 ~~iG~rIr~~R~~~-glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~ 76 (144)
+|.|+-|++-=.+- |+||.+||+.+||++.+|+.+-+|++.++.++-.+|+++||++++..++.
T Consensus 8 ~~PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspefWlNl 72 (104)
T COG3093 8 AHPGEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPEFWLNL 72 (104)
T ss_pred CCCHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf 99418899998452169899999993998999999983776789999999999929989999999
No 23
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=98.29 E-value=3.8e-06 Score=59.56 Aligned_cols=64 Identities=23% Similarity=0.416 Sum_probs=59.8
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHCCCCHHHHHCCCC
Q ss_conf 99999999998199799999987246999999852898-83589999999754999999506774
Q gi|254780424|r 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVN-RVGASRLQHISEVLESPISFFFDVSP 78 (144)
Q Consensus 15 iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~-~ps~~~L~~iA~~l~v~~~~l~~~~~ 78 (144)
+|.+++.+|+..|+||.++|.++|++..+++.||+|.. .|+...+..++..|+++..+++....
T Consensus 2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 (120)
T COG1396 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDELLEEEE 66 (120)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 78999999998699999999893988999999980787784699999999996978998840022
No 24
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.20 E-value=1.2e-06 Score=62.69 Aligned_cols=53 Identities=28% Similarity=0.485 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHHC
Q ss_conf 9999999999981997999999872469999998528988-3589999999754
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNR-VGASRLQHISEVL 66 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~-ps~~~L~~iA~~l 66 (144)
+.|+-||.+|..-+.||.|||..+|||+|-||.||.|++. |....+.++-.+|
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 25
>PRK10072 putative transcriptional regulator; Provisional
Probab=98.17 E-value=3.8e-06 Score=59.54 Aligned_cols=47 Identities=15% Similarity=0.299 Sum_probs=41.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 99999999819979999998724699999985289883589999999
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHIS 63 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA 63 (144)
.-++++|+..|++|.+||+.+|||.+++..||.|++.|+...+.-+.
T Consensus 36 ~dvkaIR~~tgl~q~eFA~~lGvSv~tvksWEq~Rr~Ptg~a~klL~ 82 (96)
T PRK10072 36 TEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMR 82 (96)
T ss_pred CCHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf 63999998809999999999777799999999678789839999999
No 26
>KOG3398 consensus
Probab=98.12 E-value=4.4e-06 Score=59.16 Aligned_cols=66 Identities=27% Similarity=0.304 Sum_probs=60.0
Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHH
Q ss_conf 899899999999999999819979999998724699999985289883589999999754999999
Q gi|254780424|r 7 IPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISF 72 (144)
Q Consensus 7 ~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~ 72 (144)
.++-++..+|+-|-..|..+||||++||.++.-.++-|..||+|+.-|+-..|.++-.+|||-..+
T Consensus 66 ~~~~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgvKlrg 131 (135)
T KOG3398 66 GHDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGVKLRG 131 (135)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCEECCC
T ss_conf 523014789999999888637548899999602861365575035674199999999985311246
No 27
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=98.09 E-value=8e-06 Score=57.50 Aligned_cols=68 Identities=18% Similarity=0.185 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC--CC----HHHHHHHHHHCCCCHHHHHCCCCCCC
Q ss_conf 9999999999981997999999872469999998528988--35----89999999754999999506774431
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNR--VG----ASRLQHISEVLESPISFFFDVSPTVC 81 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~--ps----~~~L~~iA~~l~v~~~~l~~~~~~~~ 81 (144)
++|+++|+.|+++|||++++|.+++|..+++-.+|.|.-. |. -.-|..-|++|+++.+.++.......
T Consensus 3 ~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l~~~~~~~~ 76 (284)
T COG1426 3 TLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDELLQAFEDEK 76 (284)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 77899999999849999999988577599999986677010641576789999999996899899999864104
No 28
>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=97.99 E-value=2.5e-05 Score=54.33 Aligned_cols=61 Identities=13% Similarity=0.153 Sum_probs=52.7
Q ss_pred HHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCC
Q ss_conf 9999998199-7999999872469999998528988358999999975499999950677443
Q gi|254780424|r 19 IRLRRMILGM-SQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTV 80 (144)
Q Consensus 19 Ir~~R~~~gl-TQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~~~~ 80 (144)
|.++-+..|. ||.|||+.+||+++++|.|-.... ++.+.+.++|...|+|++||+.|.++.
T Consensus 3 i~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R~~-~P~e~iv~~~~~tGvsl~WL~~G~G~~ 64 (65)
T pfam07022 3 IERLMKAYGFKSRSELADHLGVSKSTLSTWYKRDS-FPAEWVIRCALETGVSLDWLATGDGEL 64 (65)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCC-CCHHHHHHHHHHHCCCHHHHHCCCCCC
T ss_conf 99999996888699999996988888999998699-989999999999882999997089999
No 29
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria..
Probab=97.95 E-value=1.2e-05 Score=56.28 Aligned_cols=62 Identities=18% Similarity=0.183 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCC
Q ss_conf 99999999998199799999987246999999852898835899999997549999995067
Q gi|254780424|r 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 15 iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~ 76 (144)
-|.=||..|..+||||++||+++..-.|.|.++|+-.-.|......+|=+.|+|.+..=++.
T Consensus 84 yg~iIR~eREKRgwS~E~LAkki~eK~S~i~kiE~~e~eP~~k~~~kLEkllkIkL~E~~~e 145 (169)
T TIGR00270 84 YGRIIREEREKRGWSREELAKKIKEKASVIKKIEREELEPEEKVVKKLEKLLKIKLLEKVEE 145 (169)
T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCC
T ss_conf 22542200014687878999987410678888754037988899999888835010023571
No 30
>PRK10856 hypothetical protein; Provisional
Probab=97.91 E-value=4e-05 Score=53.03 Aligned_cols=65 Identities=20% Similarity=0.271 Sum_probs=55.9
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC--C----CHHHHHHHHHHCCCCHHHHHCCCC
Q ss_conf 9999999999981997999999872469999998528988--3----589999999754999999506774
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNR--V----GASRLQHISEVLESPISFFFDVSP 78 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~--p----s~~~L~~iA~~l~v~~~~l~~~~~ 78 (144)
-+|.+||+.|+++|||++++|+++.++..+|..+|+|... | .---|..-|+.||++.+.|+....
T Consensus 14 t~G~~Lr~ARE~~GlSi~dvA~~LkL~~~~ieALE~dd~~~Lp~~tF~RGylRsYAr~LglD~~~ll~~~~ 84 (332)
T PRK10856 14 TTGVRLRQAREQLGLSQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELLPGLE 84 (332)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHC
T ss_conf 88799999999859999999987089899999985782210870364799999999997889799654210
No 31
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=97.87 E-value=3.4e-05 Score=53.49 Aligned_cols=65 Identities=22% Similarity=0.325 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHHHCCCCHHHHHCCCCC
Q ss_conf 9999999999819979999998724699999985289-8835899999997549999995067744
Q gi|254780424|r 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV-NRVGASRLQHISEVLESPISFFFDVSPT 79 (144)
Q Consensus 15 iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~-~~ps~~~L~~iA~~l~v~~~~l~~~~~~ 79 (144)
+--++......+++++.+||+.+|+|.++++++..|+ ..+++++|.+||.+|.+.|.++++..+.
T Consensus 3 i~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDiley~~d 68 (73)
T COG3655 3 IAVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDILEYVPD 68 (73)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEHHHHHHHHHHCCCCHHHEEEEECC
T ss_conf 137679999997501778999984369899999728866044899999999838984054577168
No 32
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=97.82 E-value=6.1e-05 Score=51.84 Aligned_cols=64 Identities=17% Similarity=0.311 Sum_probs=59.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHH
Q ss_conf 6689989999999999999981997999999872469999998528988358999999975499999950
Q gi|254780424|r 5 KKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74 (144)
Q Consensus 5 ~~~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~ 74 (144)
.++|+|| +-||.+-..-|+|+.+||..+| |+|-+|++-+|++..+++.+.++.+-||+|.+-|.
T Consensus 56 i~aP~pv-----e~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~~lI 119 (120)
T COG5499 56 IAAPDPV-----EVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPADVLI 119 (120)
T ss_pred HHCCCHH-----HHHHHHHHHHCCCHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHC
T ss_conf 3168888-----9999999993871888899867-61889999732067669999999998695888753
No 33
>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=97.35 E-value=0.00024 Score=48.01 Aligned_cols=51 Identities=16% Similarity=0.199 Sum_probs=44.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf 99999998199799999987246999999852898835899999997549999
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~ 70 (144)
-|=.+=+.+|||| +|+..|+|+-++.+=-++.-+|+++++.+++++||+.+
T Consensus 38 ALG~iArArGMtq--lA~~tGlsREsLYkALs~~GnP~f~T~lkV~~ALG~~L 88 (91)
T TIGR02684 38 ALGVIARARGMTQ--LAKKTGLSRESLYKALSGGGNPTFDTILKVTKALGLKL 88 (91)
T ss_pred HHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEE
T ss_conf 9889986516578--99982876788788735688956688899998408602
No 34
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=96.82 E-value=0.002 Score=42.14 Aligned_cols=35 Identities=26% Similarity=0.320 Sum_probs=31.0
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 999999819979999998724699999985289883
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRV 54 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~p 54 (144)
-+.+|.+ |+||.+.|+.+|+|++++|+|-+|++.+
T Consensus 15 A~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~ 49 (119)
T COG2522 15 AKELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGS 49 (119)
T ss_pred HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHCCCCCH
T ss_conf 9999995-8869999999688899999997367736
No 35
>pfam08667 BetR BetR domain. This family includes an N-terminal helix-turn-helix domain.
Probab=96.70 E-value=0.011 Score=37.33 Aligned_cols=64 Identities=20% Similarity=0.352 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHHCCCCH----HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCC
Q ss_conf 999999999999819979----9999987246999999852898835899999997549999995067
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQ----EKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ----~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~ 76 (144)
.-|.+|+|++=...|+.- .++++-||+|.|+..+=-+|...=+++.|.++|..||+|+..||+.
T Consensus 4 ~~ia~rvr~lL~r~GI~kRqh~s~is~iL~LSfS~a~RKLkG~spW~l~Ql~kVA~~fg~~~a~L~~~ 71 (146)
T pfam08667 4 LIVAERVRKLLTRTGIAERQHNTTIANILGLSFSQAYRKLKGSIPWNLAQLQKVAQYFGVPAAILLIY 71 (146)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
T ss_conf 89999999999863997567788999997874898878735899744999999999959799999275
No 36
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=96.34 E-value=0.011 Score=37.33 Aligned_cols=52 Identities=17% Similarity=0.241 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC
Q ss_conf 99999999999819979999998724699999985289883589999999754
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVL 66 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l 66 (144)
--|+.++.+-.++|||..|+|++.|+..|++.++-+| +.|..++|.+|-+.+
T Consensus 16 ~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G-~dpr~~tl~~I~kti 67 (170)
T COG4800 16 DFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG-SDPRYDTLTRIFKTI 67 (170)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHC-CCCCHHHHHHHHHHH
T ss_conf 7999999999981999899988709989999999817-996577899999999
No 37
>PRK02866 cyanate hydratase; Validated
Probab=96.21 E-value=0.034 Score=34.29 Aligned_cols=60 Identities=15% Similarity=0.181 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 999999999998199799999987246999999852898835899999997549999995
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
.+-++|-..+.++|||=+++|+.+|.|.-++.....|....+.+...++|++|+.|.+..
T Consensus 5 ~lte~i~~aK~~kgltw~~ia~~~G~s~v~~aaa~lGQ~~~~~e~A~~l~~~L~L~~~~~ 64 (147)
T PRK02866 5 ELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDAV 64 (147)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHH
T ss_conf 999999999998499899999894989999999984677899999999999749999999
No 38
>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=96.21 E-value=0.002 Score=42.20 Aligned_cols=26 Identities=27% Similarity=0.296 Sum_probs=22.9
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 81997999999872469999998528
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
..--||.|.|..+|+|+||+|++|+-
T Consensus 193 ~~~~tQREIA~~LgISRSYVSRIEK~ 218 (228)
T TIGR02846 193 GREKTQREIAKILGISRSYVSRIEKK 218 (228)
T ss_pred CCCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf 89541789987708650045488899
No 39
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=96.13 E-value=0.014 Score=36.75 Aligned_cols=54 Identities=20% Similarity=0.454 Sum_probs=41.0
Q ss_pred CCHHHHH-HHHHHHHHHHHCCCCHHHHHHHHH------HHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 9989999-999999999981997999999872------4699999985289883589999999
Q gi|254780424|r 8 PNPVDIN-VGKRIRLRRMILGMSQEKLGECLG------ITFQQVQKYEKGVNRVGASRLQHIS 63 (144)
Q Consensus 8 ~~~~d~~-iG~rIr~~R~~~glTQ~eLA~~lG------vs~s~is~~E~G~~~ps~~~L~~iA 63 (144)
||+-... ..+..|+.|..+|+||.+++..+| .|+++|+++|+=. .|.....++-
T Consensus 4 ~~l~Ele~Fa~~fk~rRi~LG~TQ~dVG~aL~~l~g~~~SQttIcRFE~l~--LS~kn~~kLk 64 (75)
T smart00352 4 TDPRELEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQ--LSFKNMCKLK 64 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC--CCHHHHHHHH
T ss_conf 999999999999999898737759999999998618643146888988605--4798899889
No 40
>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=95.81 E-value=0.0056 Score=39.26 Aligned_cols=49 Identities=20% Similarity=0.278 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCC
Q ss_conf 99999999999981997999999872469999998528988358999999975499999950677
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVS 77 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~ 77 (144)
+||=++||+++.+.+-.-++|++++| +.|++ .-||+.|+|+.+......
T Consensus 80 vrVPRrlkEl~~~~~~a~eeL~~~lg-------------R~Pt~---~EiAe~L~~s~EEv~~al 128 (229)
T TIGR02980 80 VRVPRRLKELRLKINKATEELTQRLG-------------RSPTV---AEIAEELGVSEEEVVEAL 128 (229)
T ss_pred EECCHHHHHHHHHHHHHHHHHHHHHC-------------CCCCH---HHHHHHHCCCHHHHHHHH
T ss_conf 66051389889999999999999828-------------89887---899988588999999999
No 41
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=95.64 E-value=0.017 Score=36.11 Aligned_cols=49 Identities=14% Similarity=0.139 Sum_probs=40.6
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCH---HHHHHHHHHCCCCHHHH
Q ss_conf 81997999999872469999998528988358---99999997549999995
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRVGA---SRLQHISEVLESPISFF 73 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~---~~L~~iA~~l~v~~~~l 73 (144)
.+.+|..++|+.+|||.+|+|++-||....+- ++..++|+-||-.++..
T Consensus 4 ~kkvTi~dIA~~aGVS~aTVSrvLn~~~~Vs~eTr~rV~~aa~elgY~pn~~ 55 (342)
T PRK10014 4 AKKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRNRQ 55 (342)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 9988799999998969999999977989999999999999999948997867
No 42
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=95.64 E-value=0.037 Score=34.02 Aligned_cols=55 Identities=15% Similarity=0.111 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHH
Q ss_conf 999999999981997999999872469999998528988358999999975499999
Q gi|254780424|r 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPIS 71 (144)
Q Consensus 15 iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~ 71 (144)
|-.-+-..-..+|||| +|++.|+|+..+.+--+..-+|+++++.+++++||+-..
T Consensus 39 i~~alg~var~~GMsq--vA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl~ 93 (100)
T COG3636 39 IAAALGVVARSRGMSQ--VARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRLS 93 (100)
T ss_pred HHHHHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEE
T ss_conf 9999999998657899--999949669999998478999758999999998086542
No 43
>PRK09492 treR trehalose repressor; Provisional
Probab=95.60 E-value=0.019 Score=35.91 Aligned_cols=49 Identities=10% Similarity=0.057 Sum_probs=40.7
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCH---HHHHHHHHHCCCCHHHH
Q ss_conf 81997999999872469999998528988358---99999997549999995
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRVGA---SRLQHISEVLESPISFF 73 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~---~~L~~iA~~l~v~~~~l 73 (144)
.+.+|.+++|+..|||.+|+|++-||...++- ++..++|+-||-.|+..
T Consensus 2 ~kkvTikDIA~~aGVS~aTVSrvLn~~~~vs~eTr~rV~~~a~elgY~Pn~~ 53 (315)
T PRK09492 2 QNKLTIKDIARLSGVGKSTVSRVLNNEPKVSPRTRERVEAVINQHGFSPSKS 53 (315)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 8988799999998979999999978989999999999999999969980778
No 44
>pfam00157 Pou Pou domain - N-terminal to homeobox domain.
Probab=95.52 E-value=0.036 Score=34.09 Aligned_cols=53 Identities=19% Similarity=0.381 Sum_probs=38.3
Q ss_pred CCHHHHH-HHHHHHHHHHHCCCCHHHHHHHHHH------HHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 9989999-9999999999819979999998724------69999998528988358999999
Q gi|254780424|r 8 PNPVDIN-VGKRIRLRRMILGMSQEKLGECLGI------TFQQVQKYEKGVNRVGASRLQHI 62 (144)
Q Consensus 8 ~~~~d~~-iG~rIr~~R~~~glTQ~eLA~~lGv------s~s~is~~E~G~~~ps~~~L~~i 62 (144)
+++-+.. ..+..|..|..+|+||.+++..+|. |+++|+++|+=. .|.....++
T Consensus 4 ~~l~Ele~Fa~~fk~rRi~LG~TQ~dVg~al~~l~G~~~SQttIcRFE~l~--Ls~kn~~kL 63 (75)
T pfam00157 4 TDLEELEQFAKEFKQRRIKLGYTQADVGLALGALYGPVFSQTTICRFEALQ--LSFKNMCKL 63 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC--CCHHHHHHH
T ss_conf 999999999999999898737759999999998708654235888888504--479989988
No 45
>PHA00542 putative Cro-like protein
Probab=95.50 E-value=0.034 Score=34.29 Aligned_cols=48 Identities=13% Similarity=0.195 Sum_probs=39.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHHH
Q ss_conf 9999999819979999998724699999985289-88358999999975
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV-NRVGASRLQHISEV 65 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~-~~ps~~~L~~iA~~ 65 (144)
.|-..-...||||.++++..||+++.|+++-.|+ ..|.+++..++-+.
T Consensus 22 E~V~aLi~~G~tQ~qI~~~tgv~QpsisRilsGk~kDpR~s~v~~L~~L 70 (82)
T PHA00542 22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHL 70 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCCCCHHHHHHHHH
T ss_conf 9999999822569999986087703689998088789720699999999
No 46
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=95.17 E-value=0.017 Score=36.14 Aligned_cols=49 Identities=20% Similarity=0.329 Sum_probs=34.5
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHCC-CCCCC-HHHHHHHHHHCCCCH
Q ss_conf 999981997999999872469999998528-98835-899999997549999
Q gi|254780424|r 21 LRRMILGMSQEKLGECLGITFQQVQKYEKG-VNRVG-ASRLQHISEVLESPI 70 (144)
Q Consensus 21 ~~R~~~glTQ~eLA~~lGvs~s~is~~E~G-~~~ps-~~~L~~iA~~l~v~~ 70 (144)
.+| ++||||.|.|+.+|.|++.||.+|+. ..++. ...=.++.+.++-|+
T Consensus 14 ~lR-~~G~tQ~eIA~~lgTSraNvs~iEk~A~eNIekAreTl~~~~~l~Apv 64 (139)
T PRK03975 14 RLR-KRGLTQQEIADILGTSRANISIIEKRARENIEKARNTLAFWNTLNAPV 64 (139)
T ss_pred HHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCE
T ss_conf 999-828979999999773288999999999999999999999999668988
No 47
>PRK09526 lacI lac repressor; Reviewed
Probab=95.09 E-value=0.034 Score=34.22 Aligned_cols=49 Identities=12% Similarity=0.149 Sum_probs=40.0
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHH---HHHHHHHHCCCCHHHH
Q ss_conf 819979999998724699999985289883589---9999997549999995
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRVGAS---RLQHISEVLESPISFF 73 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~---~L~~iA~~l~v~~~~l 73 (144)
.+..|-+++|+.+|||.+|+|++-||....+-+ +..+.++-+|-.++..
T Consensus 3 ~k~~TikDIA~~agVS~sTVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~~ 54 (342)
T PRK09526 3 SKPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNRV 54 (342)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 8997699999998969999999978979999999999999999839997888
No 48
>KOG3802 consensus
Probab=94.93 E-value=0.064 Score=32.50 Aligned_cols=59 Identities=22% Similarity=0.466 Sum_probs=47.0
Q ss_pred CCCHHHHH-HHHHHHHHHHHCCCCHHHHHHHHH------HHHHHHHHHHCCCCCCCHHHHHHHHHHCC
Q ss_conf 89989999-999999999981997999999872------46999999852898835899999997549
Q gi|254780424|r 7 IPNPVDIN-VGKRIRLRRMILGMSQEKLGECLG------ITFQQVQKYEKGVNRVGASRLQHISEVLE 67 (144)
Q Consensus 7 ~~~~~d~~-iG~rIr~~R~~~glTQ~eLA~~lG------vs~s~is~~E~G~~~ps~~~L~~iA~~l~ 67 (144)
.++.=|.. -.+..|..|..+|+||.+++-.+| .|..||+++|.= ..|+..++||-=.|.
T Consensus 202 ~~~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEAL--qLSFKNMCKLKPLL~ 267 (398)
T KOG3802 202 TPDLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEAL--QLSFKNMCKLKPLLE 267 (398)
T ss_pred CCCHHHHHHHHHHHHHHEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHH--CCCHHHHHHHHHHHH
T ss_conf 669999999999987650003644267888987650764430266676762--547787766379999
No 49
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=94.84 E-value=0.092 Score=31.47 Aligned_cols=57 Identities=16% Similarity=0.117 Sum_probs=46.6
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCC
Q ss_conf 999999981997999999872469999998528988358999999975499999950677
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVS 77 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~ 77 (144)
-|...=+.+|+|...|+.+.|+|.+++.+.-.-. .|..+.| ||++|||++..+..+.
T Consensus 12 dI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~rp-~pkgEri--IA~algv~P~eIWp~R 68 (82)
T COG3423 12 DIIAALKKKGTSLAALSREAGLSSSTLANALDRP-WPKGERI--IADALGVPPEEIWPSR 68 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCC-CCHHHHH--HHHHHCCCHHHHCCHH
T ss_conf 9999999856429999988087878999987478-8718899--9999589888818342
No 50
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=94.69 E-value=0.06 Score=32.67 Aligned_cols=40 Identities=15% Similarity=0.210 Sum_probs=31.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH---HHHCCC
Q ss_conf 7999999872469999998528988358999999---975499
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVNRVGASRLQHI---SEVLES 68 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~i---A~~l~v 68 (144)
|..++|+.+|||.+++|++-+|....+.++-.+| ++.||-
T Consensus 1 Ti~DIA~~agVS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY 43 (46)
T pfam00356 1 TIKDVARLAGVSKATVSRVLNNPERVSEETREKVEAAMEELGY 43 (46)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 9999999989799999999879798999999999999999789
No 51
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=94.66 E-value=0.062 Score=32.59 Aligned_cols=46 Identities=7% Similarity=0.128 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCC---CC---HHHHHHHHHHCCCCHHHH
Q ss_conf 97999999872469999998528988---35---899999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNR---VG---ASRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~---ps---~~~L~~iA~~l~v~~~~l 73 (144)
+|-+++|+..|||.+|+|++-||+.. .+ .++..+.++-||-.|+..
T Consensus 1 vTikDVA~~AGVS~aTVSrvLNg~~~~~~Vs~~Tr~rV~~aa~eLgY~Pn~~ 52 (330)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGKAKQYRISDKTVEKVMAVVREHNYHPNAV 52 (330)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 9789999997979989988838999888769999999999999968994888
No 52
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=94.66 E-value=0.064 Score=32.51 Aligned_cols=46 Identities=9% Similarity=0.062 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCH---HHHHHHHHHCCCCHHHH
Q ss_conf 97999999872469999998528988358---99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVGA---SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps~---~~L~~iA~~l~v~~~~l 73 (144)
.|.+++|+..|||.+|+|++-||....+- ++..+.|+-||-.++..
T Consensus 2 vTi~DVA~~AGVS~aTVSrvLn~~~~Vs~eTr~rV~~aa~eLgY~Pn~~ 50 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNSALVSPDTREAVMKAVSELGYRPNAN 50 (346)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 9789999998979999999977949999999999999999949984888
No 53
>PRK08099 nicotinamide-nucleotide adenylyltransferase; Provisional
Probab=94.57 E-value=0.13 Score=30.49 Aligned_cols=56 Identities=11% Similarity=0.176 Sum_probs=50.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHCCCCHHH
Q ss_conf 9999999981997999999872469999998528-9883589999999754999999
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG-VNRVGASRLQHISEVLESPISF 72 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G-~~~ps~~~L~~iA~~l~v~~~~ 72 (144)
..+++.|++.|+|..++|+..|+++.++++.-+| ..+||...|.++-++|++....
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (411)
T PRK08099 5 DYLKTAIKQQGCTLQQVADASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFPR 61 (411)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHH
T ss_conf 899999998488298876542340999999862524894378999999995886402
No 54
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=94.40 E-value=0.078 Score=31.96 Aligned_cols=45 Identities=16% Similarity=0.159 Sum_probs=35.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHH---HHHHHHHHCCCCHHHH
Q ss_conf 79999998724699999985289883589---9999997549999995
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVNRVGAS---RLQHISEVLESPISFF 73 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~~ps~~---~L~~iA~~l~v~~~~l 73 (144)
|..++|+..|||.+++|++-+|....+.+ ++..+++-||-.++.+
T Consensus 2 Ti~dvA~~aGVS~sTVSr~ln~~~~Vs~~tr~rV~~~a~~lgY~pn~~ 49 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPNRV 49 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 899999998959999999977999899999999999999978998999
No 55
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=94.38 E-value=0.052 Score=33.06 Aligned_cols=59 Identities=19% Similarity=0.217 Sum_probs=51.1
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHHHCCCCHH
Q ss_conf 999999999999819979999998724699999985289-88358999999975499999
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV-NRVGASRLQHISEVLESPIS 71 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~-~~ps~~~L~~iA~~l~v~~~ 71 (144)
-.|+..|+.+=+..+|+|++.|..+||+++-+|-+-+|+ +..+.+.|.-.....|.+++
T Consensus 27 ~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~ 86 (91)
T COG5606 27 SALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEID 86 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf 999999999999978779999998388873188998361457669999999997598552
No 56
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=94.37 E-value=0.11 Score=30.87 Aligned_cols=60 Identities=18% Similarity=0.264 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH-----CCCCCCC--------HHHHHHHHHHCCCCHHHH
Q ss_conf 99999999999819979999998724699999985-----2898835--------899999997549999995
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYE-----KGVNRVG--------ASRLQHISEVLESPISFF 73 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E-----~G~~~ps--------~~~L~~iA~~l~v~~~~l 73 (144)
.+--++..+.-.-||||.|+|+++|+|+.+++++- .|-..++ .+.=.+|-+.||.+-.+.
T Consensus 13 ~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~~a~V 85 (321)
T COG2390 13 RLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLKEAIV 85 (321)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEE
T ss_conf 9999999999846887999998839889999999999998793899967987653999999999659976999
No 57
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=94.37 E-value=0.078 Score=31.93 Aligned_cols=45 Identities=9% Similarity=0.091 Sum_probs=37.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCH---HHHHHHHHHCCCCHHHH
Q ss_conf 7999999872469999998528988358---99999997549999995
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVNRVGA---SRLQHISEVLESPISFF 73 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~~ps~---~~L~~iA~~l~v~~~~l 73 (144)
|-+++|++.|||.+|+|++-||....+. ++..+.|+.||-.++..
T Consensus 3 TIkDIA~~AGVS~sTVSrvLN~~~~Vs~~Tr~rV~~aa~eLgY~Pn~~ 50 (342)
T PRK10727 3 TIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNAN 50 (342)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 889999997969999999977979999999999999999939985888
No 58
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=94.28 E-value=0.084 Score=31.72 Aligned_cols=46 Identities=9% Similarity=0.031 Sum_probs=38.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH---HHHHHHCCCCHHHH
Q ss_conf 97999999872469999998528988358999---99997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVGASRL---QHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L---~~iA~~l~v~~~~l 73 (144)
-|-+++|+..|||.+|+|++-||....+-++- .+.|+-||-.++..
T Consensus 10 aTikDIA~~aGVS~sTVSrvLn~~~~Vs~~Tr~rV~~aa~eLgY~pn~~ 58 (341)
T PRK11041 10 ATMKDVALKAGVSTATVSRALMNPEKVSQSTRNRVEQAVLEVGYSPQSL 58 (341)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 8899999997979999999978989999999999999999819983888
No 59
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=94.11 E-value=0.16 Score=29.88 Aligned_cols=65 Identities=12% Similarity=0.016 Sum_probs=48.3
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCC
Q ss_conf 998999999999999998199799999987246999999852898835899999997549999995067
Q gi|254780424|r 8 PNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 8 ~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~ 76 (144)
+..||-|=..=+-++ ..+|+|...|+...|+|.+++.+--... .|..+.+ ||++|||++..+...
T Consensus 3 ~~~~DWH~ADIiAAL-~KrG~sLa~Lsr~aGls~sTL~nAL~rp-wPKgE~i--IA~aLGv~P~eIWPS 67 (90)
T PRK10344 3 SNFIDWHPADIIAGL-RKKGTSMAAESRRNGLSSSTLANALSRP-WPKGEMI--IAKALGTDPWVIWPS 67 (90)
T ss_pred CCCCCCCHHHHHHHH-HHCCCCHHHHHHHCCCCHHHHHHHHCCC-CCHHHHH--HHHHHCCCHHHCCCC
T ss_conf 533668999999999-9868869999999099868899987489-9567999--999978798880975
No 60
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=94.09 E-value=0.095 Score=31.38 Aligned_cols=45 Identities=11% Similarity=0.055 Sum_probs=37.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCH---HHHHHHHHHCCCCHHHH
Q ss_conf 7999999872469999998528988358---99999997549999995
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVNRVGA---SRLQHISEVLESPISFF 73 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~~ps~---~~L~~iA~~l~v~~~~l 73 (144)
|-+++|+..|||.+|+|++-||...++- ++..+.|+-||-.++..
T Consensus 3 TikDIA~~AGVS~aTVSrvLn~~~~Vs~~Tr~rV~~aa~eLgY~pn~~ 50 (335)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAV 50 (335)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 889999997989999999968969989999999999999829997877
No 61
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=94.00 E-value=0.1 Score=31.13 Aligned_cols=42 Identities=19% Similarity=0.242 Sum_probs=35.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCC--CCC---HHHHHHHHHHCCCCH
Q ss_conf 799999987246999999852898--835---899999997549999
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVN--RVG---ASRLQHISEVLESPI 70 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~--~ps---~~~L~~iA~~l~v~~ 70 (144)
|.+++|+..|||.+|+|++-||.. .++ .++..+.|+-||-.+
T Consensus 3 TikDVA~~AGVS~sTVSrvLn~~~~~~V~~~Tr~rV~~aa~elgY~~ 49 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYKT 49 (327)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 68999999788899999995898999968999999999999968998
No 62
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=93.99 E-value=0.1 Score=31.25 Aligned_cols=46 Identities=11% Similarity=0.107 Sum_probs=37.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHH---HHHHHHHHCCCCHHHH
Q ss_conf 979999998724699999985289883589---9999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVGAS---RLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps~~---~L~~iA~~l~v~~~~l 73 (144)
.|.+++|+..|||.+|+|++-||....+.+ +..+.++-||--++..
T Consensus 1 ~TikDVA~~AGVS~sTVSrvln~~~~Vs~eTr~rV~~a~~elgY~pn~~ 49 (333)
T COG1609 1 ATIKDVAKLAGVSKATVSRVLNGSPYVSEETREKVLAAIKELGYRPNAV 49 (333)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 9689999996899989889877999879999999999999978998989
No 63
>pfam08965 DUF1870 Domain of unknown function (DUF1870). This domain is found in a set of hypothetical bacterial proteins.
Probab=93.92 E-value=0.13 Score=30.45 Aligned_cols=48 Identities=19% Similarity=0.278 Sum_probs=42.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHH--HHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 999999981997999999872--469999998528988358999999975
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLG--ITFQQVQKYEKGVNRVGASRLQHISEV 65 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lG--vs~s~is~~E~G~~~ps~~~L~~iA~~ 65 (144)
-|..+|+..-||-.|-|..+| ++..+..+||+|...+..+...++...
T Consensus 4 ELQAlR~if~mti~EaA~~I~~~~~s~~Wq~WE~G~~~IP~~i~~~~~~m 53 (117)
T pfam08965 4 ELQALRKILFLTIVEAAELIGQSVSSRTWQRWEKGDIAIPDEVEAKLRKL 53 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 89999999996499999999468888999999758988999999999999
No 64
>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=93.79 E-value=0.039 Score=33.90 Aligned_cols=48 Identities=21% Similarity=0.317 Sum_probs=32.7
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCC-CCCCC-HHHHHHHHHHCCCCHHH
Q ss_conf 81997999999872469999998528-98835-89999999754999999
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKG-VNRVG-ASRLQHISEVLESPISF 72 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G-~~~ps-~~~L~~iA~~l~v~~~~ 72 (144)
++||+|++.|..||.|++-||-+|+- ..++. ..+=..|-+.+.-|+.-
T Consensus 19 ~kGl~Q~eIAk~LkTtRaNvS~iEkrA~EnIeKa~NTl~~~~~i~spv~i 68 (142)
T TIGR00721 19 EKGLKQKEIAKILKTTRANVSIIEKRALENIEKAKNTLKLYKRIKSPVRI 68 (142)
T ss_pred HCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEE
T ss_conf 33888788987726720137898887443237766389999974498258
No 65
>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=93.65 E-value=0.083 Score=31.77 Aligned_cols=34 Identities=26% Similarity=0.464 Sum_probs=29.6
Q ss_pred HHHHHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999--81997999999872469999998
Q gi|254780424|r 14 NVGKRIRLRRM--ILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 14 ~iG~rIr~~R~--~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
.||.|+|=++. ..++||.|++..+|||-++|-+=
T Consensus 41 dl~~R~~I~~~LL~~~~~QREi~~~lG~SiA~ITRG 76 (95)
T TIGR01321 41 DLGSRVRIVEELLEGEMSQREIAEKLGVSIATITRG 76 (95)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 998799999999614897478888637616678787
No 66
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=93.65 E-value=0.038 Score=33.91 Aligned_cols=51 Identities=24% Similarity=0.288 Sum_probs=37.1
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCC-CCCCC-HHHHHHHHHHCCCCHHHHH
Q ss_conf 981997999999872469999998528-98835-8999999975499999950
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKYEKG-VNRVG-ASRLQHISEVLESPISFFF 74 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~E~G-~~~ps-~~~L~~iA~~l~v~~~~l~ 74 (144)
.++||||+|.|+.+|.+++.+|.+|+. ..++. ..+-..+++-++-|++...
T Consensus 20 RekG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnTL~l~~~i~spv~i~v 72 (143)
T COG1356 20 REKGLTQSEIARILKTTRANVSAIEKRALENIEKARNTLLLWEQINSPVSITV 72 (143)
T ss_pred HHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf 64056489999997545101799999999989999889999998469758985
No 67
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=93.51 E-value=0.06 Score=32.65 Aligned_cols=46 Identities=24% Similarity=0.281 Sum_probs=42.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCC--CCHHHHH
Q ss_conf 799999987246999999852898835899999997549--9999950
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLE--SPISFFF 74 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~--v~~~~l~ 74 (144)
.|..+|..+|||.+++++|-+|.+....+.-..|..+-+ |+...|=
T Consensus 14 ~q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~g~Vs~~elr 61 (96)
T COG4197 14 GQKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATSGQVSREELR 61 (96)
T ss_pred CHHHHHHHHCCCCHHHHHHHHHEEECCCCCCHHHHHHHCCCCCHHHHC
T ss_conf 389999997268147887765201047553328999853771599976
No 68
>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=93.38 E-value=0.084 Score=31.72 Aligned_cols=23 Identities=26% Similarity=0.478 Sum_probs=21.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 97999999872469999998528
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G 50 (144)
||-+|||+.+|+|+++|++|=+-
T Consensus 1 mT~eELa~~~G~srQtINkwaRk 23 (122)
T pfam07037 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHHCCHHHHHHHHHHH
T ss_conf 98789988747129999999997
No 69
>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=93.36 E-value=0.024 Score=35.21 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHH------CCCCHHHHHHHHHHHHHH-HHHHHCCCC
Q ss_conf 999999999998------199799999987246999-999852898
Q gi|254780424|r 14 NVGKRIRLRRMI------LGMSQEKLGECLGITFQQ-VQKYEKGVN 52 (144)
Q Consensus 14 ~iG~rIr~~R~~------~glTQ~eLA~~lGvs~s~-is~~E~G~~ 52 (144)
.+|++|+.-|.. +-=|-+|||+.+|+++-. +...|.+.+
T Consensus 94 ~la~k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~ 139 (231)
T TIGR02885 94 ELARKIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARS 139 (231)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCC
T ss_conf 9999998779999998389988899988758788786644202576
No 70
>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=93.27 E-value=0.024 Score=35.20 Aligned_cols=33 Identities=21% Similarity=0.475 Sum_probs=27.6
Q ss_pred HHHHCCCCHHHHHHHHHHHHHH-HHHHHCCCCCC
Q ss_conf 9998199799999987246999-99985289883
Q gi|254780424|r 22 RRMILGMSQEKLGECLGITFQQ-VQKYEKGVNRV 54 (144)
Q Consensus 22 ~R~~~glTQ~eLA~~lGvs~s~-is~~E~G~~~p 54 (144)
+=.--|+||.|+|++||+|-|+ -|++=+|+...
T Consensus 111 L~el~G~sQ~e~A~kLGlSlSGaKSRVQRGR~~L 144 (170)
T TIGR02959 111 LTELEGLSQKEIAEKLGLSLSGAKSRVQRGRKKL 144 (170)
T ss_pred HHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 8750799827998761753351567889999999
No 71
>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=93.04 E-value=0.15 Score=30.17 Aligned_cols=47 Identities=11% Similarity=0.224 Sum_probs=38.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC----------------CCCCHHHHHHHHHHCCCCHHHHH
Q ss_conf 979999998724699999985289----------------88358999999975499999950
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGV----------------NRVGASRLQHISEVLESPISFFF 74 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~----------------~~ps~~~L~~iA~~l~v~~~~l~ 74 (144)
||--+||++.||..|++.-||.-. .....=.+.|+|...|+|...+=
T Consensus 2 lTvG~lA~R~GVAVSALHFYE~KGLI~S~Rn~GnQRRy~Rd~LRRVa~Ik~AQ~vGipL~~I~ 64 (142)
T TIGR01950 2 LTVGELAKRAGVAVSALHFYESKGLIHSVRNAGNQRRYKRDVLRRVAVIKVAQRVGIPLAEIA 64 (142)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 861016556557888776541035610113688834232001115674332332589888999
No 72
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=92.90 E-value=0.28 Score=28.42 Aligned_cols=54 Identities=20% Similarity=0.194 Sum_probs=42.6
Q ss_pred HHH-HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCC--HHHHHC
Q ss_conf 999-819979999998724699999985289883589999999754999--999506
Q gi|254780424|r 22 RRM-ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESP--ISFFFD 75 (144)
Q Consensus 22 ~R~-~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~--~~~l~~ 75 (144)
+|. +.-+|-+||+..+|++.+.+++|=+|+..|+.++-..|-+.++-. +..++.
T Consensus 17 LR~lK~~~tykELs~~~gip~s~L~RYv~g~vlPs~e~A~~i~~~l~~~~~l~~~l~ 73 (238)
T PRK08558 17 LRSLKKTYTYEELSSILGLPESVLSRYVNGHVLPSVERAREIVEKLKPYYPLEEEVK 73 (238)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999850268999998879799998505348878758999999998421144999999
No 73
>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=92.65 E-value=0.35 Score=27.74 Aligned_cols=46 Identities=11% Similarity=0.111 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf 9999999999981997999999872469999998528988358999
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRL 59 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L 59 (144)
++.+-||.+-...+++|.++++..|++.|.+|.|-+-...++..+-
T Consensus 115 ~v~~~Ik~~m~~h~ipQ~~vv~~TGlnQS~lSq~LnkGt~Mk~~kr 160 (177)
T pfam04814 115 RVAKMIKSYMQQHNIPQREVVDATGLNQSHLSQHLNKGTPMKTQKR 160 (177)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHCCCCCHHHHH
T ss_conf 9999999999876884667876106559999999966884078999
No 74
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=92.55 E-value=0.2 Score=29.36 Aligned_cols=43 Identities=12% Similarity=0.117 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHH---HHHHHHHHCCCCHHHH
Q ss_conf 999998724699999985289883589---9999997549999995
Q gi|254780424|r 31 EKLGECLGITFQQVQKYEKGVNRVGAS---RLQHISEVLESPISFF 73 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E~G~~~ps~~---~L~~iA~~l~v~~~~l 73 (144)
+++|+..|||.+|+|++-||....+-+ +..+.|+-||-.|+.+
T Consensus 2 kDIA~~AGVS~sTVSrvLn~~~~Vs~~tr~rV~~aa~elgY~pn~~ 47 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSAL 47 (327)
T ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 6898786989999999978959999999999999999829986888
No 75
>KOG1168 consensus
Probab=92.51 E-value=0.087 Score=31.64 Aligned_cols=44 Identities=23% Similarity=0.561 Sum_probs=36.7
Q ss_pred CCHHHHH-HHHHHHHHHHHCCCCHHHHHHHHH---------HHHHHHHHHHCCC
Q ss_conf 9989999-999999999981997999999872---------4699999985289
Q gi|254780424|r 8 PNPVDIN-VGKRIRLRRMILGMSQEKLGECLG---------ITFQQVQKYEKGV 51 (144)
Q Consensus 8 ~~~~d~~-iG~rIr~~R~~~glTQ~eLA~~lG---------vs~s~is~~E~G~ 51 (144)
.+|.+-. -.+|.|++|.++|.||++++..+- .|+|+|.++|+=.
