Query gi|254780444|ref|YP_003064857.1| bacteriophage repressor protein C1 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 223
No_of_seqs 143 out of 2241
Neff 9.8
Searched_HMMs 39220
Date Sun May 29 16:30:53 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780444.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2932 Predicted transcriptio 100.0 3.8E-28 9.7E-33 202.4 15.1 209 3-223 1-211 (214)
2 PRK00215 LexA repressor; Valid 99.9 3.2E-23 8.2E-28 170.5 18.8 190 3-219 1-198 (204)
3 PRK12423 LexA repressor; Provi 99.9 2.5E-22 6.3E-27 164.7 18.6 187 1-219 1-196 (202)
4 PHA00361 cI Repressor 99.9 1.7E-22 4.4E-27 165.7 13.3 148 60-219 1-158 (165)
5 COG1974 LexA SOS-response tran 99.9 3E-21 7.6E-26 157.7 16.4 185 16-219 7-194 (201)
6 cd06529 S24_LexA-like Peptidas 99.7 1.2E-16 3.1E-21 127.8 10.3 81 138-219 1-81 (81)
7 PRK10276 DNA polymerase V subu 99.7 2.9E-16 7.4E-21 125.4 12.0 123 84-221 9-134 (139)
8 cd06462 Peptidase_S24_S26 The 99.6 1.1E-14 2.8E-19 115.2 8.8 81 138-218 1-84 (84)
9 pfam00717 Peptidase_S24 Peptid 99.5 3.1E-14 7.9E-19 112.3 8.2 67 141-208 1-67 (67)
10 PRK09706 transcriptional repre 99.3 6.5E-12 1.7E-16 97.2 7.2 74 4-82 1-74 (135)
11 PRK09943 DNA-binding transcrip 99.2 5.1E-10 1.3E-14 85.0 12.6 65 8-77 7-71 (185)
12 PHA01976 helix-turn-helix prot 99.2 9.4E-11 2.4E-15 89.7 6.9 64 9-77 3-66 (67)
13 TIGR02754 sod_Ni_protease nick 98.8 1.7E-08 4.3E-13 75.1 6.7 81 140-220 1-90 (90)
14 PRK13890 conjugal transfer pro 98.7 2.5E-08 6.3E-13 74.0 6.1 64 10-78 7-70 (119)
15 TIGR03070 couple_hipB transcri 98.7 4.8E-08 1.2E-12 72.2 6.8 58 7-69 1-58 (58)
16 smart00530 HTH_XRE Helix-turn- 98.6 7.4E-08 1.9E-12 70.9 6.1 56 12-72 1-56 (56)
17 TIGR00498 lexA LexA repressor; 98.6 2.1E-07 5.4E-12 68.0 8.4 207 1-220 1-220 (227)
18 pfam01381 HTH_3 Helix-turn-hel 98.6 6.4E-08 1.6E-12 71.4 5.5 55 13-72 1-55 (55)
19 PRK09726 DNA-binding transcrip 98.5 4.7E-07 1.2E-11 65.8 7.7 65 2-71 6-70 (88)
20 TIGR02227 sigpep_I_bact signal 98.4 1.3E-06 3.3E-11 62.9 7.7 60 138-197 21-101 (203)
21 cd00093 HTH_XRE Helix-turn-hel 98.4 8.5E-07 2.2E-11 64.1 6.3 57 11-72 2-58 (58)
22 cd06530 S26_SPase_I The S26 Ty 98.4 1.2E-06 3.1E-11 63.1 6.3 75 139-218 2-85 (85)
23 COG1476 Predicted transcriptio 98.3 1.3E-06 3.4E-11 62.9 5.9 59 12-75 5-63 (68)
24 PRK08154 anaerobic benzoate ca 98.3 2.1E-06 5.4E-11 61.5 6.9 66 8-78 28-93 (304)
25 COG3620 Predicted transcriptio 98.1 6.1E-06 1.6E-10 58.5 5.6 54 11-69 8-61 (187)
26 pfam07022 Phage_CI_repr Bacter 98.0 1.5E-05 3.8E-10 56.0 6.1 62 12-79 2-64 (65)
27 COG1813 Predicted transcriptio 97.8 8.2E-05 2.1E-09 51.2 7.4 66 7-77 78-143 (165)
28 TIGR02607 antidote_HigA addict 97.6 0.0001 2.6E-09 50.6 5.0 58 14-76 13-70 (81)
29 TIGR02612 mob_myst_A mobile my 97.6 0.00012 3E-09 50.2 4.9 62 13-77 30-91 (150)
30 PRK08359 transcription factor; 97.6 0.00038 9.7E-09 46.9 7.5 61 9-74 84-144 (175)
31 PRK06424 transcription factor; 97.6 0.00035 9E-09 47.1 7.2 59 8-71 84-142 (144)
32 PRK04140 hypothetical protein; 97.6 0.0003 7.7E-09 47.6 6.8 61 10-75 127-187 (319)