T Consensus 214 tDPReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLT 267 (385)
T KOG1168 214 TDPRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLT 267 (385)
T ss_pred CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEC
T ss_conf 888999999999875454306427777889872768875532312133210000
No 76
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=92.51 E-value=0.18 Score=29.68 Aligned_cols=57 Identities=18% Similarity=0.150 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHC--CC--CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHH
Q ss_conf 99999999999981--99--7999999872469999998528988358999999975499999950
Q gi|254780424|r 13 INVGKRIRLRRMIL--GM--SQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74 (144)
Q Consensus 13 ~~iG~rIr~~R~~~--gl--TQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~ 74 (144)
+-.|.=++.+|..- -+ +..+.+.++.-....+ .-|.| +.|+.+- ||+.||++....+
T Consensus 84 ~I~Gei~d~LR~~~~v~vpR~~~~~~~~i~~~~~~l-~~el~-r~pt~~E---IA~~L~i~~ee~~ 144 (247)
T COG1191 84 RIRGEILDYLRKNDSVKVPRSLRELGRRIEEAIDEL-EQELG-REPTDEE---IAEELGIDKEEYI 144 (247)
T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH-HHHHC-CCCCHHH---HHHHHCCCHHHHH
T ss_conf 999999999984787467689988877889999999-99847-9986899---9989698999999
No 77
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=92.50 E-value=0.18 Score=29.62 Aligned_cols=37 Identities=16% Similarity=0.362 Sum_probs=32.0
Q ss_pred HHHHHHHHHH--HHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999999999--981997999999872469999998528
Q gi|254780424|r 14 NVGKRIRLRR--MILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 14 ~iG~rIr~~R--~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
.+++|++-.+ ...|+||.++|+.+|+|..||++.=+-
T Consensus 34 ala~R~~va~~LL~~~~syreI~~~~g~S~aTItRvsr~ 72 (88)
T pfam01371 34 ALAQRLRIAKELLRGELSQREIAQELGASIATITRGSNC 72 (88)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999999999978998999999859852314788999
No 78
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=92.15 E-value=0.1 Score=31.15 Aligned_cols=42 Identities=19% Similarity=0.290 Sum_probs=31.2
Q ss_pred HHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC
Q ss_conf 9999999--819979999998724699999985289883589999999754
Q gi|254780424|r 18 RIRLRRM--ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVL 66 (144)
Q Consensus 18 rIr~~R~--~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l 66 (144)
-+-.+|. -.||||+|-|++.|||++|++++-..- -.++|++|
T Consensus 41 E~EAiRL~D~egl~QeeaA~~MgVSR~Tf~ril~~A-------RkKvA~aL 84 (100)
T pfam02001 41 EFEAIRLVDYEDYTQEEAAKLMGISRRTVWRLLTSA-------RKKIADAL 84 (100)
T ss_pred HHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHH-------HHHHHHHH
T ss_conf 999999873607989999988497699999999999-------99999998
No 79
>PRK07773 replicative DNA helicase; Validated
Probab=91.93 E-value=0.25 Score=28.73 Aligned_cols=56 Identities=18% Similarity=0.223 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf 99999999999998199799999987246999999852898835899999997549999
Q gi|254780424|r 12 DINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70 (144)
Q Consensus 12 d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~ 70 (144)
-.++-..+|....+.|+|..++++.+|+.....+-| +..+|-+++.++|.+|+-+.
T Consensus 709 P~evw~~Vr~a~~~~g~t~r~~~~~~g~~~~g~~~~---k~~~SR~Rl~~~A~~l~~~~ 764 (868)
T PRK07773 709 PKKVWKQVRPRLQAKQMTTRQLHEPIGTSYCGSTLW---KHSPSRERAHRVAARIQSRE 764 (868)
T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHH---CCCCCHHHHHHHHHHHCCHH
T ss_conf 589999999999860654899998725454640132---03422778999998747888
No 80
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=91.84 E-value=0.41 Score=27.30 Aligned_cols=41 Identities=15% Similarity=0.158 Sum_probs=34.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 998766899899999999999999819979999998724699999
Q gi|254780424|r 1 MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQ 45 (144)
Q Consensus 1 ~~~~~~~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is 45 (144)
||.|-|++ .+|.. =|+.+.+..-+|-.++|+++|+|.++++
T Consensus 1 m~~~~klD-~~D~~---IL~~Lq~d~R~s~~eiA~~lglS~stv~ 41 (153)
T PRK11179 1 MMENYQID-NLDRG---ILEALMENARTPYAELAKQFGVSPGTIH 41 (153)
T ss_pred CCCCCCCC-HHHHH---HHHHHHHCCCCCHHHHHHHHCCCHHHHH
T ss_conf 98657678-99999---9999998489999999999892999999
No 81
>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=91.77 E-value=0.22 Score=29.11 Aligned_cols=40 Identities=18% Similarity=0.252 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHH---HHHHHCCCCH
Q ss_conf 999998724699999985289883589999---9997549999
Q gi|254780424|r 31 EKLGECLGITFQQVQKYEKGVNRVGASRLQ---HISEVLESPI 70 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~---~iA~~l~v~~ 70 (144)
.++|+++|||.+|+|++-+|...++-++-. ..++-||..+
T Consensus 1 ~diA~~~gvS~~TVSr~ln~~~~Vs~~tr~~I~~~~~elgY~~ 43 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRP 43 (52)
T ss_pred CHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 9288887859999999987989899999999999999988897
No 82
>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=91.64 E-value=0.27 Score=28.53 Aligned_cols=30 Identities=23% Similarity=0.432 Sum_probs=24.5
Q ss_pred HHHHHH--HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999--981997999999872469999998
Q gi|254780424|r 18 RIRLRR--MILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 18 rIr~~R--~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
.+.++| .+.|.|..++|..+|||+++|.+|
T Consensus 10 q~~~ar~l~~~G~~~~~iA~~~GVsr~Tiyr~ 41 (42)
T cd00569 10 QIEEARRLLAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999997898999999979799999865
No 83
>PHA00675 hypothetical protein
Probab=91.64 E-value=0.35 Score=27.75 Aligned_cols=47 Identities=23% Similarity=0.175 Sum_probs=35.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH---CCCCCC
Q ss_conf 766899899999999999999819979999998724699999985---289883
Q gi|254780424|r 4 NKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYE---KGVNRV 54 (144)
Q Consensus 4 ~~~~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E---~G~~~p 54 (144)
|.+.+| ..=++||++|+.-||+-..||....+++++|.++. +-..+|
T Consensus 20 na~ltd----~~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtIAkICqYeRR~Qt~ 69 (78)
T PHA00675 20 NAKLTD----AEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYERRGQFA 69 (78)
T ss_pred CCCCCH----HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCC
T ss_conf 565778----99999999998728438999999727568999998898824674
No 84
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=91.56 E-value=1.2 Score=24.41 Aligned_cols=68 Identities=18% Similarity=0.211 Sum_probs=60.3
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCC
Q ss_conf 998999999999999998199799999987246999999852898835899999997549999995067
Q gi|254780424|r 8 PNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 8 ~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~ 76 (144)
+|.| -.|.+.|=...+.+|+|-+++++.+|.+..++...-.|....+.+--.+++.+||.+-+.+...
T Consensus 3 ~~~i-~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygq~~~~~~ear~v~e~L~L~~~~v~~L 70 (151)
T COG1513 3 RNII-LDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEALDLDEDAILLL 70 (151)
T ss_pred CCHH-HHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf 0058-9999999997875499699997550833999999997620289999999999819987889984
No 85
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=91.51 E-value=0.57 Score=26.40 Aligned_cols=52 Identities=17% Similarity=0.324 Sum_probs=35.3
Q ss_pred HHHHHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 99999999999--81997999999872469999998528988358999999975
Q gi|254780424|r 14 NVGKRIRLRRM--ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEV 65 (144)
Q Consensus 14 ~iG~rIr~~R~--~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~ 65 (144)
.+|.|++-++. ...+||.|++..+|||-.+|-+=-|.-.+.+.+....+.+.
T Consensus 45 al~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~ 98 (103)
T COG2973 45 ALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKV 98 (103)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHCCCHHHHCCCCHHHHHHHHHH
T ss_conf 999999999999956353999999858625655044444235987899999997
No 86
>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=91.30 E-value=0.72 Score=25.75 Aligned_cols=57 Identities=11% Similarity=0.072 Sum_probs=48.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 999999998199799999987246999999852898835899999997549999995
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
.+||..=.++--||..+|..+|+|..++|.=-+|+..-..+.+.+.++.|++|.+.+
T Consensus 6 ~kLrgrI~Ek~gtq~~Fa~~lg~se~tlslkln~~v~w~q~ei~kai~lL~i~~d~i 62 (69)
T pfam05339 6 SKLKGRILEKYGTQYNFASAIGLSERSLSLKLNDKVIWVANEIEKAIDLLGIPKDDI 62 (69)
T ss_pred HHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
T ss_conf 886032889956798999995811768889876867753999999999968998887
No 87
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=91.26 E-value=0.36 Score=27.67 Aligned_cols=57 Identities=21% Similarity=0.203 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH-HHHHHHCCCCHH
Q ss_conf 9999999999981997999999872469999998528988358999-999975499999
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRL-QHISEVLESPIS 71 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L-~~iA~~l~v~~~ 71 (144)
..=+.+|++=.--|+||..+|..+|+|.+++|+|-+| ..+..... .+|+..++-+..
T Consensus 6 ~~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g-~~g~~~~~~a~ia~~le~~~~ 63 (297)
T COG2842 6 IEIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNG-YKGDYATNEAKIAAFLEKKGV 63 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCC-CCCHHHHHHHHHHHHHCCCCC
T ss_conf 9999999999861666999998736684457878437-674177789999999727776
No 88
>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=91.25 E-value=0.15 Score=30.17 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=20.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 997999999872469999998528
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
.-||+++|+.+|+|+|+||+.|+-
T Consensus 198 e~tqk~vad~lGisqsyisrlek~ 221 (234)
T TIGR02835 198 EKTQKEVADLLGISQSYISRLEKR 221 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 146788898862468999999999
No 89
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=91.07 E-value=0.24 Score=28.85 Aligned_cols=51 Identities=12% Similarity=0.014 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHC---CC----CCCCHHHHHHHHHHCC
Q ss_conf 99999999999819-9799999987246999999852---89----8835899999997549
Q gi|254780424|r 14 NVGKRIRLRRMILG-MSQEKLGECLGITFQQVQKYEK---GV----NRVGASRLQHISEVLE 67 (144)
Q Consensus 14 ~iG~rIr~~R~~~g-lTQ~eLA~~lGvs~s~is~~E~---G~----~~ps~~~L~~iA~~l~ 67 (144)
|-+.-...++...| +.+. .|+-+ +--.++--|.. +. .+| ..-|++||.-+-
T Consensus 22 h~~~L~~~l~~Rl~~~~~~-~AeDl-~QDvFlrl~~~~~~~~~~~i~~p-~a~L~rIA~Nl~ 80 (178)
T PRK12529 22 NHAWLRNWLAYRLRSWGRG-VADDL-AHDIFLRILASRDGGQREAIRQP-RAYLARIANCVL 80 (178)
T ss_pred HHHHHHHHHHHHHCCCCCC-CHHHH-HHHHHHHHHHHCCCCCCCHHHHH-HHHHHHHHHHHH
T ss_conf 9999999999982899835-46999-99999999973444564323348-999999999999
No 90
>PRK01381 Trp operon repressor; Provisional
Probab=90.90 E-value=0.25 Score=28.70 Aligned_cols=52 Identities=15% Similarity=0.397 Sum_probs=36.7
Q ss_pred HHHHHHHHHH-HHCC-CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 9999999999-9819-97999999872469999998528988358999999975
Q gi|254780424|r 14 NVGKRIRLRR-MILG-MSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEV 65 (144)
Q Consensus 14 ~iG~rIr~~R-~~~g-lTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~ 65 (144)
.||.|++-++ ...| +||.++|+.+|||-++|.+=-|--...+.+....+.+.
T Consensus 40 al~~R~~I~~~Ll~ge~sQReIa~~lgvsiAtITRGSn~LK~~~~~~k~~l~~~ 93 (99)
T PRK01381 40 ALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQL 93 (99)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEECCCCHHHHHCCCHHHHHHHHHH
T ss_conf 999999999999948764999999849740200002698853999999999998
No 91
>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=90.50 E-value=0.29 Score=28.32 Aligned_cols=34 Identities=32% Similarity=0.541 Sum_probs=29.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999999981997999999872469999998528
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
+.|=.+|--.|+|+.|+|+.+|+|.+++++.++.
T Consensus 10 r~ii~l~y~~~~t~~EIA~~lgis~~~V~~~~~r 43 (50)
T pfam04545 10 REVLVLRFGEGLTLEEIGERLGISRERVRQIEKR 43 (50)
T ss_pred HHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999987068824999999989799999999999
No 92
>PRK04217 hypothetical protein; Provisional
Probab=90.36 E-value=0.2 Score=29.31 Aligned_cols=42 Identities=19% Similarity=0.362 Sum_probs=31.7
Q ss_pred HHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC
Q ss_conf 9999999--819979999998724699999985289883589999999754
Q gi|254780424|r 18 RIRLRRM--ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVL 66 (144)
Q Consensus 18 rIr~~R~--~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l 66 (144)
-+-.+|. -.||||+|-|++.|||++|++++-..- -.++|++|
T Consensus 47 E~EaiRL~D~egl~qeeaA~~M~VSR~Tf~ril~~A-------R~KvA~aL 90 (110)
T PRK04217 47 EFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSA-------RKKVAQML 90 (110)
T ss_pred HHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHH-------HHHHHHHH
T ss_conf 999999873607989999988497699999999999-------99999998
No 93
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=89.87 E-value=0.87 Score=25.23 Aligned_cols=45 Identities=20% Similarity=0.150 Sum_probs=34.3
Q ss_pred CCCCCCCCC-HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 998766899-899999999999999819979999998724699999
Q gi|254780424|r 1 MVGNKKIPN-PVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQ 45 (144)
Q Consensus 1 ~~~~~~~~~-~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is 45 (144)
|++-|+.|. .+|..==+=|+.++...-+|..+||+++|+|++++.
T Consensus 1 ~~~~~~r~~~~LD~~D~~IL~~Lq~daR~s~~eLA~~vglS~stv~ 46 (164)
T PRK11169 1 MVDSKKRPGKDLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCL 46 (164)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHH
T ss_conf 9867669964551999999999998489999999999892999999
No 94
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=89.44 E-value=0.49 Score=26.83 Aligned_cols=19 Identities=16% Similarity=0.464 Sum_probs=10.4
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q ss_conf 7999999872469999998
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~ 47 (144)
|-+|+|+.+|+|...+..+
T Consensus 131 t~~EiA~~l~is~~~v~~~ 149 (256)
T PRK07408 131 TDQEIAQALDISLEEWQEI 149 (256)
T ss_pred CHHHHHHHHCCCHHHHHHH
T ss_conf 8999998959699999999
No 95
>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=89.38 E-value=0.27 Score=28.43 Aligned_cols=41 Identities=20% Similarity=0.211 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCC
Q ss_conf 9979999998724699999985289883589999999754999
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESP 69 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~ 69 (144)
=++|..+|+.+||..|+||+|-.+-. |....|..+-+ +||.
T Consensus 23 ~~gq~~~A~~~Gv~es~ISRwK~~~~-~~~smllAvLE-~Gv~ 63 (91)
T pfam05269 23 MLGQRKTAEAVGVDESQISRWKRDWI-PKFSMLLAVLE-WGVV 63 (91)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHH-HHHHHHHHHHH-HCCC
T ss_conf 98436689996888998634443069-99999999999-5556
No 96
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=89.02 E-value=0.54 Score=26.57 Aligned_cols=18 Identities=22% Similarity=0.383 Sum_probs=10.3
Q ss_pred CHHHHHHHHHHHHHHHHH
Q ss_conf 799999987246999999
Q gi|254780424|r 29 SQEKLGECLGITFQQVQK 46 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~ 46 (144)
|-+|+|+.+|++...+..
T Consensus 144 t~~EiA~~lg~~~~~v~~ 161 (263)
T PRK07122 144 TASELAAELGMDREEVVE 161 (263)
T ss_pred CHHHHHHHHCCCHHHHHH
T ss_conf 999999896939999999
No 97
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=88.95 E-value=0.37 Score=27.60 Aligned_cols=42 Identities=19% Similarity=0.314 Sum_probs=31.3
Q ss_pred HHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC
Q ss_conf 9999999--819979999998724699999985289883589999999754
Q gi|254780424|r 18 RIRLRRM--ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVL 66 (144)
Q Consensus 18 rIr~~R~--~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l 66 (144)
-+-.+|. -.||||+|-|.+.|||++|+++.-+. -..++|.+|
T Consensus 38 ElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~s-------AR~KvA~aL 81 (99)
T COG1342 38 ELEALRLVDYEGLTQEEAALRMGISRQTFWRLLTS-------ARKKVADAL 81 (99)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHH
T ss_conf 98899988686105789999846429999999999-------999999998
No 98
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=88.86 E-value=0.5 Score=26.76 Aligned_cols=11 Identities=27% Similarity=0.238 Sum_probs=5.0
Q ss_pred HCCCCHHHHHH
Q ss_conf 81997999999
Q gi|254780424|r 25 ILGMSQEKLGE 35 (144)
Q Consensus 25 ~~glTQ~eLA~ 35 (144)
..|+...+|-+
T Consensus 79 ~~G~~l~DLIq 89 (239)
T PRK08301 79 NTGINIEDLIS 89 (239)
T ss_pred CCCCCHHHHHH
T ss_conf 89979899999
No 99
>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=88.74 E-value=0.33 Score=27.96 Aligned_cols=23 Identities=17% Similarity=0.440 Sum_probs=20.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 97999999872469999998528
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G 50 (144)
||-.|+|+.+|||..|+.+|++-
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 100
>PRK05572 sporulation sigma factor SigF; Validated
Probab=88.69 E-value=0.55 Score=26.50 Aligned_cols=18 Identities=39% Similarity=0.512 Sum_probs=8.9
Q ss_pred CHHHHHHHHHHHHHHHHH
Q ss_conf 799999987246999999
Q gi|254780424|r 29 SQEKLGECLGITFQQVQK 46 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~ 46 (144)
|-+++|+.+|++...+..
T Consensus 134 s~~eia~~lg~~~~~v~~ 151 (251)
T PRK05572 134 TIEELAEYLGVTPEEVVL 151 (251)
T ss_pred CHHHHHHHHCCCHHHHHH
T ss_conf 899999997939999999
No 101
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=88.63 E-value=0.55 Score=26.50 Aligned_cols=31 Identities=29% Similarity=0.368 Sum_probs=15.3
Q ss_pred HHHHHHHHHCCC--CHHHHHHHHHHHHHHHHHH
Q ss_conf 999999998199--7999999872469999998
Q gi|254780424|r 17 KRIRLRRMILGM--SQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 17 ~rIr~~R~~~gl--TQ~eLA~~lGvs~s~is~~ 47 (144)
+-.++++.++|= |-+|+|+.+|++...+..+
T Consensus 103 ~a~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~ 135 (229)
T PRK12427 103 EAIRQIAKRLGHEPNFEEISAELNLTADEYQEY 135 (229)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999998588999999998919999999999
No 102
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=88.60 E-value=0.59 Score=26.30 Aligned_cols=19 Identities=16% Similarity=0.333 Sum_probs=11.7
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q ss_conf 7999999872469999998
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~ 47 (144)
|-+++|+.+|++...+..+
T Consensus 134 t~~eiA~~l~~s~e~v~~~ 152 (257)
T PRK08583 134 KISEIADRLGVSEEEVLEA 152 (257)
T ss_pred CHHHHHHHHCCCHHHHHHH
T ss_conf 7999998959599999999
No 103
>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=88.47 E-value=0.28 Score=28.34 Aligned_cols=52 Identities=17% Similarity=0.266 Sum_probs=44.7
Q ss_pred HHHHC--CCCHHHHHHHHHHHH--HHHHHHHCCCCCCCHHHHHHHHHHCCCC---HHHH
Q ss_conf 99981--997999999872469--9999985289883589999999754999---9995
Q gi|254780424|r 22 RRMIL--GMSQEKLGECLGITF--QQVQKYEKGVNRVGASRLQHISEVLESP---ISFF 73 (144)
Q Consensus 22 ~R~~~--glTQ~eLA~~lGvs~--s~is~~E~G~~~ps~~~L~~iA~~l~v~---~~~l 73 (144)
.|+.. -.|-..+|+++|.|. +.+..+-.|+.+.|...+.+++++|+.+ -.||
T Consensus 20 ~rk~~~~~FS~R~fa~KaGfsS~r~~~~~~~~GK~~Lt~~~i~k~~~~l~Lde~E~~YF 78 (281)
T TIGR02147 20 ERKKTDRAFSWRSFAEKAGFSSKRSYLKRIIKGKKNLTKRMIPKFAEALGLDEKEAAYF 78 (281)
T ss_pred HHHHCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf 98501543308999986488987778889986667530003576665524672268999
No 104
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=88.27 E-value=0.59 Score=26.33 Aligned_cols=20 Identities=15% Similarity=0.453 Sum_probs=9.6
Q ss_pred CCHHHHHHHHHHHHHHHHHH
Q ss_conf 97999999872469999998
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~ 47 (144)
-|.+++|+.+|++...+..+
T Consensus 131 pt~~eia~~lg~~~~~v~~~ 150 (261)
T PRK06288 131 PTDDEIAKELGISLEEYHSL 150 (261)
T ss_pred CCHHHHHHHCCCCHHHHHHH
T ss_conf 98788887819999999999
No 105
>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=88.08 E-value=1.5 Score=23.68 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCC
Q ss_conf 9799999987246999999852-89883
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRV 54 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~p 54 (144)
+|-.++|+.+|||..++-.||+ |--.|
T Consensus 2 YtIgevA~~~Gvs~~tLR~yE~~GLl~P 29 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLLSP 29 (91)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 6589999998929999999998599798
No 106
>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=88.00 E-value=2 Score=22.85 Aligned_cols=63 Identities=14% Similarity=0.170 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCC
Q ss_conf 999999999998199799999987246999999852898835899999997549999995067
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~ 76 (144)
-|...|=+..+.+|||=+++++.+|-+..++...=.|....+.+-..+++..||.+=+.+...
T Consensus 13 dl~~~lle~Kk~kgltfad~~~~lG~~ev~~aa~~ygqa~a~~dea~~v~~~L~L~ed~~~eL 75 (156)
T TIGR00673 13 DLAKKLLEAKKKKGLTFADVEDKLGKAEVYVAAVLYGQAAADADEAKKVAELLDLEEDEVAEL 75 (156)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHH
T ss_conf 789999998873599789986531875999999998420688889999998709981134665
No 107
>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=87.96 E-value=0.77 Score=25.56 Aligned_cols=33 Identities=27% Similarity=0.415 Sum_probs=26.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999998199799999987246999999852
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+.+=.+|--.|+|++|+|+.+|||.++|.+...
T Consensus 120 r~~~~l~~~~~~s~~eIA~~lg~s~~~v~~~~~ 152 (162)
T TIGR02937 120 REVLVLRYLEGLSYKEIAEILGISEGTVKSRLK 152 (162)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999997189988999986899999999999
No 108
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=87.91 E-value=0.69 Score=25.87 Aligned_cols=16 Identities=13% Similarity=0.270 Sum_probs=6.8
Q ss_pred CHHHHHHHHHHHHHHH
Q ss_conf 7999999872469999
Q gi|254780424|r 29 SQEKLGECLGITFQQV 44 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~i 44 (144)
|-+++|+.+|++...+
T Consensus 141 t~~eiA~~l~i~~~~v 156 (257)
T PRK08215 141 TVSEIAKELEVPREEV 156 (257)
T ss_pred CHHHHHHHHCCCHHHH
T ss_conf 9999998809899999
No 109
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=87.46 E-value=0.9 Score=25.12 Aligned_cols=49 Identities=14% Similarity=-0.068 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC----CCCCHHHHHHHHHHC
Q ss_conf 99999999999819979999998724699999985289----883589999999754
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV----NRVGASRLQHISEVL 66 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~----~~ps~~~L~~iA~~l 66 (144)
|=+.-.+.++...| ..+.|+-+ +--.++.-|++.. .+| ..-|+.||.-+
T Consensus 19 ~~~~L~~~~~r~~g--~~~~AEDi-vQd~Flrl~~~~~~~~~~~~-~ayL~~iA~n~ 71 (167)
T PRK12528 19 HHHWLTGWLRRRLG--CPQSAADL-AQDTFVKVLVARETAQIIEP-RAFLTTIAKRV 71 (167)
T ss_pred HHHHHHHHHHHHHC--CHHHHHHH-HHHHHHHHHHCCCCCCCCCH-HHHHHHHHHHH
T ss_conf 99999999999939--88579999-99999999965654465679-99999999999
No 110
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=87.27 E-value=0.67 Score=25.97 Aligned_cols=52 Identities=13% Similarity=-0.031 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC----CCCCHHHHHHHHHHCCCC
Q ss_conf 99999999999819979999998724699999985289----883589999999754999
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV----NRVGASRLQHISEVLESP 69 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~----~~ps~~~L~~iA~~l~v~ 69 (144)
|=..-.+.++...|= .+.|+-+ |--.++.-|+... .+| ..-|+.||.-+-++
T Consensus 18 ~y~~L~~~~~r~lg~--~~~AeDi-vQe~Flr~~~~~~~~~~~~~-~a~L~~iArnl~~d 73 (168)
T PRK12525 18 DYDWLCKKLSRQLGC--PHSAEDI-ASETFLQVLALPDPASIREP-RALLTTIARRLMYE 73 (168)
T ss_pred HHHHHHHHHHHHHCC--HHHHHHH-HHHHHHHHHHCCCCCCCCCH-HHHHHHHHHHHHHH
T ss_conf 999999999999498--8579999-99999999867774554588-99999999999999
No 111
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=87.13 E-value=1 Score=24.81 Aligned_cols=52 Identities=15% Similarity=-0.027 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC----CCCCCHHHHHHHHHHCCC
Q ss_conf 99999999999981997999999872469999998528----988358999999975499
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG----VNRVGASRLQHISEVLES 68 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G----~~~ps~~~L~~iA~~l~v 68 (144)
.|=+.-.+.+|...| -.+.|+-+ |--.++--|.+. ..+| ..-|+.||.-+-+
T Consensus 18 ~~~~~L~~~~~r~~~--~~e~AEDi-vQd~Flrl~~~~~~~~~~~~-~a~Lf~iarNl~~ 73 (172)
T PRK12523 18 DHRGWLLAWLRRNLA--CRQRAEDL-SQDTFVRLLGRPELPTPREP-RAFLAAVAKGLMF 73 (172)
T ss_pred HHHHHHHHHHHHHHC--CHHHHHHH-HHHHHHHHHHCCCCCCCCCH-HHHHHHHHHHHHH
T ss_conf 999999999999949--88689999-99999999827765673459-9999999999999
No 112
>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=86.90 E-value=1.8 Score=23.16 Aligned_cols=46 Identities=11% Similarity=0.181 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCC----------CH-----HHHHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-89883----------58-----99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRV----------GA-----SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~p----------s~-----~~L~~iA~~l~v~~~~l 73 (144)
||-.|+|++.|||.+||-.||. |--.| +. -.+.+.++.+|.|++.+
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 113
>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=86.61 E-value=0.49 Score=26.83 Aligned_cols=30 Identities=17% Similarity=0.125 Sum_probs=24.5
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 819979999998724699999985289883
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRV 54 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~p 54 (144)
..|++|.++|+++|-|.++||++-.=...|
T Consensus 1 ~~G~kk~~IAk~LGks~s~VS~hlaL~d~P 30 (93)
T pfam08535 1 AKGVKQAEIAKKLGKSKSFVSQHLALLDMP 30 (93)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf 998779999999788988999999983486
No 114
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=86.31 E-value=0.81 Score=25.42 Aligned_cols=20 Identities=15% Similarity=0.298 Sum_probs=8.8
Q ss_pred CCHHHHHHHHHHHHHHHHHH
Q ss_conf 97999999872469999998
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~ 47 (144)
-|-+++|+.+|++...+..+
T Consensus 122 ps~~eia~~lg~s~~~v~~~ 141 (250)
T PRK07670 122 VTPSEVAAELGMSEEEVVTT 141 (250)
T ss_pred CCHHHHHHHCCCCHHHHHHH
T ss_conf 98889987719999999999
No 115
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=86.03 E-value=0.87 Score=25.21 Aligned_cols=20 Identities=15% Similarity=0.426 Sum_probs=10.8
Q ss_pred CHHHHHHHHHHHHHHHHHHH
Q ss_conf 79999998724699999985
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E 48 (144)
|.+|+|+.+|++...+....
T Consensus 113 t~~eia~~l~~s~e~v~~~~ 132 (234)
T PRK06986 113 TDTEVAEKLGLSLEEYREML 132 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHH
T ss_conf 89999989594999999999
No 116
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=85.92 E-value=0.6 Score=26.27 Aligned_cols=24 Identities=25% Similarity=0.419 Sum_probs=20.8
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 819979999998724699999985
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
..-+||+++|+.+|+++.++|+.-
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 117
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=85.92 E-value=0.86 Score=25.25 Aligned_cols=30 Identities=27% Similarity=0.302 Sum_probs=16.8
Q ss_pred HHHHHCC--CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999819--97999999872469999998528
Q gi|254780424|r 21 LRRMILG--MSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 21 ~~R~~~g--lTQ~eLA~~lGvs~s~is~~E~G 50 (144)
.++...| -|-+|+|+.+|++...+..+...
T Consensus 118 ~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~ 149 (257)
T PRK05911 118 SLRQSLGKEPTDGELCEYLNISQQELSGWFSS 149 (257)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99998688999999998839799999999985
No 118
>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=85.28 E-value=0.92 Score=25.08 Aligned_cols=31 Identities=19% Similarity=0.175 Sum_probs=26.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999819979999998724699999985
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
-|..+...-|+||.+||+.+++++++++++=
T Consensus 8 vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i 38 (59)
T pfam01047 8 ILRILYEHGPLTVSELAEKLGVDRSTVTRVL 38 (59)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999994699299999999885865499999
No 119
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=85.10 E-value=0.86 Score=25.28 Aligned_cols=32 Identities=25% Similarity=0.331 Sum_probs=24.5
Q ss_pred HHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999819-979999998724699999985
Q gi|254780424|r 17 KRIRLRRMILG-MSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 17 ~rIr~~R~~~g-lTQ~eLA~~lGvs~s~is~~E 48 (144)
+-|+.+|..-| .+|+||.+.+|.|++++|++-
T Consensus 199 ~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L 231 (258)
T COG2512 199 EILDLIRERGGRITQAELRRALGLSKTTVSRIL 231 (258)
T ss_pred HHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHHH
T ss_conf 999999985897869998886099767799999
No 120
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=84.89 E-value=0.8 Score=25.48 Aligned_cols=55 Identities=15% Similarity=-0.003 Sum_probs=49.1
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHC
Q ss_conf 99999819979999998724699999985289883589999999754999999506
Q gi|254780424|r 20 RLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFD 75 (144)
Q Consensus 20 r~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~ 75 (144)
-+.+++.+.+|+++++..|+++ ++..|.++.+.+|...+....++|+..-.++..
T Consensus 5 trrq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~g~i~~~ 59 (201)
T COG1974 5 TRRQKELLDFIRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERKGYIRRD 59 (201)
T ss_pred HHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEC
T ss_conf 6889998999999999728993-089998751789848999999997308858745
No 121
>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=84.68 E-value=2.6 Score=22.20 Aligned_cols=46 Identities=15% Similarity=0.208 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH----------------HHHHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358----------------99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA----------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~----------------~~L~~iA~~l~v~~~~l 73 (144)
||-.|+|+..|||..||-.||+ |--.|.. -.+.+.++.+|.|+..+
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 122
>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=84.68 E-value=3 Score=21.78 Aligned_cols=46 Identities=9% Similarity=0.282 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH-----------HH-----HHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358-----------99-----999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA-----------SR-----LQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~-----------~~-----L~~iA~~l~v~~~~l 73 (144)
||=.|+|+.+|||..||-.||. |--.|.. +. ..+.++.+|+|+..+
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 123
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=84.62 E-value=3.3 Score=21.51 Aligned_cols=60 Identities=15% Similarity=0.189 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH-HHHHHHCCCC
Q ss_conf 899999999999999-81997999999872469999998528988358999-9999754999
Q gi|254780424|r 10 PVDINVGKRIRLRRM-ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRL-QHISEVLESP 69 (144)
Q Consensus 10 ~~d~~iG~rIr~~R~-~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L-~~iA~~l~v~ 69 (144)
+-++.|.+.|-.-.. ..-+|-.+||+.+|||.++|.++.+--..-.+..+ ..++..+...
T Consensus 18 ~~er~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~~l~~~l~~~ 79 (281)
T COG1737 18 KSERKIADYILANPDEVALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKLALAQELAEG 79 (281)
T ss_pred HHHHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC
T ss_conf 99999999999396788561499999881998889999999859998899999999997633
No 124
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=84.52 E-value=1.1 Score=24.61 Aligned_cols=28 Identities=11% Similarity=0.191 Sum_probs=13.5
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998199799999987246999999
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
|..++..-++||.+||+.+|++++++++
T Consensus 46 L~~L~~~~~~t~~eLa~~l~id~~tvt~ 73 (144)
T PRK11512 46 LCSIRCAACITPVELKKVLSVDLGALTR 73 (144)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999986997999999997888878999
No 125
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=84.20 E-value=0.84 Score=25.32 Aligned_cols=24 Identities=17% Similarity=0.232 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 199799999987246999999852
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
++.|..+||+.+|||+++++..-+
T Consensus 22 R~~~l~elA~~lgis~sT~~~hLr 45 (53)
T pfam04967 22 RRVTLKDLAKELGISKSTLSEHLR 45 (53)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 768899999996989999999999
No 126
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=84.18 E-value=1.1 Score=24.52 Aligned_cols=28 Identities=18% Similarity=0.130 Sum_probs=16.4
Q ss_pred HHHHH-HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999-81997999999872469999998
Q gi|254780424|r 20 RLRRM-ILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 20 r~~R~-~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
..+.. .-|+||.+||+.+||+++++++.
T Consensus 38 ~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ 66 (144)
T PRK03573 38 HNIHQLPPDQSQIQLAKAIGIEQPSLVRT 66 (144)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99997398989999999979878369999
No 127
>PRK06930 positive control sigma-like factor; Validated
Probab=84.14 E-value=1.6 Score=23.57 Aligned_cols=18 Identities=33% Similarity=0.591 Sum_probs=7.3
Q ss_pred HHHHHHHH-HCCCCCCCHHH
Q ss_conf 69999998-52898835899
Q gi|254780424|r 40 TFQQVQKY-EKGVNRVGASR 58 (144)
Q Consensus 40 s~s~is~~-E~G~~~ps~~~ 58 (144)
+-.+.-.| |.| ..|...+
T Consensus 40 dleYaieWme~G-~~Pg~~r 58 (170)
T PRK06930 40 DLEYVIEWMEKG-REPGNRR 58 (170)
T ss_pred HHHHHHHHHHHC-CCCCCCH
T ss_conf 799999999857-8986300
No 128
>pfam02084 Bindin Bindin.
Probab=84.10 E-value=3.5 Score=21.36 Aligned_cols=70 Identities=17% Similarity=0.182 Sum_probs=42.2
Q ss_pred HHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 99852898835899999997549999995067744311111014542112038678999999872899999999999999
Q gi|254780424|r 45 QKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVR 124 (144)
Q Consensus 45 s~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~l~~~~~r~~i~~l~~ 124 (144)
+..+.+.+++|..++.+|-.+|+-+--+| +.++... +.--+.-+...-...+..+|.|+++|+.++..+.
T Consensus 90 ss~~e~etTIsAkvm~~IKAVLGATKIDL-------PVDINDP---YDLGLLLRHLRHHSNLLANIGDPeVReQVLsAMQ 159 (239)
T pfam02084 90 SSIEEGDTTISADVMEKIKAVLGATKIDL-------PVDINDP---YDLGLLLRHLRHHSNLLANIGDPEVREQVLSAMQ 159 (239)
T ss_pred CCCCCCCCEEEHHHHHHHHHHHCCCCCCC-------CCCCCCH---HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 22347875350999998999857543467-------4436873---3678999998877778764388899999999876
No 129
>PRK09954 hypothetical protein; Provisional
Probab=83.70 E-value=1.3 Score=24.14 Aligned_cols=29 Identities=17% Similarity=0.189 Sum_probs=22.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999981997999999872469999998
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
++-+|+.==+||.|||+++|+|+|++...
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 130
>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=83.62 E-value=3.6 Score=21.28 Aligned_cols=47 Identities=15% Similarity=0.227 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCC-----------HHHH-----HHHHHHCCCCHHHHH
Q ss_conf 9799999987246999999852-898835-----------8999-----999975499999950
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVG-----------ASRL-----QHISEVLESPISFFF 74 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps-----------~~~L-----~~iA~~l~v~~~~l~ 74 (144)
+|-.|+|+.+|||..|+-.||+ |--.|. .+.+ .+.++.+|+|++.+-
T Consensus 1 y~Ige~Ak~~gvs~~TLRyYe~~GLl~p~~~~~ngYR~Y~~~~~~~l~~I~~~r~lG~sL~eI~ 64 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIK 64 (97)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 9789999998969999999996699898613999984279999999999999999699999999
No 131
>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=83.56 E-value=0.36 Score=27.65 Aligned_cols=42 Identities=10% Similarity=0.234 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCC
Q ss_conf 997999999872469999998528988358999999975499
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLES 68 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v 68 (144)
.||-.+.|+..||++||+|++-++.+..+..+=+++-.+.+-
T Consensus 1 kLTIkDIArLagVgKSTVSRVLnNe~~V~~~tRERVE~viq~ 42 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNNESKVSIETRERVEAVIQQ 42 (311)
T ss_pred CCHHHHHHHHHCCCCEEEEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf 961777697708862023315616888872033688888751
No 132
>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=83.50 E-value=1.2 Score=24.38 Aligned_cols=30 Identities=23% Similarity=0.516 Sum_probs=26.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998199799999987246999999
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
.+|=++|-=.|||.+|.|+.+|||.+||-+
T Consensus 151 a~~veLr~F~Gl~~~E~A~~L~~S~~Tv~R 180 (194)
T TIGR02999 151 AEVVELRFFAGLTVEEIAELLGVSVRTVER 180 (194)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 998853110488989999986888878998
No 133
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=83.22 E-value=2.4 Score=22.38 Aligned_cols=46 Identities=11% Similarity=0.194 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH--------------HH--HHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358--------------99--999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA--------------SR--LQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~--------------~~--L~~iA~~l~v~~~~l 73 (144)
||-.|+|+.+|||..|+-.||+ |--.|.. .. +.+.++.+|+|+..+
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 134
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=83.07 E-value=1 Score=24.82 Aligned_cols=29 Identities=14% Similarity=0.272 Sum_probs=24.1
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99981997999999872469999998528
Q gi|254780424|r 22 RRMILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 22 ~R~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
.=...|+|..++|.++|||.+|+.+|=+-
T Consensus 16 ~~~~~G~S~re~Ak~~gvs~sTvy~wv~r 44 (138)
T COG3415 16 AVVGEGLSCREAAKRFGVSISTVYRWVRR 44 (138)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99976854999999969229999999987
No 135
>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=83.06 E-value=2.3 Score=22.51 Aligned_cols=25 Identities=20% Similarity=0.432 Sum_probs=21.5
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9819979999998724699999985
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
..+.||++|+|+.+|.|+.|+|+.-
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 136
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=82.91 E-value=1.4 Score=23.81 Aligned_cols=31 Identities=19% Similarity=0.247 Sum_probs=24.4
Q ss_pred HHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999819-979999998724699999985
Q gi|254780424|r 18 RIRLRRMILG-MSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 18 rIr~~R~~~g-lTQ~eLA~~lGvs~s~is~~E 48 (144)
-|..++...+ +|-.+||+.+|||+.+|.+.=
T Consensus 5 il~~L~~~~~~vt~~~La~~l~VSr~TV~rdi 36 (55)
T pfam08279 5 ILELLLQAREPISGQELAEKLGVSRRTIRRDI 36 (55)
T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999976999189999999698899999999
No 137
>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=82.82 E-value=1.8 Score=23.14 Aligned_cols=12 Identities=8% Similarity=-0.003 Sum_probs=5.9
Q ss_pred HHHHHHHHHHCC
Q ss_conf 469999998528
Q gi|254780424|r 39 ITFQQVQKYEKG 50 (144)
Q Consensus 39 vs~s~is~~E~G 50 (144)
|-..++.-|.+.
T Consensus 53 vqe~Flrl~~~~ 64 (185)
T pfam07638 53 VHEAFVRLVDTE 64 (185)
T ss_pred HHHHHHHHHHCC
T ss_conf 999999998402
No 138
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=82.74 E-value=2.1 Score=22.84 Aligned_cols=15 Identities=20% Similarity=0.213 Sum_probs=7.9
Q ss_pred HHHHHHHHHCCCCHHHH
Q ss_conf 99999997549999995
Q gi|254780424|r 57 SRLQHISEVLESPISFF 73 (144)
Q Consensus 57 ~~L~~iA~~l~v~~~~l 73 (144)
.-|+.|+.-+ -++++
T Consensus 64 awL~~iarN~--~id~l 78 (183)
T PRK07037 64 AYLFQMVRNL--AIDHC 78 (183)
T ss_pred HHHHHHHHHH--HHHHH
T ss_conf 9999999999--99999
No 139
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=82.50 E-value=2.9 Score=21.91 Aligned_cols=41 Identities=24% Similarity=0.367 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 9999999999998199799999987246999999852898835899999997549999995
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
|||=++|..+++. |.||+..+| +.||. .-||.+|+++++.+
T Consensus 190 iH~~EKLnkiKK~----qReL~q~lG-------------R~Ps~---~EiAe~lel~~~qv 230 (336)
T TIGR02997 190 IHITEKLNKIKKV----QRELSQKLG-------------RRPSE---AEIAEALELEPEQV 230 (336)
T ss_pred CCHHHHHHHHHHH----HHHHHHHHC-------------CCCCH---HHHHHHHCCCHHHH
T ss_conf 1076666899899----899999838-------------89786---89998838898899
No 140
>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=82.50 E-value=4 Score=20.96 Aligned_cols=22 Identities=23% Similarity=0.478 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9799999987246999999852
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+|-.|+|+.+|||.++|-.||+
T Consensus 1 ytIgevA~~~Gvs~~tlRyYE~ 22 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9488999998979999999998
No 141
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=82.36 E-value=1.1 Score=24.64 Aligned_cols=20 Identities=15% Similarity=0.511 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999987246999999852
Q gi|254780424|r 30 QEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 30 Q~eLA~~lGvs~s~is~~E~ 49 (144)
.+++|+.+|++...+..++.
T Consensus 151 ~~eiA~~l~~~~~~v~~~~~ 170 (289)
T PRK07500 151 HREIATALGVSLSDVEMMDA 170 (289)
T ss_pred HHHHHHHHCCCHHHHHHHHH
T ss_conf 99999880999999999999
No 142
>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=82.22 E-value=2.2 Score=22.61 Aligned_cols=33 Identities=30% Similarity=0.411 Sum_probs=27.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999998199799999987246999999852
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+.+=.+|--.|+|++|+|+.+|+|.+++..+..
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 143
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=82.00 E-value=1.7 Score=23.39 Aligned_cols=33 Identities=18% Similarity=0.145 Sum_probs=26.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999998199799999987246999999852
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
.-|..+...-|+||.+||+.++++++++++.=+
T Consensus 14 ~vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v~ 46 (101)
T smart00347 14 LVLRILYEEGPLSVSELAKRLGVSPSTVTRVLD 46 (101)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999976997999999998968879999999
No 144
>PHA01083 hypothetical protein
Probab=81.71 E-value=3.7 Score=21.20 Aligned_cols=60 Identities=15% Similarity=0.160 Sum_probs=50.1
Q ss_pred HHHHHHHHHCCCCH-HHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHCCCCHHHHHCC
Q ss_conf 99999999819979-9999987246999999852898-835899999997549999995067
Q gi|254780424|r 17 KRIRLRRMILGMSQ-EKLGECLGITFQQVQKYEKGVN-RVGASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 17 ~rIr~~R~~~glTQ-~eLA~~lGvs~s~is~~E~G~~-~ps~~~L~~iA~~l~v~~~~l~~~ 76 (144)
+-|....+.+++.| +++|.-+|++++.||.+-+|.+ -.+-+...-||+.-|++++.-+-|
T Consensus 3 ~LldAYK~aknYvQdKQIAhDlg~~pq~iS~~RkG~R~Ylsd~eAifLAe~~GiD~E~aLlG 64 (153)
T PHA01083 3 KLLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESAGIDPEIALLG 64 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCHHHHCCHHHHHHHHHHCCCCHHHHHHH
T ss_conf 78999999998888999999809998999999812376435388999898709988888998
No 145
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=81.70 E-value=1 Score=24.84 Aligned_cols=43 Identities=26% Similarity=0.330 Sum_probs=28.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCH--HHHHHHHH-HCCCCHHHH
Q ss_conf 7999999872469999998528988358--99999997-549999995
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVNRVGA--SRLQHISE-VLESPISFF 73 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~~ps~--~~L~~iA~-~l~v~~~~l 73 (144)
|+..+|..+|||.+.||+| |..-|.. -.|.+|.. .|.++++-.
T Consensus 12 sk~klA~aLgIs~~aVsqW--ge~IPE~rAy~le~iT~G~Lk~~p~lY 57 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW--GELVPEGRAMRLQEASGGELQYDPKVY 57 (75)
T ss_pred CHHHHHHHHCCCHHHHHHH--HHHCCHHHHHHHHHHHCCCEECCHHHH
T ss_conf 2999999949987999887--401606889999998588512588999
No 146
>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=81.42 E-value=4.4 Score=20.71 Aligned_cols=32 Identities=16% Similarity=0.081 Sum_probs=26.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999998199799999987246999999852
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+++=... +.|.|-.|.|...|||.+++.+|-+
T Consensus 9 ~rVl~~v-e~G~S~~eaA~~F~Is~~Tv~rWlk 40 (120)
T pfam01710 9 KKVIDYI-ESGGSITEASKVFQIGRATIYRWLK 40 (120)
T ss_pred HHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999-8699999999993702999999985
No 147
>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=81.18 E-value=0.85 Score=25.30 Aligned_cols=44 Identities=14% Similarity=0.253 Sum_probs=33.3
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCC-CHHHHHCCC
Q ss_conf 81997999999872469999998528988358999999975499-999950677
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLES-PISFFFDVS 77 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v-~~~~l~~~~ 77 (144)
..-||+.++|+.+|++.||||+.-+|+.-- --.|+ |+.+||...
T Consensus 47 l~PLtlk~iA~~l~lh~STVSRav~~Kyi~---------tp~Gi~~lk~fFs~~ 91 (160)
T pfam04552 47 LRPLTLREVAEALGMHESTVSRATTNKYLA---------TPRGLFELKYFFSSA 91 (160)
T ss_pred CCCCCHHHHHHHCCCCCCHHHHHHHHHHHH---------CCCCEEEHHHHHHCC
T ss_conf 757619999988099810699999613976---------799516599985013
No 148
>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=81.16 E-value=4.3 Score=20.76 Aligned_cols=47 Identities=11% Similarity=0.173 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCC-CCCC----------CH-----HHHHHHHHHCCCCHHHH
Q ss_conf 997999999872469999998528-9883----------58-----99999997549999995
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKYEKG-VNRV----------GA-----SRLQHISEVLESPISFF 73 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~E~G-~~~p----------s~-----~~L~~iA~~l~v~~~~l 73 (144)
.||-.|+|++.|||.++|-.||+- --.| +- -.+.+.++.+|.+++.+
T Consensus 1 ~mtIgelA~~~gvs~~tiRyYE~~GLl~p~R~~~gyR~Y~~~~l~rl~~I~~~r~lGfsL~eI 63 (139)
T cd01110 1 ELSVGEVAKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEI 63 (139)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 997899999988788999999987884666789887704989999999999999859989999
No 149
>PRK11753 cAMP-regulatory protein; Provisional
Probab=80.35 E-value=1.3 Score=24.05 Aligned_cols=20 Identities=15% Similarity=0.458 Sum_probs=11.3
Q ss_pred CCHHHHHHHHHHHHHHHHHH
Q ss_conf 97999999872469999998
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~ 47 (144)
+||++||..+|+|+.++++.
T Consensus 169 lt~~eLA~~lG~sretvsR~ 188 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRV 188 (211)
T ss_pred CCHHHHHHHHCCCHHHHHHH
T ss_conf 69999998869989999999
No 150
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=80.34 E-value=3.2 Score=21.61 Aligned_cols=37 Identities=22% Similarity=0.266 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 8998999999999999998199799999987246999999
Q gi|254780424|r 7 IPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 7 ~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+-+.+|+. =|+.++.....|+.++|+.+|+|.+++++
T Consensus 5 ~lD~~D~~---IL~~L~~d~r~~~~eia~~lglS~~~v~~ 41 (154)
T COG1522 5 KLDDIDRR---ILRLLQEDARISNAELAERVGLSPSTVLR 41 (154)
T ss_pred CCCHHHHH---HHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 53799999---99999972765799999997979899999
No 151
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=80.34 E-value=3.7 Score=21.22 Aligned_cols=46 Identities=13% Similarity=0.076 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCC-CH----------------HHHHHHHHHCCCCHHHH
Q ss_conf 979999998724699999985289883-58----------------99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRV-GA----------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~p-s~----------------~~L~~iA~~l~v~~~~l 73 (144)
|+-.|||++.||+..||-.||+-.--| .. -.+.+-|+.||.+++..
T Consensus 1 M~IgelAk~tGv~~~TIRyYE~~GLl~~~~R~~~GyR~Y~~~~l~rL~fI~~ar~lGfsL~EI 63 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEES 63 (135)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 968999999896999999999838977343289992177899999999999998879999999
No 152
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=79.97 E-value=3 Score=21.77 Aligned_cols=53 Identities=9% Similarity=-0.114 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC----CCCCHHHHHHHHHHCCCC
Q ss_conf 999999999999819979999998724699999985289----883589999999754999
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV----NRVGASRLQHISEVLESP 69 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~----~~ps~~~L~~iA~~l~v~ 69 (144)
.|-+.-.+.++... .-.+.|+-+ |--.++.-|++.. .+| ..-|+.||.-+-++
T Consensus 18 ~~~~~l~~~~~~~~--~~~~~AeDi-vQe~Flr~~~~~~~~~~~~~-~a~L~~iarn~~id 74 (172)
T PRK09651 18 THHGWLKSWLTRKL--QSAFDADDI-AQDTFLRVMVSETLSTIRDP-RSFLCTIAKRVMVD 74 (172)
T ss_pred HHHHHHHHHHHHHH--CCHHHHHHH-HHHHHHHHHHCCCCCCCCCH-HHHHHHHHHHHHHH
T ss_conf 99999999999995--988689999-99999999863852334688-99999999999999
No 153
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=79.86 E-value=5 Score=20.38 Aligned_cols=56 Identities=14% Similarity=0.231 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH-HHHHHHCCC
Q ss_conf 999999999999-81997999999872469999998528988358999-999975499
Q gi|254780424|r 13 INVGKRIRLRRM-ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRL-QHISEVLES 68 (144)
Q Consensus 13 ~~iG~rIr~~R~-~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L-~~iA~~l~v 68 (144)
+.|++.|-.--. ...+|-.+||+.+|||.++|.++.+.-.-..+..| ..+++.+..
T Consensus 19 k~iA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~efK~~l~~~l~~ 76 (284)
T PRK11302 19 RKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPDFKLHLAQSLAN 76 (284)
T ss_pred HHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf 9999999809899976669999989699888999999995789789999999999753
No 154
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=79.85 E-value=3 Score=21.83 Aligned_cols=33 Identities=9% Similarity=-0.044 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCC---HHHHHHHHH
Q ss_conf 9999987246999999852898835---899999997
Q gi|254780424|r 31 EKLGECLGITFQQVQKYEKGVNRVG---ASRLQHISE 64 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E~G~~~ps---~~~L~~iA~ 64 (144)
.+.|+-+ |.-.++.-|++....+. ..-|++||.
T Consensus 19 ~~~AeDi-vQd~F~k~~~~~~~~~~~~~~a~L~~ia~ 54 (159)
T PRK12527 19 RQAAEDV-AHDAYLRVLERSSSAQIEHPRAFLYRTAL 54 (159)
T ss_pred HHHHHHH-HHHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf 9999999-99999999986663554569999999999
No 155
>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=79.79 E-value=1.5 Score=23.69 Aligned_cols=24 Identities=13% Similarity=0.585 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 199799999987246999999852
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
..+|.++||+.+|||..+|.+|-.
T Consensus 1 ~~vnk~elA~~~gVS~~tv~~W~~ 24 (164)
T pfam07471 1 MEVNKKQLAEIFGVSIRTIDNWQS 24 (164)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 967899999996988889999998
No 156
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=79.73 E-value=1.2 Score=24.29 Aligned_cols=42 Identities=12% Similarity=0.220 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCC-CHHHHHCC
Q ss_conf 1997999999872469999998528988358999999975499-99995067
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLES-PISFFFDV 76 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v-~~~~l~~~ 76 (144)
+-||++++|+.+|++.||||+.=+|+.--+ -.|+ |+.+||+.
T Consensus 348 kPL~lkdiA~~lglheSTVSRav~~Kyi~t---------p~G~~~lk~fFs~ 390 (461)
T PRK05932 348 KPLVLKDIAEALGMHESTISRATTNKYMAT---------PRGIFELKYFFSS 390 (461)
T ss_pred CCCCHHHHHHHCCCCHHHHHHHHHCCEECC---------CCCEEEHHHHHHH
T ss_conf 676399999873998125889871661148---------9744669997423
No 157
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=79.67 E-value=1.5 Score=23.80 Aligned_cols=22 Identities=23% Similarity=0.555 Sum_probs=15.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9979999998724699999985
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~E 48 (144)
-|||++||+.+|.|+.++++.-
T Consensus 184 ~lt~~dLA~~lG~trEtVsR~L 205 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLL 205 (235)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
T ss_conf 3789999988789899999999
No 158
>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=79.49 E-value=1.6 Score=23.56 Aligned_cols=27 Identities=22% Similarity=0.284 Sum_probs=23.7
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 981997999999872469999998528
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
..-|.|..++|..+||+.++|.+|=+-
T Consensus 20 ~~~g~sv~~var~~gi~~~~l~~W~k~ 46 (75)
T pfam01527 20 LEPGASVSELAREHGVSPATLYKWRKK 46 (75)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 809984999999989599999999999
No 159
>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=79.25 E-value=1.6 Score=23.48 Aligned_cols=59 Identities=17% Similarity=0.109 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHCCC----CHHHHHHHH-HHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHH
Q ss_conf 8999999999999998199----799999987-2469999998528988358999999975499999950
Q gi|254780424|r 10 PVDINVGKRIRLRRMILGM----SQEKLGECL-GITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74 (144)
Q Consensus 10 ~~d~~iG~rIr~~R~~~gl----TQ~eLA~~l-Gvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~ 74 (144)
++-.-||+-=|.+|....+ +..++|-+. -|...-+++. ...|+. ..||+.|++|-....
T Consensus 91 avPmiiGeirrylrdn~~irvsrslrd~ay~alqvr~~l~~~~---~~eP~~---~~ia~~l~~~~~~~v 154 (254)
T TIGR02850 91 AVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRDKLVSKN---SKEPTV---SEIAKELDVPKEEVV 154 (254)
T ss_pred HHHHHHHHHHHHHHCCCCEEEHHHHHHHHHHHHHHHHHHHHHH---CCCCCH---HHHHHHHCCCHHHHH
T ss_conf 4667889889985248741303558899999999999998531---258758---899987347557877
No 160
>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=79.24 E-value=4.7 Score=20.53 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHH-HHHHHHHHHHHC
Q ss_conf 9999999999998199799999987-246999999852
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECL-GITFQQVQKYEK 49 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~l-Gvs~s~is~~E~ 49 (144)
..|.++|++.=+..+++|+-||+.+ |.|++++|.+-+
T Consensus 6 ~~i~~~i~~eL~~~~I~Q~~Fa~~vL~rsQGtlSdLL~ 43 (81)
T pfam02376 6 AEIARRIKEELKRANISQALFAEVVLGRSQGSLSDLLR 43 (81)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999999999994976999999997318378999881
No 161
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=78.91 E-value=1.2 Score=24.29 Aligned_cols=43 Identities=14% Similarity=0.161 Sum_probs=32.7
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCC-CHHHHHCC
Q ss_conf 81997999999872469999998528988358999999975499-99995067
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLES-PISFFFDV 76 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v-~~~~l~~~ 76 (144)
.+-||++++|+.+|++.||||+.=+|+.- ..-.|+ ++.+||..
T Consensus 361 lkPL~lkdiA~~lglheSTVSRav~~Kyi---------~tp~Gi~~lk~FFs~ 404 (475)
T PRK12469 361 LKPLVLRDVAEELGLHESTVSRATGNKYM---------ATPRGTFEFKHFFPR 404 (475)
T ss_pred CCCCCHHHHHHHHCCCCCHHHHHHCCCEE---------CCCCCEEEHHHHHHH
T ss_conf 36734999999819982037688627502---------379854669986232
No 162
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=78.68 E-value=2.8 Score=22.01 Aligned_cols=24 Identities=21% Similarity=0.162 Sum_probs=18.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 997999999872469999998528
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
.-|-+++|+.+|++...+..+..-
T Consensus 192 ~pt~eEIA~~lg~~~~~v~~~l~~ 215 (328)
T PRK05657 192 EPSAEEIAELLDKPVDDVSRMLAL 215 (328)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 998999999969599999999974
No 163
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=78.37 E-value=1.8 Score=23.24 Aligned_cols=23 Identities=30% Similarity=0.561 Sum_probs=15.2
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 81997999999872469999998
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
...+||+++|..+|+|+.++++.
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 164
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=78.21 E-value=2.8 Score=21.99 Aligned_cols=10 Identities=20% Similarity=0.175 Sum_probs=4.2
Q ss_pred CCCCHHHHHH
Q ss_conf 1997999999
Q gi|254780424|r 26 LGMSQEKLGE 35 (144)
Q Consensus 26 ~glTQ~eLA~ 35 (144)
.|+...+|-+
T Consensus 71 ~g~~l~DLIQ 80 (228)
T PRK05803 71 TGEDVDDLIS 80 (228)
T ss_pred CCCCHHHHHH
T ss_conf 9989899999
No 165
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=78.04 E-value=5.6 Score=20.03 Aligned_cols=49 Identities=8% Similarity=0.151 Sum_probs=37.6
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCH-----------------HHHHHHHHHCCCCHHHH
Q ss_conf 81997999999872469999998528988358-----------------99999997549999995
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRVGA-----------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~-----------------~~L~~iA~~l~v~~~~l 73 (144)
..+||-.|||++.|||..+|-.||+-.--|.. -.+.+-|+.||.+++..
T Consensus 5 m~~m~IgelAk~~gvs~~tIRyYE~~GLl~~~~R~~~gyR~Y~~~~v~rL~fI~~~r~lGfsL~eI 70 (144)
T PRK13752 5 LENLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEI 70 (144)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 223829999999789845667987259979877799998247999999999999999879989999
No 166
>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=77.96 E-value=1.4 Score=23.95 Aligned_cols=27 Identities=19% Similarity=0.222 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 979999998724699999985289883
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRV 54 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~p 54 (144)
||-+|.|+.+|||.+|+-+|=....-|
T Consensus 2 lTv~EaA~yLgv~~~t~~~l~~~g~l~ 28 (49)
T TIGR01764 2 LTVEEAAEYLGVSKSTVYRLIEEGELP 28 (49)
T ss_pred CCHHHHHHHCCCCHHHHHHHHHCCCCC
T ss_conf 877889977199905789999718985
No 167
>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=77.95 E-value=2.3 Score=22.52 Aligned_cols=32 Identities=9% Similarity=0.133 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf 97999999872469999998528988358999
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVGASRL 59 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L 59 (144)
+...|+++.+|+|+++|.++.+...-|.--.|
T Consensus 4 lr~~eV~~~~glsrstiyr~i~~G~FP~pikl 35 (51)
T pfam05930 4 LRLKEVEQLTGLSRSTIYRLIKDGEFPKPIKL 35 (51)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEEE
T ss_conf 37999999989899999999987999998760
No 168
>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=77.66 E-value=2.7 Score=22.04 Aligned_cols=37 Identities=27% Similarity=0.239 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 8998999999999999998199799999987246999999
Q gi|254780424|r 7 IPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 7 ~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+|+..|+. |+=..=++.||-|+.-|+.||+|+-|++.
T Consensus 526 A~~l~eRE---Rli~AlE~aGWVQAKAARlLg~TPRQVgY 562 (574)
T TIGR01817 526 APTLSERE---RLIAALEKAGWVQAKAARLLGLTPRQVGY 562 (574)
T ss_pred CCCCCCHH---HHHHHHHHCCHHHHHHHHHHCCCHHHHHH
T ss_conf 88723178---99999975153799999973786558999
No 169
>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=77.64 E-value=3.5 Score=21.35 Aligned_cols=31 Identities=29% Similarity=0.433 Sum_probs=25.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999981997999999872469999998
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
+.+=.++.-.|+|.+|.|+.+|+|.+++..+
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 170
>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=77.53 E-value=2.5 Score=22.31 Aligned_cols=22 Identities=9% Similarity=0.300 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9799999987246999999852
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+|-.|+|+.+||+..+|-.||+
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 171
>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=77.28 E-value=1.3 Score=24.07 Aligned_cols=46 Identities=9% Similarity=0.067 Sum_probs=37.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCC------CCCCHHHHHHHHHHCCCCHHHHH
Q ss_conf 79999998724699999985289------88358999999975499999950
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGV------NRVGASRLQHISEVLESPISFFF 74 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~------~~ps~~~L~~iA~~l~v~~~~l~ 74 (144)
|..|.|+..|||+.|.|.+=||+ ..=|.++..+|++..|-.|+..=
T Consensus 1 tL~dIA~LAGVS~TTASyViNGka~~~Ris~~T~erV~Avv~e~~Y~Pn~~A 52 (335)
T TIGR02417 1 TLDDIAKLAGVSKTTASYVINGKAKEYRISEETVERVMAVVEEQGYKPNVAA 52 (335)
T ss_pred CCHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf 9005766608232322120004311101367878899998987378577554
No 172
>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=77.25 E-value=2 Score=22.97 Aligned_cols=32 Identities=22% Similarity=0.455 Sum_probs=25.7
Q ss_pred HHHHHHHH--HCCCCHHHHHHHHH-HHHHH-HHHHH
Q ss_conf 99999999--81997999999872-46999-99985
Q gi|254780424|r 17 KRIRLRRM--ILGMSQEKLGECLG-ITFQQ-VQKYE 48 (144)
Q Consensus 17 ~rIr~~R~--~~glTQ~eLA~~lG-vs~s~-is~~E 48 (144)
+||..||+ ..|+|-.++|+.|| ||+.+ |++.-
T Consensus 6 Erve~LkkLW~eGlSaSqIA~~LGgvTRNAVIGKaH 41 (162)
T pfam07750 6 ERVELLKKLWLEGLSASQIAAQLGGVSRNAVIGKVH 41 (162)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCCCCEEEHHH
T ss_conf 999999999985365999999976554000000224
No 173
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=77.11 E-value=1.9 Score=23.03 Aligned_cols=23 Identities=17% Similarity=0.268 Sum_probs=16.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 19979999998724699999985
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E 48 (144)
..+||+|||..+|.|+.++++.-
T Consensus 144 l~lT~~eLA~~iGttREtVsR~L 166 (201)
T PRK13918 144 IYATHDELAAAVGSVRETVTKVV 166 (201)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 05799999988598689999999
No 174
>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=77.08 E-value=3.8 Score=21.12 Aligned_cols=59 Identities=15% Similarity=0.210 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHH-HHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH-HHHHHHCCC
Q ss_conf 8999999999999-9981997999999872469999998528988358999-999975499
Q gi|254780424|r 10 PVDINVGKRIRLR-RMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRL-QHISEVLES 68 (144)
Q Consensus 10 ~~d~~iG~rIr~~-R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L-~~iA~~l~v 68 (144)
+-+..|++.|-.- .....+|-.+||+++|||.++|.++.+--.--.+.-+ ..||.-+..
T Consensus 16 ~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kklG~~Gf~efk~~La~~~~~ 76 (106)
T pfam01418 16 KSEKKIADYILASPDNAIHLSIAELAKAAGVSEASVVRFCRKLGFSGFSDLKVALAGELAQ 76 (106)
T ss_pred HHHHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCC
T ss_conf 9999999999929999988339999989699899999999995899899999999998653
No 175
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=77.07 E-value=6 Score=19.85 Aligned_cols=46 Identities=13% Similarity=0.186 Sum_probs=30.4
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH-HHHHHHCC
Q ss_conf 99981997999999872469999998528988358999-99997549
Q gi|254780424|r 22 RRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRL-QHISEVLE 67 (144)
Q Consensus 22 ~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L-~~iA~~l~ 67 (144)
......+|-.|||+.+|||.++|.+..+-----.+..| ..++..+.
T Consensus 42 ~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~~~~~ 88 (293)
T PRK11337 42 GNLSCATALKDVAEALAVSEAMIVKVAKLLGFSGFRNLRSALEDYFS 88 (293)
T ss_pred HHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 89997666999998959988899999999578978999999999986
No 176
>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=77.06 E-value=1.4 Score=23.92 Aligned_cols=25 Identities=16% Similarity=0.276 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 1997999999872469999998528
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
-.++..++|+.||||.++|++|-+-
T Consensus 21 G~~~l~~IA~~L~vs~~~IrkWKs~ 45 (60)
T pfam10668 21 GTMKLKDIANKLNVSESQIRKWKSQ 45 (60)
T ss_pred CCEEHHHHHHHHCCCHHHHHHCCHH
T ss_conf 9644999999968798887603114
No 177
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=77.02 E-value=3 Score=21.76 Aligned_cols=35 Identities=14% Similarity=0.188 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 98999999999999998199799999987246999999
Q gi|254780424|r 9 NPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 9 ~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
|.+|.. =|+.++..-.+|-.++|+.+|+|.+++.+
T Consensus 2 D~~D~~---Il~~L~~n~R~s~~~iA~~lg~S~~tv~~ 36 (108)
T smart00344 2 DEIDRK---ILEELQKDARISLAELAKKVGLSPSTVHN 36 (108)
T ss_pred CHHHHH---HHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 889999---99999982899999999998939999999
No 178
>PRK09480 slmA nucleoid occlusion protein; Provisional
Probab=76.86 E-value=6.1 Score=19.82 Aligned_cols=61 Identities=13% Similarity=0.101 Sum_probs=38.0
Q ss_pred HHHHHHHHHHH---CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHC
Q ss_conf 99999999998---19979999998724699999985289883589999999754999999506
Q gi|254780424|r 15 VGKRIRLRRMI---LGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFD 75 (144)
Q Consensus 15 iG~rIr~~R~~---~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~ 75 (144)
|=+-+.++=.. .++|-.++|+++|||.+++.++=.++..+=...+..+.+.|---++....
T Consensus 15 Il~a~~~ll~~~~~~~iTt~~iA~~~gvs~aalYrHF~sK~~i~~~lie~ie~~l~~~i~~i~~ 78 (194)
T PRK09480 15 ILQTLAQMLESPPGERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEESLFTRINQILA 78 (194)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999986279764229999989099789999975879999999999999999999999986
No 179
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=76.82 E-value=2.9 Score=21.89 Aligned_cols=39 Identities=23% Similarity=0.410 Sum_probs=30.3
Q ss_pred HHHHHHHHHCC-CCHHHHHHHHHHHHHHHH----HHHCCCCCCCHH
Q ss_conf 99999999819-979999998724699999----985289883589
Q gi|254780424|r 17 KRIRLRRMILG-MSQEKLGECLGITFQQVQ----KYEKGVNRVGAS 57 (144)
Q Consensus 17 ~rIr~~R~~~g-lTQ~eLA~~lGvs~s~is----~~E~G~~~ps~~ 57 (144)
.++-.+|+ | |+-.|+|..+|||++.++ +||.|...|.-+
T Consensus 10 dYv~yF~e--G~L~D~eIA~~LGVsr~nV~kmRqKwes~~dsv~ed 53 (181)
T pfam04645 10 DYVAYFKE--GSLSDAEIAKELGVSRVNVWRMRQKWESGEDSVNED 53 (181)
T ss_pred HHHHHHHC--CCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 99999961--787579999997830999999999998127885556
No 180
>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=76.35 E-value=0.74 Score=25.67 Aligned_cols=48 Identities=19% Similarity=0.400 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCC
Q ss_conf 999999999981997999999872469999998528988358999999975499
Q gi|254780424|r 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLES 68 (144)
Q Consensus 15 iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v 68 (144)
|-+-.+++|..-|||..| |..|++.+||+|+.-||.+...++-+.|.-
T Consensus 415 inkdmkrlrilfGmtrne------vnvsyyakyenGkeiPsyeivkkflnslkP 462 (1145)
T TIGR00491 415 INKDMKRLRILFGMTRNE------VNVSYYAKYENGKEIPSYEIVKKFLNSLKP 462 (1145)
T ss_pred CHHHHHHHHHHHCCCCCC------EEEEEEEEECCCCCCCHHHHHHHHHHHCCC
T ss_conf 303445534432121000------345555430478637508999999852275
No 181
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=76.13 E-value=2.2 Score=22.63 Aligned_cols=31 Identities=29% Similarity=0.457 Sum_probs=17.4
Q ss_pred HHHHHHHCCC----CHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999998199----799999987246999999852
Q gi|254780424|r 19 IRLRRMILGM----SQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 19 Ir~~R~~~gl----TQ~eLA~~lGvs~s~is~~E~ 49 (144)
+|..+...++ +.+++|+.+|++...+..++.
T Consensus 139 lr~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~ 173 (284)
T PRK06596 139 LRKAKKRLGWLNPEEVEMIAEELGVSEEEVREMES 173 (284)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999987145986299999997919999999999
No 182
>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=76.11 E-value=3.2 Score=21.62 Aligned_cols=41 Identities=12% Similarity=0.139 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCH----HHHHHHHHHCCCCHHHH
Q ss_conf 999999872469999998528988358----99999997549999995
Q gi|254780424|r 30 QEKLGECLGITFQQVQKYEKGVNRVGA----SRLQHISEVLESPISFF 73 (144)
Q Consensus 30 Q~eLA~~lGvs~s~is~~E~G~~~ps~----~~L~~iA~~l~v~~~~l 73 (144)
-.+.|+-+ |.-..++-||+-..-... .-|..+++ |-.+++|
T Consensus 24 ~~e~AEdI-VqdvF~~lWe~r~~l~~~~~~~~YL~~~v~--N~~ln~L 68 (167)
T TIGR02985 24 DEEDAEDI-VQDVFLKLWENRESLEESESIKAYLFTIVK--NRCLNYL 68 (167)
T ss_pred CHHHHHHH-HHHHHHHHHHCCCCCCCCCCCCHHHHHHHH--HHHHHHH
T ss_conf 89999999-999999997314525621352179999999--9899899
No 183
>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=75.60 E-value=6.3 Score=19.74 Aligned_cols=38 Identities=18% Similarity=0.143 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 999999999981997999999872469999998528988
Q gi|254780424|r 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNR 53 (144)
Q Consensus 15 iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ 53 (144)
+-.-|..+|.- +||+...|..-||+.++++..-+|...
T Consensus 5 l~~Al~av~~g-~~S~~kAa~~ygIP~sTL~~r~~g~~~ 42 (45)
T pfam05225 5 LAEALEAVRNG-KMSLRKAARKYGIPRSTLWRRLRGKYS 42 (45)
T ss_pred HHHHHHHHHCC-CCCHHHHHHHHCCCHHHHHHHHCCCCC
T ss_conf 99999999919-967999999978985899999756343
No 184
>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=75.56 E-value=3.6 Score=21.26 Aligned_cols=36 Identities=17% Similarity=0.132 Sum_probs=28.3
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf 99999981997999999872469999998528988358
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGA 56 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~ 56 (144)
|.++=.+.| |...|+.+||.+++||+--+-.+++-+
T Consensus 5 L~dyv~~~G--Q~kaA~~lGV~Q~AISKAlragR~I~v 40 (58)
T pfam09048 5 LSDYVEEHG--QAKAAKDLGVNQSAISKALRAGRNIEV 40 (58)
T ss_pred HHHHHHHHC--HHHHHHHCCCCHHHHHHHHHCCCEEEE
T ss_conf 899999976--598999829758999999964881799
No 185
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=75.11 E-value=3.9 Score=21.09 Aligned_cols=29 Identities=41% Similarity=0.463 Sum_probs=23.0
Q ss_pred HHHHHHHCC--CCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999819--97999999872469999998
Q gi|254780424|r 19 IRLRRMILG--MSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 19 Ir~~R~~~g--lTQ~eLA~~lGvs~s~is~~ 47 (144)
+.-+....+ .|.++||+.+|+|+.+|++.
T Consensus 9 ~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~ 39 (79)
T COG1654 9 LLLLLLLTGNFVSGEKLAEELGISRTAVWKH 39 (79)
T ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999973799666899999978659999999
No 186
>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=74.52 E-value=7 Score=19.43 Aligned_cols=46 Identities=13% Similarity=0.145 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH---------------HHHHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358---------------99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA---------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~---------------~~L~~iA~~l~v~~~~l 73 (144)
++-.++|+.+||++.|+-.||+ |--.|.- ..+.++++.+|++++..
T Consensus 2 y~Ig~vA~l~gv~~~TLR~YEr~GLi~P~R~~G~RlYs~~Di~rLrfIkrL~~e~G~nlagI 63 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERHGLIKPARRNGQRLYSNNDLKRLRFIKKLINEKGLNIAGV 63 (120)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 24899999978688999999985896888889822779999999999999999759689999
No 187
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=74.46 E-value=7 Score=19.42 Aligned_cols=50 Identities=12% Similarity=0.078 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC-CCCC----HHHHHHHHH
Q ss_conf 9999999999999819979999998724699999985289-8835----899999997
Q gi|254780424|r 12 DINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV-NRVG----ASRLQHISE 64 (144)
Q Consensus 12 d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~-~~ps----~~~L~~iA~ 64 (144)
+.|-+.-.+..+.-. ...+.|+-+ |--.++.-|++-. -.|. ..=|..||.
T Consensus 37 ~~y~~~l~~~~~~~~--~d~~~AeDi-vQevFl~~~~~~~~~~~~~~~~~~WL~~Ia~ 91 (194)
T PRK09646 37 DRTASRVYGLVRRVL--RDPGYSEET-TQEVYLEVWRTASRFDPARGSALAWLLTLAH 91 (194)
T ss_pred HHHHHHHHHHHHHHH--CCHHHHHHH-HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 999999999999992--999999999-9999999999752147542659999999999
No 188
>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=74.34 E-value=2.5 Score=22.29 Aligned_cols=23 Identities=17% Similarity=0.307 Sum_probs=20.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 97999999872469999998528
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G 50 (144)
+|-.|+|+.+|||..+|-.||+-
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 189
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=74.19 E-value=3.7 Score=21.20 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=25.3
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999981997999999872469999998528
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
.++. ..+.|.+-.++|...|||++|+-+|-+.
T Consensus 13 ~v~~-L~~~G~~i~~IA~~~~vsrsTvYRyl~~ 44 (45)
T pfam02796 13 EVIT-LLEEGISIKQIAKIFGISRSTVYRYLAA 44 (45)
T ss_pred HHHH-HHHCCCCHHHHHHHHCCHHHHHHHHCCC
T ss_conf 9999-9987994999999986008888764458
No 190
>PRK09775 hypothetical protein; Provisional
Probab=74.01 E-value=3.6 Score=21.24 Aligned_cols=31 Identities=16% Similarity=0.161 Sum_probs=27.6
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999819979999998724699999985
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
-|+.++..--+|-.||++++|||+.|+|+--
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 191
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=73.98 E-value=5.1 Score=20.32 Aligned_cols=30 Identities=20% Similarity=0.202 Sum_probs=26.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998199799999987246999999
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+.|.+.=...|+.+.+.|+.+|+|++++.+
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 192
>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=73.84 E-value=7.3 Score=19.32 Aligned_cols=44 Identities=14% Similarity=0.159 Sum_probs=29.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHH--CC-----CCCCCHHHHHHHHHHCCCC
Q ss_conf 19979999998724699999985--28-----9883589999999754999
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYE--KG-----VNRVGASRLQHISEVLESP 69 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E--~G-----~~~ps~~~L~~iA~~l~v~ 69 (144)
.++|-.+||+.+|++..-+-+.- .| ....+.+....||..||+.
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 193
>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=73.55 E-value=3.8 Score=21.10 Aligned_cols=23 Identities=13% Similarity=0.329 Sum_probs=20.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 97999999872469999998528
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G 50 (144)
+|-.|+|+.+|||.++|-.||.-
T Consensus 2 ~tIgeva~~~gvs~~tLRyye~~ 24 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEK 24 (88)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 67899999989599999999994
No 194
>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=73.47 E-value=2.8 Score=21.99 Aligned_cols=46 Identities=22% Similarity=0.286 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH--------------H--HHHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358--------------9--9999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA--------------S--RLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~--------------~--~L~~iA~~l~v~~~~l 73 (144)
||-.|+|+.+|||.++|-.||. |--.|.- . .+....+.+|.|+..+
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 195
>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=73.28 E-value=3 Score=21.76 Aligned_cols=36 Identities=17% Similarity=0.208 Sum_probs=28.9
Q ss_pred HHHHHH-HHHCCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 999999-998199799999987246999999852898
Q gi|254780424|r 17 KRIRLR-RMILGMSQEKLGECLGITFQQVQKYEKGVN 52 (144)
Q Consensus 17 ~rIr~~-R~~~glTQ~eLA~~lGvs~s~is~~E~G~~ 52 (144)
+++.-+ |.+.|-|-.+||...||..||++.|-.++.
T Consensus 11 eKi~iI~~~e~G~s~~~lar~~gi~~STl~~I~Knke 47 (53)
T pfam04218 11 EKIEVIQRSEEGESKASLARRFNVPRSTLRDILKNKE 47 (53)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9999999998589688999996987979999998099
No 196
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=73.09 E-value=2.9 Score=21.93 Aligned_cols=24 Identities=13% Similarity=0.292 Sum_probs=20.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 979999998724699999985289
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
+|-.|+|+.+|||.++|-.||+-.
T Consensus 1 ytI~e~a~~~gvs~~tlR~ye~~G 24 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIG 24 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 978899999896999999999858
No 197
>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=73.00 E-value=2.9 Score=21.92 Aligned_cols=24 Identities=17% Similarity=0.321 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 979999998724699999985289
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
|+-.|||++.|||..||-.||+-.
T Consensus 1 M~IgelA~~tGvs~~TIRyYe~~G 24 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREG 24 (95)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 978999999897899999999978
No 198
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=72.78 E-value=2.5 Score=22.25 Aligned_cols=31 Identities=16% Similarity=0.379 Sum_probs=25.9
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 9981997999999872469999998528988
Q gi|254780424|r 23 RMILGMSQEKLGECLGITFQQVQKYEKGVNR 53 (144)
Q Consensus 23 R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ 53 (144)
--..||...++|+++|||+.||.+|-+-...
T Consensus 15 ~yl~gmk~~dIAeklGvspntiksWKrr~gW 45 (279)
T COG5484 15 DYLKGMKLKDIAEKLGVSPNTIKSWKRRDGW 45 (279)
T ss_pred HHHHHCCHHHHHHHHCCCHHHHHHHHHHCCC
T ss_conf 9984341999999968986888877874088
No 199
>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=72.76 E-value=3 Score=21.82 Aligned_cols=46 Identities=11% Similarity=0.205 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH------------H-----HHHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358------------9-----9999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA------------S-----RLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~------------~-----~L~~iA~~l~v~~~~l 73 (144)
||-.|+|+.+|||.+||-.||+ |--.|.. + .+...++.+|+|++..
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 200
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=72.71 E-value=7.7 Score=19.15 Aligned_cols=46 Identities=15% Similarity=0.058 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC-CCCC--------------H--HHHHHHHHHCCCCHHHH
Q ss_conf 979999998724699999985289-8835--------------8--99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGV-NRVG--------------A--SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~-~~ps--------------~--~~L~~iA~~l~v~~~~l 73 (144)
++-.|+|+++|||..||-.||+-. -.|. + -.+.+-|+.||.|+...
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 201
>PHA01082 putative transcription regulator
Probab=72.55 E-value=7.8 Score=19.13 Aligned_cols=48 Identities=21% Similarity=0.208 Sum_probs=38.6
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC-HHHHHHHHHHCC--CCHHH
Q ss_conf 8199799999987246999999852898835-899999997549--99999
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRVG-ASRLQHISEVLE--SPISF 72 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps-~~~L~~iA~~l~--v~~~~ 72 (144)
+-|||-+|-|+..--|..++-.|-.|+.-|. -.+|+++-+.=. ..-+|
T Consensus 28 eCgLsveeaA~LCfKtVrtVk~WD~G~~IPPeCkRLMRm~~gREl~~~e~W 78 (133)
T PHA01082 28 ECGLSVEEAAKLCFKTVSEVKQWDAGEKIPPICKRLMRMNKGRELSSCEEW 78 (133)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCCH
T ss_conf 137639999999999788886304899498799999988517704564104
No 202
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=72.43 E-value=3.1 Score=21.71 Aligned_cols=17 Identities=12% Similarity=0.085 Sum_probs=5.9
Q ss_pred CCHHHHHHHHHHCCCCH
Q ss_conf 35899999997549999
Q gi|254780424|r 54 VGASRLQHISEVLESPI 70 (144)
Q Consensus 54 ps~~~L~~iA~~l~v~~ 70 (144)
|.--.+..||+.|||+.
T Consensus 176 PR~~~l~dLA~~lGISk 192 (215)
T COG3413 176 PRRVSLKDLAKELGISK 192 (215)
T ss_pred CCCCCHHHHHHHHCCCH
T ss_conf 76589999999959988
No 203
>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=72.18 E-value=1.8 Score=23.26 Aligned_cols=49 Identities=14% Similarity=0.217 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCC
Q ss_conf 99999999999981997999999872469999998528988358999999975499999950677
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVS 77 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~ 77 (144)
+||=+|||++=-.-...-+||-..+- +.| ++.-||+.||++=...++.+
T Consensus 106 vHVPRRIKelGpkIkk~~dELT~~lq-------------rSP---~i~EIA~~lg~SEEEVLE~M 154 (256)
T TIGR02941 106 VHVPRRIKELGPKIKKAVDELTDELQ-------------RSP---KIAEIADRLGVSEEEVLEIM 154 (256)
T ss_pred CCCCCCHHCCCCCCHHHHHHHHHHHC-------------CCC---CHHHHHHHCCCCHHHHHHHH
T ss_conf 01574110037720145566444421-------------487---06546412177488898776
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=72.02 E-value=3.7 Score=21.23 Aligned_cols=22 Identities=14% Similarity=0.250 Sum_probs=19.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9799999987246999999852
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+|-.|+|+.+||+..++-.||+
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
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=71.88 E-value=8.1 Score=19.03 Aligned_cols=35 Identities=20% Similarity=0.306 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHH-----------CCCCCCCHHHHHHH
Q ss_conf 979999998724699999985-----------28988358999999
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYE-----------KGVNRVGASRLQHI 62 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E-----------~G~~~ps~~~L~~i 62 (144)
|.-.++|.++|||+.||.+|- .|..-.+-+.|..+
T Consensus 1 mkT~~vAk~LGVspkTVQRWvKq~ni~~~rNE~GHy~Ft~e~l~~l 46 (178)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQLNLPIERNEYGHYIFTEDDLDQL 46 (178)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEEECHHHHHHH
T ss_conf 9717889993999299999999958995536554433249899999
No 206
>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=71.68 E-value=3.7 Score=21.20 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=23.7
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9981997999999872469999998528
Q gi|254780424|r 23 RMILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 23 R~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
-...|+|-.|.|+.+|+|.+|+..+=+.
T Consensus 11 ~~~~G~s~~eIA~~L~is~~TV~~~~~~ 38 (57)
T cd06170 11 LLAEGKTNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9980799999999989789999999999
No 207
>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=71.55 E-value=4.6 Score=20.62 Aligned_cols=47 Identities=15% Similarity=0.182 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH--------------HH--HHHHHHHCCCCHHHHH
Q ss_conf 9799999987246999999852-8988358--------------99--9999975499999950
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA--------------SR--LQHISEVLESPISFFF 74 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~--------------~~--L~~iA~~l~v~~~~l~ 74 (144)
+|-.++|+.+|||..|+-.||+ |--.|+. .+ +....+.+|.|+..+-
T Consensus 2 ~tI~e~Ak~~gvs~~TLRyYe~~GLl~P~~r~~nGYR~Ys~~dl~rL~~I~~lr~lG~sL~eIk 65 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIR 65 (172)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 9789999998949889999998879899884999870779999999999999998799999999
No 208
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=71.37 E-value=3.4 Score=21.41 Aligned_cols=21 Identities=19% Similarity=0.339 Sum_probs=13.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 997999999872469999998
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~ 47 (144)
.+||.++|..+|+|+.++|+.
T Consensus 173 ~~t~~~lA~~lG~tretvsR~ 193 (236)
T PRK09392 173 PYEKRTLASYLGMTPENLSRA 193 (236)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
T ss_conf 478999999878989999999
No 209
>pfam00376 MerR MerR family regulatory protein.