33 COG1709 Predicted transcriptio 97.4 0.00019 4.8E-09 48.9 3.9 59 7-70 26-84 (241)
34 COG2944 Predicted transcriptio 97.2 0.00065 1.6E-08 45.4 5.3 37 11-47 47-83 (104)
35 COG3655 Predicted transcriptio 97.2 0.0009 2.3E-08 44.5 6.1 65 10-78 4-68 (73)
36 COG4800 Predicted transcriptio 97.2 0.0013 3.3E-08 43.5 6.7 55 5-65 13-67 (170)
37 TIGR02684 dnstrm_HI1420 probab 97.2 0.00096 2.4E-08 44.3 5.7 55 9-70 35-89 (91)
38 TIGR02228 sigpep_I_arch signal 97.2 0.0016 4E-08 42.9 6.7 75 142-218 42-135 (175)
39 KOG1568 consensus 97.1 0.0046 1.2E-07 39.9 8.7 83 137-219 31-145 (174)
40 COG3093 VapI Plasmid maintenan 97.1 0.0011 2.7E-08 44.0 4.9 63 9-76 10-73 (104)
41 KOG3398 consensus 97.1 0.0016 4.1E-08 42.8 5.8 60 7-71 72-131 (135)
42 COG0681 LepB Signal peptidase 97.0 0.0013 3.2E-08 43.5 4.7 58 138-195 32-93 (166)
43 PRK10861 lsignal peptidase I; 96.9 0.002 5.1E-08 42.2 5.2 57 139-195 84-158 (324)
44 PRK10072 putative transcriptio 96.9 0.0019 4.7E-08 42.4 4.9 35 13-47 38-72 (96)
45 KOG0171 consensus 96.8 0.0024 6E-08 41.8 4.7 55 139-193 35-96 (176)
46 COG1395 Predicted transcriptio 96.7 0.0051 1.3E-07 39.6 5.9 57 10-71 127-183 (313)
47 KOG3342 consensus 96.7 0.0028 7.2E-08 41.3 4.4 81 139-219 50-144 (180)
48 PRK13355 bifunctional HTH-doma 96.6 0.0061 1.6E-07 39.1 6.0 66 8-78 5-75 (518)
49 COG3423 Nlp Predicted transcri 96.1 0.015 3.9E-07 36.5 5.4 54 12-73 12-65 (82)
50 PRK10344 DNA-binding transcrip 96.0 0.016 4.1E-07 36.4 5.4 53 13-73 13-65 (90)
51 COG1396 HipB Predicted transcr 95.7 0.054 1.4E-06 33.0 6.8 61 9-73 2-62 (120)
52 pfam01726 LexA_DNA_bind LexA D 95.6 0.026 6.6E-07 35.1 5.0 41 1-41 1-46 (65)
53 COG1426 Predicted transcriptio 95.6 0.034 8.6E-07 34.3 5.5 74 8-81 3-77 (284)
54 TIGR00270 TIGR00270 conserved 95.5 0.029 7.3E-07 34.8 4.9 62 7-73 82-143 (169)
55 PHA00542 putative Cro-like pro 95.4 0.043 1.1E-06 33.6 5.6 44 13-61 24-67 (82)
56 COG3636 Predicted transcriptio 95.1 0.061 1.5E-06 32.6 5.6 56 9-71 39-94 (100)
57 COG2522 Predicted transcriptio 94.7 0.071 1.8E-06 32.2 5.1 38 7-45 4-46 (119)
58 pfam08667 BetR BetR domain. Th 94.7 0.14 3.6E-06 30.2 6.6 66 8-78 5-74 (146)
59 PRK10856 hypothetical protein; 94.7 0.15 3.8E-06 30.1 6.6 69 9-77 15-84 (332)
60 pfam01527 Transposase_8 Transp 94.6 0.11 2.8E-06 31.0 5.8 46 2-48 5-50 (75)
61 COG5606 Uncharacterized conser 94.5 0.056 1.4E-06 32.9 4.1 64 3-70 23-86 (91)
62 cd00569 HTH_Hin_like Helix-tur 94.3 0.11 2.8E-06 31.0 5.2 38 2-41 4-41 (42)
63 PRK08099 nicotinamide-nucleoti 94.0 0.18 4.6E-06 29.6 5.9 144 11-160 5-159 (411)
64 PRK03975 tfx putative transcri 93.9 0.21 5.3E-06 29.2 6.0 43 1-45 1-43 (139)
65 COG2390 DeoR Transcriptional r 93.6 0.17 4.3E-06 29.8 5.2 72 3-74 8-87 (321)
66 PRK09526 lacI lac repressor; R 93.3 0.12 3.1E-06 30.7 4.1 53 17-71 1-53 (342)
67 COG5499 Predicted transcriptio 93.3 0.21 5.4E-06 29.1 5.2 58 10-73 62-119 (120)
68 PRK13756 tetracycline represso 93.2 0.2 5.1E-06 29.3 5.0 43 1-43 1-46 (205)
69 pfam04218 CENP-B_N CENP-B N-te 93.2 0.22 5.6E-06 29.0 5.2 41 2-44 5-45 (53)
70 PRK02866 cyanate hydratase; Va 93.0 0.66 1.7E-05 25.9 7.4 65 4-73 1-65 (147)
71 PRK10014 DNA-binding transcrip 93.0 0.18 4.6E-06 29.5 4.5 52 18-71 3-54 (342)
72 cd04762 HTH_MerR-trunc Helix-T 92.3 0.18 4.5E-06 29.7 3.7 41 22-62 1-47 (49)
73 pfam05225 HTH_psq helix-turn-h 91.8 0.36 9.1E-06 27.7 4.8 40 5-45 1-40 (45)
74 pfam04814 HNF-1_N Hepatocyte n 91.7 0.41 1.1E-05 27.3 5.0 37 9-45 116-152 (177)
75 PRK09492 treR trehalose repres 91.3 0.37 9.3E-06 27.6 4.4 51 20-72 3-53 (315)
76 PRK10339 DNA-binding transcrip 91.0 0.32 8.1E-06 28.0 3.9 47 23-69 3-49 (327)
77 pfam02001 DUF134 Protein of un 91.0 0.52 1.3E-05 26.6 4.9 42 11-65 43-84 (100)
78 COG2524 Predicted transcriptio 90.6 1.4 3.6E-05 23.8 8.8 41 1-41 1-45 (294)
79 PRK11303 DNA-binding transcrip 90.5 0.69 1.8E-05 25.8 5.2 50 22-73 1-53 (330)
80 PRK09480 slmA nucleoid occlusi 90.5 1.2 3.1E-05 24.2 6.4 37 6-42 12-51 (194)
81 pfam00356 LacI Bacterial regul 90.3 0.6 1.5E-05 26.2 4.8 37 23-64 1-37 (46)
82 PRK03902 manganese transport t 89.8 0.82 2.1E-05 25.3 5.1 42 1-42 1-43 (142)
83 smart00352 POU Found in Pit-Oc 89.7 0.78 2E-05 25.4 4.9 55 9-70 12-72 (75)
84 PRK04217 hypothetical protein; 89.5 0.8 2E-05 25.4 4.9 42 11-65 49-90 (110)
85 PRK10681 DNA-binding transcrip 89.3 0.62 1.6E-05 26.1 4.2 40 1-40 1-40 (252)
86 PRK10668 DNA-binding transcrip 89.3 0.78 2E-05 25.5 4.7 39 5-43 12-53 (216)
87 PRK10401 DNA-binding transcrip 89.2 0.84 2.1E-05 25.2 4.8 48 22-71 2-49 (346)
88 PRK09685 DNA-binding transcrip 89.1 0.68 1.7E-05 25.8 4.3 16 149-164 92-107 (303)
89 PRK11161 fumarate/nitrate redu 88.9 1.9 4.9E-05 22.9 6.8 36 6-41 157-204 (235)
90 PRK10727 DNA-binding transcrip 88.8 0.9 2.3E-05 25.1 4.7 48 23-72 3-50 (342)
91 PRK11050 manganese transport r 88.5 0.87 2.2E-05 25.1 4.5 37 6-42 38-75 (155)
92 COG1609 PurR Transcriptional r 88.4 0.96 2.4E-05 24.9 4.7 47 23-71 2-48 (333)
93 PRK11512 DNA-binding transcrip 88.4 0.8 2.1E-05 25.4 4.2 32 10-41 43-74 (144)
94 smart00354 HTH_LACI helix_turn 88.2 1 2.6E-05 24.7 4.7 48 23-72 2-49 (70)
95 COG4197 Uncharacterized protei 88.2 0.34 8.7E-06 27.8 2.2 49 19-73 11-61 (96)
96 pfam07037 DUF1323 Putative tra 88.1 0.52 1.3E-05 26.6 3.1 25 22-46 1-25 (122)
97 PRK11041 DNA-binding transcrip 88.0 1.1 2.8E-05 24.5 4.7 48 23-72 11-58 (341)
98 PRK03573 transcriptional regul 87.8 0.92 2.3E-05 25.0 4.3 32 10-41 34-66 (144)
99 PRK11179 DNA-binding transcrip 87.8 1 2.6E-05 24.7 4.5 39 2-40 3-42 (153)
100 PRK10703 DNA-binding transcrip 87.8 1.1 2.9E-05 24.4 4.7 48 23-72 3-50 (335)
101 COG1356 tfx Transcriptional re 87.7 0.44 1.1E-05 27.1 2.6 29 17-45 19-47 (143)
102 COG1342 Predicted DNA-binding 87.5 1.2 2.9E-05 24.4 4.6 42 11-65 40-81 (99)
103 TIGR00721 tfx DNA-binding prot 87.2 0.56 1.4E-05 26.4 2.9 40 4-46 7-46 (142)
104 pfam01047 MarR MarR family. Th 87.1 1.1 2.9E-05 24.4 4.4 33 10-42 6-38 (59)
105 smart00347 HTH_MARR helix_turn 86.9 1.3 3.4E-05 24.0 4.6 33 10-42 13-45 (101)
106 TIGR01321 TrpR trp operon repr 86.7 1.1 2.8E-05 24.5 4.2 34 6-40 39-75 (95)
107 PRK09975 DNA-binding transcrip 86.7 1.4 3.5E-05 23.8 4.6 40 4-43 11-53 (213)
108 COG1349 GlpR Transcriptional r 86.6 1.1 2.9E-05 24.4 4.2 38 3-40 1-38 (253)