Probab=71.05 E-value=3.2 Score=21.57 Aligned_cols=25 Identities=20% Similarity=0.238 Sum_probs=20.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 7999999872469999998528988
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVNR 53 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~~ 53 (144)
|-.|+|+.+|||.++|-.||+-.--
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gli 25 (38)
T pfam00376 1 TIGEVAKLLGVSPRTLRYYEKIGLL 25 (38)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCC
T ss_conf 9899999988799999999986898
No 210
>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=70.98 E-value=8.4 Score=18.90 Aligned_cols=46 Identities=15% Similarity=0.019 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCC-CCH--------------H--HHHHHHHHCCCCHHHH
Q ss_conf 97999999872469999998528988-358--------------9--9999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNR-VGA--------------S--RLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~-ps~--------------~--~L~~iA~~l~v~~~~l 73 (144)
+|-.|+|+..|||..||-.||+-.-- |.. . .+.+-|+.+|.|++.+
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 211
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=70.91 E-value=4 Score=20.98 Aligned_cols=33 Identities=9% Similarity=0.121 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999999998199799999987246999999852
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
|..+-.+..+.. +...+.|+-+ |--..+.-|.+
T Consensus 22 ~~p~L~~~a~~l--~~~~~dAEDl-vQetflk~~~~ 54 (190)
T PRK12516 22 SLPSLRAFAVSL--IGQHDRADDL-VQDTIMKAWAK 54 (190)
T ss_pred HHHHHHHHHHHH--CCCHHHHHHH-HHHHHHHHHHH
T ss_conf 899999999999--0999999999-99999999999
No 212
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=70.77 E-value=8.5 Score=18.87 Aligned_cols=72 Identities=28% Similarity=0.346 Sum_probs=53.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHH--HCC---CCHHHHHHHHHHHHHHHHHH-----HCCCCCCC---HHHHHHHHHHCC
Q ss_conf 998766899899999999999999--819---97999999872469999998-----52898835---899999997549
Q gi|254780424|r 1 MVGNKKIPNPVDINVGKRIRLRRM--ILG---MSQEKLGECLGITFQQVQKY-----EKGVNRVG---ASRLQHISEVLE 67 (144)
Q Consensus 1 ~~~~~~~~~~~d~~iG~rIr~~R~--~~g---lTQ~eLA~~lGvs~s~is~~-----E~G~~~ps---~~~L~~iA~~l~ 67 (144)
||..++.|.+.=..+-.++|.++. +.| .|=.+||+.+|++.++|-+= +.|++..- -+.+..|.++||
T Consensus 1 ~~~~~~Ip~~ti~RLp~Y~r~L~~l~~~g~~~iSS~eLa~~~gi~~~qVRKDls~fG~fG~~G~GY~V~~L~~~i~~iLG 80 (211)
T PRK05472 1 MMKQKKIPEATIKRLPLYYRYLKELLEEGVERVSSKELAEAVGVDSAQIRKDLSYFGELGKRGVGYNVKELLDFIEKILG 80 (211)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEECHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf 98657899899999999999999999859838979999999698999999899986457999988129999999999968
Q ss_pred CCHHH
Q ss_conf 99999
Q gi|254780424|r 68 SPISF 72 (144)
Q Consensus 68 v~~~~ 72 (144)
++-.|
T Consensus 81 ~~~~~ 85 (211)
T PRK05472 81 LDKTT 85 (211)
T ss_pred CCCCC
T ss_conf 99975
No 213
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=70.60 E-value=8.6 Score=18.85 Aligned_cols=30 Identities=23% Similarity=0.251 Sum_probs=24.0
Q ss_pred HHHH-HHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999-99819979999998724699999985
Q gi|254780424|r 19 IRLR-RMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 19 Ir~~-R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
|..+ +...++|..|+|+.+|++++++.++-
T Consensus 17 Le~l~~~~~~lslsela~~lglpksTv~RlL 47 (264)
T PRK09834 17 LRALNRLDGGATVGLLAELTGLHRTTVRRLL 47 (264)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9987417999799999999790999999999
No 214
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=70.05 E-value=6.1 Score=19.79 Aligned_cols=56 Identities=13% Similarity=0.043 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC--CC-C-HHHHHHHHHHCCCCHHHH
Q ss_conf 9999999999998199799999987246999999852898--83-5-899999997549999995
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVN--RV-G-ASRLQHISEVLESPISFF 73 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~--~p-s-~~~L~~iA~~l~v~~~~l 73 (144)
.|-+.-.+.++...| -.+.|+-+ |--.++.-|.+-.. .. + ..=|..||. +.-++++
T Consensus 9 ~y~~~l~~~~~~~~~--d~~~AEDi-vQe~flk~~~~~~~~~~~~~~~~WL~~Iar--N~~id~~ 68 (181)
T PRK09637 9 EYKAQLKAFLHSRVS--NEADVDDL-LQEVLIKTHSNLHSLKDGSSIKSWLYQIAN--NTIIDFY 68 (181)
T ss_pred HHHHHHHHHHHHHCC--CHHHHHHH-HHHHHHHHHHHHHCCCCCCCHHHHHHHHHH--HHHHHHH
T ss_conf 999999999999959--99999999-999999999852205882349999999999--9999999
No 215
>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=69.81 E-value=3.8 Score=21.15 Aligned_cols=46 Identities=20% Similarity=0.190 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC-CCCCCH----------------HHHHHHHHHCCCCHHHH
Q ss_conf 97999999872469999998528-988358----------------99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKG-VNRVGA----------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G-~~~ps~----------------~~L~~iA~~l~v~~~~l 73 (144)
||-.|+|+..|||..||-.||+- --.|.- -.+.+-++.+|.|++.+
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 216
>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=69.65 E-value=3.7 Score=21.20 Aligned_cols=47 Identities=21% Similarity=0.168 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCC----------CCCHHH-----HHHHHHHCCCCHHHHH
Q ss_conf 9799999987246999999852-898----------835899-----9999975499999950
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVN----------RVGASR-----LQHISEVLESPISFFF 74 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~----------~ps~~~-----L~~iA~~l~v~~~~l~ 74 (144)
||-.|+|+.+|||.+||-.||+ |-- .-+.+. +.+.++.+|+|++.+-
T Consensus 2 ~~Ige~A~~~gvs~~TlRyYe~~GLl~~~R~~ngyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~ 64 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECL 64 (102)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 809999999897999999999869989881999995069999999999999999799899999
No 217
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=69.57 E-value=8.2 Score=18.99 Aligned_cols=58 Identities=12% Similarity=0.089 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC-CCCCC---CH-HHHHHHHHHCCCCHHHH
Q ss_conf 999999999999998199799999987246999999852-89883---58-99999997549999995
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEK-GVNRV---GA-SRLQHISEVLESPISFF 73 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~-G~~~p---s~-~~L~~iA~~l~v~~~~l 73 (144)
++.|-+.-.+..+.-. .-.+.|+-+ |--.++.-|++ +.-.| +. .-|..||. +.-++++
T Consensus 29 ~~ry~~~l~~~~~~~~--~d~~~AEDi-vQe~flki~~~~~~~~~~~~~~~~wL~~ia~--n~~~d~~ 91 (187)
T PRK13919 29 FRRYAGSFLALARRMG--LDGAAAEDV-VQEAMIRVWQKAKEFDPRRGSARAFLLTLGH--HAAVDEV 91 (187)
T ss_pred HHHHHHHHHHHHHHHC--CCHHHHHHH-HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH--HHHHHHH
T ss_conf 9999999999999990--999999999-9999999999998768764649999999999--9999999
No 218
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=69.55 E-value=7.8 Score=19.14 Aligned_cols=18 Identities=17% Similarity=0.200 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHHHHHC
Q ss_conf 9999987246999999852
Q gi|254780424|r 31 EKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E~ 49 (144)
.+.|+-+ +.-..+.-|.+
T Consensus 37 ~~~AeDi-~Qe~fi~l~~~ 54 (180)
T PRK11924 37 RALAEDA-VQEAFLRAWRK 54 (180)
T ss_pred HHHHHHH-HHHHHHHHHHH
T ss_conf 9999999-99999999886
No 219
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=69.24 E-value=5.5 Score=20.07 Aligned_cols=59 Identities=19% Similarity=0.191 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHH-HHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 999999999999998199--799999987246999-999852898835899999997549999995
Q gi|254780424|r 11 VDINVGKRIRLRRMILGM--SQEKLGECLGITFQQ-VQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~gl--TQ~eLA~~lGvs~s~-is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
+..|...--+.++...|= .-+++.+.+=+..-. +..| .+... -..=|..|+. |.-++++
T Consensus 21 ~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~~~~-~~~wl~~Ia~--n~~iD~~ 82 (182)
T COG1595 21 LERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RGRSS-FKAWLYRIAR--NLAIDRL 82 (182)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHC-CCCCC-HHHHHHHHHH--HHHHHHH
T ss_conf 9999999999999996884309999999999999733311-67887-8999999999--9999999
No 220
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=69.18 E-value=5.7 Score=19.98 Aligned_cols=32 Identities=34% Similarity=0.375 Sum_probs=29.5
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 99981997999999872469999998528988
Q gi|254780424|r 22 RRMILGMSQEKLGECLGITFQQVQKYEKGVNR 53 (144)
Q Consensus 22 ~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ 53 (144)
.|...|+|-.+.|+.+|.+.+++-++-.|...
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 221
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=69.17 E-value=4.5 Score=20.68 Aligned_cols=26 Identities=23% Similarity=0.404 Sum_probs=22.8
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 98199799999987246999999852
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
...|+|-.|.|+.+|+|.+++..+=+
T Consensus 15 l~~G~s~~eIA~~L~is~~TV~~h~~ 40 (58)
T pfam00196 15 LAAGKSNKEIADILGISEKTVKVHRS 40 (58)
T ss_pred HHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98079999999997888999999999
No 222
>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=69.02 E-value=4 Score=20.98 Aligned_cols=46 Identities=17% Similarity=0.150 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCC-CC-----------HH-----HHHHHHHHCCCCHHHH
Q ss_conf 97999999872469999998528988-35-----------89-----9999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNR-VG-----------AS-----RLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~-ps-----------~~-----~L~~iA~~l~v~~~~l 73 (144)
||-.|||+..|||..||-.||+-.-- |. .+ .+.+-++.+|.|++.+
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 223
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=69.01 E-value=4.5 Score=20.67 Aligned_cols=27 Identities=22% Similarity=0.365 Sum_probs=23.0
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 998199799999987246999999852
Q gi|254780424|r 23 RMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 23 R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
-...|+|-.+.|+.+|+|.+|+..+=+
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 224
>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=68.93 E-value=4 Score=20.96 Aligned_cols=46 Identities=15% Similarity=0.160 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCC-CCH----------------HHHHHHHHHCCCCHHHH
Q ss_conf 97999999872469999998528988-358----------------99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNR-VGA----------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~-ps~----------------~~L~~iA~~l~v~~~~l 73 (144)
||-.|+|+..|||..+|-.||.-.-- |.. -.+.+.++.+|.|+..+
T Consensus 1 m~Ige~A~~~gvs~~tlR~Ye~~GLl~~~~R~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI 63 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEI 63 (123)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEECCCCCEEEHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 968999999895999999999818987514679995621377878899999999869999999
No 225
>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=68.80 E-value=4.1 Score=20.94 Aligned_cols=23 Identities=22% Similarity=0.458 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 97999999872469999998528
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G 50 (144)
+|-.|+|+.+||+..++-.||+.
T Consensus 1 YtI~eva~~~Gv~~~tLRyyEk~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 97899999988687899999873
No 226
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=68.54 E-value=4.1 Score=20.95 Aligned_cols=41 Identities=10% Similarity=0.228 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCC
Q ss_conf 9799999987246999999852898835899999997549999995067
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~ 76 (144)
|+..++|+.+|++.||||+.=+++.--+---++ ++-|||..
T Consensus 331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~f--------eLk~FFs~ 371 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAITNKYLATPRGLF--------ELKYFFSS 371 (444)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCEE--------EHHHHHHH
T ss_conf 319999988371288899998254104886334--------48988777
No 227
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=68.52 E-value=7.9 Score=19.10 Aligned_cols=55 Identities=22% Similarity=0.308 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH-HHHHHHC
Q ss_conf 999999999999-981997999999872469999998528988358999-9999754
Q gi|254780424|r 12 DINVGKRIRLRR-MILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRL-QHISEVL 66 (144)
Q Consensus 12 d~~iG~rIr~~R-~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L-~~iA~~l 66 (144)
.+-|.+.|-.-. ....+|-.|||+.+|||.++|.++.+-----.+.-| ..+++.+
T Consensus 18 Ek~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~~~~ 74 (282)
T PRK11557 18 DRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLALSEAL 74 (282)
T ss_pred HHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 999999998098999765699999896999889999999938998999999999998
No 228
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=68.46 E-value=7.2 Score=19.35 Aligned_cols=35 Identities=17% Similarity=0.217 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999998199799999987246999999852
Q gi|254780424|r 12 DINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 12 d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+.|-+.-.+..+...| -.+.|+-+ +--..+.-|++
T Consensus 37 ~ry~~~ly~~a~~~~~--~~~dAEDl-vQevFlk~~~~ 71 (231)
T PRK11922 37 RRHNRRLYRLARAILR--DDAEAEDV-VQEAYLRAFRA 71 (231)
T ss_pred HHHHHHHHHHHHHHHC--CHHHHHHH-HHHHHHHHHHH
T ss_conf 9999999999999929--99999999-99999999987
No 229
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=68.38 E-value=8.5 Score=18.90 Aligned_cols=17 Identities=24% Similarity=0.415 Sum_probs=9.0
Q ss_pred HHHHHHHHHCCCHHHHHH
Q ss_conf 999999872899999999
Q gi|254780424|r 101 LQLNRYFIQIDDVKVRQK 118 (144)
Q Consensus 101 ~~l~~~~~~l~~~~~r~~ 118 (144)
.++.++...+|+.+ |..
T Consensus 123 ~~l~~~l~~Lp~~~-r~v 139 (184)
T PRK12539 123 LDLGRLLARLPEKM-RLA 139 (184)
T ss_pred HHHHHHHHCCCHHH-HHH
T ss_conf 99999998499999-999
No 230
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=68.11 E-value=9 Score=18.73 Aligned_cols=33 Identities=9% Similarity=0.113 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999819979999998724699999985
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
.|-..-.+..+...| -.+.|+-+ +--.++.-|.
T Consensus 34 ry~~~l~~~a~~~l~--d~~~AEDl-vQe~Fl~~~~ 66 (196)
T PRK12524 34 RLAPRALAVATRVLG--NRAEAEDV-TQEAMLRLWR 66 (196)
T ss_pred HHHHHHHHHHHHHHC--CHHHHHHH-HHHHHHHHHH
T ss_conf 999999999999919--99999999-9999999999
No 231
>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=68.06 E-value=4.3 Score=20.78 Aligned_cols=46 Identities=11% Similarity=0.186 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCC-H----------------HHHHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852898835-8----------------99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVG-A----------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps-~----------------~~L~~iA~~l~v~~~~l 73 (144)
||-.|+|+..|||..||-.||.-.--|+ . -.+.+.++.+|.|++.+
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 232
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=67.66 E-value=9.2 Score=18.68 Aligned_cols=58 Identities=14% Similarity=0.161 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCCH----HHHHHHHHHCCCCHHHH
Q ss_conf 999999999999998199799999987246999999852898-8358----99999997549999995
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVN-RVGA----SRLQHISEVLESPISFF 73 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~-~ps~----~~L~~iA~~l~v~~~~l 73 (144)
++.|-+.-.+..+...| -.+.|+-+ |--.++.-|++-.. .|.. .=|..||. |.-++++
T Consensus 26 ~~~y~~~l~~~~~~~~~--d~~~AeDi-vQe~fl~~~~~~~~~~~~~~~~~~wL~~ia~--n~~~d~~ 88 (186)
T PRK05602 26 VARKLPRLLALATRMLG--DPAEAEDV-AQETFLRIWNQAPSWRPGEARFDTWLHRVVL--NLCYDRL 88 (186)
T ss_pred HHHHHHHHHHHHHHHCC--CHHHHHHH-HHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH--HHHHHHH
T ss_conf 99999999999999929--99999999-9999999998722258862039999999999--9999999
No 233
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=67.24 E-value=7.7 Score=19.15 Aligned_cols=49 Identities=18% Similarity=0.178 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHCCC-CH--HHHHHHHHHH-HHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 999999999998199-79--9999987246-999999852898835899999997
Q gi|254780424|r 14 NVGKRIRLRRMILGM-SQ--EKLGECLGIT-FQQVQKYEKGVNRVGASRLQHISE 64 (144)
Q Consensus 14 ~iG~rIr~~R~~~gl-TQ--~eLA~~lGvs-~s~is~~E~G~~~ps~~~L~~iA~ 64 (144)
|-.+-++..|..++= .. +++.+-+=+. ...+..++ |...+ ..=|++||.
T Consensus 14 ~r~~L~~fa~~~L~~~~d~AEDlvQEtflka~~~~~~f~-~~s~f-~tWL~~Iar 66 (195)
T PRK12532 14 SRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQ-GRALV-NSWLFAILK 66 (195)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCC-CCCCH-HHHHHHHHH
T ss_conf 899999999998089875799999999999998687458-98878-889999999
No 234
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=67.21 E-value=7.1 Score=19.38 Aligned_cols=37 Identities=19% Similarity=0.255 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 9799999987246999999852898835899999997
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISE 64 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~ 64 (144)
||.+++|+.+|+|.+++++.=+-....+...+....+
T Consensus 2 lsl~~lA~~~~~S~~~l~~~f~~~~g~s~~~~i~~~R 38 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRDRR 38 (84)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 8999999988909999999999988939999999999
No 235
>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=67.09 E-value=4.7 Score=20.56 Aligned_cols=46 Identities=17% Similarity=0.268 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH----------H-----HHHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358----------9-----9999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA----------S-----RLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~----------~-----~L~~iA~~l~v~~~~l 73 (144)
+|-.++|+.+|||.++|-.||+ |--.|.- + .+.+....+|+|++.+
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 236
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=66.97 E-value=9.5 Score=18.58 Aligned_cols=50 Identities=8% Similarity=-0.035 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC--HHHHHHHHH
Q ss_conf 99999999999998199799999987246999999852898835--899999997
Q gi|254780424|r 12 DINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVG--ASRLQHISE 64 (144)
Q Consensus 12 d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps--~~~L~~iA~ 64 (144)
+.|-+.-.+.++...| -.+.|+-+ +.-..+.-|.+.....+ ..=|..||.
T Consensus 10 ~~y~~~l~~~~~~~~~--d~~~AeDl-~Qe~flk~~~~~~~~~~~~~~wL~~ia~ 61 (166)
T PRK09639 10 KQYYQDVVQQIIYIVK--DRTQAEDL-AQEVFLRLLRSDWKGIENEKGWLIKSAR 61 (166)
T ss_pred HHHHHHHHHHHHHHHC--CHHHHHHH-HHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf 9999999999999929--99999999-9999999987263544678999999999
No 237
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=66.96 E-value=7.8 Score=19.11 Aligned_cols=42 Identities=7% Similarity=0.139 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHCC-CCCC---C-HHHHHHHHHHCCCCHHHH
Q ss_conf 7999999872469999998528-9883---5-899999997549999995
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKG-VNRV---G-ASRLQHISEVLESPISFF 73 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G-~~~p---s-~~~L~~iA~~l~v~~~~l 73 (144)
.-.+.|+-+ |--.++.-|++- .-.+ + ..=|+.||. |.-++++
T Consensus 60 ~d~~~AEDv-vQetFlkvw~~~~~~~~~~~~f~tWL~~Iar--N~~~d~l 106 (206)
T PRK12526 60 GNEAQANEL-VQETMSNVWRKAHLYNGDKGAATTWVYTVMR--NAAFDML 106 (206)
T ss_pred CCHHHHHHH-HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH--HHHHHHH
T ss_conf 999999999-9999999998387658642529999999999--9999999
No 238
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=66.90 E-value=5.4 Score=20.15 Aligned_cols=13 Identities=23% Similarity=0.404 Sum_probs=6.8
Q ss_pred HHHHHHHHCCCHH
Q ss_conf 9999987289999
Q gi|254780424|r 102 QLNRYFIQIDDVK 114 (144)
Q Consensus 102 ~l~~~~~~l~~~~ 114 (144)
++..++..||+.+
T Consensus 106 ~l~~aL~~LP~~~ 118 (188)
T PRK12546 106 DFRAAFAQLPDEQ 118 (188)
T ss_pred HHHHHHHCCCHHH
T ss_conf 9999998699999
No 239
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=66.70 E-value=9.4 Score=18.61 Aligned_cols=58 Identities=19% Similarity=0.201 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCC---HHHHHHHHHHCCCCHHHH
Q ss_conf 999999999999998199799999987246999999852898-835---899999997549999995
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVN-RVG---ASRLQHISEVLESPISFF 73 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~-~ps---~~~L~~iA~~l~v~~~~l 73 (144)
++.|-+.-.+..+...| -.+.|+-+ |--..+.-|++-.. .|. ..=|..||. |+-++++
T Consensus 24 ~~~y~~~l~~~~~~~~~--~~~~AeD~-vQe~flk~~~~~~~~~~~~~~~~WL~~Ia~--N~~~d~~ 85 (187)
T PRK09641 24 VDLYKDKIYQLCYRMLG--NRHEAEDI-AQEAFIRAYVNIDSFDINRKFSTWLYRIAT--NLTIDRL 85 (187)
T ss_pred HHHHHHHHHHHHHHHCC--CHHHHHHH-HHHHHHHHHHHCCCCCCCCCHHHHHHHHHH--HHHHHHH
T ss_conf 99999999999999909--99999999-999999999846125741349999999999--9999999
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=66.65 E-value=6 Score=19.85 Aligned_cols=50 Identities=24% Similarity=0.243 Sum_probs=36.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf 99999998199799999987246999999852898835899999997549999
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~ 70 (144)
|==+.|...|.|-+++|+..|++...|-+|+.- +-.++-+.+..+..+++
T Consensus 59 reIQarIRaGas~eevA~~~g~~~~rVerfa~P---Vl~ER~~iae~A~~~~~ 108 (169)
T pfam11268 59 REIQARIRAGASAEEVAEAAGVPEERVERFEGP---VLAERARVAELARAVHP 108 (169)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHCCCH---HHHHHHHHHHHHHHCCC
T ss_conf 999999887999999999959999998742233---88999999999860877
No 241
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=66.62 E-value=5.1 Score=20.29 Aligned_cols=10 Identities=30% Similarity=0.484 Sum_probs=4.5
Q ss_pred CCHHHHHHHH
Q ss_conf 9799999987
Q gi|254780424|r 28 MSQEKLGECL 37 (144)
Q Consensus 28 lTQ~eLA~~l 37 (144)
++|+++-..+
T Consensus 134 ~~Q~~iD~~~ 143 (225)
T PRK10046 134 ASQKQIDEMF 143 (225)
T ss_pred CCHHHHHHHH
T ss_conf 8999999996
No 242
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=66.44 E-value=10 Score=18.35 Aligned_cols=58 Identities=10% Similarity=0.002 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCC---HHHHHHHHHHCCCCHHHH
Q ss_conf 999999999999998199799999987246999999852898-835---899999997549999995
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVN-RVG---ASRLQHISEVLESPISFF 73 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~-~ps---~~~L~~iA~~l~v~~~~l 73 (144)
.+.|-+.-.+.++.-.| -.+.|+-+ |.-.++.-|++-.. .|. ..=|..||. +.-++++
T Consensus 25 ~~~y~~~l~~~~~~~~~--~~~~AeDi-vQe~fl~~~~~~~~~~~~~~~~~wL~~ia~--n~~~d~~ 86 (177)
T PRK09638 25 LQQHYNFLYGYVLKLTL--NPDLAEDL-VQETMLKAIENIHQFQGRSKFSTWLISIAS--RLYLDHL 86 (177)
T ss_pred HHHHHHHHHHHHHHHCC--CHHHHHHH-HHHHHHHHHHHHHHCCCCHHHHHHHHHHHH--HHHHHHH
T ss_conf 99999999999999919--99999999-999999999988770650079999999999--9999999
No 243
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=66.42 E-value=9.7 Score=18.53 Aligned_cols=34 Identities=15% Similarity=0.046 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCH----HHHHHHHH
Q ss_conf 999999872469999998528988358----99999997
Q gi|254780424|r 30 QEKLGECLGITFQQVQKYEKGVNRVGA----SRLQHISE 64 (144)
Q Consensus 30 Q~eLA~~lGvs~s~is~~E~G~~~ps~----~~L~~iA~ 64 (144)
..+.|+-+ +--.++.-|++....+.. .=|..|+.
T Consensus 52 ~~~~AeDl-vQe~fl~~~~~~~~~~~~~~~~~wL~~ia~ 89 (194)
T PRK12519 52 NSQEAEDL-TQEIFLSLWRKSSYDPKRGSLSSYLLTLTR 89 (194)
T ss_pred CHHHHHHH-HHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 99999999-999999999863316662429999999999
No 244
>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=66.42 E-value=4.9 Score=20.41 Aligned_cols=47 Identities=13% Similarity=0.130 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCC--------------H--HHHHHHHHHCCCCHHHHH
Q ss_conf 9799999987246999999852-898835--------------8--999999975499999950
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVG--------------A--SRLQHISEVLESPISFFF 74 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps--------------~--~~L~~iA~~l~v~~~~l~ 74 (144)
|+-.|||++.|||.++|-.||. |--.|. + -.+.+-++.+|.+++.+-
T Consensus 1 M~IgelA~~~gvs~~tlR~YE~~GLl~p~~r~~nGyR~Y~~~~i~~l~~I~~~r~lGfsL~eI~ 64 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIR 64 (131)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 9789999998878899999997799898776999975349999999999999999699999999
No 245
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=66.38 E-value=10 Score=18.30 Aligned_cols=52 Identities=8% Similarity=0.100 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHH------HCCCCCCCHHHHHHHHHHC
Q ss_conf 9999999999819-97999999872469999998------5289883589999999754
Q gi|254780424|r 15 VGKRIRLRRMILG-MSQEKLGECLGITFQQVQKY------EKGVNRVGASRLQHISEVL 66 (144)
Q Consensus 15 iG~rIr~~R~~~g-lTQ~eLA~~lGvs~s~is~~------E~G~~~ps~~~L~~iA~~l 66 (144)
|-+-.++.+.+-| |||+++|-.+|+|.++|+++ |+|..-|+.-+...|...+
T Consensus 92 i~Ri~~EA~~QgglLT~~Dla~LL~~S~~TI~~~ik~ye~~~g~vvPtRG~i~DiGp~v 150 (220)
T pfam07900 92 IVRIFNEAYEQGALLTHADIAILLGVSTTTISRHVKEYEERTGEVVPTRGIIKDIGPSV 150 (220)
T ss_pred HHHHHHHHHHCCCEEEHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf 99999999973885117669999889888999999999997096635787203458762
No 246
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=66.16 E-value=7 Score=19.41 Aligned_cols=15 Identities=20% Similarity=0.224 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999998
Q gi|254780424|r 11 VDINVGKRIRLRRMI 25 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~ 25 (144)
++.|-..-.+.++..
T Consensus 53 v~rh~~~vy~~a~r~ 67 (222)
T PRK09647 53 VRQHADRVYRLAYRL 67 (222)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999999999998
No 247
>PHA00361 cI Repressor
Probab=66.16 E-value=3.2 Score=21.57 Aligned_cols=19 Identities=5% Similarity=0.225 Sum_probs=16.1
Q ss_pred HHHHHCCCCHHHHHCCCCC
Q ss_conf 9997549999995067744
Q gi|254780424|r 61 HISEVLESPISFFFDVSPT 79 (144)
Q Consensus 61 ~iA~~l~v~~~~l~~~~~~ 79 (144)
+||++||++++||+.+...
T Consensus 1 ~lA~~Lg~s~~~Ll~g~~~ 19 (165)
T PHA00361 1 KLAKALGTSVDDLLQEDLS 19 (165)
T ss_pred CHHHHHCCCHHHHHCCCCC
T ss_conf 9568669899998557556
No 248
>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=66.16 E-value=5 Score=20.34 Aligned_cols=46 Identities=9% Similarity=0.203 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH-----------H-----HHHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358-----------9-----9999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA-----------S-----RLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~-----------~-----~L~~iA~~l~v~~~~l 73 (144)
+|-.|+|+.+|||.+++-.||. |--.|.. + .+....+.+|+|+..+
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 249
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=66.11 E-value=11 Score=18.29 Aligned_cols=12 Identities=0% Similarity=0.008 Sum_probs=6.0
Q ss_pred HHHHHHHHCCCH
Q ss_conf 999998728999
Q gi|254780424|r 102 QLNRYFIQIDDV 113 (144)
Q Consensus 102 ~l~~~~~~l~~~ 113 (144)
++..+...+|+.
T Consensus 105 ~l~~al~~Lp~~ 116 (164)
T PRK12547 105 DFRKALNLLPAD 116 (164)
T ss_pred HHHHHHHHCCHH
T ss_conf 999999858999
No 250
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=65.91 E-value=8.6 Score=18.86 Aligned_cols=41 Identities=7% Similarity=0.098 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCC---CC-C-HHHHHHHHHHCCCCHHHH
Q ss_conf 99999987246999999852898---83-5-899999997549999995
Q gi|254780424|r 30 QEKLGECLGITFQQVQKYEKGVN---RV-G-ASRLQHISEVLESPISFF 73 (144)
Q Consensus 30 Q~eLA~~lGvs~s~is~~E~G~~---~p-s-~~~L~~iA~~l~v~~~~l 73 (144)
-.+.|+-+ |--.++.-|.+-.. .. + ..=|+.||. +.-++++
T Consensus 50 d~~~AeDl-vQe~Flk~~~~~~~~~~~~s~f~tWl~~Ia~--N~~~d~l 95 (194)
T PRK12531 50 NEQVAMEM-VQETMSTVWQKAHLFDGQKSALSTWIYTIIR--NLCFDLL 95 (194)
T ss_pred CHHHHHHH-HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH--HHHHHHH
T ss_conf 99999999-9999999999888667653609999999999--9999999
No 251
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=65.75 E-value=10 Score=18.31 Aligned_cols=57 Identities=11% Similarity=0.214 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCC---H-HHHHHHHHHCCCCHHHH
Q ss_conf 99999999999998199799999987246999999852898-835---8-99999997549999995
Q gi|254780424|r 12 DINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVN-RVG---A-SRLQHISEVLESPISFF 73 (144)
Q Consensus 12 d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~-~ps---~-~~L~~iA~~l~v~~~~l 73 (144)
+.|-+.-.+..+.-. ...+.|+-+ |.-..+.-|.+-.. .|. + .=|+.|+. |.-++++
T Consensus 30 ~~y~~~l~~~~~~~~--~d~~~AeDi-vQe~Fl~~~~~~~~~~~~~~~~~~WL~~Iar--n~~~~~l 91 (184)
T PRK12537 30 QQESARLLGVARRIV--RDRALAEDI-VHDAFIKIWTKAASFDAARGSARGWIYSVTR--HLALNTL 91 (184)
T ss_pred HHHHHHHHHHHHHHH--CCHHHHHHH-HHHHHHHHHHHHCCCCCCCCCHHHHHHHHHH--HHHHHHH
T ss_conf 999999999999992--999999999-9999999998604168442639999999999--9999999
No 252
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=65.66 E-value=11 Score=18.29 Aligned_cols=35 Identities=17% Similarity=0.098 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999819979999998724699999985
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
++.|-+.-.+-.+.-.+ . .+.|+-+ +--..+.-|.
T Consensus 25 ~~~y~~~l~~~~~~~~~-~-~~~aeDv-~Qe~fl~l~~ 59 (192)
T PRK09652 25 VRKYQPRLYRLLSRLVR-D-PADAEDL-AQETFIKAYR 59 (192)
T ss_pred HHHHHHHHHHHHHHHCC-C-HHHHHHH-HHHHHHHHHH
T ss_conf 99999999999999969-9-9999998-7599999887
No 253
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=65.64 E-value=10 Score=18.37 Aligned_cols=18 Identities=17% Similarity=0.122 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHHHHHC
Q ss_conf 9999987246999999852
Q gi|254780424|r 31 EKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E~ 49 (144)
.+.|+-+ |.-.++.-|++
T Consensus 43 ~~~AeD~-vQe~Flk~~~~ 60 (190)
T PRK12543 43 KTDVDDV-VQEVYIQLYES 60 (190)
T ss_pred HHHHHHH-HHHHHHHHHHH
T ss_conf 9999999-99999999999
No 254
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=65.61 E-value=5.3 Score=20.20 Aligned_cols=34 Identities=18% Similarity=0.097 Sum_probs=25.9
Q ss_pred HHHH--HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999--9999998199799999987246999999852
Q gi|254780424|r 15 VGKR--IRLRRMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 15 iG~r--Ir~~R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+++| |..++ ..|+|-.|+|..+|..+|||++=-+
T Consensus 10 ~~eR~~I~~l~-~~~~S~reIA~~LgRh~sTIsRElk 45 (318)
T COG2826 10 LFERYEIERLL-KAKMSIREIAKQLNRHHSTISRELK 45 (318)
T ss_pred HHHHHHHHHHH-HCCCCHHHHHHHHCCCCCHHHHHHH
T ss_conf 88899999999-8599899999985768620427986
No 255
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=65.55 E-value=8.7 Score=18.81 Aligned_cols=16 Identities=19% Similarity=0.275 Sum_probs=7.8
Q ss_pred HHHHHHHHHHCCCCHHHH
Q ss_conf 899999997549999995
Q gi|254780424|r 56 ASRLQHISEVLESPISFF 73 (144)
Q Consensus 56 ~~~L~~iA~~l~v~~~~l 73 (144)
..=|+.||. |.-++++
T Consensus 56 ~~WL~~Ia~--N~~~d~~ 71 (161)
T PRK12541 56 RPWLFTIAY--NAFIDWY 71 (161)
T ss_pred HHHHHHHHH--HHHHHHH
T ss_conf 899999999--9999999
No 256
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=65.47 E-value=5.6 Score=20.05 Aligned_cols=31 Identities=10% Similarity=0.116 Sum_probs=24.0
Q ss_pred HHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999-8199799999987246999999852
Q gi|254780424|r 19 IRLRRM-ILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 19 Ir~~R~-~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
|..+.. ..++|..|+|+.+|++++++.++-+
T Consensus 9 L~~~~~~~~~~~l~eia~~~gl~kstv~RlL~ 40 (52)
T pfam09339 9 LEALAEAPGGLSLTEIARRTGLPKSTAHRLLQ 40 (52)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99986289998999999998919999999999
No 257
>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=65.11 E-value=5.3 Score=20.19 Aligned_cols=46 Identities=15% Similarity=0.158 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCC-H-------------H--HHHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-898835-8-------------9--9999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVG-A-------------S--RLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps-~-------------~--~L~~iA~~l~v~~~~l 73 (144)
+|=.|||+.+|||.++|-.||+ |--.|. . . .+...++.+|.|++.+
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 258
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=64.64 E-value=9.4 Score=18.60 Aligned_cols=11 Identities=27% Similarity=0.422 Sum_probs=4.9
Q ss_pred HHHHHHHCCCH
Q ss_conf 99998728999
Q gi|254780424|r 103 LNRYFIQIDDV 113 (144)
Q Consensus 103 l~~~~~~l~~~ 113 (144)
+..+...+|+.
T Consensus 122 l~~~l~~Lp~~ 132 (188)
T PRK12517 122 LRRQIAKLDPE 132 (188)
T ss_pred HHHHHHCCCHH
T ss_conf 99999769999
No 259
>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=64.50 E-value=4.1 Score=20.94 Aligned_cols=48 Identities=17% Similarity=0.241 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 1997999999872469999998528-98835899999997549999995
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYEKG-VNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E~G-~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
-|||-+++|.--|+++||||+|=.. +...=-.+=..+|.-|+-+...|
T Consensus 181 ~~Ls~~r~g~my~~~~STvsR~~~~ARe~lle~Tr~~La~RL~L~~~El 229 (249)
T TIGR03001 181 EGLSMDRLGAMYQVHRSTVSRWVAQARERLLERTRRRLAERLKLSSREL 229 (249)
T ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf 0332999987745775078999999999999999999999748880578
No 260
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=64.39 E-value=6.5 Score=19.61 Aligned_cols=59 Identities=14% Similarity=0.049 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHCCCCH---HHHHHHHHHH-HHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 99999999999999819979---9999987246-999999852898835899999997549999995
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQ---EKLGECLGIT-FQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ---~eLA~~lGvs-~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
++.+-+.-.+.++...+-.. +++.+.+=+. ...+.+|..+. +=..=|..||. +.-++++
T Consensus 24 ~~~y~~~l~~~~~~~l~~~~~~AEDl~Qe~fl~~~~~~~~~~~~~--~~~~WL~~Ia~--n~~~d~~ 86 (178)
T PRK12536 24 LTELARHLRAFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRPDQ--PLTAWVQAIAR--YKLADFL 86 (178)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHH--HHHHHHH
T ss_conf 999999999999999099876899999999999999787669999--68999999999--9999999
No 261
>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=64.36 E-value=5.6 Score=20.05 Aligned_cols=46 Identities=13% Similarity=0.137 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCC----------CHHH-----HHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-89883----------5899-----999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRV----------GASR-----LQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~p----------s~~~-----L~~iA~~l~v~~~~l 73 (144)
|+-.|+|+.+|||..+|-.||+ |--.| +.+. +...++.+|.|++.+
T Consensus 1 M~Ige~a~~~gvs~~tlRyYe~~GLl~p~r~~~gyR~Y~~~~~~~l~~I~~lr~~G~sl~eI 62 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEI 62 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 96899999989799999999984899998089987005999999999999999969999999
No 262
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=64.21 E-value=11 Score=18.09 Aligned_cols=57 Identities=16% Similarity=0.100 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC---CC-C-HHHHHHHHHHCCCCHHHH
Q ss_conf 99999999999998199799999987246999999852898---83-5-899999997549999995
Q gi|254780424|r 12 DINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVN---RV-G-ASRLQHISEVLESPISFF 73 (144)
Q Consensus 12 d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~---~p-s-~~~L~~iA~~l~v~~~~l 73 (144)
+.|-+.-.+....-.| -.+.|+-+ +--.++.-|.+-.. .. + ..=|..||. |.-++++
T Consensus 26 ~~y~~~l~~~a~~~~~--d~~~AeDi-~Qe~fl~~~~~~~~~~~~~~~~~~wL~~iar--N~~id~~ 87 (179)
T PRK12514 26 DATSAKLFGICLRVLK--DRSEAEEA-LQDVYVKIWTKADRFAVSGLSPMTWLITIAR--NHAIDRL 87 (179)
T ss_pred HHHHHHHHHHHHHHCC--CHHHHHHH-HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH--HHHHHHH
T ss_conf 9999999999999909--99999999-9999999998875157665539999999999--9999999
No 263
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=64.20 E-value=11 Score=18.24 Aligned_cols=15 Identities=20% Similarity=0.268 Sum_probs=6.5
Q ss_pred HHHHHHHHHCCCCHHHH
Q ss_conf 99999997549999995
Q gi|254780424|r 57 SRLQHISEVLESPISFF 73 (144)
Q Consensus 57 ~~L~~iA~~l~v~~~~l 73 (144)
.=|..||. |.-++++
T Consensus 53 ~WL~~Ia~--n~~~d~~ 67 (165)
T PRK09644 53 PWLFKVAY--HTFIDFV 67 (165)
T ss_pred HHHHHHHH--HHHHHHH
T ss_conf 99999999--9999999
No 264
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=64.08 E-value=5.5 Score=20.10 Aligned_cols=39 Identities=26% Similarity=0.381 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHH-------HCC--CCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 999999999999-------819--979999998724699999985289
Q gi|254780424|r 13 INVGKRIRLRRM-------ILG--MSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 13 ~~iG~rIr~~R~-------~~g--lTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
+|+-++++.+++ +.| -|-+|+|+.+|++...+..+..-.
T Consensus 162 ~~~~~~~~ki~~~~~~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~~ 209 (318)
T PRK07405 162 IHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERA 209 (318)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 789999999999999999871898648999988599999999999980
No 265
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=64.07 E-value=7.8 Score=19.12 Aligned_cols=12 Identities=0% Similarity=0.108 Sum_probs=5.6
Q ss_pred HHHHHHHCCCHH
Q ss_conf 999987289999
Q gi|254780424|r 103 LNRYFIQIDDVK 114 (144)
Q Consensus 103 l~~~~~~l~~~~ 114 (144)
+..+...||+.+
T Consensus 100 l~~ai~~Lp~~q 111 (161)
T PRK09047 100 IEEAIQKLPARQ 111 (161)
T ss_pred HHHHHHHCCHHH
T ss_conf 999998199999
No 266
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=63.92 E-value=11 Score=18.08 Aligned_cols=25 Identities=16% Similarity=0.356 Sum_probs=10.2
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 8199799999987246999999852
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
..|=|...+|.+.|||.+.+-+|.+
T Consensus 349 r~GDtL~~IA~ky~vsv~~L~~~N~ 373 (449)
T PRK10783 349 RSGDTLSGIASRLGVSTKDLQQWNN 373 (449)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 8999899999997979999999839
No 267
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=63.84 E-value=11 Score=18.10 Aligned_cols=52 Identities=12% Similarity=0.121 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC-----CCCCHHHHHHHHHH
Q ss_conf 99999999999999819979999998724699999985289-----88358999999975
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV-----NRVGASRLQHISEV 65 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~-----~~ps~~~L~~iA~~ 65 (144)
.+.|-+.-.+.++...| =.+.|+-+ |.-..+.-|++-. ..+-..=|..|+.-
T Consensus 13 y~~~~~~l~~~~~~~~~--d~~~AeDi-vQe~F~k~~~~~~~~~~~~~~~~~wL~~Ia~n 69 (171)
T PRK09645 13 YDEHAAALWRYALRLTG--DRARAEDV-VQETLLRAWQHPEVLADPTRSARAWLFTVARN 69 (171)
T ss_pred HHHHHHHHHHHHHHHCC--CHHHHHHH-HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf 99999999999999909--99999999-99999999985887066414199999999999
No 268
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=63.69 E-value=11 Score=18.15 Aligned_cols=18 Identities=11% Similarity=0.082 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHHHHHHHC
Q ss_conf 9999987246999999852
Q gi|254780424|r 31 EKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E~ 49 (144)
.+.|+-+ +--.++.-|.+
T Consensus 33 ~~~AEDi-vQe~Flk~~~~ 50 (185)
T PRK12542 33 IQQAEDA-VQETFITLYKN 50 (185)
T ss_pred HHHHHHH-HHHHHHHHHHH
T ss_conf 9999999-99999999998
No 269
>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=63.62 E-value=4 Score=20.98 Aligned_cols=23 Identities=9% Similarity=0.118 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHCCCCHHHHHCCC
Q ss_conf 58999999975499999950677
Q gi|254780424|r 55 GASRLQHISEVLESPISFFFDVS 77 (144)
Q Consensus 55 s~~~L~~iA~~l~v~~~~l~~~~ 77 (144)
+.++|++||+-+||+++.|....