109 PRK10906 DNA-binding transcrip 86.6 1.1 2.9E-05 24.4 4.2 38 3-40 1-38 (252)
110 PRK11202 DNA-binding transcrip 86.5 0.91 2.3E-05 25.0 3.6 40 4-43 11-54 (203)
111 PRK10219 DNA-binding transcrip 86.3 2.4 6.1E-05 22.3 5.7 42 4-45 1-45 (107)
112 pfam02954 HTH_8 Bacterial regu 86.1 1.9 5E-05 22.9 5.1 30 11-40 8-37 (42)
113 PRK13918 CRP/FNR family transc 85.6 2.9 7.5E-05 21.7 7.0 62 6-67 118-199 (201)
114 PRK10434 srlR DNA-bindng trans 85.6 1.3 3.4E-05 23.9 4.1 38 3-40 1-38 (256)
115 pfam00157 Pou Pou domain - N-t 85.6 1.9 4.9E-05 22.9 4.9 55 10-71 13-73 (75)
116 pfam01325 Fe_dep_repress Iron 85.6 1.6 4E-05 23.5 4.5 38 5-42 3-41 (58)
117 PRK09744 DNA-binding transcrip 85.5 1 2.6E-05 24.7 3.5 29 18-47 8-36 (75)
118 COG4565 CitB Response regulato 85.3 0.84 2.1E-05 25.2 3.0 17 50-66 152-168 (224)
119 cd00092 HTH_CRP helix_turn_hel 85.3 2.4 6.1E-05 22.3 5.3 37 6-42 2-46 (67)
120 pfam02042 RWP-RK RWP-RK domain 85.2 2 5E-05 22.8 4.8 42 13-56 7-48 (52)
121 KOG3802 consensus 85.1 0.96 2.4E-05 24.9 3.2 58 10-74 212-275 (398)
122 cd00090 HTH_ARSR Arsenical Res 84.9 2 5E-05 22.9 4.7 39 2-41 2-40 (78)
123 pfam01710 Transposase_14 Trans 84.9 2.2 5.7E-05 22.5 5.0 34 6-44 8-41 (120)
124 cd01110 HTH_SoxR Helix-Turn-He 84.8 2.3 5.8E-05 22.5 5.0 54 22-75 2-66 (139)
125 PRK10870 transcriptional repre 84.6 1.2 3.1E-05 24.2 3.5 38 4-41 35-91 (176)
126 PRK13509 transcriptional repre 84.4 1.7 4.4E-05 23.2 4.2 39 3-41 1-39 (251)
127 PRK10423 transcriptional repre 84.3 1.9 4.7E-05 23.0 4.3 46 25-72 2-47 (327)
128 PRK00767 transcriptional regul 84.1 2.7 6.8E-05 22.0 5.1 38 6-43 11-51 (197)
129 PRK11753 cAMP-regulatory prote 83.6 3.2 8.2E-05 21.5 5.4 19 22-40 169-187 (211)
130 cd01392 HTH_LacI Helix-turn-he 83.2 1.8 4.5E-05 23.1 3.9 40 25-69 1-43 (52)
131 smart00344 HTH_ASNC helix_turn 83.1 1.7 4.4E-05 23.2 3.8 29 12-40 8-36 (108)
132 COG1522 Lrp Transcriptional re 83.1 2.5 6.3E-05 22.2 4.6 37 4-40 4-41 (154)
133 PRK08558 adenine phosphoribosy 83.0 3.8 9.7E-05 21.0 6.5 43 21-68 23-65 (238)
134 COG1321 TroR Mn-dependent tran 82.9 3 7.7E-05 21.6 5.0 40 3-42 5-45 (154)
135 cd04781 HTH_MerR-like_sg6 Heli 82.7 3.5 9E-05 21.2 5.3 55 22-76 1-66 (120)
136 PRK10046 dpiA two-component re 82.7 1.6 4E-05 23.5 3.4 61 2-66 107-172 (225)
137 PRK11169 leucine-responsive tr 82.6 1.8 4.7E-05 23.0 3.8 30 11-40 18-47 (164)
138 TIGR01950 SoxR redox-sensitive 82.3 0.97 2.5E-05 24.8 2.2 53 21-73 1-64 (142)
139 COG2826 Tra8 Transposase and i 82.1 1.8 4.6E-05 23.1 3.6 41 6-47 7-50 (318)
140 pfam02796 HTH_7 Helix-turn-hel 81.7 2.2 5.6E-05 22.5 3.9 38 3-42 5-42 (45)
141 PRK09775 hypothetical protein; 81.5 2.6 6.6E-05 22.1 4.2 33 11-43 2-34 (443)
142 PHA00675 hypothetical protein 81.4 3.8 9.8E-05 21.0 5.0 36 7-42 25-60 (78)
143 PRK07773 replicative DNA helic 81.1 4.4 0.00011 20.6 10.1 52 7-66 710-761 (868)
144 cd04783 HTH_MerR1 Helix-Turn-H 81.0 4.5 0.00011 20.5 5.3 54 22-75 1-66 (126)
145 PRK10227 DNA-binding transcrip 80.9 3.9 1E-04 20.9 4.9 54 22-75 1-66 (135)
146 pfam01371 Trp_repressor Trp re 80.0 4.2 0.00011 20.7 4.9 39 4-42 27-70 (88)
147 PRK10411 DNA-binding transcrip 79.9 3 7.7E-05 21.6 4.1 37 4-40 1-37 (240)
148 TIGR02293 TIGR02293 conserved 79.9 3.4 8.8E-05 21.3 4.4 59 11-72 26-88 (138)
149 PRK10141 DNA-binding transcrip 79.9 3.4 8.7E-05 21.3 4.4 40 3-42 10-49 (106)
150 PRK11337 DNA-binding transcrip 79.8 2.9 7.4E-05 21.8 4.0 39 6-44 31-70 (293)
151 cd04761 HTH_MerR-SF Helix-Turn 79.5 3 7.7E-05 21.6 4.0 25 22-46 1-25 (49)
152 cd04774 HTH_YfmP Helix-Turn-He 79.3 5.1 0.00013 20.2 5.3 56 22-77 1-68 (96)
153 COG1309 AcrR Transcriptional r 79.2 5 0.00013 20.2 5.0 39 5-43 13-54 (201)
154 PRK11302 DNA-binding transcrip 78.8 3.2 8E-05 21.5 3.9 40 6-45 18-58 (284)
155 TIGR02959 SigZ RNA polymerase 78.4 1.3 3.4E-05 24.0 1.9 30 11-42 107-136 (170)
156 cd04764 HTH_MlrA-like_sg1 Heli 78.3 3.5 9E-05 21.2 4.0 24 22-45 1-24 (67)
157 PRK06759 RNA polymerase factor 78.2 2.4 6.1E-05 22.3 3.1 29 17-45 118-146 (154)
158 PRK13182 racA polar chromosome 77.9 2.2 5.5E-05 22.6 2.8 49 23-71 2-56 (178)
159 TIGR03384 betaine_BetI transcr 77.8 5.6 0.00014 19.9 6.6 40 4-43 8-50 (189)
160 pfam08279 HTH_11 HTH domain. T 77.7 3.6 9.1E-05 21.2 3.9 31 11-41 4-35 (55)
161 COG3888 Predicted transcriptio 77.5 2.5 6.5E-05 22.1 3.1 40 1-41 1-40 (321)
162 pfam06056 Terminase_5 Putative 77.3 4.1 0.0001 20.8 4.1 26 19-44 11-36 (58)
163 COG2963 Transposase and inacti 77.2 5.8 0.00015 19.8 4.9 41 3-44 7-48 (116)
164 pfam02376 CUT CUT domain. The 77.1 5.9 0.00015 19.8 5.0 61 4-67 3-68 (81)
165 PRK09413 insertion sequence 2 77.0 3.8 9.8E-05 21.0 3.9 33 17-49 25-57 (121)
166 pfam01418 HTH_6 Helix-turn-hel 77.0 4 0.0001 20.9 4.0 40 6-45 18-58 (106)
167 smart00418 HTH_ARSR helix_turn 76.5 3.8 9.8E-05 21.0 3.8 28 13-41 3-30 (66)
168 PRK10430 DNA-binding transcrip 76.5 6.1 0.00016 19.7 5.1 16 50-65 156-171 (239)
169 TIGR02702 SufR_cyano iron-sulf 76.4 3.4 8.7E-05 21.3 3.5 36 5-43 2-37 (215)
170 smart00346 HTH_ICLR helix_turn 76.4 5.9 0.00015 19.8 4.7 36 7-42 5-41 (91)
171 pfam09048 Cro Cro. Members of 76.3 4.2 0.00011 20.7 4.0 31 13-45 5-35 (58)
172 cd01111 HTH_MerD Helix-Turn-He 76.3 6.2 0.00016 19.6 5.3 54 22-75 1-66 (107)
173 PRK11557 putative DNA-binding 76.3 4.3 0.00011 20.6 4.0 39 6-44 18-57 (282)
174 COG1414 IclR Transcriptional r 76.3 5.8 0.00015 19.8 4.7 35 8-42 5-40 (246)
175 COG2973 TrpR Trp operon repres 76.2 5.6 0.00014 19.9 4.6 46 6-55 43-91 (103)
176 pfam07471 Phage_Nu1 Phage DNA 76.0 3.3 8.3E-05 21.4 3.3 24 21-44 2-25 (164)
177 COG3415 Transposase and inacti 75.9 6.3 0.00016 19.6 7.5 58 8-65 8-76 (138)
178 cd04773 HTH_TioE_rpt2 Second H 75.6 4.7 0.00012 20.4 4.0 54 22-75 1-66 (108)
179 PRK12523 RNA polymerase sigma 75.2 4 0.0001 20.8 3.6 28 15-42 129-156 (172)
180 COG1737 RpiR Transcriptional r 75.0 4.9 0.00013 20.3 4.0 39 6-44 20-59 (281)
181 PRK10163 DNA-binding transcrip 74.9 6.7 0.00017 19.4 4.8 33 10-42 28-61 (271)
182 TIGR02417 fruct_sucro_rep D-fr 74.9 2.5 6.3E-05 22.2 2.5 51 23-73 1-52 (335)
183 PRK06930 positive control sigm 74.9 6.4 0.00016 19.5 4.6 28 15-42 124-151 (170)
184 PRK09834 DNA-binding transcrip 74.5 6.7 0.00017 19.4 4.6 32 11-42 15-47 (264)
185 pfam00376 MerR MerR family reg 74.3 5.2 0.00013 20.1 4.0 25 23-47 1-25 (38)