T Consensus 3 ~GDtlWkiA~kygV~~~~Li~~N 25 (44)
T TIGR02899 3 KGDTLWKIAKKYGVDLDELIQAN 25 (44)
T ss_pred CCCHHHHHHHHHCCCHHHHHHHC
T ss_conf 88214777877178767886416
No 270
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=63.53 E-value=5.2 Score=20.27 Aligned_cols=41 Identities=20% Similarity=0.121 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCC-CC---CHHHHHHHHHHCCCCHHHH
Q ss_conf 99999987246999999852898-83---5899999997549999995
Q gi|254780424|r 30 QEKLGECLGITFQQVQKYEKGVN-RV---GASRLQHISEVLESPISFF 73 (144)
Q Consensus 30 Q~eLA~~lGvs~s~is~~E~G~~-~p---s~~~L~~iA~~l~v~~~~l 73 (144)
-.+.|+-+ |--.++.-|++... .+ -..=|+.|+. |.-++++
T Consensus 27 d~~dAEDl-vQetflk~~~~~~~~~~~~~~~~WL~~Iar--N~~id~~ 71 (182)
T PRK12511 27 DSAEAEDL-VHDALVRALERRASFRSGGNLRTWLMSILH--NAFIDEL 71 (182)
T ss_pred CHHHHHHH-HHHHHHHHHHHHHHCCCCCCHHHHHHHHHH--HHHHHHH
T ss_conf 99999999-999999999998866886649999999999--9999999
No 271
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=63.47 E-value=10 Score=18.36 Aligned_cols=41 Identities=15% Similarity=0.080 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCC-CCCCC----HHHHHHHHHHCCCCHHHH
Q ss_conf 999999872469999998528-98835----899999997549999995
Q gi|254780424|r 30 QEKLGECLGITFQQVQKYEKG-VNRVG----ASRLQHISEVLESPISFF 73 (144)
Q Consensus 30 Q~eLA~~lGvs~s~is~~E~G-~~~ps----~~~L~~iA~~l~v~~~~l 73 (144)
..+.|+-+ +--.++.-|.+- .-.|+ ..=|..||. |.-++++
T Consensus 48 ~~~~AeDv-~Qe~Fl~vw~~~~~~~~~~~~~~tWl~~Iar--N~~~d~l 93 (187)
T PRK12534 48 QRAEAEEV-LQDVFTLIWHKAGQFDPSRARGLTWLAMIAR--NKAIDHL 93 (187)
T ss_pred CHHHHHHH-HHHHHHHHHHHHCCCCCCCCCHHHHHHHHHH--HHHHHHH
T ss_conf 99999999-9999999998753368752218999999999--9999999
No 272
>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=63.46 E-value=12 Score=17.95 Aligned_cols=28 Identities=25% Similarity=0.246 Sum_probs=22.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHH-CCCCCCC
Q ss_conf 979999998724699999985-2898835
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYE-KGVNRVG 55 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E-~G~~~ps 55 (144)
|+-.|||+..|||..||-.|| .|--.|.
T Consensus 1 m~Ige~Ak~~~vs~~TlRyYe~~GLl~P~ 29 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDLGLLIPE 29 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 96899999969989888999985886887
No 273
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=63.45 E-value=7.3 Score=19.31 Aligned_cols=32 Identities=9% Similarity=0.133 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf 97999999872469999998528988358999
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVGASRL 59 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L 59 (144)
|...|+++.+|+|+++|.++.+....|.--.|
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvkl 45 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVKL 45 (70)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCCCCCCEEC
T ss_conf 20899999977668999999804779998622
No 274
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=63.40 E-value=5.9 Score=19.92 Aligned_cols=35 Identities=3% Similarity=-0.046 Sum_probs=25.8
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 99999999819979999998724699999985289
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
.++=..+--.+.|-.++|+++|||++++..|=.++
T Consensus 6 ~~l~~~~G~~~~s~~~Ia~~agvs~~~iy~~F~~K 40 (47)
T pfam00440 6 LELFAEKGYDATTVREIAKEAGVSKGALYRHFPSK 40 (47)
T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCCCH
T ss_conf 99999869150779999999796988999887699
No 275
>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=62.79 E-value=12 Score=17.87 Aligned_cols=31 Identities=35% Similarity=0.345 Sum_probs=21.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999981997999999872469999998
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
+.|=.+|-..|++-+++|+++|.|.+++.+.
T Consensus 121 R~Ll~~rY~~G~~~~~~A~~~g~~~~A~~~~ 151 (163)
T TIGR02989 121 RELLQLRYQRGVSLEALAEQLGRTVNAVYKA 151 (163)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCHHHHHHHH
T ss_conf 9999998227978789998847138999999
No 276
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=62.67 E-value=12 Score=17.86 Aligned_cols=42 Identities=10% Similarity=-0.039 Sum_probs=17.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCC--CCCH--HHHHHHHHHCCCCHHHH
Q ss_conf 799999987246999999852898--8358--99999997549999995
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVN--RVGA--SRLQHISEVLESPISFF 73 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~--~ps~--~~L~~iA~~l~v~~~~l 73 (144)
+-.+.|+-+ +--..+.-|.+-.. .+.. .=|+.||. |+-.+++
T Consensus 32 ~~~~~AEDi-~Qd~fik~~~~~~~~~~~~~~~~wl~~ia~--N~~~d~~ 77 (175)
T PRK12518 32 CGRELLDDL-VQEVFLRVWKGLPKLRNPAYFSTWLYRITW--NVATDAR 77 (175)
T ss_pred CCHHHHHHH-HHHHHHHHHHCCCCCCCCCHHHHHHHHHHH--HHHHHHH
T ss_conf 799889999-999999998711127982359999999999--9999999
No 277
>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=62.60 E-value=12 Score=17.85 Aligned_cols=47 Identities=11% Similarity=0.022 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCH-----------H-----HHHHHHHHCCCCHHHHH
Q ss_conf 97999999872469999998528988358-----------9-----99999975499999950
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVGA-----------S-----RLQHISEVLESPISFFF 74 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps~-----------~-----~L~~iA~~l~v~~~~l~ 74 (144)
+|-.|+|+.+|||.+|+-.||+-.--|.. + .+...++.+|+|++.+-
T Consensus 2 ~~Ige~a~~~gis~~tlRyYe~~GLl~~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sL~eIk 64 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIA 64 (102)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 878999999894999999999879999873999996378999999999999999699999999
No 278
>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=62.53 E-value=8 Score=19.07 Aligned_cols=36 Identities=19% Similarity=0.129 Sum_probs=29.0
Q ss_pred HHHHHHHHHCCC-CHHHHHHHH-----H-HHHHHHHHHHCCCC
Q ss_conf 999999998199-799999987-----2-46999999852898
Q gi|254780424|r 17 KRIRLRRMILGM-SQEKLGECL-----G-ITFQQVQKYEKGVN 52 (144)
Q Consensus 17 ~rIr~~R~~~gl-TQ~eLA~~l-----G-vs~s~is~~E~G~~ 52 (144)
++||++=.+.++ ||+||.+.| - |+++|+|+|-+=-.
T Consensus 5 ~~Ik~Ii~~e~~~tQ~El~~~L~~~G~~nvTQaTvSRDL~el~ 47 (155)
T TIGR01529 5 EAIKEIITEEKISTQEELVALLKKEGVKNVTQATVSRDLRELG 47 (155)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHCCCCEECCCCHHHHHHHHC
T ss_conf 9999998743767988999999865975112340678787522
No 279
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=62.12 E-value=13 Score=17.80 Aligned_cols=36 Identities=11% Similarity=0.125 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999999999981997999999872469999998528
Q gi|254780424|r 12 DINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 12 d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
+.|-+.-.+..+.- +...+.|+-+ |--.++.-|++-
T Consensus 29 ~ry~~~l~~~~~~~--~~~~~~AeDi-vQe~Fl~~~~~~ 64 (189)
T PRK12515 29 GRHHVRVYRFGLRL--VRDEQTAEDL-VSEVFLDVWRQA 64 (189)
T ss_pred HHHHHHHHHHHHHH--CCCHHHHHHH-HHHHHHHHHHHH
T ss_conf 99999999999999--2999999999-999999999865
No 280
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=61.68 E-value=7.7 Score=19.15 Aligned_cols=11 Identities=0% Similarity=0.015 Sum_probs=5.0
Q ss_pred HHHHHHHCCCH
Q ss_conf 99998728999
Q gi|254780424|r 103 LNRYFIQIDDV 113 (144)
Q Consensus 103 l~~~~~~l~~~ 113 (144)
+..+...+++.
T Consensus 105 l~~al~~Lp~~ 115 (181)
T PRK12540 105 FRAALEKLPQD 115 (181)
T ss_pred HHHHHHCCCHH
T ss_conf 99999819999
No 281
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=61.46 E-value=13 Score=17.72 Aligned_cols=64 Identities=22% Similarity=0.208 Sum_probs=52.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHC
Q ss_conf 766899899999999999999819979999998724699999985289883589999999754999999506
Q gi|254780424|r 4 NKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFD 75 (144)
Q Consensus 4 ~~~~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~ 75 (144)
.+..||..+.| +-++..+..-+ +|.++..++ +=..++.|++--..++|..||...|.+.+.+-.
T Consensus 96 ~~~~~nt~~Ah--~l~~~A~~~G~-~~~~~~~~l-----f~AyF~eg~nI~D~dVL~diA~~~GLD~~~~~~ 159 (225)
T COG2761 96 IVPAPNTLDAH--RLIKAAELQGK-AQDRFLEAL-----FEAYFEEGRNIGDEDVLADIAEEVGLDREEFKA 159 (225)
T ss_pred CCCCCCHHHHH--HHHHHHHHHCC-HHHHHHHHH-----HHHHHCCCCCCCCHHHHHHHHHHHCCCHHHHHH
T ss_conf 14788628999--99999999583-389999999-----999722488888489999999994988999999
No 282
>PRK05949 RNA polymerase sigma factor; Validated
Probab=61.05 E-value=6.9 Score=19.48 Aligned_cols=42 Identities=10% Similarity=0.223 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHH---------CCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 9999999999998---------19979999998724699999985289883
Q gi|254780424|r 13 INVGKRIRLRRMI---------LGMSQEKLGECLGITFQQVQKYEKGVNRV 54 (144)
Q Consensus 13 ~~iG~rIr~~R~~---------~glTQ~eLA~~lGvs~s~is~~E~G~~~p 54 (144)
+|+.++++.+++. +.-|-.|+|+.+|++...+..+..-...|
T Consensus 171 ~~~~~~~~ki~~~~~~l~~~lgr~pt~~EiA~~l~i~~~~v~~~l~~~~~~ 221 (327)
T PRK05949 171 IHITEKLNKIKKTQRELSQKLGRSATPAEIAKALELEPSQIREYLSMARQP 221 (327)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf 789999999999999999981889988999989499999999999841887
No 283
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=61.03 E-value=6.9 Score=19.46 Aligned_cols=46 Identities=17% Similarity=0.191 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH------------HH--HHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358------------99--999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA------------SR--LQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~------------~~--L~~iA~~l~v~~~~l 73 (144)
+|-.|+|+.+|||..||-.||. |--.|.- .. +..-++.+|.|+..+
T Consensus 1 ytIge~A~~~gvs~~tlRyYe~~GLl~p~r~~g~R~Y~~~~~~~l~~I~~~r~~G~sL~eI 61 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEI 61 (118)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 9588999998979999999998699875557986860899999999999999829989999
No 284
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=60.74 E-value=7.9 Score=19.08 Aligned_cols=28 Identities=25% Similarity=0.326 Sum_probs=23.0
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998199799999987246999999
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+..+++..-+|-.+||+.+|||..|+-+
T Consensus 6 l~~l~~~~~~~i~~La~~~~VS~~TiRR 33 (53)
T smart00420 6 LELLAQQGKVSVEELAELLGVSEMTIRR 33 (53)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999986979799999998979999999
No 285
>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=60.53 E-value=2.8 Score=21.95 Aligned_cols=23 Identities=26% Similarity=0.449 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 9999987246999999852898835899999997
Q gi|254780424|r 31 EKLGECLGITFQQVQKYEKGVNRVGASRLQHISE 64 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~ 64 (144)
+|||+++|||+.|+ -++|.+||+
T Consensus 34 RELsElIGVTRTTL-----------REVLQRLAR 56 (275)
T TIGR02812 34 RELSELIGVTRTTL-----------REVLQRLAR 56 (275)
T ss_pred HHHHHHCCCCCCHH-----------HHHHHHHHH
T ss_conf 65754237663037-----------899988764
No 286
>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=60.52 E-value=7.2 Score=19.33 Aligned_cols=50 Identities=8% Similarity=0.119 Sum_probs=41.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCC-HHHH
Q ss_conf 9819979999998724699999985289883589999999754999-9995
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESP-ISFF 73 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~-~~~l 73 (144)
...|++++.++..+|++++.+|++-+=...+..+.+..|.-+-+|= +.|+
T Consensus 174 ~~~g~~r~~I~~aL~vdks~lSrml~Va~~iP~elI~aIGpAp~iGR~RW~ 224 (325)
T TIGR03454 174 EDRGFDRDTIMAALSVDKTELSRMISVARRIPEELIEAIGPAPGIGRPRWM 224 (325)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHH
T ss_conf 984999999999988899999999999997899999973798734733799
No 287
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=60.47 E-value=9 Score=18.72 Aligned_cols=28 Identities=11% Similarity=-0.142 Sum_probs=16.3
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999819979999998724699999985
Q gi|254780424|r 21 LRRMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 21 ~~R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
.+-...-+|+.+||+.+-||++|+.+.-
T Consensus 86 ~lL~~~~i~l~dLAd~lfVSrsTi~~dl 113 (585)
T PRK09863 86 NLLLNTFTPMGQLASALFLSRTWVAERL 113 (585)
T ss_pred HHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9862689889999998583999999999
No 288
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=60.21 E-value=8.5 Score=18.87 Aligned_cols=20 Identities=10% Similarity=0.187 Sum_probs=12.6
Q ss_pred CCHHHHHHHHHHHHHHHHCC
Q ss_conf 99899999999999999819
Q gi|254780424|r 8 PNPVDINVGKRIRLRRMILG 27 (144)
Q Consensus 8 ~~~~d~~iG~rIr~~R~~~g 27 (144)
|-.++.+-++-+|..|...|
T Consensus 22 ~~l~e~y~~~L~r~A~r~l~ 41 (207)
T PRK12544 22 PVFLEDLRAQMLKFAKLQLR 41 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHC
T ss_conf 99999999999999999949
No 289
>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=60.14 E-value=5.5 Score=20.09 Aligned_cols=20 Identities=15% Similarity=0.313 Sum_probs=15.8
Q ss_pred CCCHHHHHHHHHHCCCCHHH
Q ss_conf 83589999999754999999
Q gi|254780424|r 53 RVGASRLQHISEVLESPISF 72 (144)
Q Consensus 53 ~ps~~~L~~iA~~l~v~~~~ 72 (144)
.|.+..|.+||++++||+.-
T Consensus 90 EPDV~ALlRLc~V~nIPlAt 109 (143)
T TIGR00160 90 EPDVKALLRLCDVYNIPLAT 109 (143)
T ss_pred CCCHHHHHHHHHHCCCHHHH
T ss_conf 80078898786450250344
No 290
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=60.04 E-value=8.7 Score=18.84 Aligned_cols=26 Identities=8% Similarity=0.192 Sum_probs=12.3
Q ss_pred HHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 999852898835899999997549999995
Q gi|254780424|r 44 VQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 44 is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
+.+|. |...+ ..=|+.||. |+-++++
T Consensus 65 l~~f~-~~s~f-~tWL~~IA~--N~~~d~~ 90 (185)
T PRK09649 65 IPRFS-ARSSA-RTWLLAIAR--HVVADHI 90 (185)
T ss_pred HHHCC-CCCCH-HHHHHHHHH--HHHHHHH
T ss_conf 87628-87618-999999999--9999999
No 291
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=59.89 E-value=8.2 Score=18.98 Aligned_cols=25 Identities=20% Similarity=0.311 Sum_probs=21.4
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 8199799999987246999999852
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
..++|..|+|+.+|++++++.++-+
T Consensus 18 ~~~~sl~eia~~~~l~ksT~~RlL~ 42 (91)
T smart00346 18 PGGLTLAELAERLGLSKSTAHRLLN 42 (91)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9998999999998909999999999
No 292
>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=59.71 E-value=7.6 Score=19.19 Aligned_cols=46 Identities=13% Similarity=0.190 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH-----------H---H--HHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358-----------9---9--999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA-----------S---R--LQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~-----------~---~--L~~iA~~l~v~~~~l 73 (144)
++-.|+|+.+|||..|+-.||. |--.|.. + . +....+.+|+|++.+
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 293
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=59.69 E-value=9.8 Score=18.50 Aligned_cols=27 Identities=22% Similarity=0.213 Sum_probs=21.7
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999981997999999872469999998
Q gi|254780424|r 20 RLRRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 20 r~~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
..++ ...++-.|+|+.+|+|++++|+-
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 294
>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=59.68 E-value=7.7 Score=19.17 Aligned_cols=46 Identities=17% Similarity=0.175 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCC-CCH-----------H-----HHHHHHHHCCCCHHHH
Q ss_conf 97999999872469999998528988-358-----------9-----9999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNR-VGA-----------S-----RLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~-ps~-----------~-----~L~~iA~~l~v~~~~l 73 (144)
|.-.|+|+.+|||..+|-.||+-.-- |.. + .+.+-++.+|.|+..+
T Consensus 1 M~Ige~a~~~gvs~~tlRyYE~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~GfsL~eI 63 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEI 63 (127)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEECCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 968999999894999999999858988753479995436399999999999998649879999
No 295
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=59.52 E-value=9.1 Score=18.71 Aligned_cols=12 Identities=0% Similarity=-0.017 Sum_probs=5.5
Q ss_pred HHHHHHHHCCCH
Q ss_conf 999998728999
Q gi|254780424|r 102 QLNRYFIQIDDV 113 (144)
Q Consensus 102 ~l~~~~~~l~~~ 113 (144)
++..+...|++.
T Consensus 125 ~l~~~l~~Lp~~ 136 (195)
T PRK12535 125 DVRTLIDALPPE 136 (195)
T ss_pred HHHHHHHCCCHH
T ss_conf 999999849998
No 296
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=59.00 E-value=14 Score=17.54 Aligned_cols=35 Identities=9% Similarity=-0.030 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999998199799999987246999999852
Q gi|254780424|r 12 DINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 12 d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+.|-+.-.+.++.-. .-.+.|+-+ +--.++.-|.+
T Consensus 27 ~~y~~~l~~~~~~~~--~d~~~AeDi-~Qe~f~~~~~~ 61 (193)
T PRK11923 27 LKYQHKILGLIVRFV--HDTHEAQDV-AQEAFIKAYRA 61 (193)
T ss_pred HHHHHHHHHHHHHHC--CCHHHHHHH-HHHHHHHHHHC
T ss_conf 999999999999990--999999999-99999999861
No 297
>pfam09571 RE_XcyI XcyI restriction endonuclease. This family includes the XcyI (recognizes and cleaves C^CCGGG) restriction endonucleases.
Probab=58.93 E-value=3.7 Score=21.24 Aligned_cols=63 Identities=21% Similarity=0.280 Sum_probs=46.8
Q ss_pred HHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHH-CCCCCCC-HHHHHHHHHHCCCCHHHHHCCCCCC
Q ss_conf 9999999819979999998-724699999985-2898835-8999999975499999950677443
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGEC-LGITFQQVQKYE-KGVNRVG-ASRLQHISEVLESPISFFFDVSPTV 80 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~-lGvs~s~is~~E-~G~~~ps-~~~L~~iA~~l~v~~~~l~~~~~~~ 80 (144)
-|-..|.-+|+||+++-.. -|......-.+| +|+..+- -..+..+|-+|.-+-+.|+++.+..
T Consensus 76 L~GYYRLLlG~SQK~fy~~d~g~g~g~fksmE~kG~i~k~~~p~i~dlc~af~~sas~Ll~~~g~~ 141 (318)
T pfam09571 76 LIGYYRLLLGYSQKRFYRMDSGLGFGPFKSMEKKGKINKALRPHIPDLCSAFIASASKLLDGLGIQ 141 (318)
T ss_pred HHHHHHHHHCCCHHHHCCCCCCCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCH
T ss_conf 566899985665998646777778761220465176451013320789999999999998542521
No 298
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=58.72 E-value=14 Score=17.42 Aligned_cols=45 Identities=7% Similarity=0.040 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 99999999999999--8199799999987246999999852898835
Q gi|254780424|r 11 VDINVGKRIRLRRM--ILGMSQEKLGECLGITFQQVQKYEKGVNRVG 55 (144)
Q Consensus 11 ~d~~iG~rIr~~R~--~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps 55 (144)
.|-.|-+-++.+.. ...+|.++||+.+|+|++++++.=+.....|
T Consensus 181 ~d~ri~~a~~yI~~h~~~~isl~~lA~~~~lS~s~l~rlFk~~~G~s 227 (290)
T PRK10572 181 MDPRVREACQYISDHLASEFDIESVAQHVCLSPSRLSHLFRQQLGIS 227 (290)
T ss_pred CCHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCC
T ss_conf 68999999999998637999999999896979999999999864989
No 299
>PRK13749 transcriptional regulator MerD; Provisional
Probab=58.53 E-value=14 Score=17.40 Aligned_cols=48 Identities=15% Similarity=0.090 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHC-CCCCCCH----------------HHHHHHHHHCCCCHHHH
Q ss_conf 199799999987246999999852-8988358----------------99999997549999995
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYEK-GVNRVGA----------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E~-G~~~ps~----------------~~L~~iA~~l~v~~~~l 73 (144)
..+|-.+||+..|||..+|-.||. |--.|.. -.+.+-|..+|.+++.+
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 300
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=58.43 E-value=14 Score=17.47 Aligned_cols=57 Identities=11% Similarity=0.233 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHH----HHH-HHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 999999999999998199799999987----246-999999852898835899999997549999995
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQEKLGECL----GIT-FQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ~eLA~~l----Gvs-~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
+..+-++-.+..+...| -.+.|+-+ -+. ...+..++ |...+ ..=|++||. |.-++++
T Consensus 15 ~e~yr~~L~~fa~~~l~--d~~~AEDlvQEtFlka~~~~~~f~-~~~~f-~tWL~~Ia~--N~~id~l 76 (191)
T PRK12530 15 LEEIRLQMLKFATLQLK--DADLAEDVVQEAFTSALKNIDSFK-GQSAL-KTWIFAILK--NKIIDYI 76 (191)
T ss_pred HHHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHHHHHCC-CCCCH-HHHHHHHHH--HHHHHHH
T ss_conf 99999999999999939--999999999999999998688637-87729-999999999--9999999
No 301
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=58.27 E-value=15 Score=17.37 Aligned_cols=13 Identities=8% Similarity=0.151 Sum_probs=6.3
Q ss_pred HHHHHHHHCCCHH
Q ss_conf 9999987289999
Q gi|254780424|r 102 QLNRYFIQIDDVK 114 (144)
Q Consensus 102 ~l~~~~~~l~~~~ 114 (144)
++..+...+++.+
T Consensus 124 ~l~~~L~~Lp~~~ 136 (184)
T PRK12512 124 DVGRHLETLPPRQ 136 (184)
T ss_pred HHHHHHHCCCHHH
T ss_conf 9999996899999
No 302
>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=58.16 E-value=2 Score=22.97 Aligned_cols=46 Identities=11% Similarity=0.234 Sum_probs=37.4
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCC-CHHHHHCCC
Q ss_conf 9981997999999872469999998528988358999999975499-999950677
Q gi|254780424|r 23 RMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLES-PISFFFDVS 77 (144)
Q Consensus 23 R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v-~~~~l~~~~ 77 (144)
+.-+=||.+++|+.+|++.||||+.=+|+. |+.-+|| ++-+||...
T Consensus 361 ~~LkPL~L~~vA~el~~heSTiSRai~~KY---------l~T~~G~f~Lk~FFS~~ 407 (477)
T TIGR02395 361 AALKPLTLREVAEELGLHESTISRAINNKY---------LQTPRGVFELKYFFSSG 407 (477)
T ss_pred HCCCCCCHHHHHHHHCCCCCCEEEEECCCE---------EECCCCCHHHHHHCCHH
T ss_conf 006886389999885889872463317735---------76076403365431201
No 303
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=57.86 E-value=15 Score=17.33 Aligned_cols=51 Identities=10% Similarity=0.195 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH------HCCCCCCCHHHHHHHHHH
Q ss_conf 9999999999999981997999999872469999998------528988358999999975
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKY------EKGVNRVGASRLQHISEV 65 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~------E~G~~~ps~~~L~~iA~~ 65 (144)
.++|-+.-.+..+... .-.+.|+-+ +--.++.-| ..|...+ ..=|++||.-
T Consensus 69 y~ry~~~l~~~a~r~l--~d~~dAEDv-vQEvFlk~w~~~~~f~~g~s~f-~tWL~~IA~N 125 (233)
T PRK12538 69 VERHIDRAYAIALRIV--GNRADAEDV-VQDTMLKVWTHRGRWQHGRAKF-STWLYRVVSN 125 (233)
T ss_pred HHHHHHHHHHHHHHHH--CCHHHHHHH-HHHHHHHHHHHHHCCCCCCCHH-HHHHHHHHHH
T ss_conf 9999999999999995--999999999-9999999999884477786739-9999999999
No 304
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=57.80 E-value=15 Score=17.33 Aligned_cols=32 Identities=6% Similarity=-0.012 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999819979999998724699999985
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
|-..-.+.++.-. .-.+.|+-+ +--..+.-|+
T Consensus 35 y~~~l~~~~~~~~--~d~~~AeDl-~Qevfl~~~~ 66 (194)
T PRK12513 35 HRTGLYRFLLRLA--RDPALADDI-FQETWLRVIR 66 (194)
T ss_pred HHHHHHHHHHHHC--CCHHHHHHH-HHHHHHHHHH
T ss_conf 9999999999996--999999999-9899999998
No 305
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=57.70 E-value=15 Score=17.31 Aligned_cols=51 Identities=14% Similarity=0.132 Sum_probs=25.5
Q ss_pred HHHHHHCCCC-HHHHHHHHHHHHHHHHHHHCCCC-CC---C-HHHHHHHHHHCCCCHHHH
Q ss_conf 9999981997-99999987246999999852898-83---5-899999997549999995
Q gi|254780424|r 20 RLRRMILGMS-QEKLGECLGITFQQVQKYEKGVN-RV---G-ASRLQHISEVLESPISFF 73 (144)
Q Consensus 20 r~~R~~~glT-Q~eLA~~lGvs~s~is~~E~G~~-~p---s-~~~L~~iA~~l~v~~~~l 73 (144)
+-.+..+|.+ ..+.|+-+ |.-.++.-|.+-.. .+ + ..=|..||. +.-++++
T Consensus 31 ~~~~~~l~~~~~~~~aeD~-vQevFi~~~~~~~~~~~~~~~f~~WL~~Ia~--n~~~d~~ 87 (185)
T PRK06811 31 KIVHKVLGTDQYKQLIEEC-VNDIFLSIWNNIDKFDEEKGSFKNWIAAISK--YKAIDYK 87 (185)
T ss_pred HHHHHHHCCCCCHHHHHHH-HHHHHHHHHHHCHHCCCCCCCHHHHHHHHHH--HHHHHHH
T ss_conf 9999996776889899999-9999999998370038864529999999999--9999999
No 306
>pfam10654 DUF2481 Protein of unknown function (DUF2481). This is a hypothetical protein family homologous to Lmo2305 in Bacteriophage A118 systems.
Probab=57.43 E-value=12 Score=18.00 Aligned_cols=24 Identities=8% Similarity=0.219 Sum_probs=16.3
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 819979999998724699999985
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
..|||+.++|+..+||+|++-++-
T Consensus 78 hAGlt~~aIAD~F~iS~s~~~nft 101 (126)
T pfam10654 78 HAGLTGYAIADHFKVSKSVVFNFT 101 (126)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 558860799999747799999999
No 307
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=57.15 E-value=8.6 Score=18.86 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=17.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 997999999872469999998528
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
.-|-+|+|+.+|++...+..+..-
T Consensus 185 ~Pt~eEIA~~lgi~~~~v~~~l~~ 208 (320)
T PRK07921 185 EATDEELAEESGIPEEKINDLLEH 208 (320)
T ss_pred CCCHHHHHHHCCCCHHHHHHHHHH
T ss_conf 998999998819999999999997
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=57.10 E-value=8.1 Score=19.01 Aligned_cols=27 Identities=22% Similarity=0.230 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 979999998724699999985289883
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRV 54 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~p 54 (144)
++-.|+|+.+|||..+|-.||+-.--|
T Consensus 1 Yri~ElA~~~Gvs~~tiR~YE~~GLlp 27 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGLIP 27 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC
T ss_conf 978999999896999999999969999
No 309
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=57.08 E-value=9.4 Score=18.62 Aligned_cols=25 Identities=12% Similarity=0.291 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9979999998724699999985289
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
.|+.++.|+.+|||..|+.+|=+-.
T Consensus 1 ~m~~~e~~~~lgis~~Tl~rw~r~G 25 (193)
T COG2452 1 LLRPKEACQLLGISYSTLLRWIREG 25 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 9888999998394799999998768
No 310
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=56.99 E-value=9.7 Score=18.53 Aligned_cols=30 Identities=7% Similarity=0.003 Sum_probs=23.9
Q ss_pred HHHH-HHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999-99819979999998724699999985
Q gi|254780424|r 19 IRLR-RMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 19 Ir~~-R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
|+.+ +...++|..|+|+.+|+++++++++-
T Consensus 31 L~~la~~~~~ltl~eia~~lglpksT~~RlL 61 (271)
T PRK10163 31 LQYLEKSGGSSSVSDISLNLDLPLSTTFRLL 61 (271)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999747999799999999791999999999
No 311
>TIGR02293 TIGR02293 conserved hypothetical protein TIGR02293; InterPro: IPR011979 Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. The function is unknown..
Probab=56.98 E-value=10 Score=18.37 Aligned_cols=56 Identities=23% Similarity=0.395 Sum_probs=42.8
Q ss_pred HCCCCHHH-HHHHHHHHHHHHHHHHCCCC-CCC---HHHHHHHHHHCCCCHHHHHCCC-CCCC
Q ss_conf 81997999-99987246999999852898-835---8999999975499999950677-4431
Q gi|254780424|r 25 ILGMSQEK-LGECLGITFQQVQKYEKGVN-RVG---ASRLQHISEVLESPISFFFDVS-PTVC 81 (144)
Q Consensus 25 ~~glTQ~e-LA~~lGvs~s~is~~E~G~~-~ps---~~~L~~iA~~l~v~~~~l~~~~-~~~~ 81 (144)
-..+...| |.+.+||+..++++|-.-.+ ..+ .++|+++|.++++-++-| +++ ....
T Consensus 35 ~~~~~k~esl~~~~gi~~atl~RR~~~~~krl~~eES~RlaR~ArV~~~A~D~f-g~d~~eA~ 96 (138)
T TIGR02293 35 YLAIGKAESLLKATGIPKATLQRRKKADNKRLSSEESDRLARVARVLKAAVDVF-GGDKAEAR 96 (138)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC-CCCHHHHH
T ss_conf 238874589999844635447887506798688212479999999999999652-79878899
No 312
>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=56.93 E-value=8.6 Score=18.87 Aligned_cols=22 Identities=27% Similarity=0.398 Sum_probs=19.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9799999987246999999852
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+|-.++|+.+||+++++-.||+
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 313
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=56.45 E-value=13 Score=17.69 Aligned_cols=26 Identities=27% Similarity=0.296 Sum_probs=21.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 98199799999987246999999852
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
...++|..|+|+++|+++++++++-+
T Consensus 16 ~~~~l~l~ela~~~glpksT~~RlL~ 41 (246)
T COG1414 16 GPGGLSLAELAERLGLPKSTVHRLLQ 41 (246)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 88888799999987919889999999
No 314
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=56.37 E-value=13 Score=17.69 Aligned_cols=40 Identities=15% Similarity=0.316 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHH-------HCCC--CHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 999999999999-------8199--799999987246999999852898
Q gi|254780424|r 13 INVGKRIRLRRM-------ILGM--SQEKLGECLGITFQQVQKYEKGVN 52 (144)
Q Consensus 13 ~~iG~rIr~~R~-------~~gl--TQ~eLA~~lGvs~s~is~~E~G~~ 52 (144)
+|+.+.++.+++ .+|- |-+|+|..+|++...+..+-+...
T Consensus 228 ~h~~e~l~ki~k~~~~L~~~lGr~Pt~eEIA~~l~i~~e~v~~~~~~~~ 276 (385)
T PRK07406 228 VHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQ 276 (385)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 8999999999999999998708998699999993999999999998548
No 315
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=56.19 E-value=11 Score=18.08 Aligned_cols=31 Identities=23% Similarity=0.249 Sum_probs=24.1
Q ss_pred HHHHHHHHHCC--CCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999819--97999999872469999998
Q gi|254780424|r 17 KRIRLRRMILG--MSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 17 ~rIr~~R~~~g--lTQ~eLA~~lGvs~s~is~~ 47 (144)
+-||.++.+.+ +.|.|+-+..|.|+|++|-.
T Consensus 8 klir~Lk~a~~~GI~Q~eIeel~GlSKStvSEa 40 (321)
T COG3888 8 KLIRELKRAGPEGIDQTEIEELMGLSKSTVSEA 40 (321)
T ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999862877765878898857456479999
No 316
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=55.86 E-value=16 Score=17.12 Aligned_cols=24 Identities=17% Similarity=0.084 Sum_probs=21.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 981997999999872469999998
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
...++|-+++|+.++.++|++++-
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rs 62 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRS 62 (126)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 469957999999978319999999
No 317
>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=55.80 E-value=9.7 Score=18.51 Aligned_cols=27 Identities=19% Similarity=0.252 Sum_probs=21.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC--CCCCC
Q ss_conf 9799999987246999999852--89883
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK--GVNRV 54 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~--G~~~p 54 (144)
+|-.|+|+.+||+.+++-.||. |...|
T Consensus 1 ysIgEva~~~gv~~~tLRywE~~~~~~~P 29 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETEFPQLKP 29 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHCCCCCC
T ss_conf 97889999989499999999987477488
No 318
>pfam08822 DUF1804 Protein of unknown function (DUF1804). This family of bacterial protein is uncharacterized.
Probab=55.66 E-value=16 Score=17.10 Aligned_cols=42 Identities=10% Similarity=0.294 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 89989999999999999981997999999872469999998528
Q gi|254780424|r 7 IPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 7 ~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
|+||- ..-..+|..=---++|.+..|.+.|||.+|.-+|-+.
T Consensus 1 MAH~~--e~r~~vR~~Yv~~~~~Le~aA~~~gV~~~TArrWK~~ 42 (165)
T pfam08822 1 MAHPK--ETRDAVRRLYVFDRLTLEVAAAKAGVSYSTARRWKRE 42 (165)
T ss_pred CCCCH--HHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHH
T ss_conf 99968--9999999999966787999998809988889999998
No 319
>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=55.08 E-value=7.4 Score=19.28 Aligned_cols=28 Identities=14% Similarity=0.275 Sum_probs=23.9
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 8199799999987246999999852898
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVN 52 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~ 52 (144)
-.|+|-.+.|+.+|++..+|..|-.-..
T Consensus 11 ~qg~~~~eIA~~Lg~~~~tVysWk~r~~ 38 (58)
T pfam06056 11 WQGYRPAEIAQELGLKARTVYSWKDRDK 38 (58)
T ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHCC
T ss_conf 9689899999997899314565865248
No 320
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=54.85 E-value=10 Score=18.43 Aligned_cols=37 Identities=16% Similarity=0.204 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHH-------HCC--CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999999999-------819--9799999987246999999852
Q gi|254780424|r 13 INVGKRIRLRRM-------ILG--MSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 13 ~~iG~rIr~~R~-------~~g--lTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+|+.+++..+++ ..| -|-+|+|..+|++...+..+..
T Consensus 250 ~h~~e~l~ki~r~~r~L~q~lGR~Pt~eEIA~~lg~s~e~V~~~l~ 295 (410)
T PRK07598 250 VHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL 295 (410)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 0299999999999999998759999799999880999999999998
No 321
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=54.73 E-value=7.9 Score=19.10 Aligned_cols=49 Identities=22% Similarity=0.345 Sum_probs=35.4
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHCCCCHHHH
Q ss_conf 819979999998724699999985289883-5899999997549999995
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRV-GASRLQHISEVLESPISFF 73 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~p-s~~~L~~iA~~l~v~~~~l 73 (144)
--|+|.+.+|.--|+++||+++|=.+...- --.+=..+|.-|..+-..+
T Consensus 38 ~~gLsldR~~~lY~~hrStvaR~v~~are~Ll~~Tr~~LaeRL~L~~~el 87 (106)
T TIGR02233 38 VEGLSLDRLGTLYGVHRSTVARWVAGARELLLERTRQELAERLRLTSSEL 87 (106)
T ss_pred HCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 23655899998847886169999999999999998998767407886778
No 322
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=54.54 E-value=17 Score=16.99 Aligned_cols=56 Identities=14% Similarity=0.262 Sum_probs=40.6
Q ss_pred HHHHHHHHHHH----------CCCCHHHHHHHHHHHHHHHHHHHCCCC----------------CCCHHHHHHHHHHCCC
Q ss_conf 99999999998----------199799999987246999999852898----------------8358999999975499
Q gi|254780424|r 15 VGKRIRLRRMI----------LGMSQEKLGECLGITFQQVQKYEKGVN----------------RVGASRLQHISEVLES 68 (144)
Q Consensus 15 iG~rIr~~R~~----------~glTQ~eLA~~lGvs~s~is~~E~G~~----------------~ps~~~L~~iA~~l~v 68 (144)
+-++|+.+|.. +-+|-.|.|+.+|||.+++-+.+.... .-+++.+..|-+.|+.
T Consensus 17 ~~~~l~~~~~~~~~P~~~K~lR~Fs~~EvA~l~gvs~~~lr~~~~~g~~P~p~~~~~gr~~~R~~Ytl~~i~~lR~~~~~ 96 (388)
T PRK13705 17 MTKAIAIAQFNDDSPEARKITRRWRIGEAADLVGVSSQAIRDAEKAGRLPHPDMEMRGRVEQRVGYTIEQINHMRDVFGT 96 (388)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf 99999998624799821125588887999999399999999786468999997687776554551069999999999643
Q ss_pred CH
Q ss_conf 99
Q gi|254780424|r 69 PI 70 (144)
Q Consensus 69 ~~ 70 (144)
.+
T Consensus 97 ~p 98 (388)
T PRK13705 97 RL 98 (388)
T ss_pred CC
T ss_conf 88
No 323
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=54.41 E-value=14 Score=17.59 Aligned_cols=28 Identities=14% Similarity=0.253 Sum_probs=23.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998199799999987246999999
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
|..++.+.++.-.|+|+.+|.++|+++.
T Consensus 29 l~lL~~k~plNvneiAe~lgLpqst~s~ 56 (308)
T COG4189 29 LQLLHRKGPLNVNEIAEALGLPQSTMSA 56 (308)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999871798789999885886566665
No 324
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=54.39 E-value=11 Score=18.07 Aligned_cols=31 Identities=23% Similarity=0.100 Sum_probs=24.6
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 8199799999987246999999852898835
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRVG 55 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps 55 (144)
...+|.++||+.+|+|+++++++=+.....+
T Consensus 23 ~~~lsl~~lA~~~~~S~~~l~r~Fk~~~G~s 53 (127)
T PRK11511 23 ESPLSLEKVSERSGYSKWHLQRMFKKETGHS 53 (127)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHCCC
T ss_conf 8999999999998959999999999998919
No 325
>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=54.28 E-value=9.3 Score=18.64 Aligned_cols=24 Identities=17% Similarity=0.203 Sum_probs=18.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 981997999999872469999998
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
-.-.+|..|.|+..|||+++++..
T Consensus 30 y~eDlSL~EIAe~~~iSRQaV~D~ 53 (101)
T pfam04297 30 YLDDLSLSEIAEEFNVSRQAVYDN 53 (101)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 876398999998819859999999
No 326
>PRK11569 transcriptional repressor IclR; Provisional
Probab=54.09 E-value=12 Score=18.04 Aligned_cols=23 Identities=9% Similarity=0.125 Sum_probs=21.1
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 81997999999872469999998
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
..+||..|+|+.+|++++++.++
T Consensus 41 ~~~lsl~eia~~lglpksT~~Rl 63 (274)
T PRK11569 41 NGSVALTELAQQAGLPNSTTHRL 63 (274)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99989999999879199999999
No 327
>PRK11050 manganese transport regulator MntR; Provisional
Probab=53.84 E-value=14 Score=17.50 Aligned_cols=26 Identities=23% Similarity=0.248 Sum_probs=12.4
Q ss_pred HHHHCCC-CHHHHHHHHHHHHHHHHHH
Q ss_conf 9998199-7999999872469999998
Q gi|254780424|r 22 RRMILGM-SQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 22 ~R~~~gl-TQ~eLA~~lGvs~s~is~~ 47 (144)
+-...|. -+.++|+++|||+++++++
T Consensus 48 L~~~~G~aR~~DIA~~LgVs~pSVt~m 74 (155)
T PRK11050 48 LIAEVGEARQVDIAARLGVSQPTVAKM 74 (155)
T ss_pred HHHCCCCEEHHHHHHHHCCCCHHHHHH
T ss_conf 998269564999998909993319999
No 328
>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=53.69 E-value=17 Score=16.90 Aligned_cols=43 Identities=14% Similarity=0.003 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHCC----------CCCCCHHHHHHHHHHCCCCH-HHHHCCCC
Q ss_conf 872469999998528----------98835899999997549999-99506774
Q gi|254780424|r 36 CLGITFQQVQKYEKG----------VNRVGASRLQHISEVLESPI-SFFFDVSP 78 (144)
Q Consensus 36 ~lGvs~s~is~~E~G----------~~~ps~~~L~~iA~~l~v~~-~~l~~~~~ 78 (144)
+++-|++|++-+|.- ++.|+.+-|..|.+.||+++ ..++-..+
T Consensus 8 RCSkSR~tLalL~dkgi~P~vV~YL~~pp~~seL~~~~~~LG~~~ar~~~R~ke 61 (114)
T TIGR00014 8 RCSKSRQTLALLEDKGIEPEVVKYLKNPPTKSELKALLAKLGISSAREMIRTKE 61 (114)
T ss_pred CCCHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCCHHHHHCCCCC
T ss_conf 872468999999856999547414589748688999998708970363011765
No 329
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=53.69 E-value=12 Score=18.02 Aligned_cols=22 Identities=27% Similarity=0.496 Sum_probs=19.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9979999998724699999985
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~E 48 (144)
-||-.++|+.+|.+..++|+.-
T Consensus 2 pmsrqdIadylGlt~ETVsR~l 23 (32)
T pfam00325 2 PMSRQEIADYLGLTRETVSRLL 23 (32)
T ss_pred CCCHHHHHHHHCCHHHHHHHHH
T ss_conf 8658899998472599999999
No 330
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=53.67 E-value=7.6 Score=19.21 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=22.0
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 999819979999998724699999985
Q gi|254780424|r 22 RRMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 22 ~R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
.|. .++|-.+||.++|+|.++.++|-
T Consensus 15 ~~~-~~~t~~ela~~l~~S~qta~R~l 40 (214)
T COG1339 15 VRG-VKVTSSELAKRLGVSSQTAARKL 40 (214)
T ss_pred HCC-CCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 037-60208999988574707788998
No 331
>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=53.53 E-value=17 Score=16.88 Aligned_cols=36 Identities=22% Similarity=0.383 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9989999999999999981997999999872469999998
Q gi|254780424|r 8 PNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 8 ~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
.|+....| ++.+. ..++|..|+|+.+|+|++++++-
T Consensus 5 ~~~~r~~I---l~~L~-~~~~~~~eia~~l~is~~~vs~h 40 (78)
T cd00090 5 SDPTRLRI---LRLLL-EGPLTVSELAERLGLSQSTVSRH 40 (78)
T ss_pred CCHHHHHH---HHHHH-HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 79999999---99998-48906999987778487899999
No 332
>PRK00118 putative DNA-binding protein; Validated
Probab=53.34 E-value=10 Score=18.37 Aligned_cols=26 Identities=15% Similarity=0.086 Sum_probs=20.6
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99981997999999872469999998
Q gi|254780424|r 22 RRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 22 ~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
+=-.-.+|..|.|+..|||+++++..