186 cd04772 HTH_TioE_rpt1 First He 74.3 4.8 0.00012 20.4 3.8 26 22-47 1-26 (99)
187 PRK11642 exoribonuclease R; Pr 74.1 7 0.00018 19.3 13.0 69 141-211 109-182 (813)
188 pfam00440 TetR_N Bacterial reg 74.0 5.2 0.00013 20.1 4.0 34 10-43 2-38 (47)
189 COG2378 Predicted transcriptio 73.7 6.1 0.00015 19.7 4.2 42 1-42 2-43 (311)
190 pfam09339 HTH_IclR IclR helix- 73.6 7.2 0.00018 19.2 4.9 35 8-42 4-39 (52)
191 cd01104 HTH_MlrA-CarA Helix-Tu 73.4 4.6 0.00012 20.4 3.6 23 22-44 1-23 (68)
192 smart00422 HTH_MERR helix_turn 73.1 4 0.0001 20.9 3.2 24 22-45 1-24 (70)
193 COG2842 Uncharacterized ATPase 73.1 3.3 8.5E-05 21.4 2.8 34 11-44 9-42 (297)
194 pfam04967 HTH_10 HTH DNA bindi 73.0 4.2 0.00011 20.7 3.3 24 20-43 22-45 (53)
195 PRK11886 biotin--protein ligas 73.0 7.5 0.00019 19.1 4.6 38 5-42 2-39 (319)
196 PRK09802 DNA-binding transcrip 72.9 6.1 0.00016 19.7 4.1 36 5-40 15-50 (269)
197 cd04780 HTH_MerR-like_sg5 Heli 72.7 6.3 0.00016 19.6 4.1 55 22-76 1-68 (95)
198 TIGR02944 suf_reg_Xantho FeS a 72.5 1.9 4.9E-05 22.9 1.4 26 17-42 21-46 (130)
199 COG0789 SoxR Predicted transcr 72.5 7.7 0.0002 19.0 5.4 55 22-76 1-67 (124)
200 cd01107 HTH_BmrR Helix-Turn-He 71.6 4.5 0.00011 20.5 3.2 55 22-76 1-68 (108)
201 cd00592 HTH_MerR-like Helix-Tu 71.6 6.6 0.00017 19.4 4.0 56 22-77 1-67 (100)
202 pfam08535 KorB KorB domain. Th 71.0 4.1 0.00011 20.8 2.9 24 19-42 1-24 (93)
203 cd04768 HTH_BmrR-like Helix-Tu 70.6 4.8 0.00012 20.3 3.1 55 22-76 1-67 (96)
204 TIGR03613 RutR pyrimidine util 70.6 8.4 0.00021 18.8 4.9 39 5-43 9-50 (202)
205 cd01105 HTH_GlnR-like Helix-Tu 70.6 8.4 0.00022 18.8 5.2 52 22-73 2-65 (88)
206 cd04763 HTH_MlrA-like Helix-Tu 70.3 5.6 0.00014 19.9 3.4 40 22-61 1-47 (68)
207 pfam01402 RHH_1 Ribbon-helix-h 69.8 6.5 0.00017 19.5 3.7 26 6-31 7-32 (35)
208 COG1438 ArgR Arginine represso 69.6 8.8 0.00023 18.6 4.5 41 3-43 1-47 (150)
209 cd01279 HTH_HspR-like Helix-Tu 69.6 8.9 0.00023 18.6 5.1 50 22-71 2-63 (98)
210 cd01108 HTH_CueR Helix-Turn-He 69.5 5.3 0.00014 20.0 3.2 55 22-76 1-67 (127)
211 cd04787 HTH_HMRTR_unk Helix-Tu 69.2 5.5 0.00014 20.0 3.2 55 22-76 1-67 (133)
212 pfam11268 DUF3071 Protein of u 69.2 9 0.00023 18.6 4.4 35 3-42 55-89 (169)
213 PRK05066 arginine repressor; P 69.1 8.2 0.00021 18.8 4.1 40 4-43 5-51 (156)
214 cd04789 HTH_Cfa Helix-Turn-Hel 69.0 8.1 0.00021 18.9 4.0 55 22-76 2-67 (102)
215 cd04785 HTH_CadR-PbrR-like Hel 68.8 5.6 0.00014 19.9 3.2 55 22-76 1-67 (126)
216 cd04766 HTH_HspR Helix-Turn-He 68.0 8.6 0.00022 18.7 4.0 53 22-74 2-66 (91)
217 PRK07037 extracytoplasmic-func 68.0 9.5 0.00024 18.4 6.7 45 15-68 133-177 (183)
218 cd04770 HTH_HMRTR Helix-Turn-H 67.9 6 0.00015 19.7 3.2 54 22-75 1-66 (123)
219 pfam01022 HTH_5 Bacterial regu 67.5 9.8 0.00025 18.4 4.5 30 13-43 8-37 (47)
220 PRK09508 leuO leucine transcri 67.3 9.9 0.00025 18.3 5.6 31 9-41 26-56 (314)
221 PRK12515 RNA polymerase sigma 67.1 9.9 0.00025 18.3 4.4 47 16-71 142-188 (189)
222 smart00419 HTH_CRP helix_turn_ 66.9 6.3 0.00016 19.6 3.1 22 20-41 7-28 (48)
223 PRK01905 DNA-binding protein F 66.8 8.4 0.00021 18.8 3.7 28 13-40 42-69 (77)