T Consensus 28 lyy~~DlSl~EIAe~~~iSRQaV~D~ 53 (105)
T PRK00118 28 LYYLDDYSLGEIAEEFNVSRQAVYDN 53 (105)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99885499999989969859999999
No 333
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=53.24 E-value=18 Score=16.85 Aligned_cols=35 Identities=11% Similarity=0.105 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999819979999998724699999985
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
++.|-+.-.+.+..-.| -.+.|+-+ +--.++.-|.
T Consensus 9 ~~~y~~~l~~~~~~~~~--~~~~AeDl-~Qe~flk~~~ 43 (173)
T PRK12522 9 IDIYKDQIYSLCYKLAK--TKEDAEDI-FQETWIKVFS 43 (173)
T ss_pred HHHHHHHHHHHHHHHCC--CHHHHHHH-HHHHHHHHHH
T ss_conf 99999999999999919--99999999-9999999999
No 334
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=52.99 E-value=12 Score=17.89 Aligned_cols=30 Identities=23% Similarity=0.315 Sum_probs=24.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998199799999987246999999
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+=+..+++..-++-++||+.+|||..||-+
T Consensus 9 ~Il~~l~~~g~v~v~eLa~~~~VS~~TIRR 38 (253)
T COG1349 9 KILELLKEKGKVSVEELAELFGVSEMTIRR 38 (253)
T ss_pred HHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 999999985969799999885978999986
No 335
>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=52.95 E-value=12 Score=18.04 Aligned_cols=46 Identities=13% Similarity=0.164 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCC----------H---HH--HHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-898835----------8---99--999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVG----------A---SR--LQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps----------~---~~--L~~iA~~l~v~~~~l 73 (144)
++-.|+|+..|||..||-.||+ |--.|. . .+ +...++.+|.|++.+
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 336
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.88 E-value=18 Score=16.82 Aligned_cols=33 Identities=15% Similarity=0.115 Sum_probs=25.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHH-HHHHHHHHHC
Q ss_conf 99999999819979999998724-6999999852
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGI-TFQQVQKYEK 49 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGv-s~s~is~~E~ 49 (144)
.++-++....|.|..++|...|| +.+++.+|=+
T Consensus 14 ~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 14 LEAVALYLRGGDTVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred HHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 9999999817835999999948775378999999
No 337
>pfam01726 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.
Probab=52.77 E-value=18 Score=16.81 Aligned_cols=35 Identities=17% Similarity=0.205 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHCCC--CHHHHHHHHHH-HHHHHHHH
Q ss_conf 9999999999998199--79999998724-69999998
Q gi|254780424|r 13 INVGKRIRLRRMILGM--SQEKLGECLGI-TFQQVQKY 47 (144)
Q Consensus 13 ~~iG~rIr~~R~~~gl--TQ~eLA~~lGv-s~s~is~~ 47 (144)
..|=+.|+..-.+.|+ |..|+|+.+|+ |.+++..+
T Consensus 9 ~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~ 46 (65)
T pfam01726 9 REVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEH 46 (65)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 99999999999982889879999999389980999999
No 338
>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=52.69 E-value=16 Score=17.07 Aligned_cols=29 Identities=21% Similarity=0.159 Sum_probs=22.5
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999819979999998724699999985
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
|+.++. .-+|-.++|+.+|++++++|+--
T Consensus 8 l~~L~~-~~~~v~el~~~l~~sq~~vS~HL 36 (47)
T pfam01022 8 LYLLSE-GELCVCELAEILGLSQSTVSHHL 36 (47)
T ss_pred HHHHHC-CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999980-89969999999895886999999
No 339
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=52.39 E-value=13 Score=17.65 Aligned_cols=28 Identities=25% Similarity=0.380 Sum_probs=22.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998199799999987246999999
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+..++...-++-.+||+.+|||..||-+
T Consensus 6 l~~l~~~~~v~i~~La~~f~VS~~TiRR 33 (57)
T pfam08220 6 LELLKQQGTLSVEELAELLGVSEMTIRR 33 (57)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999986979799999998959999999
No 340
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=51.63 E-value=19 Score=16.69 Aligned_cols=56 Identities=13% Similarity=0.039 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC--CCC--HHHHHHHHHHCCCCHHHH
Q ss_conf 9999999999998199799999987246999999852898--835--899999997549999995
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVN--RVG--ASRLQHISEVLESPISFF 73 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~--~ps--~~~L~~iA~~l~v~~~~l 73 (144)
.|-+.-.+.++...| ..+.|+-+ +--.++.-|++-.. .++ ..=|++||. +.-.+++
T Consensus 24 ~y~~~v~~~~~~~~~--d~~~AeD~-~Qe~fl~~~~~~~~~~~~~~~~~Wl~~ia~--N~~~d~~ 83 (177)
T PRK09415 24 KYGQEVLQLVYSYVK--NKEVAEDL-TQEIFVKCYKSLHTYKGKSNLKTWLYRIAI--NHCKDYL 83 (177)
T ss_pred HHHHHHHHHHHHHCC--CHHHHHHH-HHHHHHHHHHHHHHCCCCCCHHHHHHHHHH--HHHHHHH
T ss_conf 999999999999909--99999999-999999999987455885549999999999--9999999
No 341
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=51.49 E-value=19 Score=16.68 Aligned_cols=53 Identities=13% Similarity=0.189 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHCC-CC-----HHHHHHHHHHHH-HHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 99999999999999819-97-----999999872469-99999852898835899999997
Q gi|254780424|r 11 VDINVGKRIRLRRMILG-MS-----QEKLGECLGITF-QQVQKYEKGVNRVGASRLQHISE 64 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~g-lT-----Q~eLA~~lGvs~-s~is~~E~G~~~ps~~~L~~iA~ 64 (144)
++.|-+.-.+.+|...| ++ -+++.+.+=+.. ..+.+|. +...|=..=|..||.
T Consensus 28 ~~~~~~~v~r~~~~~l~~~~~~~~dAeDl~Qe~fl~~~~~l~~f~-~~~~~f~~Wl~~Ia~ 87 (187)
T PRK09648 28 LETIHPLVVRYCRARLGTVERSGLSADDVAQEVCLAVITALPRYR-DQGRPFLAFVYGIAA 87 (187)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHH
T ss_conf 999999999999999714458764399999999999998376626-677849999999999
No 342
>pfam09572 RE_XamI XamI restriction endonuclease. This family includes the XamI (recognizes GTCGAC but cleavage site unknown) restriction endonuclease.
Probab=51.45 E-value=16 Score=17.13 Aligned_cols=49 Identities=18% Similarity=0.186 Sum_probs=37.7
Q ss_pred HHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHH------HHHHHHHC
Q ss_conf 999999981--99799999987246999999852898835899------99999754
Q gi|254780424|r 18 RIRLRRMIL--GMSQEKLGECLGITFQQVQKYEKGVNRVGASR------LQHISEVL 66 (144)
Q Consensus 18 rIr~~R~~~--glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~------L~~iA~~l 66 (144)
-+-.+|..- -++-..|....|||++.+-.+|.|+-.|...- |.+|+.++
T Consensus 18 ~L~~LR~~t~ppia~d~l~~lagvsk~lv~~le~~kl~~~~~~~~l~~~l~ki~~iI 74 (251)
T pfam09572 18 TLPTLRMLTCPPIARDRLVGLAGGSKNLVKSLEPKKLPPKMKADVLDEHLQKVVAVI 74 (251)
T ss_pred HHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 777878613998308787665166678887642278983222436899999999999
No 343
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=51.45 E-value=19 Score=16.67 Aligned_cols=58 Identities=12% Similarity=0.010 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC--CCCC--HHHHHHHHHHCCCCHHHH
Q ss_conf 99999999999999819979999998724699999985289--8835--899999997549999995
Q gi|254780424|r 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV--NRVG--ASRLQHISEVLESPISFF 73 (144)
Q Consensus 11 ~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~--~~ps--~~~L~~iA~~l~v~~~~l 73 (144)
++.|-..-.+..+...+ -.+.|+-+ |--.++.-|.+-. ..++ ..=|+.|+. |.-++++
T Consensus 33 ~~ry~~~l~~~a~~~~~--~~~~AeDv-vQe~flk~~~~~~~~~~~~~f~~WL~~Ia~--N~~~d~~ 94 (197)
T PRK09643 33 FRRHHRQLWRLARRTSG--TREDAADA-LQDAMLSAHRGAGSFRGDAAVSSWLHRIVV--NACLDRL 94 (197)
T ss_pred HHHHHHHHHHHHHHHHC--CHHHHHHH-HHHHHHHHHHHHHHCCCCCHHHHHHHHHHH--HHHHHHH
T ss_conf 99999999999999919--99999999-999999999988633886349999999999--9999999
No 344
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=51.38 E-value=11 Score=18.18 Aligned_cols=25 Identities=32% Similarity=0.375 Sum_probs=20.7
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 8199799999987246999999852
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+-...|.|.|+.+|||.+++|.+=+
T Consensus 23 qp~v~q~eIA~~lgiT~QaVsehiK 47 (260)
T COG1497 23 QPRVKQKEIAKKLGITLQAVSEHIK 47 (260)
T ss_pred CCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 8877888999870987999999999
No 345
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=51.08 E-value=13 Score=17.71 Aligned_cols=42 Identities=7% Similarity=0.076 Sum_probs=31.5
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 998199799999987246999999852898835899999997
Q gi|254780424|r 23 RMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISE 64 (144)
Q Consensus 23 R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~ 64 (144)
+--.++|-.++|+++||+++++.+|-.++...-...+..+..
T Consensus 28 ~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K~~l~~~~~~~~~~ 69 (201)
T COG1309 28 KGYAATTVDEIAKAAGVSKGTLYRHFPSKEDLLLALLERALE 69 (201)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 593228999999887949789998878999999999999999
No 346
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=50.32 E-value=16 Score=17.18 Aligned_cols=18 Identities=17% Similarity=0.156 Sum_probs=8.2
Q ss_pred HHHHHCCCCCCCHHHHHHHHH
Q ss_conf 999852898835899999997
Q gi|254780424|r 44 VQKYEKGVNRVGASRLQHISE 64 (144)
Q Consensus 44 is~~E~G~~~ps~~~L~~iA~ 64 (144)
+.+|. |. .+ ..=|+.|+.
T Consensus 63 l~~fr-g~-~~-~tWL~rIa~ 80 (217)
T PRK12533 63 FDSCR-GD-NA-RPWLLAIVR 80 (217)
T ss_pred HHHHC-CC-CH-HHHHHHHHH
T ss_conf 77623-44-24-899999999
No 347
>PRK00215 LexA repressor; Validated
Probab=50.20 E-value=20 Score=16.55 Aligned_cols=35 Identities=20% Similarity=0.258 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHCCC--CHHHHHHHHHH-HHHHHHHH
Q ss_conf 9999999999998199--79999998724-69999998
Q gi|254780424|r 13 INVGKRIRLRRMILGM--SQEKLGECLGI-TFQQVQKY 47 (144)
Q Consensus 13 ~~iG~rIr~~R~~~gl--TQ~eLA~~lGv-s~s~is~~ 47 (144)
..|=+.|++.-.+.|+ |.+|+|+.+|+ |++++.++
T Consensus 7 ~~il~fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~ 44 (204)
T PRK00215 7 QEILDFIKDRIEETGYPPSRREIADALGLRSPSAVHEH 44 (204)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHH
T ss_conf 99999999999974889989999998099981899999
No 348
>pfam04539 Sigma70_r3 Sigma-70 region 3. 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 as 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.
Probab=49.63 E-value=20 Score=16.49 Aligned_cols=41 Identities=22% Similarity=0.299 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHCCC--CHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 999999999998199--79999998724699999985289883
Q gi|254780424|r 14 NVGKRIRLRRMILGM--SQEKLGECLGITFQQVQKYEKGVNRV 54 (144)
Q Consensus 14 ~iG~rIr~~R~~~gl--TQ~eLA~~lGvs~s~is~~E~G~~~p 54 (144)
.|-+-.++++..+|- |.+|+|+.+|+|...|..+-.-.+.|
T Consensus 5 ki~ka~~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~~~~ 47 (78)
T pfam04539 5 KIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREP 47 (78)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf 9999999999998889999999999694999999999875898
No 349
>PRK05066 arginine repressor; Provisional
Probab=49.32 E-value=20 Score=16.46 Aligned_cols=32 Identities=22% Similarity=0.179 Sum_probs=24.3
Q ss_pred HHHHHHHHHCCC-CHHHHHHHH---H---HHHHHHHHHH
Q ss_conf 999999998199-799999987---2---4699999985
Q gi|254780424|r 17 KRIRLRRMILGM-SQEKLGECL---G---ITFQQVQKYE 48 (144)
Q Consensus 17 ~rIr~~R~~~gl-TQ~eLA~~l---G---vs~s~is~~E 48 (144)
+.||++=....+ ||+||.+.+ | ||++|+|+--
T Consensus 12 ~aIk~lI~~~~I~tQeeL~~~L~~~G~~~VTQATvSRDl 50 (156)
T PRK05066 12 KAFKALLKEEKFGSQGEIVTALQEQGFDNINQSKVSRML 50 (156)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 999999851896679999999997398612088888789
No 350
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=49.11 E-value=20 Score=16.44 Aligned_cols=47 Identities=17% Similarity=0.155 Sum_probs=28.6
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC---CHHHHHHHHHHCCC
Q ss_conf 9999999819979999998724699999985289883---58999999975499
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRV---GASRLQHISEVLES 68 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~p---s~~~L~~iA~~l~v 68 (144)
+-+.++....++|+++-+.++...++- .-...| +..+|.+|.+.|..
T Consensus 120 ~r~~l~~~~~~sQ~~lD~l~~~~~k~~----~~~~LPkGi~~~Tl~~i~~~~~~ 169 (224)
T COG4565 120 KRHALESHQQLSQKELDQLFNIQSKEQ----PPDDLPKGLDELTLQKVREALKE 169 (224)
T ss_pred HHHHHHHHCCCCHHHHHHHHHCCCCCC----CCCCCCCCCCHHHHHHHHHHHHC
T ss_conf 999986201027999999983225456----75547877679999999999867
No 351
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=48.95 E-value=21 Score=16.43 Aligned_cols=29 Identities=14% Similarity=0.080 Sum_probs=23.3
Q ss_pred HHHHHHH--HCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999--8199799999987246999999
Q gi|254780424|r 18 RIRLRRM--ILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 18 rIr~~R~--~~glTQ~eLA~~lGvs~s~is~ 46 (144)
.||.++. ..|++-.+-|+++++|++++|+
T Consensus 5 QLryf~~va~~~~n~t~AA~~L~iSQPavS~ 35 (324)
T PRK12681 5 QLRYIVEVVNHNLNVSATAESLYTSQPGISK 35 (324)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999999997699999999997897779999
No 352
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=48.21 E-value=21 Score=16.35 Aligned_cols=39 Identities=8% Similarity=0.016 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHCC-----CCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 99999872469999998528-----98835899999997549999995
Q gi|254780424|r 31 EKLGECLGITFQQVQKYEKG-----VNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E~G-----~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
.+.|+-+ |--..+.-|.+- ...+ ..=|+.|+. |.-+++|
T Consensus 32 ~~~AEDl-vQEtflka~~~~~~F~g~ss~-~TWL~~Ia~--N~~id~l 75 (201)
T PRK12545 32 ADAAEDA-VQEALAAAWSQAGRFAGQSAH-KTWVFGILR--NKLIDTL 75 (201)
T ss_pred HHHHHHH-HHHHHHHHHHHHCCCCCCCHH-HHHHHHHHH--HHHHHHH
T ss_conf 9899999-999999999854045875238-999999999--9999999
No 353
>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=48.15 E-value=21 Score=16.35 Aligned_cols=55 Identities=11% Similarity=0.205 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHH----------CCCCHHHHHHHHHHHHHHHHHHH------------CCCCCCCHHHHHHHHHHCCC
Q ss_conf 999999999998----------19979999998724699999985------------28988358999999975499
Q gi|254780424|r 14 NVGKRIRLRRMI----------LGMSQEKLGECLGITFQQVQKYE------------KGVNRVGASRLQHISEVLES 68 (144)
Q Consensus 14 ~iG~rIr~~R~~----------~glTQ~eLA~~lGvs~s~is~~E------------~G~~~ps~~~L~~iA~~l~v 68 (144)
.+...|.++|.. +-+|-.|+|+.+||+.+++-+.+ +|++.-|++.+..+-..|+.
T Consensus 10 ~ls~~l~~~r~~~~~P~~~K~lr~f~~~e~a~l~gv~~~~lr~~~~~g~~p~p~~~~~grR~ytl~ei~~lR~~l~~ 86 (387)
T TIGR03453 10 ELSSQLQALRERLFPPNAQKTLRRFTSGEAAKLLGVTDSYLRQLSLEGKGPQPEVLANGRRSYTLEQINELRRHLAQ 86 (387)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEEEEHHHHHHHHHHHHH
T ss_conf 99999999999737996556668888899998849699999999866999998758998258439999999999986
No 354
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=48.07 E-value=14 Score=17.49 Aligned_cols=21 Identities=19% Similarity=0.330 Sum_probs=14.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHC
Q ss_conf 799999987246999999852
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~ 49 (144)
|-+|+|+.+|++...+..+.+
T Consensus 235 t~eEIA~~lgi~~e~V~~i~~ 255 (368)
T PRK09210 235 TPEEIAEEMDMPPEKVREILK 255 (368)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 889999894998999999998
No 355
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=47.38 E-value=16 Score=17.06 Aligned_cols=30 Identities=7% Similarity=0.140 Sum_probs=24.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998199799999987246999999
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+=+..+++..-++-.|||+.+|||..||-+
T Consensus 11 ~Il~~L~~~g~v~v~eLa~~~~VS~~TIRR 40 (252)
T PRK10681 11 QLLQALKRSDKLHLKDAAALLGVSEMTIRR 40 (252)
T ss_pred HHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 999999986979999999887979989987
No 356
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=47.20 E-value=15 Score=17.34 Aligned_cols=29 Identities=28% Similarity=0.271 Sum_probs=18.6
Q ss_pred HHHHCC--CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999819--97999999872469999998528
Q gi|254780424|r 22 RRMILG--MSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 22 ~R~~~g--lTQ~eLA~~lGvs~s~is~~E~G 50 (144)
+...+| -|-+|+|+.+|++...+..+..-
T Consensus 255 l~~~~gr~Pt~eEiA~~lg~~~~~v~~~~~~ 285 (398)
T PRK05901 255 LLQELGREPTPEELAEEMDFTPEKVREIQKY 285 (398)
T ss_pred HHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9998489999999998819999999999997
No 357
>pfam06322 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=46.77 E-value=16 Score=17.17 Aligned_cols=27 Identities=19% Similarity=0.188 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 199799999987246999999852898
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYEKGVN 52 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E~G~~ 52 (144)
.-=.|.|+|..+++++.++-+|-..+.
T Consensus 15 ~~GN~teVaR~L~c~R~TVrkY~~D~~ 41 (64)
T pfam06322 15 TYGNQTEVARRLNCSRNTVRKYAEDKE 41 (64)
T ss_pred HHCCHHHHHHHHCCHHHHHHHHHCCCC
T ss_conf 707799997885110888998723555
No 358
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=46.72 E-value=22 Score=16.21 Aligned_cols=15 Identities=13% Similarity=0.344 Sum_probs=7.4
Q ss_pred HHHHHHHHHCCCCHHHH
Q ss_conf 99999997549999995
Q gi|254780424|r 57 SRLQHISEVLESPISFF 73 (144)
Q Consensus 57 ~~L~~iA~~l~v~~~~l 73 (144)
.=|.+||. |..++++
T Consensus 47 ~WL~~Ia~--N~~~d~~ 61 (160)
T PRK09642 47 TWMARIAT--NHAIDYK 61 (160)
T ss_pred HHHHHHHH--HHHHHHH
T ss_conf 99999999--9999999
No 359
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=46.52 E-value=22 Score=16.19 Aligned_cols=39 Identities=13% Similarity=0.172 Sum_probs=25.9
Q ss_pred HHHHHHH--HHCCCCHHHHHHHHHHHHHHHH-HHH---CCCCCCC
Q ss_conf 9999999--9819979999998724699999-985---2898835
Q gi|254780424|r 17 KRIRLRR--MILGMSQEKLGECLGITFQQVQ-KYE---KGVNRVG 55 (144)
Q Consensus 17 ~rIr~~R--~~~glTQ~eLA~~lGvs~s~is-~~E---~G~~~ps 55 (144)
+-|+..| +.+|||-.|.|+.++||+.|.. -.. .+...|.
T Consensus 6 eLi~kA~eLk~~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~ 50 (203)
T COG0856 6 ELIKKARELKSKGLTTGEIADELNVSRETATWLLTRAFKKESVPA 50 (203)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCC
T ss_conf 999999999877985777676641048778888754431147888
No 360
>pfam05732 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Probab=46.49 E-value=14 Score=17.58 Aligned_cols=52 Identities=23% Similarity=0.305 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH-HHCCCCHHHHHCCCCC
Q ss_conf 19979999998724699999985289883589999999-7549999995067744
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHIS-EVLESPISFFFDVSPT 79 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA-~~l~v~~~~l~~~~~~ 79 (144)
.=.||+++|+..|+|.+++..--+--.. ...+.+-. .++-++|+-+|-|...
T Consensus 74 lI~T~R~lae~~gvs~~TV~~tmK~L~e--~~fIkk~t~GvymiNP~i~~kG~~~ 126 (165)
T pfam05732 74 LIMTQREIAEETGISLETVRQTMKALEE--GNFLKKKTSGVYMINPDLLFKGDDT 126 (165)
T ss_pred EEEEHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEEECCCEEEECHHHHHCCCHH
T ss_conf 9987899999839529999999999975--8926861387699885895068727
No 361
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=46.41 E-value=17 Score=16.96 Aligned_cols=45 Identities=24% Similarity=0.426 Sum_probs=26.8
Q ss_pred CCCCCCCCHHHHHHHHHHHH----HHHHCC--C-CHHHHHHHHHHHHHHH----HHHH
Q ss_conf 98766899899999999999----999819--9-7999999872469999----9985
Q gi|254780424|r 2 VGNKKIPNPVDINVGKRIRL----RRMILG--M-SQEKLGECLGITFQQV----QKYE 48 (144)
Q Consensus 2 ~~~~~~~~~~d~~iG~rIr~----~R~~~g--l-TQ~eLA~~lGvs~s~i----s~~E 48 (144)
|+|++.+ ..| .|.+.||. -...-| | |-.+||+.+|||++.+ ...|
T Consensus 1 ~~~~r~~-l~e-~V~~~ir~~I~~g~l~pG~~LP~E~eLae~~gVSR~~VREAL~~L~ 56 (251)
T PRK09990 1 MKDERRP-IAD-VVAERIERLIVDGVLKVGQALPSERRLTEKLGVSRSALREGLKVLR 56 (251)
T ss_pred CCCCCCC-HHH-HHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9976673-999-9999999999809999929792399999998979599999999999
No 362
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=46.32 E-value=18 Score=16.83 Aligned_cols=28 Identities=25% Similarity=0.271 Sum_probs=22.2
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998199799999987246999999
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+..++...-+|-.+||+.+|||..||-+
T Consensus 11 l~~l~~~g~v~v~eLa~~~~VS~~TIRR 38 (252)
T PRK10906 11 IELVKQQGYVSTEELVEHFSVSPQTIRR 38 (252)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999986989999999987969989988
No 363
>PRK00767 transcriptional regulator BetI; Validated
Probab=46.06 E-value=23 Score=16.14 Aligned_cols=50 Identities=12% Similarity=0.238 Sum_probs=38.0
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHH
Q ss_conf 81997999999872469999998528988358999999975499999950
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~ 74 (144)
-.|.|-.++|+..|||.+.+..|=.++...-...+..+.+-+......-+
T Consensus 27 ~~~~t~~~IA~~AGvs~g~v~~yF~~k~~Ll~~a~~~~~~~~~~~~~~~~ 76 (197)
T PRK00767 27 LLDTTIAQIARRAGVSSGIISHYFGGKDGLLEATMRHLLRQLGQAVLARL 76 (197)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 35288999999959989999999087999999999999999999999997
No 364
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=45.92 E-value=18 Score=16.77 Aligned_cols=28 Identities=14% Similarity=0.197 Sum_probs=22.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998199799999987246999999
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+..++...-.+-.+||+.+|||..||-+
T Consensus 23 l~~L~~~g~v~v~eLae~~~VS~~TIRR 50 (269)
T PRK09802 23 IQRLRQQGSVQVNDLSALYGVSTVTIRN 50 (269)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999986989999999987969889998
No 365
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=45.86 E-value=18 Score=16.73 Aligned_cols=28 Identities=18% Similarity=0.299 Sum_probs=22.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998199799999987246999999
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+..++...-++-.+||+.+|||..||-+
T Consensus 10 l~~L~~~g~v~v~eLa~~~~VS~~TIRR 37 (240)
T PRK10411 10 VDLLLNHTSLTTEALAEQLNVSKETIRR 37 (240)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999986979999999988959989998
No 366
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=45.70 E-value=23 Score=16.11 Aligned_cols=14 Identities=14% Similarity=-0.256 Sum_probs=5.8
Q ss_pred HHHHHHCCCCHHHH
Q ss_conf 99997549999995
Q gi|254780424|r 60 QHISEVLESPISFF 73 (144)
Q Consensus 60 ~~iA~~l~v~~~~l 73 (144)
..+|..-.+.++.+
T Consensus 427 ~~~~~g~~i~~~di 440 (513)
T PRK10820 427 LTQLEGYELRPQDI 440 (513)
T ss_pred HHHCCCCCCCHHHC
T ss_conf 99579985349982
No 367
>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=45.64 E-value=14 Score=17.50 Aligned_cols=18 Identities=22% Similarity=0.429 Sum_probs=11.7
Q ss_pred CHHHHHHHHHHHHHHHHH
Q ss_conf 799999987246999999
Q gi|254780424|r 29 SQEKLGECLGITFQQVQK 46 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~ 46 (144)
|..+||+..|||++++.+
T Consensus 26 s~~~La~~~~vSr~tvr~ 43 (64)
T pfam00392 26 SERELAAEFGVSRTTVRE 43 (64)
T ss_pred HHHHHHHHHCCCHHHHHH
T ss_conf 799999997969999999
No 368
>PRK11886 biotin--protein ligase; Provisional
Probab=45.53 E-value=21 Score=16.32 Aligned_cols=30 Identities=30% Similarity=0.101 Sum_probs=21.6
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999981997999999872469999998
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
-|+.+..-.=.|=++||+++|||+.+|++.
T Consensus 9 lL~~L~~g~~~SGe~la~~LgvSR~aVwK~ 38 (319)
T PRK11886 9 LLSLLADGDFHSGEQLAEELGISRAAIWKH 38 (319)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999973799296999999879889999999
No 369
>COG1438 ArgR Arginine repressor [Transcription]
Probab=45.45 E-value=23 Score=16.08 Aligned_cols=33 Identities=27% Similarity=0.153 Sum_probs=25.4
Q ss_pred HHHHHHHHHCCC-CHHHHHHHHH-----HHHHHHHHHHC
Q ss_conf 999999998199-7999999872-----46999999852
Q gi|254780424|r 17 KRIRLRRMILGM-SQEKLGECLG-----ITFQQVQKYEK 49 (144)
Q Consensus 17 ~rIr~~R~~~gl-TQ~eLA~~lG-----vs~s~is~~E~ 49 (144)
+.||++=.+..+ ||+||.+.+- |+++|+|+.-+
T Consensus 9 ~~Ik~iI~~~~i~TQ~Elv~~L~~~Gi~vTQaTvSRDlk 47 (150)
T COG1438 9 ELIKEIITEEKISTQEELVELLQEEGIEVTQATVSRDLK 47 (150)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHCCCEEEHHHHHHHHH
T ss_conf 999999986777789999999998297586398787799
No 370
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=45.17 E-value=16 Score=17.19 Aligned_cols=33 Identities=21% Similarity=0.350 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHCC--C-CHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999819--9-799999987246999999
Q gi|254780424|r 14 NVGKRIRLRRMILG--M-SQEKLGECLGITFQQVQK 46 (144)
Q Consensus 14 ~iG~rIr~~R~~~g--l-TQ~eLA~~lGvs~s~is~ 46 (144)
+|-++|..-+..-| | |..+||+..|||++++.+
T Consensus 4 ~i~~~I~~g~~~~G~~LPs~~~la~~~~vSr~tvr~ 39 (60)
T smart00345 4 RLREDIVSGELRPGDKLPSERELAAQLGVSRTTVRE 39 (60)
T ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999839999839881099999998949999999
No 371
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=45.13 E-value=21 Score=16.40 Aligned_cols=56 Identities=14% Similarity=0.269 Sum_probs=40.6
Q ss_pred HHHHHHHHHH----------HCCCCHHHHHHHHHHHHHHHHHHHCCCCC----------------CCHHHHHHHHHHCCC
Q ss_conf 9999999999----------81997999999872469999998528988----------------358999999975499
Q gi|254780424|r 15 VGKRIRLRRM----------ILGMSQEKLGECLGITFQQVQKYEKGVNR----------------VGASRLQHISEVLES 68 (144)
Q Consensus 15 iG~rIr~~R~----------~~glTQ~eLA~~lGvs~s~is~~E~G~~~----------------ps~~~L~~iA~~l~v 68 (144)
+-++|+..|. -+-+|-.|.|+.+|||.+++-+.+....- -+++.+..|-..|+.
T Consensus 17 ~~~~~~~~~~~~~~P~~~k~lR~Fs~~E~A~l~gvs~~~lR~~~~~g~~P~p~~~~~gr~~~rr~ytl~~i~~lR~~l~~ 96 (387)
T PHA02519 17 MTQAIAIAQFGDDSPEARAITRRWGITEVADLIGVTPQAIRDAEKSGRLPPPDFETRGRVERRAGYTIDQISHMRDHFGN 96 (387)
T ss_pred HHHHHHHHHHCCCCCHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf 99999999721589633124477888999999599989998787568999997688887553343579999999998645
Q ss_pred CH
Q ss_conf 99
Q gi|254780424|r 69 PI 70 (144)
Q Consensus 69 ~~ 70 (144)
+.
T Consensus 97 ~~ 98 (387)
T PHA02519 97 PN 98 (387)
T ss_pred CC
T ss_conf 66
No 372
>PRK09409 insertion element IS2 transposase InsD; Reviewed
Probab=44.80 E-value=23 Score=16.15 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=22.2
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 98199799999987246999999852
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
.+.|++-..+++.+|||+|.+..|-+
T Consensus 8 ~a~g~~v~~~cr~LgVSRS~~y~~~~ 33 (301)
T PRK09409 8 IARGWGVSLVSRCLRVSRAQLHVILR 33 (301)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 96897499999997866877444302
No 373
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=44.66 E-value=24 Score=16.00 Aligned_cols=34 Identities=9% Similarity=0.177 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999981997999999872469999998
Q gi|254780424|r 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
.+..=|-.+|....+|-.+||+.+|||..||.+-
T Consensus 9 RL~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RD 42 (311)
T COG2378 9 RLLQIIQILRAKETVTAAELADEFEVSVRTIYRD 42 (311)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHH
T ss_conf 9999999998576045999998729889999999
No 374
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=44.56 E-value=18 Score=16.83 Aligned_cols=44 Identities=20% Similarity=0.160 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 199799999987246999999852898835899999997549999995
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
.|.|..++|+..|||+++|..+=.++... |..+.....-.+..+
T Consensus 30 ~~ttl~dIA~~AGVS~GaiY~HF~sK~dL----l~av~~~~~~~~~~~ 73 (216)
T PRK10668 30 SATSLADIAKAAGVTRGAIYWHFKNKSDL----FSEIWELSESKIGEL 73 (216)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHCCCHHHH----HHHHHHHHHHHHHHH
T ss_conf 51889999999689857999875999999----999999987179999
No 375
>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=43.81 E-value=25 Score=15.92 Aligned_cols=46 Identities=20% Similarity=0.274 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCCH---------------HHHHHHHHHCCCCHHHH
Q ss_conf 9799999987246999999852-8988358---------------99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK-GVNRVGA---------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~-G~~~ps~---------------~~L~~iA~~l~v~~~~l 73 (144)
|+-.|+|+++|||..||-.||. |--.|.. -.+...++.+|+|++.+
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 376
>PRK09413 insertion sequence 2 OrfA protein; Reviewed
Probab=43.54 E-value=20 Score=16.46 Aligned_cols=34 Identities=18% Similarity=0.279 Sum_probs=23.7
Q ss_pred HHHHHHH--HHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999999--981997999999872469999998528
Q gi|254780424|r 17 KRIRLRR--MILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 17 ~rIr~~R--~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
++++-.. .+-|+|-.++|.+-||+.+++-+|=+-
T Consensus 17 EK~~IV~es~ePG~sVs~VARrHGi~~~qlf~WRr~ 52 (121)
T PRK09413 17 EKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999999569984999999949989999999999
No 377
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=43.48 E-value=22 Score=16.29 Aligned_cols=29 Identities=21% Similarity=0.179 Sum_probs=23.1
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999981997999999872469999998
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
+..+++..-++-.|||+.+|||..||-+-
T Consensus 11 l~~L~~~g~v~v~eLa~~~~VS~~TIRRD 39 (251)
T PRK13509 11 LDMLAQLGFVTVEKVIERLGISPATARRD 39 (251)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHHH
T ss_conf 99999869898999999989699899983
No 378
>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=42.72 E-value=18 Score=16.75 Aligned_cols=32 Identities=25% Similarity=0.387 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHCC--C-CHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999819--9-799999987246999999
Q gi|254780424|r 15 VGKRIRLRRMILG--M-SQEKLGECLGITFQQVQK 46 (144)
Q Consensus 15 iG~rIr~~R~~~g--l-TQ~eLA~~lGvs~s~is~ 46 (144)
|-.+|..-+..-| | |..+||+..|||++++.+
T Consensus 10 i~~~I~~g~~~~G~~LPs~~~La~~~~vSr~tvr~ 44 (66)
T cd07377 10 LREAILSGELKPGDRLPSERELAEELGVSRTTVRE 44 (66)
T ss_pred HHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 99999859999919992799999997988899999
No 379
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=42.25 E-value=20 Score=16.47 Aligned_cols=15 Identities=13% Similarity=0.129 Sum_probs=7.5
Q ss_pred HHHHHHHCCCCHHHH
Q ss_conf 999997549999995
Q gi|254780424|r 59 LQHISEVLESPISFF 73 (144)
Q Consensus 59 L~~iA~~l~v~~~~l 73 (144)
...||..+|++..-+
T Consensus 159 ~~elA~~lG~Sretl 173 (213)
T PRK10402 159 HTQAAEYLGVSYRHL 173 (213)
T ss_pred HHHHHHHHCCCHHHH
T ss_conf 999999979889999
No 380
>TIGR02534 mucon_cyclo muconate and chloromuconate cycloisomerases; InterPro: IPR013370 This family consists of muconate cycloisomerase (5.5.1.1 from EC) and chloromuconate cycloisomerase (5.5.1.7 from EC), enzymes that often overlap in specificity. It does not include more distantly related proteins such as mandelate racemase (5.1.2.2 from EC).; GO: 0018849 muconate cycloisomerase activity, 0018850 chloromuconate cycloisomerase activity, 0030145 manganese ion binding.
Probab=41.86 E-value=20 Score=16.55 Aligned_cols=43 Identities=19% Similarity=0.217 Sum_probs=28.7
Q ss_pred HHHHHHHCC----CCCCCHHHHHHHHHHCCCCHHHHHCCCCCCCCCC
Q ss_conf 999998528----9883589999999754999999506774431111
Q gi|254780424|r 42 QQVQKYEKG----VNRVGASRLQHISEVLESPISFFFDVSPTVCSDI 84 (144)
Q Consensus 42 s~is~~E~G----~~~ps~~~L~~iA~~l~v~~~~l~~~~~~~~~~~ 84 (144)
..|.++=+| +.-+....+..=|+-||||++.||+|.--...+.
T Consensus 88 ~~l~k~~~gnRFAK~Av~tAL~DAqA~rLgVPV~eLLGG~~Rd~vdV 134 (369)
T TIGR02534 88 ADLEKVVAGNRFAKAAVDTALLDAQARRLGVPVSELLGGAVRDSVDV 134 (369)
T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHCCCCEECCCCH
T ss_conf 99999872061368899999899877647872344278741144540
No 381
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=41.70 E-value=15 Score=17.27 Aligned_cols=35 Identities=17% Similarity=0.240 Sum_probs=23.3
Q ss_pred HHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999-819979999998724699999985
Q gi|254780424|r 14 NVGKRIRLRRM-ILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 14 ~iG~rIr~~R~-~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
-+|+-.--+=. ..-||..|+++.+|+|++.+|.--
T Consensus 27 tVG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~l 62 (177)
T COG1510 27 TVGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGL 62 (177)
T ss_pred HHHHHHHHHEECCCCCCHHHHHHHHCCCCCHHHHHH
T ss_conf 277786540006999669999999777801288999
No 382
>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=41.69 E-value=27 Score=15.72 Aligned_cols=25 Identities=24% Similarity=0.401 Sum_probs=22.7
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9819979999998724699999985
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
..+|++.+.++..+||+.+++++.-
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 383
>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=41.65 E-value=9.6 Score=18.55 Aligned_cols=23 Identities=30% Similarity=0.508 Sum_probs=14.0
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 99819979999998724699999
Q gi|254780424|r 23 RMILGMSQEKLGECLGITFQQVQ 45 (144)
Q Consensus 23 R~~~glTQ~eLA~~lGvs~s~is 45 (144)
|---+||-+|.|+.+|||.+|+-
T Consensus 125 RY~eDlSe~~~A~~LG~SvGTVK 147 (165)
T TIGR02983 125 RYYEDLSEAEVAEVLGISVGTVK 147 (165)
T ss_pred ECCCCCCHHHHHHHHCCCCHHHH
T ss_conf 04578986899988199932289
No 384
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=41.32 E-value=27 Score=15.68 Aligned_cols=31 Identities=10% Similarity=0.063 Sum_probs=23.1
Q ss_pred HHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999---819979999998724699999985
Q gi|254780424|r 18 RIRLRRM---ILGMSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 18 rIr~~R~---~~glTQ~eLA~~lGvs~s~is~~E 48 (144)
|++-+.. ...++--++++.+|+|++++|+--
T Consensus 16 Rl~Il~lL~~~gelcV~eL~~~l~~sQs~vS~HL 49 (106)
T PRK10141 16 RLGIVLLLRESGELCVCDLCTALDQSQPKISRHL 49 (106)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999987499569999988699888999999
No 385
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=40.87 E-value=27 Score=15.63 Aligned_cols=30 Identities=10% Similarity=0.162 Sum_probs=23.8
Q ss_pred HHHHHHHHH--CCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998--199799999987246999999
Q gi|254780424|r 17 KRIRLRRMI--LGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R~~--~glTQ~eLA~~lGvs~s~is~ 46 (144)
+.||.++.- .|++-.+-|+++++|++++|+
T Consensus 4 ~QLr~f~~va~~~~s~t~AAe~L~iSQPavS~ 35 (316)
T PRK12679 4 QQLKIIREAARQDYNLTEVANMLFTSQSGVSR 35 (316)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 99999999998689999999997897789999
No 386
>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=40.65 E-value=14 Score=17.43 Aligned_cols=19 Identities=32% Similarity=0.581 Sum_probs=14.6
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q ss_conf 7999999872469999998
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~ 47 (144)
|..++|+.+|+++++|+++
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 387
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=40.50 E-value=25 Score=15.90 Aligned_cols=28 Identities=18% Similarity=0.128 Sum_probs=20.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998199799999987246999999
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+..++...-++-.+||+.+|||..||-+
T Consensus 11 l~~L~~~g~v~v~eLa~~l~VS~~TIRR 38 (256)
T PRK10434 11 LEYLQKQGKCSVEELAQYFDTTGTTIRK 38 (256)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999986979999999987969989998
No 388
>PRK03837 transcriptional regulator NanR; Provisional
Probab=40.24 E-value=16 Score=17.14 Aligned_cols=34 Identities=21% Similarity=0.285 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHCC--C-CHHHHHHHHHHHHHH----HHHHH
Q ss_conf 9999999999819--9-799999987246999----99985
Q gi|254780424|r 15 VGKRIRLRRMILG--M-SQEKLGECLGITFQQ----VQKYE 48 (144)
Q Consensus 15 iG~rIr~~R~~~g--l-TQ~eLA~~lGvs~s~----is~~E 48 (144)
|-+.|-.-+..-| | |..+||+.+|||++. +...|
T Consensus 23 lr~~I~~g~l~pG~rLp~E~eLae~lgVSRtpVREAL~~L~ 63 (243)
T PRK03837 23 LEQMIRSGEFGPGEQLPSERELMAFFGVGRPSVREALQALK 63 (243)
T ss_pred HHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 99999839999949793599999997969789999999999
No 389
>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=40.18 E-value=28 Score=15.61 Aligned_cols=12 Identities=25% Similarity=0.216 Sum_probs=4.1
Q ss_pred HHHHHHHHHCCC
Q ss_conf 999999998199
Q gi|254780424|r 17 KRIRLRRMILGM 28 (144)
Q Consensus 17 ~rIr~~R~~~gl 28 (144)
..+++++...|+
T Consensus 22 ~~l~~~~~~~Gf 33 (232)
T TIGR03541 22 DAVREFAQNLGY 33 (232)
T ss_pred HHHHHHHHHCCC
T ss_conf 999999998499
No 390
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=40.09 E-value=28 Score=15.56 Aligned_cols=35 Identities=11% Similarity=-0.015 Sum_probs=25.2
Q ss_pred HHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 99999999--819979999998724699999985289
Q gi|254780424|r 17 KRIRLRRM--ILGMSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 17 ~rIr~~R~--~~glTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
+-+..+.. ...+|.++||+.+|+|++++++.=+..