224 TIGR03454 partition_RepB plasm 66.7 8.7 0.00022 18.7 3.8 30 15-44 171-200 (325)
225 PRK13752 putative transcriptio 66.6 7.7 0.0002 19.0 3.5 56 20-75 6-73 (144)
226 pfam09862 DUF2089 Protein of u 66.3 10 0.00026 18.2 5.7 35 4-40 34-68 (113)
227 cd04786 HTH_MerR-like_sg7 Heli 66.0 6.9 0.00018 19.3 3.2 55 22-76 1-67 (131)
228 pfam08822 DUF1804 Protein of u 66.0 10 0.00027 18.2 5.3 39 8-46 6-44 (165)
229 COG1339 Transcriptional regula 65.9 10 0.00027 18.1 4.2 25 20-44 18-42 (214)
230 PRK09392 ftrB transcriptional 65.7 11 0.00027 18.1 5.1 20 22-41 174-193 (236)
231 PRK09393 ftrA transcriptional 65.7 11 0.00027 18.1 5.1 37 7-43 216-254 (320)
232 pfam05269 Phage_CII Bacterioph 65.4 4.1 0.00011 20.8 1.9 38 20-63 22-59 (91)
233 cd04775 HTH_Cfa-like Helix-Tur 65.4 11 0.00027 18.1 4.1 55 22-76 2-67 (102)
234 PRK13832 plasmid partitioning 65.3 11 0.00027 18.1 4.7 39 4-43 102-140 (518)
235 COG3140 Uncharacterized protei 65.1 6.1 0.00016 19.7 2.7 25 1-26 5-32 (60)
236 PRK09651 RNA polymerase sigma 64.1 9.7 0.00025 18.4 3.6 27 15-41 129-155 (172)
237 TIGR02043 ZntR Zn(II)-responsi 63.8 7.6 0.00019 19.1 3.0 53 24-76 4-68 (132)
238 cd01282 HTH_MerR-like_sg3 Heli 63.7 12 0.00029 17.9 4.1 54 22-75 1-65 (112)
239 cd01109 HTH_YyaN Helix-Turn-He 63.5 8.2 0.00021 18.8 3.2 53 22-74 1-65 (113)
240 PRK11569 transcriptional repre 63.2 12 0.0003 17.8 5.0 32 10-41 31-63 (274)
241 PRK12681 cysB transcriptional 63.2 12 0.0003 17.8 5.8 24 18-41 13-36 (324)
242 COG1725 Predicted transcriptio 63.1 12 0.0003 17.8 4.8 35 7-41 14-55 (125)
243 PRK09391 fixK transcriptional 62.7 12 0.00031 17.8 5.4 10 150-159 36-45 (224)
244 TIGR02051 MerR Hg(II)-responsi 62.7 3.3 8.5E-05 21.4 1.0 54 23-76 1-66 (126)
245 pfam10654 DUF2481 Protein of u 62.5 11 0.00029 17.9 3.7 35 9-45 70-104 (126)
246 PRK02277 orotate phosphoribosy 62.4 12 0.00031 17.7 4.0 35 6-41 4-38 (201)
247 pfam04545 Sigma70_r4 Sigma-70, 62.4 9.6 0.00024 18.4 3.3 28 16-43 15-42 (50)
248 cd04782 HTH_BltR Helix-Turn-He 62.4 8.9 0.00023 18.6 3.2 55 22-76 1-67 (97)
249 COG1318 Predicted transcriptio 62.1 11 0.00029 17.9 3.7 30 17-46 57-86 (182)
250 cd04769 HTH_MerR2 Helix-Turn-H 62.1 12 0.00031 17.7 5.2 54 22-75 1-65 (116)
251 PRK00430 fis DNA-binding prote 62.0 12 0.00031 17.8 3.8 28 13-40 63-90 (98)
252 cd06170 LuxR_C_like C-terminal 61.6 9.6 0.00025 18.4 3.2 26 19-44 13-38 (57)
253 pfam09824 ArsR ArsR transcript 61.6 13 0.00032 17.6 4.9 28 13-40 113-140 (160)
254 smart00420 HTH_DEOR helix_turn 61.5 10 0.00026 18.2 3.3 28 13-40 6-33 (53)
255 pfam07750 GcrA GcrA cell cycle 61.4 9.8 0.00025 18.3 3.3 37 11-48 9-47 (162)
256 cd04790 HTH_Cfa-like_unk Helix 61.3 9.4 0.00024 18.5 3.1 57 22-78 2-70 (172)
257 PRK11552 putative DNA-binding 61.1 13 0.00033 17.6 4.7 38 5-42 14-53 (224)
258 PRK09863 putative frv operon r 60.8 13 0.00033 17.6 3.9 33 7-40 4-36 (585)
259 cd01106 HTH_TipAL-Mta Helix-Tu 60.8 9.7 0.00025 18.4 3.1 55 22-76 1-67 (103)
260 PRK13749 transcriptional regul 60.8 13 0.00033 17.5 4.7 55 21-75 3-69 (121)
261 TIGR02812 fadR_gamma fatty aci 60.7 6 0.00015 19.7 2.0 32 151-186 180-211 (275)