T Consensus 9 ~~~~yI~~h~~~~i~l~~lA~~~~~S~~~l~r~Fk~~ 45 (107)
T PRK10219 9 TLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999999866999999999989893999999999999
No 391
>PRK13503 transcriptional activator RhaS; Provisional
Probab=39.82 E-value=25 Score=15.92 Aligned_cols=23 Identities=9% Similarity=0.283 Sum_probs=12.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99799999987246999999852
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
.+|.+++|+.+|+|.++++++=+
T Consensus 187 ~isl~~lA~~~~lS~~~l~r~FK 209 (278)
T PRK13503 187 EVNWEAVADQFSLSLRTLHRQLK 209 (278)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999999897959999999999
No 392
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=39.72 E-value=24 Score=15.99 Aligned_cols=29 Identities=3% Similarity=0.044 Sum_probs=23.1
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 81997999999872469999998528988
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNR 53 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ 53 (144)
=.+-|.+++|+..|||+++|..+=.++..
T Consensus 29 ~~~tTl~~IA~~AGVt~GaiY~HF~nKe~ 57 (213)
T PRK09975 29 VANTTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHCCCHHH
T ss_conf 45588999999968984899987799999
No 393
>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=39.68 E-value=25 Score=15.85 Aligned_cols=27 Identities=15% Similarity=0.118 Sum_probs=22.0
Q ss_pred HCCCCHHHHHHHHHH-HHHHHHHHHCCC
Q ss_conf 819979999998724-699999985289
Q gi|254780424|r 25 ILGMSQEKLGECLGI-TFQQVQKYEKGV 51 (144)
Q Consensus 25 ~~glTQ~eLA~~lGv-s~s~is~~E~G~ 51 (144)
..+|+-.++|..+|+ |.++.++.-+-.
T Consensus 6 ~~~~~i~~IA~~~g~~s~~~f~r~fk~~ 33 (43)
T pfam00165 6 STNWTIADIAEELGFSSQSYFSRLFKKY 33 (43)
T ss_pred CCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 0899799999996899768999999998
No 394
>pfam06971 Put_DNA-bind_N Putative DNA-binding protein N-terminus. This family represents the N-terminus (approximately 50 residues) of a number of putative bacterial DNA-binding proteins.
Probab=39.67 E-value=29 Score=15.52 Aligned_cols=40 Identities=28% Similarity=0.390 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHHHHHHHH--CC---CCHHHHHHHHHHHHHHHHH
Q ss_conf 8998999999999999998--19---9799999987246999999
Q gi|254780424|r 7 IPNPVDINVGKRIRLRRMI--LG---MSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 7 ~~~~~d~~iG~rIr~~R~~--~g---lTQ~eLA~~lGvs~s~is~ 46 (144)
.|.+.=..+--++|.+... .| .|=++||+.+||+.++|-+
T Consensus 2 IP~ati~RLp~Y~R~L~~L~~~g~~~vSS~eLa~~~gv~~aqiRK 46 (49)
T pfam06971 2 IPEATIKRLPLYYRYLEELLEEGVERVSSKELSEAIGIDAAQIRK 46 (49)
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHC
T ss_conf 888999999999999999998599049799999997939999614
No 395
>PRK04280 arginine repressor; Provisional
Probab=39.55 E-value=29 Score=15.50 Aligned_cols=31 Identities=23% Similarity=0.187 Sum_probs=24.1
Q ss_pred HHHHHHHHHCCC-CHHHHHHHH-----HHHHHHHHHH
Q ss_conf 999999998199-799999987-----2469999998
Q gi|254780424|r 17 KRIRLRRMILGM-SQEKLGECL-----GITFQQVQKY 47 (144)
Q Consensus 17 ~rIr~~R~~~gl-TQ~eLA~~l-----Gvs~s~is~~ 47 (144)
+.|+++=.+.-+ ||+||.+.+ .|+++|+|+-
T Consensus 8 ~~I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATlSRD 44 (149)
T PRK04280 8 IKIREIITNEEIETQDELVDRLREYGFNVTQATVSRD 44 (149)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHHH
T ss_conf 9999999748977899999999985975538988987
No 396
>PRK11525 dinD DNA-damage-inducible protein D; Provisional
Probab=39.33 E-value=29 Score=15.48 Aligned_cols=42 Identities=19% Similarity=0.124 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCC
Q ss_conf 9799999987246999999852898835899999997549999995067
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~ 76 (144)
|+-.+|+..+| |+.|++-. +-+++-...|...|.++++-|..
T Consensus 22 W~ARdL~~~Lg-----Y~~w~~F~--~vI~rA~~ac~~~g~~v~dHF~~ 63 (279)
T PRK11525 22 WSARELAPLLG-----YSEWRNFQ--KVIARAKTACENSGHAVSDHFVE 63 (279)
T ss_pred EEHHHHHHHCC-----CHHHHHHH--HHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 40998788639-----28899899--99999999999869986787898
No 397
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=39.16 E-value=29 Score=15.47 Aligned_cols=27 Identities=15% Similarity=0.123 Sum_probs=10.4
Q ss_pred CCHHHH-HHHHHHCCCCHHHHHCCCCCC
Q ss_conf 358999-999975499999950677443
Q gi|254780424|r 54 VGASRL-QHISEVLESPISFFFDVSPTV 80 (144)
Q Consensus 54 ps~~~L-~~iA~~l~v~~~~l~~~~~~~ 80 (144)
|.+..+ ..|.++-..+..-|+.|....
T Consensus 146 ~am~~v~~~i~~~A~s~~pVLI~GE~GT 173 (441)
T PRK10365 146 PAMQHLLSEIALVAPSEATVLIHGDSGT 173 (441)
T ss_pred HHHHHHHHHHHHHHCCCCCEEEECCCCH
T ss_conf 9999999999998488994899899981
No 398
>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=39.04 E-value=20 Score=16.52 Aligned_cols=16 Identities=19% Similarity=0.198 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9998724699999985
Q gi|254780424|r 33 LGECLGITFQQVQKYE 48 (144)
Q Consensus 33 LA~~lGvs~s~is~~E 48 (144)
+|+..|.++.++..|.
T Consensus 17 laDlsg~tkGQL~A~~ 32 (230)
T pfam06323 17 TADLSGATKGQLEAWL 32 (230)
T ss_pred HHHHCCCCHHHHHHHH
T ss_conf 8774435215699986
No 399
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=38.90 E-value=26 Score=15.76 Aligned_cols=45 Identities=22% Similarity=0.321 Sum_probs=27.4
Q ss_pred CCCCCCCCCHHHHH-HHHHHHHHHHHCC--C-CHHHHHHHHHHHHHHHH
Q ss_conf 99876689989999-9999999999819--9-79999998724699999
Q gi|254780424|r 1 MVGNKKIPNPVDIN-VGKRIRLRRMILG--M-SQEKLGECLGITFQQVQ 45 (144)
Q Consensus 1 ~~~~~~~~~~~d~~-iG~rIr~~R~~~g--l-TQ~eLA~~lGvs~s~is 45 (144)
||-..+.|...--. |=+.|..-+..-| | +..|||+.+|||+.++-
T Consensus 1 ~~~~a~~pa~~ae~~i~~~I~~g~~~~G~~LP~EreLa~~~gVsR~tvR 49 (239)
T PRK04984 1 MVIKAQSPAGFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLR 49 (239)
T ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHH
T ss_conf 9731358679999999999986999999989889999999798889999
No 400
>pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
Probab=38.82 E-value=29 Score=15.43 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=15.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 997999999872469999998
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~ 47 (144)
..+-.++|+++|||+++++..
T Consensus 20 ~v~~~~iA~~L~Vs~~SVt~m 40 (58)
T pfam01325 20 VVKTKDLAERLNVSPSTVSEM 40 (58)
T ss_pred CEEHHHHHHHHCCCCHHHHHH
T ss_conf 612999999959992529999
No 401
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.66 E-value=23 Score=16.07 Aligned_cols=22 Identities=14% Similarity=0.241 Sum_probs=16.5
Q ss_pred HCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 8199799999987246999999
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~ 46 (144)
...+|..|.|+..+||+++|..
T Consensus 31 ~dDlSl~EIAee~~VSRqAIyD 52 (105)
T COG2739 31 LDDLSLSEIAEEFNVSRQAIYD 52 (105)
T ss_pred HHHCCHHHHHHHHCCCHHHHHH
T ss_conf 8116699999995750999999
No 402
>pfam05848 CtsR Firmicute transcriptional repressor of class III stress genes (CtsR). This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon.
Probab=38.50 E-value=25 Score=15.93 Aligned_cols=42 Identities=10% Similarity=0.035 Sum_probs=32.6
Q ss_pred CHHHHHHHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9899999999999999819-----979999998724699999985289
Q gi|254780424|r 9 NPVDINVGKRIRLRRMILG-----MSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 9 ~~~d~~iG~rIr~~R~~~g-----lTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
|..| .|-+.||++=.+.+ +.-.|||++.+|.+|+|+.+-+.+
T Consensus 2 nlSD-~IE~yiK~ll~~s~~~~ieI~R~eLA~~F~CvPSQINYVl~TR 48 (151)
T pfam05848 2 NISD-IIEEYLKQLLAQSEDEVIEIKRSELADQFNCVPSQINYVINTR 48 (151)
T ss_pred CHHH-HHHHHHHHHHHHCCCCEEEEEHHHHHHHCCCCHHHCEEEEEEE
T ss_conf 6578-9999999999738788399758998987197713512676533
No 403
>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=38.50 E-value=14 Score=17.56 Aligned_cols=45 Identities=18% Similarity=0.220 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCH---------------HHH--HHHHHHCCCCHHHH
Q ss_conf 7999999872469999998528988358---------------999--99997549999995
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVNRVGA---------------SRL--QHISEVLESPISFF 73 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~~ps~---------------~~L--~~iA~~l~v~~~~l 73 (144)
.=.|||+++||+..||=-||+-.--|.- ++| ..=|..|+.+.+.+
T Consensus 2 kIGeLA~~t~v~v~TIRFYE~~gLLPeP~R~~nnYRlYt~~hvErL~FI~~CR~Ldmsl~EI 63 (127)
T TIGR02047 2 KIGELAKKTGVSVETIRFYEKEGLLPEPARADNNYRLYTEEHVERLAFIRNCRTLDMSLAEI 63 (127)
T ss_pred CHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHH
T ss_conf 41345455334400224644137853865447795103888999999998316230018999
No 404
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=38.02 E-value=23 Score=16.10 Aligned_cols=23 Identities=4% Similarity=-0.104 Sum_probs=16.0
Q ss_pred CCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 98835899999997549999995
Q gi|254780424|r 51 VNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 51 ~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
...|+.+.+..||..+|++...+
T Consensus 22 ~~~P~~~~~~~La~~~~l~~~qV 44 (59)
T cd00086 22 NPYPSREEREELAKELGLTERQV 44 (59)
T ss_pred CCCCCHHHHHHHHHHHCCCHHHH
T ss_conf 79999999999999979299999
No 405
>PRK13502 transcriptional activator RhaR; Provisional
Probab=37.55 E-value=31 Score=15.31 Aligned_cols=21 Identities=0% Similarity=-0.046 Sum_probs=10.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 997999999872469999998
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~ 47 (144)
.+|.+++|+.+|+|++++++.
T Consensus 192 ~isl~~lA~~~~~S~~~lsr~ 212 (282)
T PRK13502 192 PFALDAFCQQEQCSERVLRQQ 212 (282)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
T ss_conf 988999998979799999999
No 406
>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=37.45 E-value=31 Score=15.30 Aligned_cols=36 Identities=17% Similarity=0.264 Sum_probs=25.5
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCC
Q ss_conf 999999819979999998724699999985289883589999999754999
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESP 69 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~ 69 (144)
+..++.--.+.+.+.|..+||+.++ |.++|..+||+
T Consensus 7 ~~dl~~~F~lpi~~AA~~Lgv~~T~---------------LKk~CR~~gI~ 42 (52)
T pfam02042 7 LEDLSKYFHLPIKEAAKELGVCLTV---------------LKKICRQLGIP 42 (52)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHH---------------HHHHHHHCCCC
T ss_conf 9999998187599999996877999---------------99999987998
No 407
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; InterPro: IPR014305 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 and represent a conserved family.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=37.45 E-value=28 Score=15.53 Aligned_cols=30 Identities=27% Similarity=0.368 Sum_probs=24.2
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999981997999999872469999998528
Q gi|254780424|r 21 LRRMILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 21 ~~R~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
-+|..+||.=.|.|+.||.|...++.--.-
T Consensus 153 ~LRdvlGw~A~E~A~~L~~s~ASVnSaLQR 182 (329)
T TIGR02960 153 LLRDVLGWKAAEVAELLGTSVASVNSALQR 182 (329)
T ss_pred HHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 989883555568998743832678658888
No 408
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=37.43 E-value=18 Score=16.85 Aligned_cols=24 Identities=25% Similarity=0.376 Sum_probs=20.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 799999987246999999852898
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVN 52 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~ 52 (144)
|..+.|+.+|+++++|+++-++..
T Consensus 19 Si~~aak~l~~~~~~I~~~l~~~~ 42 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNTGK 42 (53)
T ss_pred HHHHHHHHHCCCCCCHHHHHCCCC
T ss_conf 799999985888323888706775
No 409
>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=37.37 E-value=31 Score=15.29 Aligned_cols=58 Identities=16% Similarity=0.174 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHHHHHHC-CCCCCCH----------------HHHHHHHHHCCCCHHHH---HCCCCCCCCCCCCH
Q ss_conf 99999987246999999852-8988358----------------99999997549999995---06774431111101
Q gi|254780424|r 30 QEKLGECLGITFQQVQKYEK-GVNRVGA----------------SRLQHISEVLESPISFF---FDVSPTVCSDISSE 87 (144)
Q Consensus 30 Q~eLA~~lGvs~s~is~~E~-G~~~ps~----------------~~L~~iA~~l~v~~~~l---~~~~~~~~~~~~~~ 87 (144)
--|||++.||+.=|+--||+ |--.|+. =++..=|+.||.+.+.+ ++..-+.....+.+
T Consensus 4 IGeLAklc~V~~DTlRfYEK~gl~~p~~RtdsGYRlYtd~d~~rlRFIl~AK~lGftLdeI~eLLsI~ld~~~h~Cae 81 (132)
T TIGR02043 4 IGELAKLCDVTADTLRFYEKNGLLKPAERTDSGYRLYTDEDLKRLRFILKAKELGFTLDEIKELLSIKLDKDEHACAE 81 (132)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCCCHHH
T ss_conf 022476617984333477677430556677876534177568988899988774687888787631222777664156
No 410
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=37.15 E-value=31 Score=15.27 Aligned_cols=30 Identities=13% Similarity=0.053 Sum_probs=24.2
Q ss_pred HHHHHHHH--CCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999998--1997999999872469999998
Q gi|254780424|r 18 RIRLRRMI--LGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 18 rIr~~R~~--~glTQ~eLA~~lGvs~s~is~~ 47 (144)
.||.++.- .|++-.+-|+++++|++++|+-
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 411
>pfam03333 PapB Adhesin biosynthesis transcription regulatory protein. This family includes PapB, DaaA, FanA, FanB, and AfaA.
Probab=36.86 E-value=24 Score=16.04 Aligned_cols=30 Identities=20% Similarity=0.125 Sum_probs=17.7
Q ss_pred HHHHHHHH--HCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999999--8199799999987246999999
Q gi|254780424|r 17 KRIRLRRM--ILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R~--~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+-|-++|. -.|.|+++..++-||+.+++|.
T Consensus 41 kvI~AL~dylV~G~srkevCe~~~Vn~gyfS~ 72 (91)
T pfam03333 41 KVINALRDYLVDGYSRKEVCERHNVNNGYFSI 72 (91)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHH
T ss_conf 99999999987686499999872977999999
No 412
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=36.76 E-value=31 Score=15.27 Aligned_cols=25 Identities=4% Similarity=0.028 Sum_probs=15.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 1997999999872469999998528
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
..+|.+++|+.+|+|+++.+++=+-
T Consensus 206 e~IsL~diA~~~~lS~~y~sr~FKk 230 (302)
T PRK10371 206 QALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999998979599999999999
No 413
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=36.67 E-value=22 Score=16.23 Aligned_cols=40 Identities=13% Similarity=0.112 Sum_probs=25.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHH------CCCCHHHHHHHHHHHHHHH
Q ss_conf 7668998999999999999998------1997999999872469999
Q gi|254780424|r 4 NKKIPNPVDINVGKRIRLRRMI------LGMSQEKLGECLGITFQQV 44 (144)
Q Consensus 4 ~~~~~~~~d~~iG~rIr~~R~~------~glTQ~eLA~~lGvs~s~i 44 (144)
..+.+..-| .|-+.||+.=.. --|+..+||+.+|||++.+
T Consensus 6 ~i~~~sL~~-~v~~~lr~~I~~g~l~pG~~L~E~~La~~~gVSRtpv 51 (212)
T TIGR03338 6 LLQSSSLTT-LVQDEIERAILSGELPPGAKLNESDIAARLGVSRGPV 51 (212)
T ss_pred CCCCCCHHH-HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHH
T ss_conf 567899999-9999999999839999909818999999889694999
No 414
>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=36.64 E-value=26 Score=15.72 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=14.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9799999987246999999852
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~ 49 (144)
++-+|+|++-|||++++.++-+
T Consensus 26 v~~~~ia~~~~Is~~yL~K~l~ 47 (133)
T TIGR00738 26 VSVKEIAERQGISRSYLEKVLR 47 (133)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 0789999884899879999999
No 415
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=36.43 E-value=32 Score=15.19 Aligned_cols=23 Identities=35% Similarity=0.495 Sum_probs=12.4
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf 99981997999999872469999
Q gi|254780424|r 22 RRMILGMSQEKLGECLGITFQQV 44 (144)
Q Consensus 22 ~R~~~glTQ~eLA~~lGvs~s~i 44 (144)
+|.-.||+-+|.|+.+|+|..++
T Consensus 167 LRdV~g~s~~EiAe~Lg~S~aAV 189 (341)
T PRK08241 167 LRDVLGWSAAEVAEALGTSTAAV 189 (341)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHH
T ss_conf 29752998899999978999999
No 416
>PRK11891 aspartate carbamoyltransferase; Provisional
Probab=36.27 E-value=29 Score=15.49 Aligned_cols=35 Identities=14% Similarity=0.185 Sum_probs=30.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 99999999819979999998724699999985289
Q gi|254780424|r 17 KRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 17 ~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
..||..-..++||-..+|+++||...++..|---.
T Consensus 7 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ 41 (430)
T PRK11891 7 AFLRDAMRRLNMTREAFANRIGVSRRALDTWLLPD 41 (430)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHCCCC
T ss_conf 99999987626679999998614443630112777
No 417
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=36.00 E-value=33 Score=15.15 Aligned_cols=10 Identities=10% Similarity=-0.071 Sum_probs=3.4
Q ss_pred HHHCCCCCCC
Q ss_conf 9852898835
Q gi|254780424|r 46 KYEKGVNRVG 55 (144)
Q Consensus 46 ~~E~G~~~ps 55 (144)
.+-+|....+
T Consensus 123 ~v~~G~~~l~ 132 (216)
T PRK10100 123 GVLRGECYFT 132 (216)
T ss_pred HHHCCCCCCC
T ss_conf 9987997239
No 418
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA; InterPro: IPR011983 This putative transcriptional regulator, which contains both the substrate-binding, dimerisation domain and the helix-turn-helix DNA-binding domain of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway ..
Probab=35.95 E-value=33 Score=15.15 Aligned_cols=42 Identities=12% Similarity=0.195 Sum_probs=31.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf 999999981997999999872469999998528988358999
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRL 59 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L 59 (144)
++=+-+-+..|+..+-|+++|||.|-++.+++--..-|..+|
T Consensus 198 ~LIe~nY~~hl~~~~Y~~~LG~sesrLn~iCr~~a~~SsKRL 239 (292)
T TIGR02297 198 ALIEENYKQHLRLPEYAERLGLSESRLNDICRRIADLSSKRL 239 (292)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCHHHHHHHHHHHHHCCCCCHH
T ss_conf 578888771687145676640107789899999827897224
No 419
>KOG2252 consensus
Probab=35.77 E-value=33 Score=15.13 Aligned_cols=57 Identities=12% Similarity=0.165 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHH-HHHHHHHHHHHCCC-----CCCCHHHHHHHHHHCCCCH
Q ss_conf 9999999999998199799999987-24699999985289-----8835899999997549999
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECL-GITFQQVQKYEKGV-----NRVGASRLQHISEVLESPI 70 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~l-Gvs~s~is~~E~G~-----~~ps~~~L~~iA~~l~v~~ 70 (144)
..|.+||+..-+..++.|+-||+++ +.|++++|-.-+.- ..---+++.++++-|. ++
T Consensus 329 keia~rI~~eLk~~sIpQaiFAervLcRSQGTLSDLLrnPKPW~klKsGRetFrRM~~WL~-eP 391 (558)
T KOG2252 329 KEIAQRIKAELKRYSIPQAIFAERVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMANWLE-EP 391 (558)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHCCCCHHHHCCCCHHHHHHHHHHC-CH
T ss_conf 9999999999864577378888888612522299996389952544032099999998742-78
No 420
>pfam01316 Arg_repressor Arginine repressor, DNA binding domain.
Probab=35.66 E-value=33 Score=15.12 Aligned_cols=32 Identities=22% Similarity=0.086 Sum_probs=22.7
Q ss_pred HHHHHHHHHCCC-CHHHHHHHHH-----HHHHHHHHHH
Q ss_conf 999999998199-7999999872-----4699999985
Q gi|254780424|r 17 KRIRLRRMILGM-SQEKLGECLG-----ITFQQVQKYE 48 (144)
Q Consensus 17 ~rIr~~R~~~gl-TQ~eLA~~lG-----vs~s~is~~E 48 (144)
..|+++=....+ ||+||...+. |+++|+|+.-
T Consensus 8 ~~I~~li~~~~i~tQ~eL~~~L~~~G~~vTQATlSRDl 45 (70)
T pfam01316 8 ELIKEIITEEKISTQEELVALLKAEGINVTQATVSRDL 45 (70)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHCCCCEEEHHHHHHH
T ss_conf 99999997089789999999999769856417888779
No 421
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=35.62 E-value=33 Score=15.11 Aligned_cols=24 Identities=8% Similarity=0.027 Sum_probs=18.4
Q ss_pred HHHHHHHHHCCCCHHHHHCCCCCC
Q ss_conf 999999975499999950677443
Q gi|254780424|r 57 SRLQHISEVLESPISFFFDVSPTV 80 (144)
Q Consensus 57 ~~L~~iA~~l~v~~~~l~~~~~~~ 80 (144)
..+..+|+.|||+++.+++..-..
T Consensus 3 ~I~~~Va~~~~v~~~~i~~~~R~~ 26 (90)
T cd06571 3 LIIEAVAEYFGISVEDLRSKSRKK 26 (90)
T ss_pred HHHHHHHHHHCCCHHHHHCCCCCC
T ss_conf 899999999799899984698871
No 422
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=35.54 E-value=24 Score=15.98 Aligned_cols=23 Identities=4% Similarity=-0.006 Sum_probs=17.8
Q ss_pred CCCCHHHHHHHHHHHHHH----HHHHH
Q ss_conf 199799999987246999----99985
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQ----VQKYE 48 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~----is~~E 48 (144)
-.|+..+||+++|||+.. +.+.+
T Consensus 29 ~~L~e~~Lae~lgVSRtPVREAL~rL~ 55 (224)
T PRK11534 29 EKLRMSLLTSRYALGVGPLREALSQLV 55 (224)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 955899999997988589999999999
No 423
>TIGR02318 phosphono_phnM phosphonate metabolism protein PhnM; InterPro: IPR012696 This family consists of proteins from in the PhnM family. PhnM is a protein associated with phosphonate utilization in a number of bacterial species. Pseudomonas stutzeri WM88, has a related protein that is part of a system for the oxidation of phosphites (another form of reduced phosphorous compound), which is not contained in this entry..
Probab=35.43 E-value=33 Score=15.09 Aligned_cols=55 Identities=13% Similarity=0.149 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHH
Q ss_conf 9999999999819--97999999872469999998528988358999999975499999
Q gi|254780424|r 15 VGKRIRLRRMILG--MSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPIS 71 (144)
Q Consensus 15 iG~rIr~~R~~~g--lTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~ 71 (144)
+=+++..++++.| ||-+++++.+. ...-.+=+.+...++...|.++|..-++++.
T Consensus 182 ~~~yr~~~~~k~grvlsd~~~~~~~~--~r~~~~~~~~~~~~~r~~i~ala~~~~i~lA 238 (391)
T TIGR02318 182 LEKYREYYQKKRGRVLSDDEFDEIVE--ERIARSAEYADVEANRSEIAALARARGIPLA 238 (391)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHH--HHHHHHCCCCCHHHHHHHHHHHHHHCCCCEE
T ss_conf 57899987245267458999999999--9999735863258999999999985799532
No 424
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=35.40 E-value=33 Score=15.09 Aligned_cols=46 Identities=13% Similarity=0.281 Sum_probs=35.1
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf 8199799999987246999999852898835899999997549999
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~ 70 (144)
-.|.|..++|+..|||++.+..|=.++...=...+..+..-+...+
T Consensus 26 ~~~~t~~~IA~~AGvS~G~v~~yF~sK~~Ll~~~~~~~~~~~~~~~ 71 (189)
T TIGR03384 26 SLDVTIAQIARRAGVSSGIISHYFGGKQGLLEATMRHLLSELRAAV 71 (189)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 3528899999996999999999838899999999999999999999
No 425
>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=35.34 E-value=27 Score=15.69 Aligned_cols=20 Identities=35% Similarity=0.350 Sum_probs=13.4
Q ss_pred CCHHHHHHHHHHHHHHHHHH
Q ss_conf 97999999872469999998
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~ 47 (144)
+|.+|+++.+|+|..++.++
T Consensus 53 ft~~el~~~L~~s~~~v~k~ 72 (76)
T pfam06970 53 FTNEELMELLNCSKQKVIKI 72 (76)
T ss_pred EEHHHHHHHHCCCHHHHHHH
T ss_conf 64999999978788899999
No 426
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=35.30 E-value=33 Score=15.08 Aligned_cols=42 Identities=19% Similarity=0.176 Sum_probs=24.9
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCC----HHHHHHHHHHC
Q ss_conf 8199799999987246999999852898-835----89999999754
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVN-RVG----ASRLQHISEVL 66 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~-~ps----~~~L~~iA~~l 66 (144)
.-+||-+.+|+.+|||..++.++=.+.. +|+ -.+|.+..+.|
T Consensus 213 dp~Ls~~~iA~~~giS~R~L~rlF~~~G~t~~~~I~~~RL~~a~~~L 259 (303)
T PRK09685 213 EEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYIRNRRLDRCADDL 259 (303)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf 99989999999979999999999998599899999999999999960
No 427
>PRK13866 plasmid partitioning protein RepB; Provisional
Probab=35.15 E-value=32 Score=15.16 Aligned_cols=57 Identities=11% Similarity=0.124 Sum_probs=41.4
Q ss_pred HHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCC-HHHH
Q ss_conf 99999999-819979999998724699999985289883589999999754999-9995
Q gi|254780424|r 17 KRIRLRRM-ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESP-ISFF 73 (144)
Q Consensus 17 ~rIr~~R~-~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~-~~~l 73 (144)
+-+=..+. ..|+++..+...++++.+.+|++-.=...+..+.+..|.-+-+|- +.|+
T Consensus 168 rAlFA~~l~~~g~~r~~i~~aL~~dk~~lS~m~~v~~~iP~~~i~aIG~Ap~iGR~rW~ 226 (336)
T PRK13866 168 KALFALRLEDAGFDRATIIAALSTDKADLSRYITVARGIPLNLATQIGPASKAGRSRWV 226 (336)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHH
T ss_conf 99999999976998889999967888899999999997899999974788867707899
No 428
>pfam00046 Homeobox Homeobox domain.
Probab=34.47 E-value=26 Score=15.76 Aligned_cols=23 Identities=9% Similarity=-0.041 Sum_probs=18.1
Q ss_pred CCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 98835899999997549999995
Q gi|254780424|r 51 VNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 51 ~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
...|+.+....||..+|++...+
T Consensus 22 ~~~P~~~~~~~LA~~l~l~~~~V 44 (57)
T pfam00046 22 NRYPSAEEREELAKKLGLTERQV 44 (57)
T ss_pred CCCCCHHHHHHHHHHHCCCHHHH
T ss_conf 79999899999999839998997
No 429
>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=34.25 E-value=20 Score=16.51 Aligned_cols=21 Identities=10% Similarity=0.164 Sum_probs=17.1
Q ss_pred HHHHHHHHHHCCCCHHHHHCC
Q ss_conf 899999997549999995067
Q gi|254780424|r 56 ASRLQHISEVLESPISFFFDV 76 (144)
Q Consensus 56 ~~~L~~iA~~l~v~~~~l~~~ 76 (144)
.++|+.||+.++++++.+...
T Consensus 6 GDtl~~IA~~~~v~~~~i~~~ 26 (43)
T pfam01476 6 GDTLSSIAKRYGITVEELAEL 26 (43)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
T ss_conf 987999999989689999998
No 430
>smart00257 LysM Lysin motif.
Probab=34.02 E-value=20 Score=16.57 Aligned_cols=24 Identities=13% Similarity=0.200 Sum_probs=18.9
Q ss_pred CHHHHHHHHHHCCCCHHHHHCCCC
Q ss_conf 589999999754999999506774
Q gi|254780424|r 55 GASRLQHISEVLESPISFFFDVSP 78 (144)
Q Consensus 55 s~~~L~~iA~~l~v~~~~l~~~~~ 78 (144)
+.++|+.||..+++++..|....+
T Consensus 6 ~GDTl~~IA~~~~v~~~~l~~~N~ 29 (44)
T smart00257 6 KGDTLSSIARRYGISVSDLLELNN 29 (44)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 898899999998968999998769
No 431
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=33.61 E-value=28 Score=15.59 Aligned_cols=35 Identities=23% Similarity=0.337 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHC----C--C-CHHHHHHHHHHHHHHH----HHHH
Q ss_conf 9999999999981----9--9-7999999872469999----9985
Q gi|254780424|r 14 NVGKRIRLRRMIL----G--M-SQEKLGECLGITFQQV----QKYE 48 (144)
Q Consensus 14 ~iG~rIr~~R~~~----g--l-TQ~eLA~~lGvs~s~i----s~~E 48 (144)
.|-++|++.=... | | +..+||+.+|||++.+ ...|
T Consensus 6 ~V~e~Lr~~I~~g~l~pG~~LP~E~eLae~~GVSRt~VREAL~~L~ 51 (253)
T PRK10421 6 EVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLV 51 (253)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9999999999819999859593399999997969899999999999
No 432
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=33.56 E-value=30 Score=15.41 Aligned_cols=22 Identities=5% Similarity=-0.087 Sum_probs=15.8
Q ss_pred CCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 8835899999997549999995
Q gi|254780424|r 52 NRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 52 ~~ps~~~L~~iA~~l~v~~~~l 73 (144)
..|+.+.+..||..+|++...+
T Consensus 23 ~~P~~~~~~~La~~l~l~~~~I 44 (56)
T smart00389 23 PYPSREEREELAAKLGLSERQV 44 (56)
T ss_pred CCCCHHHHHHHHHHHCCCHHHH
T ss_conf 9999899999999969499999
No 433
>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=33.52 E-value=18 Score=16.75 Aligned_cols=23 Identities=9% Similarity=0.182 Sum_probs=18.7
Q ss_pred HHHHHHHHHHCCCCHHHHHCCCC
Q ss_conf 89999999754999999506774
Q gi|254780424|r 56 ASRLQHISEVLESPISFFFDVSP 78 (144)
Q Consensus 56 ~~~L~~iA~~l~v~~~~l~~~~~ 78 (144)
.++|+.||..+++++..|....+
T Consensus 8 GDTl~~Ia~~~~v~~~~l~~~N~ 30 (46)
T cd00118 8 GDTLSSIAQRYGISVEELLKLNG 30 (46)
T ss_pred CCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 99999999998967999998669
No 434
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=33.42 E-value=36 Score=14.89 Aligned_cols=54 Identities=9% Similarity=0.149 Sum_probs=40.5
Q ss_pred HHHHHHHHHHH----------CCCCHHHHHHHHHHHHHHHHHHH------------CCCCCCCHHHHHHHHHHCCC
Q ss_conf 99999999998----------19979999998724699999985------------28988358999999975499
Q gi|254780424|r 15 VGKRIRLRRMI----------LGMSQEKLGECLGITFQQVQKYE------------KGVNRVGASRLQHISEVLES 68 (144)
Q Consensus 15 iG~rIr~~R~~----------~glTQ~eLA~~lGvs~s~is~~E------------~G~~~ps~~~L~~iA~~l~v 68 (144)
++..+.++|.+ +-+|-.|+|+.+||+.+++-+.+ +|++.-+++.+..+-..|.-
T Consensus 26 ls~~l~~~r~~~~~P~~~K~lr~fs~~e~a~l~gv~~~~lr~~~~~g~~p~p~~~~~grr~ytl~~i~~lR~~l~~ 101 (405)
T PRK13869 26 LSSQLQAMSEALFPPTSHKSLRKFTSGEAARLMKISDSTLRKMTLAGEGPQPELASNGRRFYTLGQINEIRGMLAG 101 (405)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCEECHHHHHHHHHHHHH
T ss_conf 9999999998508996656658788899999969699999999865999999878998543019999999999974
No 435
>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=32.76 E-value=37 Score=14.82 Aligned_cols=51 Identities=22% Similarity=0.280 Sum_probs=38.1
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf 998199799999987246999999852898835899999997549999995
Q gi|254780424|r 23 RMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73 (144)
Q Consensus 23 R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l 73 (144)
+--.|-|-.++|+..||+++.+..|=.++...=...|..+-+.+.-+...+
T Consensus 24 ~G~~g~~~~~Ia~~ag~~k~~i~yyF~~Ke~l~~avl~~~~~~~~~~~~~~ 74 (202)
T TIGR03613 24 FGFHGTSLEQIAELAGVSKTNLLYYFPSKDALYLAVLRQILDIWLSPLKAF 74 (202)
T ss_pred HCCCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 495648899999985998889999858999999999999999999788762
No 436
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=32.67 E-value=37 Score=14.81 Aligned_cols=36 Identities=17% Similarity=0.162 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9999999999819979999998724699999985289
Q gi|254780424|r 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 15 iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
+-..|.. -...++|.+++|..+|+|.+++.+.=+..
T Consensus 25 ~~~~i~~-~~~~~~~l~~la~~~g~S~~~l~r~f~~~ 60 (127)
T COG2207 25 ALDYIEE-NLAEPLTLEDLARRLGMSRRTLSRLFKKE 60 (127)
T ss_pred HHHHHHH-CCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999986-41379999999999798999999999999
No 437
>TIGR02018 his_ut_repres histidine utilization repressor; InterPro: IPR010248 This entry represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0006547 histidine metabolic process, 0045892 negative regulation of transcription DNA-dependent.
Probab=32.54 E-value=25 Score=15.83 Aligned_cols=18 Identities=17% Similarity=0.209 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHHHH
Q ss_conf 999998724699999985
Q gi|254780424|r 31 EKLGECLGITFQQVQKYE 48 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E 48 (144)
.||.+..|||+.|++|--
T Consensus 29 ~EL~~~~G~SRMTvnrAL 46 (234)
T TIGR02018 29 NELVAQFGVSRMTVNRAL 46 (234)
T ss_pred HHHHHHHCCCHHHHHHHH
T ss_conf 999977487233578999
No 438
>PRK11414 putative DNA-binding transcriptional regulator; Provisional
Probab=32.04 E-value=27 Score=15.64 Aligned_cols=35 Identities=17% Similarity=0.308 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHH------CCCCHHHHHHHHHHHHHH----HHHHH
Q ss_conf 999999999998------199799999987246999----99985
Q gi|254780424|r 14 NVGKRIRLRRMI------LGMSQEKLGECLGITFQQ----VQKYE 48 (144)
Q Consensus 14 ~iG~rIr~~R~~------~glTQ~eLA~~lGvs~s~----is~~E 48 (144)
.|-++||..=.. -.|++.+||+.+|||+.- +.+.+
T Consensus 15 qV~~~Lr~~I~~G~l~PG~~L~e~~La~~lgVSRtPVREAL~rL~ 59 (221)
T PRK11414 15 QVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLV 59 (221)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999999983998995971899999997999068999999999
No 439
>pfam12116 SpoIIID Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.
Probab=31.39 E-value=39 Score=14.68 Aligned_cols=23 Identities=13% Similarity=0.223 Sum_probs=17.3
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 98199799999987246999999
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
.+.+-|-.+-|...|||.||+.+
T Consensus 16 i~~~aTVR~tAk~FGvSKSTVHk 38 (82)
T pfam12116 16 IENKATVRQAAKVFGVSKSTVHK 38 (82)
T ss_pred HHCCHHHHHHHHHHCCCHHHHHH
T ss_conf 96262899999996960988988
No 440
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=31.33 E-value=39 Score=14.67 Aligned_cols=33 Identities=15% Similarity=0.025 Sum_probs=22.9
Q ss_pred HHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999819-979999998724699999985
Q gi|254780424|r 16 GKRIRLRRMILG-MSQEKLGECLGITFQQVQKYE 48 (144)
Q Consensus 16 G~rIr~~R~~~g-lTQ~eLA~~lGvs~s~is~~E 48 (144)
.+.|..+=...| .+..++|+.++|++++++.+-
T Consensus 12 L~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml 45 (154)
T COG1321 12 LETIYELLEEKGFARTKDIAERLKVSPPSVTEML 45 (154)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 9999999843687519999998589927899999
No 441
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=31.12 E-value=39 Score=14.65 Aligned_cols=28 Identities=7% Similarity=0.060 Sum_probs=11.6
Q ss_pred CCCHHHH-HHHHHHCCCCHHHHHCCCCCC
Q ss_conf 8358999-999975499999950677443
Q gi|254780424|r 53 RVGASRL-QHISEVLESPISFFFDVSPTV 80 (144)
Q Consensus 53 ~ps~~~L-~~iA~~l~v~~~~l~~~~~~~ 80 (144)
.|.+..+ ..|.++-..+..-|+.|....
T Consensus 149 S~~m~~v~~~i~~~A~s~~~VLI~GEsGT 177 (457)
T PRK11361 149 SPAMMDICKDTAKIALSQASVLISGESGT 177 (457)
T ss_pred CHHHHHHHHHHHHHHCCCCCEEEECCCCC
T ss_conf 99999999999998488995899889985
No 442
>PRK04435 hypothetical protein; Provisional
Probab=30.95 E-value=22 Score=16.22 Aligned_cols=30 Identities=20% Similarity=0.045 Sum_probs=23.3
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 998199799999987246999999852898
Q gi|254780424|r 23 RMILGMSQEKLGECLGITFQQVQKYEKGVN 52 (144)
Q Consensus 23 R~~~glTQ~eLA~~lGvs~s~is~~E~G~~ 52 (144)
....-.|-.|..+++|+|+|++.+|--+.-
T Consensus 29 ~~g~~~~i~EAvk~vGISRSafYKYKD~VF 58 (146)
T PRK04435 29 KSGKVKSITEAVKQVGISRSAFYKYKDYVF 58 (146)
T ss_pred HCCCCCCHHHHHHHHCCCHHHEECCCCCCC
T ss_conf 738977499999983965210112366210
No 443
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=30.86 E-value=35 Score=14.98 Aligned_cols=18 Identities=33% Similarity=0.458 Sum_probs=11.3
Q ss_pred CHHHHHHHHHHHHHHHHH
Q ss_conf 799999987246999999
Q gi|254780424|r 29 SQEKLGECLGITFQQVQK 46 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~ 46 (144)
|-.+||..+||++.|+++
T Consensus 37 SvRelA~~~~VNpnTv~r 54 (125)
T COG1725 37 SVRELAKDLGVNPNTVQR 54 (125)
T ss_pred CHHHHHHHHCCCHHHHHH
T ss_conf 599999981989889999
No 444
>pfam05344 DUF746 Domain of Unknown Function (DUF746). This is a short conserved region found in some transposons.
Probab=30.52 E-value=40 Score=14.58 Aligned_cols=27 Identities=15% Similarity=0.170 Sum_probs=22.0
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 981997999999872469999998528
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
..+-++-.|.|+.+|++...+.+|-..
T Consensus 10 Ls~p~s~~qaa~~lg~~~~~i~~wv~~ 36 (65)
T pfam05344 10 LSQPISCAQAADQLGTDEGIIRKWVRM 36 (65)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 266665999999978788899999999
No 445
>KOG0774 consensus
Probab=29.96 E-value=18 Score=16.75 Aligned_cols=21 Identities=29% Similarity=0.298 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHHCCC
Q ss_conf 999998724699999985289
Q gi|254780424|r 31 EKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E~G~ 51 (144)
+|||.+.|++.|++|+|-.++
T Consensus 222 ~eLAkqCnItvsQvsnwfgnk 242 (334)
T KOG0774 222 EELAKQCNITVSQVSNWFGNK 242 (334)
T ss_pred HHHHHHCCCEEHHHCCCCCCC
T ss_conf 999987293405632322454
No 446
>PRK12423 LexA repressor; Provisional
Probab=29.83 E-value=41 Score=14.51 Aligned_cols=35 Identities=20% Similarity=0.197 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHCCC--CHHHHHHHHHH-HHHHHHHH
Q ss_conf 9999999999998199--79999998724-69999998
Q gi|254780424|r 13 INVGKRIRLRRMILGM--SQEKLGECLGI-TFQQVQKY 47 (144)
Q Consensus 13 ~~iG~rIr~~R~~~gl--TQ~eLA~~lGv-s~s~is~~ 47 (144)
..|=+.|++.-.+.|+ |.+|+|+.+|+ |.+++.++
T Consensus 9 ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~h 46 (202)
T PRK12423 9 AAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKH 46 (202)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHH
T ss_conf 99999999999962989889999998299986789999
No 447
>COG5424 Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C [Coenzyme metabolism]
Probab=29.82 E-value=41 Score=14.51 Aligned_cols=37 Identities=14% Similarity=0.212 Sum_probs=28.6
Q ss_pred HHHHHHHCCCCCCC-HHHHHHHHHHCCCCHHHHHCCCC
Q ss_conf 99999852898835-89999999754999999506774
Q gi|254780424|r 42 QQVQKYEKGVNRVG-ASRLQHISEVLESPISFFFDVSP 78 (144)
Q Consensus 42 s~is~~E~G~~~ps-~~~L~~iA~~l~v~~~~l~~~~~ 78 (144)
.-|.--++|.+.|+ ++...++|.++||+..++.+-.+
T Consensus 79 eni~de~~g~~e~~hidlwlr~aeAlGvs~eei~s~ep 116 (242)
T COG5424 79 ENIMDEDNGYNEPNHIDLWLRLAEALGVSREEILSHEP 116 (242)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHCCC
T ss_conf 99998746778853899999999981999999851698
No 448
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=29.40 E-value=10 Score=18.44 Aligned_cols=53 Identities=19% Similarity=0.301 Sum_probs=33.7
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHH--HHHHHCCCCCCC-HHHHHHHHHH-----CCCCHHHHHC
Q ss_conf 99998199799999987246999--999852898835-8999999975-----4999999506
Q gi|254780424|r 21 LRRMILGMSQEKLGECLGITFQQ--VQKYEKGVNRVG-ASRLQHISEV-----LESPISFFFD 75 (144)
Q Consensus 21 ~~R~~~glTQ~eLA~~lGvs~s~--is~~E~G~~~ps-~~~L~~iA~~-----l~v~~~~l~~ 75 (144)
.++..==+|-+|||+.+|||-+| +-+.|-|- |. -+++..+|+- =.++.+.+.+
T Consensus 15 ~i~~nPF~TDeeLa~~f~VSiqTIRLDR~~L~I--PElReRik~vAe~~~~~vrsl~~~EviG 75 (185)
T PRK04424 15 TIEENPFITDEELAEKFGVSIQTIRLDRMELSI--PELRERIKHVAEKNYDKVKSLPLEEVVG 75 (185)
T ss_pred HHHHCCCCCHHHHHHHCCCEEEEEEECHHHCCC--HHHHHHHHHHHHHHHHHHCCCCHHHEEE
T ss_conf 998689987799998609577788822143298--7899999999997476404677134155
No 449
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=29.21 E-value=32 Score=15.16 Aligned_cols=35 Identities=26% Similarity=0.436 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHCC--CCHHHHHHHHHHHHHH----HHHHH
Q ss_conf 99999999999819--9799999987246999----99985
Q gi|254780424|r 14 NVGKRIRLRRMILG--MSQEKLGECLGITFQQ----VQKYE 48 (144)
Q Consensus 14 ~iG~rIr~~R~~~g--lTQ~eLA~~lGvs~s~----is~~E 48 (144)
+|-+.|-..+..-| +++.+||+.+|||+.. +.+.+
T Consensus 24 ~lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~ 64 (230)
T COG1802 24 ELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLE 64 (230)
T ss_pred HHHHHHHHCCCCCCCEECHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 99999982998982981799999998889079999999998
No 450
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=29.18 E-value=42 Score=14.44 Aligned_cols=32 Identities=13% Similarity=0.131 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999981997999999872469999998
Q gi|254780424|r 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 15 iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
+=.+-+++| ..|||-.|.|+.+++|+.|++-.
T Consensus 7 Li~kA~eL~-~~Gls~geIAdELnvS~eT~~WL 38 (201)
T PRK02277 7 LIEKALELR-SEGLSTGEIADELNVSRETATWL 38 (201)
T ss_pred HHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 999999999-86997666355540269999999
No 451
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=29.07 E-value=42 Score=14.43 Aligned_cols=50 Identities=14% Similarity=0.138 Sum_probs=36.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC
Q ss_conf 999999999819979999998724699999985289883589999999754
Q gi|254780424|r 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVL 66 (144)
Q Consensus 16 G~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l 66 (144)
-+-+.+-....|||-+++|..+|+|...+.++-+=+. +++..-+.+-+.|
T Consensus 12 ~~ELqeNf~~~~ls~~~iA~dL~~s~~~ve~vL~m~~-~~i~~vW~lRdyL 61 (89)
T pfam10078 12 RKELQANFELSGLTIEQVAKDLNTTPEKVEALLQLKQ-RSIEDVWILRNYL 61 (89)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCC-CCCCHHHHHHHHH
T ss_conf 9999999988389899999894999999999997346-7754138899999
No 452
>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=28.77 E-value=43 Score=14.39 Aligned_cols=21 Identities=24% Similarity=0.411 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHHHCCCCC
Q ss_conf 999872469999998528988
Q gi|254780424|r 33 LGECLGITFQQVQKYEKGVNR 53 (144)
Q Consensus 33 LA~~lGvs~s~is~~E~G~~~ 53 (144)
+|+.|||+..-+..+|+--+.
T Consensus 149 ~A~~L~V~~~eV~eMe~RlsG 169 (279)
T TIGR02392 149 IAEELGVSEEEVLEMESRLSG 169 (279)
T ss_pred HHHHCCCCHHHHHHHHHCCCC
T ss_conf 997638988899887514553
No 453
>PRK10870 transcriptional repressor MprA; Provisional
Probab=28.63 E-value=43 Score=14.40 Aligned_cols=25 Identities=4% Similarity=0.391 Sum_probs=12.6
Q ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99987289999999999999999999
Q gi|254780424|r 104 NRYFIQIDDVKVRQKIIELVRSIVSS 129 (144)
Q Consensus 104 ~~~~~~l~~~~~r~~i~~l~~~l~~~ 129 (144)
...|..+++++ ++.+..+++.+...
T Consensus 137 ~~l~s~Ls~eE-~~qL~~LL~KLL~~ 161 (176)
T PRK10870 137 HQLWSALSTTE-KDQLEQITRKLLTR 161 (176)
T ss_pred HHHHCCCCHHH-HHHHHHHHHHHHHH
T ss_conf 99872899999-99999999999981
No 454
>PRK05306 infB translation initiation factor IF-2; Validated
Probab=28.46 E-value=43 Score=14.36 Aligned_cols=53 Identities=11% Similarity=0.132 Sum_probs=41.3
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHH--CC-----CCCCCHHHHHHHHHHCCCCHHH
Q ss_conf 99999819979999998724699999985--28-----9883589999999754999999
Q gi|254780424|r 20 RLRRMILGMSQEKLGECLGITFQQVQKYE--KG-----VNRVGASRLQHISEVLESPISF 72 (144)
Q Consensus 20 r~~R~~~glTQ~eLA~~lGvs~s~is~~E--~G-----~~~ps~~~L~~iA~~l~v~~~~ 72 (144)
|.++..-++|-.|||+++|+..+.|-+.. .| ...+..++...||.-||+.+..
T Consensus 263 reIkIpEsITV~ELAekM~vKaSevi~~L~~~G~m~t~nq~lD~dtael~~~e~g~~~~~ 322 (839)
T PRK05306 263 REVVIPETITVAELANKMAVKAAEVIKKLMKLGVMVTINQSLDQDTAELVAEEFGHKVKL 322 (839)
T ss_pred EEEEECCCEEHHHHHHHHCCCHHHHHHHHHHCCCEECCCCCCCHHHHHHHHHHCCCEEEE
T ss_conf 489968964899999987889999999999778662266777999999999981977999
No 455
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=28.29 E-value=44 Score=14.34 Aligned_cols=45 Identities=4% Similarity=-0.034 Sum_probs=27.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCC------C-CHHHHHHHHHHHHHH----HHHHH
Q ss_conf 8766899899999999999999819------9-799999987246999----99985
Q gi|254780424|r 3 GNKKIPNPVDINVGKRIRLRRMILG------M-SQEKLGECLGITFQQ----VQKYE 48 (144)
Q Consensus 3 ~~~~~~~~~d~~iG~rIr~~R~~~g------l-TQ~eLA~~lGvs~s~----is~~E 48 (144)
..+|+-..-| .|-.+|++.=..-. | |..+||+.+|||++. +...|
T Consensus 2 ~~~~p~rL~e-qV~~~L~~~I~~G~l~pGdrLPsEreLAe~fGVSRt~VREAL~~Le 57 (258)
T PRK11523 2 EITEPRRLYQ-QLAADLKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLE 57 (258)
T ss_pred CCCCCHHHHH-HHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9887503999-9999999999859999979096699999997988799999999999
No 456
>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=28.16 E-value=44 Score=14.32 Aligned_cols=45 Identities=16% Similarity=0.119 Sum_probs=30.7
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf 99999998199799999987246999999852898835899999997549999
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~ 70 (144)
-+..+=.....|-.++|+.+.||.+++.+.=+ .+..+-+-+++.+
T Consensus 21 il~~lf~~~~~s~~~~a~~l~iS~sTl~R~ik--------~l~~~L~~~~l~i 65 (87)
T pfam05043 21 LLKFLFFHEFFSLTSLAQKLFISESTLYRLIK--------KLNKLLKEFDLSI 65 (87)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH--------HHHHHHHHCCEEE
T ss_conf 99999818999899999997889999999999--------9999999859688
No 457
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=28.16 E-value=44 Score=14.32 Aligned_cols=31 Identities=26% Similarity=0.415 Sum_probs=23.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf 799999987246999999852898835899999997549999
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~ 70 (144)
+-..-|+.+|||++++|+. +..+-+.||+++
T Consensus 15 s~~~AA~~l~isqs~vs~~-----------i~~LE~~lg~~L 45 (60)
T pfam00126 15 SFTAAAERLGLSQPAVSRQ-----------IKRLEEELGVPL 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHH-----------HHHHHHHHCCEE
T ss_conf 9999999979898899999-----------999999959970
No 458
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=28.02 E-value=44 Score=14.31 Aligned_cols=34 Identities=21% Similarity=0.232 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 8999999999999998199799999987246999999852
Q gi|254780424|r 10 PVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 10 ~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+|-.-.|..+.+.+.+.|... +++|...+..+++
T Consensus 365 DI~lLa~~FLe~~~~~~g~~~------~~ls~eAl~~L~~ 398 (510)
T PRK05022 365 DVLLLAGYFLEQNRLRLGLSS------LRLSPDAQAALLQ 398 (510)
T ss_pred HHHHHHHHHHHHHHHHCCCCC------CCCCHHHHHHHHC
T ss_conf 099999999999999829898------9888999999970
No 459
>COG3720 HemS Putative heme degradation protein [Inorganic ion transport and metabolism]
Probab=27.86 E-value=44 Score=14.29 Aligned_cols=36 Identities=22% Similarity=0.233 Sum_probs=31.6
Q ss_pred HHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 99999999981-9979999998724699999985289
Q gi|254780424|r 16 GKRIRLRRMIL-GMSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 16 G~rIr~~R~~~-glTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
-.+++++|.++ |+-+.++|..+|||...+-.-.-|.
T Consensus 10 y~~~r~~raE~P~~r~RD~Aa~lgisEaeLvaarvg~ 46 (349)
T COG3720 10 YTRWRALRAENPGLRARDIAALLGISEAELVAARVGH 46 (349)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 7999998742854145678988286688888877168
No 460
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=27.83 E-value=34 Score=15.04 Aligned_cols=40 Identities=18% Similarity=0.248 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 999999999981--9979999998724699999985289883
Q gi|254780424|r 15 VGKRIRLRRMIL--GMSQEKLGECLGITFQQVQKYEKGVNRV 54 (144)
Q Consensus 15 iG~rIr~~R~~~--glTQ~eLA~~lGvs~s~is~~E~G~~~p 54 (144)
|-.-++-+...- ++|-..||+++||+.+++..+=.++...
T Consensus 10 v~aAl~Lld~~Gl~alSMRrLA~~LgV~~~sLY~Hv~nK~~L 51 (205)
T PRK13756 10 INSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRAL 51 (205)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHHHHHCCCHHHH
T ss_conf 999999998238000669999999489931789873889999
No 461
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=27.77 E-value=35 Score=14.97 Aligned_cols=17 Identities=18% Similarity=0.311 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999872469999998
Q gi|254780424|r 31 EKLGECLGITFQQVQKY 47 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~ 47 (144)
.++|+.+|||+++++..
T Consensus 3 ~diA~~L~vs~~sVs~~ 19 (96)
T smart00529 3 SEIAERLNVSPPTVTQM 19 (96)
T ss_pred HHHHHHHCCCCHHHHHH
T ss_conf 88998849991679999
No 462
>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=27.58 E-value=45 Score=14.26 Aligned_cols=50 Identities=22% Similarity=0.340 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHCCC--CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 99999999998199--799999987246999999852898835899999997
Q gi|254780424|r 15 VGKRIRLRRMILGM--SQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISE 64 (144)
Q Consensus 15 iG~rIr~~R~~~gl--TQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~ 64 (144)
|.+-++++...+|= |-+|+|..+|++..-|.++.+..+.-+.--|..+-.
T Consensus 85 ~~~a~~~Le~~LgR~P~~~EiA~~Lg~~~~e~~~~~~~~~~~~~~SLd~~~~ 136 (227)
T TIGR02479 85 LEEAIEELEARLGREPTEEEIAEELGMDLKEVRQALNEINAESLVSLDELLE 136 (227)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999869898888999983999989999999988998764899984
No 463
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=27.54 E-value=45 Score=14.26 Aligned_cols=18 Identities=28% Similarity=0.412 Sum_probs=15.9
Q ss_pred CHHHHHHHHHHHHHHHHH
Q ss_conf 799999987246999999
Q gi|254780424|r 29 SQEKLGECLGITFQQVQK 46 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~ 46 (144)
|..+||+..|||+.|+-+
T Consensus 27 sE~eLa~~~~VSR~TvR~ 44 (231)
T TIGR03337 27 SERDLGERFNTTRVTIRE 44 (231)
T ss_pred CHHHHHHHHCCCHHHHHH
T ss_conf 899999997979999999
No 464
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=27.29 E-value=45 Score=14.23 Aligned_cols=26 Identities=12% Similarity=0.281 Sum_probs=16.5
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99981997999999872469999998
Q gi|254780424|r 22 RRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 22 ~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
+|.--|++-+|+|+.+|+|..++-+.
T Consensus 122 Lrdv~g~s~~EIA~iLg~s~~avR~~ 147 (289)
T PRK09636 122 LHDVFGVPFDEIASTLGRSEAACRQL 147 (289)
T ss_pred HHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 49860999999999981799999999
No 465
>KOG0775 consensus
Probab=27.25 E-value=30 Score=15.42 Aligned_cols=22 Identities=32% Similarity=0.471 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999987246999999852898
Q gi|254780424|r 31 EKLGECLGITFQQVQKYEKGVN 52 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~E~G~~ 52 (144)
.|||+..|.+..++++|=++++
T Consensus 207 ReLA~aTgLt~tQVsNWFKNRR 228 (304)
T KOG0775 207 RELAEATGLTITQVSNWFKNRR 228 (304)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9999871886300215542035
No 466
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=27.03 E-value=41 Score=14.48 Aligned_cols=34 Identities=26% Similarity=0.263 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHCC------C-CHHHHHHHHHHHHHHH----HHHH
Q ss_conf 9999999999819------9-7999999872469999----9985
Q gi|254780424|r 15 VGKRIRLRRMILG------M-SQEKLGECLGITFQQV----QKYE 48 (144)
Q Consensus 15 iG~rIr~~R~~~g------l-TQ~eLA~~lGvs~s~i----s~~E 48 (144)
|..+||..=..-. | +-.+||+.+|||++.+ ...|
T Consensus 14 V~~~Lr~~I~~G~l~PGdrLP~EreLAe~lgVSRt~VREAL~~Le 58 (257)
T PRK10225 14 VGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLE 58 (257)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999999828999979395299999997988789999999999
No 467
>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=26.94 E-value=46 Score=14.19 Aligned_cols=20 Identities=30% Similarity=0.409 Sum_probs=12.1
Q ss_pred HHHHHHH--HCCCCHHHHHHHH
Q ss_conf 9999999--8199799999987
Q gi|254780424|r 18 RIRLRRM--ILGMSQEKLGECL 37 (144)
Q Consensus 18 rIr~~R~--~~glTQ~eLA~~l 37 (144)
|||.++. .+|+|...+++.+
T Consensus 46 RL~~I~~L~~~G~tl~~I~e~l 67 (219)
T cd04778 46 RLRLINQLLERGYTLAHIAELL 67 (219)
T ss_pred HHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9999999998799889999999
No 468
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=26.93 E-value=46 Score=14.19 Aligned_cols=33 Identities=27% Similarity=0.359 Sum_probs=25.6
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999981997999999872469999998528
Q gi|254780424|r 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50 (144)
Q Consensus 18 rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G 50 (144)
+.-......|.|..|+|..+|+|..++...-..
T Consensus 10 ~~~~~l~~~G~s~~eia~~l~is~~tV~~h~~~ 42 (65)
T COG2771 10 REILRLVAQGKSNKEIARILGISEETVKTHLRN 42 (65)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999986998999999987799999999999
No 469
>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=26.67 E-value=34 Score=14.99 Aligned_cols=25 Identities=24% Similarity=0.336 Sum_probs=21.9
Q ss_pred CCCCCHHHHHHHHHHCCCCHHHHHC
Q ss_conf 9883589999999754999999506
Q gi|254780424|r 51 VNRVGASRLQHISEVLESPISFFFD 75 (144)
Q Consensus 51 ~~~ps~~~L~~iA~~l~v~~~~l~~ 75 (144)
..+|...++..+|+.|+++.+.++-
T Consensus 30 v~TP~~~TIe~la~fl~v~~~~~iK 54 (160)
T cd04334 30 VATPGQKTIEELAEFLGVPPSQTVK 54 (160)
T ss_pred ECCCCCCCHHHHHHHHCCCHHHHEE
T ss_conf 7494986399999987969888443
No 470
>pfam08280 HTH_Mga M protein trans-acting positive regulator (MGA) HTH domain. 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.
Probab=26.64 E-value=43 Score=14.36 Aligned_cols=27 Identities=15% Similarity=0.305 Sum_probs=21.1
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 819979999998724699999985289
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGV 51 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~ 51 (144)
..-++..|+|..+|.|..++..+-+.-
T Consensus 17 ~~~~~l~el~~~l~ls~~tl~~~i~~L 43 (59)
T pfam08280 17 NKSITLDELAKQLGLSELTLKSYIHEL 43 (59)
T ss_pred CCCEEHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 883649999988099799999999999
No 471
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=26.51 E-value=36 Score=14.87 Aligned_cols=31 Identities=13% Similarity=0.145 Sum_probs=23.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 9819979999998724699999985289883
Q gi|254780424|r 24 MILGMSQEKLGECLGITFQQVQKYEKGVNRV 54 (144)
Q Consensus 24 ~~~glTQ~eLA~~lGvs~s~is~~E~G~~~p 54 (144)
--.++|..|+|...||++.++.++=.++...
T Consensus 29 gf~~lslreiar~aGv~~~afYrHF~d~e~L 59 (203)
T PRK11202 29 SFSSLSLREVAREAGIAPTSFYRHFKDMDEL 59 (203)
T ss_pred CCCCCCHHHHHHHHCCCCCHHHHHCCCHHHH
T ss_conf 9330679999998489975188875988999
No 472
>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=25.91 E-value=44 Score=14.29 Aligned_cols=45 Identities=16% Similarity=0.201 Sum_probs=33.4
Q ss_pred CHHHHHHHHHHHHHHHHHHH-CCCCCCCH----------------HHHHHHHHHCCCCHHHH
Q ss_conf 79999998724699999985-28988358----------------99999997549999995
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYE-KGVNRVGA----------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E-~G~~~ps~----------------~~L~~iA~~l~v~~~~l 73 (144)
.=.++|+..|+|...|=.|| .|--.|++ =+|..=|+.+|-+.+..
T Consensus 2 NIg~~AK~tglssK~IR~YE~kGLi~Pp~Rse~GYR~Y~~~h~~~L~li~raR~~GFSLeEc 63 (127)
T TIGR02044 2 NIGQVAKLTGLSSKSIRYYEEKGLIPPPLRSEGGYRTYTDKHVDELRLISRARSVGFSLEEC 63 (127)
T ss_pred CHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 76777501477268898877632679988688888563876788889999998718988999
No 473
>PRK03341 arginine repressor; Provisional
Probab=25.78 E-value=48 Score=14.05 Aligned_cols=30 Identities=23% Similarity=0.213 Sum_probs=23.0
Q ss_pred HHHHHHHHHCCC-CHHHHHHHHH-----HHHHHHHH
Q ss_conf 999999998199-7999999872-----46999999
Q gi|254780424|r 17 KRIRLRRMILGM-SQEKLGECLG-----ITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R~~~gl-TQ~eLA~~lG-----vs~s~is~ 46 (144)
+.|+++=.+..+ ||+||.+.+. |+++|||+
T Consensus 18 ~~I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATiSR 53 (168)
T PRK03341 18 ARIVAILSSQSVRSQSELAALLADEGIDVTQATLSR 53 (168)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHCCCCEEHHHHHH
T ss_conf 999999960897889999999997698654278775
No 474
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=25.63 E-value=49 Score=14.04 Aligned_cols=34 Identities=21% Similarity=0.288 Sum_probs=26.2
Q ss_pred HHHHHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999--81997999999872469999998
Q gi|254780424|r 14 NVGKRIRLRRM--ILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 14 ~iG~rIr~~R~--~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
.|++-|...+. +.-+|.++||+++|+|.-++.+.
T Consensus 221 ~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRl 256 (328)
T COG4977 221 RLLRAIELMEANLEEPLSLEELADRAGLSRRQLERL 256 (328)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 899999999986538868999999968788789999
No 475
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=25.12 E-value=47 Score=14.10 Aligned_cols=19 Identities=11% Similarity=0.475 Sum_probs=8.7
Q ss_pred CCHHHHHHHHHHHHHHHHH
Q ss_conf 9799999987246999999
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~ 46 (144)
.|..++|..++|++.-+++
T Consensus 158 rtl~eIa~a~~V~~kei~r 176 (285)
T COG1405 158 RTLDEIAKALGVSKKEIGR 176 (285)
T ss_pred CCHHHHHHHHCCCHHHHHH
T ss_conf 3199999997789999999
No 476
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=25.10 E-value=50 Score=13.97 Aligned_cols=25 Identities=16% Similarity=0.038 Sum_probs=18.7
Q ss_pred HHHC-CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9981-997999999872469999998
Q gi|254780424|r 23 RMIL-GMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 23 R~~~-glTQ~eLA~~lGvs~s~is~~ 47 (144)
-... ..+-.++|+.+|||+++++..
T Consensus 17 ~~~~~~vr~~dIA~~L~Vs~~SVs~m 42 (142)
T PRK03902 17 IEEKGYARVSDIAEALSVHPSSVTKM 42 (142)
T ss_pred HHCCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf 82589712999999978995339999
No 477
>pfam05121 GvpK Gas vesicle protein K. These proteins are involved in the formation of gas vesicles.
Probab=24.96 E-value=50 Score=13.96 Aligned_cols=45 Identities=16% Similarity=0.166 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCH------------HHHHHHHHHCCCCHHHH
Q ss_conf 97999999872469999998528988358------------99999997549999995
Q gi|254780424|r 28 MSQEKLGECLGITFQQVQKYEKGVNRVGA------------SRLQHISEVLESPISFF 73 (144)
Q Consensus 28 lTQ~eLA~~lGvs~s~is~~E~G~~~ps~------------~~L~~iA~~l~v~~~~l 73 (144)
+|.-||=..+ +-+++|-++|.|.-+..- +.+..+|+.||+++++|
T Consensus 20 LtvVELlRql-mErQAiRRme~G~Ls~eqiErlG~tLm~le~~~~~L~~~fgl~~~dL 76 (89)
T pfam05121 20 LTVVELLRQL-MERQAIRRMESGSLSDEQIERLGESLQKLEEQLEQLCEQFGIDPEDL 76 (89)
T ss_pred HHHHHHHHHH-HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 9999999999-99999998725899999999999999999999999999829998997
No 478
>PRK13501 transcriptional activator RhaR; Provisional
Probab=24.95 E-value=50 Score=13.96 Aligned_cols=21 Identities=0% Similarity=-0.051 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 997999999872469999998
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~ 47 (144)
.+|.+++|+..|+|.++++++
T Consensus 192 ~~~l~~lA~~~~lS~~~lsrl 212 (290)
T PRK13501 192 YFDMADFCHKNQLVERSLKQL 212 (290)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999999969899999999
No 479
>pfam11300 DUF3102 Protein of unknown function (DUF3102). This family of proteins has no known function.
Probab=24.71 E-value=50 Score=13.93 Aligned_cols=42 Identities=19% Similarity=0.339 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH---CCCCCCCHHHHHHHHHHCC
Q ss_conf 999999999999819979999998724699999985---2898835899999997549
Q gi|254780424|r 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYE---KGVNRVGASRLQHISEVLE 67 (144)
Q Consensus 13 ~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E---~G~~~ps~~~L~~iA~~l~ 67 (144)
+.||+||+..... +....+.+|- -+-+.-+..+++++++.||
T Consensus 26 IEIGrrL~~~Ke~-------------l~HGef~~WLke~v~~S~rtA~~~M~v~~eyG 70 (130)
T pfam11300 26 IEIGRRLKEAKAL-------------LPHGEWGKWLKESVSYSRRTAANLMRLYEEYG 70 (130)
T ss_pred HHHHHHHHHHHHH-------------CCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHC
T ss_conf 9999999999985-------------88662999999992826999999999999975
No 480
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.28 E-value=51 Score=13.88 Aligned_cols=56 Identities=16% Similarity=0.229 Sum_probs=0.0
Q ss_pred CHHHHH-HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC
Q ss_conf 989999-9999999999819979999998724699999985289883589999999754
Q gi|254780424|r 9 NPVDIN-VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVL 66 (144)
Q Consensus 9 ~~~d~~-iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l 66 (144)
||--++ --+-+.+-+....||-+++|..+|+|..-+.++++=+..| ...+.+-++|
T Consensus 4 n~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~--~dvW~lRd~l 60 (97)
T COG4367 4 NPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRP--ADVWRLRDFL 60 (97)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHCC--CHHHHHHHHH
T ss_conf 98999988999997544064529999999588799999999885064--2368899999
No 481
>PRK00441 argR arginine repressor; Provisional
Probab=24.22 E-value=52 Score=13.87 Aligned_cols=30 Identities=27% Similarity=0.204 Sum_probs=0.0
Q ss_pred HHHHHHHHHCCC-CHHHHHHHHH-----HHHHHHHH
Q ss_conf 999999998199-7999999872-----46999999
Q gi|254780424|r 17 KRIRLRRMILGM-SQEKLGECLG-----ITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R~~~gl-TQ~eLA~~lG-----vs~s~is~ 46 (144)
+.|+++=....+ ||+||.+.+. |+++|+|+
T Consensus 7 ~~I~~lI~~~~I~tQ~eL~~~L~~~Gi~vTQATlSR 42 (149)
T PRK00441 7 AKILEIINSKEIETQEELAEELKKMGFDVTQATVSR 42 (149)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHH
T ss_conf 999999972896789999999998699766589888
No 482
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=24.12 E-value=52 Score=13.86 Aligned_cols=30 Identities=17% Similarity=0.261 Sum_probs=0.0
Q ss_pred HHHHHHH--HHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999--98199799999987246999999
Q gi|254780424|r 17 KRIRLRR--MILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R--~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+.+|.+. -+.|.|-..-|+.+|+|++++|+
T Consensus 4 ~~L~~f~~vv~~~~Sft~AA~~L~isQ~avS~ 35 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSK 35 (309)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 99999999998699999999997898789999
No 483
>pfam12368 DUF3650 Protein of unknown function (DUF3650). This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with pfam00581. There is a single completely conserved residue N that may be functionally important.
Probab=24.11 E-value=52 Score=13.86 Aligned_cols=14 Identities=29% Similarity=0.325 Sum_probs=0.0
Q ss_pred HHCCCCHHHHHHHH
Q ss_conf 98199799999987
Q gi|254780424|r 24 MILGMSQEKLGECL 37 (144)
Q Consensus 24 ~~~glTQ~eLA~~l 37 (144)
++.|||.+|+|+++
T Consensus 12 ~~h~Ls~eEv~~RL 25 (28)
T pfam12368 12 KEHNLSEEEVAERL 25 (28)
T ss_pred HHCCCCHHHHHHHH
T ss_conf 87179999999998
No 484
>pfam07600 DUF1564 Protein of unknown function (DUF1564). A family of paralogous proteins in Leptospira interrogans. Several have been annotated as possible CopG-like transcriptional regulators (see pfam01402).
Probab=24.10 E-value=52 Score=13.85 Aligned_cols=21 Identities=10% Similarity=0.178 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHCCCCHHHHHC
Q ss_conf 589999999754999999506
Q gi|254780424|r 55 GASRLQHISEVLESPISFFFD 75 (144)
Q Consensus 55 s~~~L~~iA~~l~v~~~~l~~ 75 (144)
....|-.+|.++||+.++||+
T Consensus 92 dW~~LgvlA~~hGVSrC~LFn 112 (167)
T pfam07600 92 DWALLGVLAAAHGVSRCYLFN 112 (167)
T ss_pred HHHHHHHHHHHCCCHHHHHHH
T ss_conf 499999999981831899999
No 485
>pfam06413 Neugrin Neugrin. This family consists of several mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation.
Probab=23.86 E-value=52 Score=13.82 Aligned_cols=45 Identities=13% Similarity=0.104 Sum_probs=0.0
Q ss_pred HHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH
Q ss_conf 99999999--8199799999987246999999852898835899999
Q gi|254780424|r 17 KRIRLRRM--ILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQH 61 (144)
Q Consensus 17 ~rIr~~R~--~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~ 61 (144)
+.||.++. ---||-..||+...||.-+|.++-+.+=.|+.+.-.+
T Consensus 17 e~IR~Lh~~~Pe~~t~~~LAe~F~VSpeaIrRILKSKw~Pt~e~klK 63 (225)
T pfam06413 17 EQIRYLKQEFPEEWTVPRLAEGFDVSTDVIRRVLKSKFVPTLERKLK 63 (225)
T ss_pred HHHHHHHHHCCHHCCHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHH
T ss_conf 99999987384011589998607889999999997157886888754
No 486
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=23.74 E-value=53 Score=13.81 Aligned_cols=21 Identities=10% Similarity=0.175 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 997999999872469999998
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~ 47 (144)
+||.++||..+++++.+++++
T Consensus 388 ~LtL~~la~~f~in~~Ylgql 408 (475)
T COG4753 388 NLTLKDLAKVFHINPVYLGQL 408 (475)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
T ss_conf 887999987737089999999
No 487
>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=23.61 E-value=53 Score=13.79 Aligned_cols=31 Identities=16% Similarity=0.140 Sum_probs=0.0
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999998199799999987246999999852
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQKYEK 49 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~~E~ 49 (144)
+++.=+..+=.....|+.+|||+.|+++|-+
T Consensus 627 ~~~aL~~~~G~~~a~a~~LGiSrTTLWRrL~ 657 (658)
T TIGR02329 627 VRAALERFQGDRAAAAKALGISRTTLWRRLK 657 (658)
T ss_pred HHHHHHHHCCCHHHHHHHCCCCHHHHHHHHC
T ss_conf 8999987278968998542764245777613
No 488
>PRK13558 bacterio-opsin activator; Provisional
Probab=23.53 E-value=53 Score=13.78 Aligned_cols=21 Identities=14% Similarity=0.178 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHH
Q ss_conf 199799999987246999999
Q gi|254780424|r 26 LGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 26 ~glTQ~eLA~~lGvs~s~is~ 46 (144)
+.-|=+|||+.+|||++++++
T Consensus 638 R~sTGeElAesLgIS~pTfhq 658 (674)
T PRK13558 638 RRAEGKQLAESMDIVPSTYHQ 658 (674)
T ss_pred CCCCHHHHHHHCCCCHHHHHH
T ss_conf 778789999870988388999
No 489
>PRK01905 DNA-binding protein Fis; Provisional
Probab=23.13 E-value=54 Score=13.73 Aligned_cols=28 Identities=25% Similarity=0.270 Sum_probs=0.0
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998199799999987246999999
Q gi|254780424|r 19 IRLRRMILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 19 Ir~~R~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
|...=..-+-.|...|+.+|+++.|+-+
T Consensus 42 i~~vl~~~~gNQ~kAA~~LGinR~TLRk 69 (77)
T PRK01905 42 LEVVMEQAGGNQSLAAEYLGINRNTLRK 69 (77)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999998459499999997865888999
No 490
>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=23.10 E-value=46 Score=14.17 Aligned_cols=26 Identities=8% Similarity=0.089 Sum_probs=0.0
Q ss_pred HHHHCCCCCCCHHHHHHHHHHCCCCH
Q ss_conf 99852898835899999997549999
Q gi|254780424|r 45 QKYEKGVNRVGASRLQHISEVLESPI 70 (144)
Q Consensus 45 s~~E~G~~~ps~~~L~~iA~~l~v~~ 70 (144)
+.++.|..+||...+..+.+...+|+
T Consensus 28 s~L~~GGlTPs~~~i~~~~~~~~ipv 53 (202)
T pfam03932 28 ANLAVGGLTPSYGVIKSAAQRAKIPV 53 (202)
T ss_pred CCCCCCCCCCCHHHHHHHHHHCCCCE
T ss_conf 67666897989999999998659974
No 491
>PRK06347 autolysin; Reviewed
Probab=23.07 E-value=54 Score=13.73 Aligned_cols=50 Identities=12% Similarity=0.080 Sum_probs=0.0
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCC---------------------------------------CCCHHHHHHHHHH
Q ss_conf 8199799999987246999999852898---------------------------------------8358999999975
Q gi|254780424|r 25 ILGMSQEKLGECLGITFQQVQKYEKGVN---------------------------------------RVGASRLQHISEV 65 (144)
Q Consensus 25 ~~glTQ~eLA~~lGvs~s~is~~E~G~~---------------------------------------~ps~~~L~~iA~~ 65 (144)
..|=|.-.+|.+-|++...+..|=+=+. -=+.+.|+.||.-
T Consensus 486 ksGDSLw~IA~K~GtSV~~L~swNniksd~Iy~GQkLkVs~~ssssststs~~sts~~sssst~tYTVKSGDSLw~IA~k 565 (593)
T PRK06347 486 AKGDSLWRIANNNKVTIANLKSWNNLKSDFIYPGQKLKVSAGTTTNNTNTAKPSTNKPSNSAVKTYTVKKGDSLWAISRQ 565 (593)
T ss_pred CCCCCHHHHHHHCCCCHHHHHHHHCCCCCCEEECEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHH
T ss_conf 36853788887708417775555245777335040799705654565434665555567787357898138859999998
Q ss_pred CCCCHHHHH
Q ss_conf 499999950
Q gi|254780424|r 66 LESPISFFF 74 (144)
Q Consensus 66 l~v~~~~l~ 74 (144)
|||+++.|.
T Consensus 566 yGvSV~qL~ 574 (593)
T PRK06347 566 YKTTVDNIK 574 (593)
T ss_pred HCCCHHHHH
T ss_conf 497799999
No 492
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=23.07 E-value=54 Score=13.73 Aligned_cols=18 Identities=17% Similarity=0.331 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHHHHHH
Q ss_conf 799999987246999999
Q gi|254780424|r 29 SQEKLGECLGITFQQVQK 46 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~ 46 (144)
|..+||+..|||+.|+-+
T Consensus 31 sE~eLa~~~~VSR~TvR~ 48 (239)
T PRK09764 31 TESALQTEFGVSRVTVRQ 48 (239)
T ss_pred CHHHHHHHHCCCHHHHHH
T ss_conf 999999997979999999
No 493
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=22.48 E-value=56 Score=13.65 Aligned_cols=30 Identities=17% Similarity=0.231 Sum_probs=0.0
Q ss_pred HHHHHHHHHC--CCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999981--99799999987246999999
Q gi|254780424|r 17 KRIRLRRMIL--GMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R~~~--glTQ~eLA~~lGvs~s~is~ 46 (144)
+.||.+.... |.|-..-|+++|+|++++|+
T Consensus 4 ~qLryf~~va~~~~sft~AA~~L~iSQpavS~ 35 (313)
T PRK12684 4 HQLRFVREAVRQNFNLTEAAKALYTSQPGVSK 35 (313)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 99999999998699999999997897789999
No 494
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=22.47 E-value=56 Score=13.65 Aligned_cols=66 Identities=14% Similarity=0.134 Sum_probs=0.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHH-----CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC
Q ss_conf 9987668998999999999999998-----19979999998724699999985289883589999999754
Q gi|254780424|r 1 MVGNKKIPNPVDINVGKRIRLRRMI-----LGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVL 66 (144)
Q Consensus 1 ~~~~~~~~~~~d~~iG~rIr~~R~~-----~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l 66 (144)
+..+...|-.|=..+...+|.+-.. .|.++.+++..+||.+-.+..+-+-.+..+...|.++-..+
T Consensus 240 l~~~~~~~~~il~~l~~~~r~l~~ik~~~~~g~~~~~i~~~l~i~~~~~~~~~~~~~~~s~~~L~~~l~~l 310 (336)
T PRK05574 240 LRLEGEEPIKLLAALQREFRLLLQLKILLQQGYPLQQLFKELRVWPYRRKLALRALQRLSLKQLEQAIQLL 310 (336)
T ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99779972999999999999999999998769999999988399999999999999729999999999999
No 495
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=22.22 E-value=56 Score=13.62 Aligned_cols=109 Identities=9% Similarity=0.111 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf 79999998724699999985289883589999999754999999506774431111101454211203867899999987
Q gi|254780424|r 29 SQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFI 108 (144)
Q Consensus 29 TQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~ 108 (144)
|-.++|++.|++.+.|..|=.++...=...+..||+.......-+.+..+................... .+.....
T Consensus 34 ttr~Ia~~Ag~~~~~i~yyFg~Ke~Ly~Av~~~ia~~i~~~~~p~~~~~~~~l~~~~~~~~~~~~~i~~----~~~~~~~ 109 (224)
T PRK11552 34 TTRDIAAQAGQNIAAITYYFGSKEDLYLACAQWIADFIGEQFRPHAEEAERLFAQPAPDRAAIRELILR----ACLNMIK 109 (224)
T ss_pred HHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH----HHHHHHH
T ss_conf 099999983999999988738889999999999999999985179987664015688755899999999----9999988
Q ss_pred HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 289999999999999999999999753999873
Q gi|254780424|r 109 QIDDVKVRQKIIELVRSIVSSEKKYRTIEEECM 141 (144)
Q Consensus 109 ~l~~~~~r~~i~~l~~~l~~~e~~~~~~~ee~l 141 (144)
-+.+++......-+++.+..-........++.+
T Consensus 110 l~~~~~~~~~~~fmaREq~~Pt~A~~~l~~~~i 142 (224)
T PRK11552 110 LLTQDDTVNLSKFISREQLSPTAAYHLIHEQVI 142 (224)
T ss_pred HHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 407873179999999987288499999999988
No 496
>PRK13832 plasmid partitioning protein; Provisional
Probab=22.01 E-value=57 Score=13.59 Aligned_cols=36 Identities=31% Similarity=0.504 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 989999999999999981997999999872469999998
Q gi|254780424|r 9 NPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 9 ~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~ 47 (144)
||+|.- +-|..+ ..+|||-+++|-.++++..+|-+.
T Consensus 103 npvDqW--Raierl-valGwTeeaIa~ALal~vrqiRkL 138 (518)
T PRK13832 103 NPVDQW--RAIERL-VALGWTEEAIAVALALPVRQIRKL 138 (518)
T ss_pred CHHHHH--HHHHHH-HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 869999--999999-984998899999966899999999
No 497
>PRK01770 sec-independent translocase; Provisional
Probab=21.97 E-value=46 Score=14.19 Aligned_cols=39 Identities=26% Similarity=0.381 Sum_probs=0.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 9987668998999999999999998199799999987246
Q gi|254780424|r 1 MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGIT 40 (144)
Q Consensus 1 ~~~~~~~~~~~d~~iG~rIr~~R~~~glTQ~eLA~~lGvs 40 (144)
.++-++.|..+ +.+|.-|+.+|...+=-|.+|.+.+.+.
T Consensus 19 VlGPerLP~a~-Rtvg~~v~~~R~~a~~~q~el~~el~~~ 57 (171)
T PRK01770 19 VLGPQRLPVAV-KTVAGWIRALRSLATTVQNELTQELKLQ 57 (171)
T ss_pred EECHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 05888879999-9999999999999999999999999799
No 498
>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=21.96 E-value=57 Score=13.59 Aligned_cols=21 Identities=14% Similarity=0.237 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 997999999872469999998
Q gi|254780424|r 27 GMSQEKLGECLGITFQQVQKY 47 (144)
Q Consensus 27 glTQ~eLA~~lGvs~s~is~~ 47 (144)
..|-.++|+.+|++++++...
T Consensus 22 ~~t~~eia~~~~i~r~~vY~~ 42 (68)
T pfam01978 22 PATADEIAEESGVPRSKVYEV 42 (68)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
T ss_conf 988999999959889899999
No 499
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.90 E-value=57 Score=13.58 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999872469999998
Q gi|254780424|r 31 EKLGECLGITFQQVQKY 47 (144)
Q Consensus 31 ~eLA~~lGvs~s~is~~ 47 (144)
..+|+.+|+|+.++.+|
T Consensus 195 ~~VA~~L~iSr~TVY~Y 211 (220)
T COG2964 195 NIVADRLGISRHTVYRY 211 (220)
T ss_pred HHHHHHHCCCHHHHHHH
T ss_conf 99999968875899999
No 500
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=21.64 E-value=58 Score=13.55 Aligned_cols=30 Identities=17% Similarity=0.264 Sum_probs=0.0
Q ss_pred HHHHHHH--HHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999--98199799999987246999999
Q gi|254780424|r 17 KRIRLRR--MILGMSQEKLGECLGITFQQVQK 46 (144)
Q Consensus 17 ~rIr~~R--~~~glTQ~eLA~~lGvs~s~is~ 46 (144)
+.||.+. -..|.|-..-|+.+|+|++++|+
T Consensus 4 rqL~~F~~~v~~~~s~t~AA~~L~iSQpavS~ 35 (308)
T PRK12683 4 QQLRIIREAVRQNFNLTEVANALYTSQSGVSK 35 (308)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 99999999998689999999997897779999
Done!