262 COG5484 Uncharacterized conser 60.6 8.5 0.00022 18.7 2.8 26 20-45 18-43 (279)
263 PRK09954 hypothetical protein; 60.5 13 0.00033 17.5 5.0 33 6-41 5-37 (362)
264 pfam00196 GerE Bacterial regul 60.0 11 0.00027 18.1 3.2 26 19-44 16-41 (58)
265 cd04776 HTH_GnyR Helix-Turn-He 59.9 10 0.00027 18.2 3.2 54 22-75 1-64 (118)
266 PRK12527 RNA polymerase sigma 59.9 11 0.00029 17.9 3.4 26 16-41 116-141 (159)
267 cd04784 HTH_CadR-PbrR Helix-Tu 59.8 10 0.00027 18.2 3.1 54 22-75 1-66 (127)
268 PRK09514 zntR zinc-responsive 59.4 11 0.00028 18.1 3.2 55 22-76 2-68 (140)
269 smart00421 HTH_LUXR helix_turn 59.3 11 0.00028 18.0 3.2 25 19-43 16-40 (58)
270 pfam08281 Sigma70_r4_2 Sigma-7 59.3 14 0.00035 17.4 4.9 28 15-42 20-47 (54)
271 pfam01978 TrmB Sugar-specific 59.2 14 0.00035 17.4 5.1 37 4-41 6-42 (68)
272 COG1497 Predicted transcriptio 59.0 14 0.00035 17.4 4.8 38 4-43 10-47 (260)
273 PRK09047 RNA polymerase factor 58.9 14 0.00036 17.3 5.1 45 16-69 117-161 (161)
274 TIGR01529 argR_whole arginine 58.8 11 0.00028 18.0 3.1 55 8-73 2-64 (155)
275 LOAD_arc_metj consensus 58.7 14 0.00035 17.4 3.6 26 6-31 9-34 (43)
276 TIGR01884 cas_HTH CRISPR locus 58.6 11 0.00029 17.9 3.2 33 10-42 172-205 (231)
277 PRK13877 conjugal transfer rel 58.5 9.9 0.00025 18.3 2.9 28 10-37 22-49 (114)
278 COG4189 Predicted transcriptio 58.0 14 0.00037 17.2 3.9 30 12-41 28-57 (308)
279 PRK10225 DNA-binding transcrip 57.5 15 0.00038 17.2 3.9 38 4-41 9-53 (257)
280 cd04788 HTH_NolA-AlbR Helix-Tu 56.8 12 0.00032 17.7 3.1 55 22-76 1-67 (96)
281 PRK05114 hypothetical protein; 56.7 13 0.00033 17.6 3.2 26 1-27 5-33 (60)
282 TIGR01764 excise DNA binding d 56.6 15 0.00039 17.1 4.6 24 22-45 2-25 (49)
283 PRK11511 DNA-binding transcrip 56.3 15 0.00039 17.1 4.1 35 9-44 14-48 (127)
284 pfam03701 UPF0181 Uncharacteri 56.1 14 0.00034 17.4 3.2 26 1-27 5-33 (52)
285 PRK08402 replication factor A; 55.8 16 0.0004 17.0 3.6 55 1-70 1-55 (357)
286 PRK11013 DNA-binding transcrip 55.7 16 0.0004 17.0 6.3 38 1-41 1-38 (309)
287 pfam08220 HTH_DeoR DeoR-like h 54.6 16 0.0004 17.0 3.3 28 13-40 6-33 (57)
288 PRK12682 transcriptional regul 54.4 17 0.00042 16.9 4.2 24 18-41 13-36 (309)
289 PRK04424 fatty acid biosynthes 54.2 8.2 0.00021 18.8 1.9 36 5-40 5-40 (185)
290 pfam10000 DUF2241 Uncharacteri 53.7 17 0.00043 16.8 4.5 17 145-161 12-28 (72)
291 cd04765 HTH_MlrA-like_sg2 Heli 53.4 17 0.00044 16.8 5.0 23 22-44 1-23 (99)
292 PRK10840 transcriptional regul 53.0 17 0.00044 16.7 4.4 22 21-42 165-186 (216)
293 KOG0775 consensus 52.8 8.7 0.00022 18.7 1.8 23 24-46 206-228 (304)
294 pfam04552 Sigma54_DBD Sigma-54 52.5 12 0.0003 17.8 2.5 26 20-45 48-73 (160)
295 pfam06892 Phage_CP76 Phage reg 51.7 18 0.00046 16.6 6.5 58 6-68 7-64 (163)
296 COG1513 CynS Cyanate lyase [In 51.4 18 0.00047 16.6 6.9 67 5-76 5-71 (151)
297 PRK12518 RNA polymerase sigma 51.1 19 0.00047 16.5 4.3 23 19-41 134-156 (175)
298 PRK09958 DNA-binding transcrip 51.1 19 0.00047 16.5 6.0 11 9-19 12-22 (204)
299 TIGR01455 glmM phosphoglucosam 51.0 11 0.00028 18.0 2.1 36 6-41 343-380 (450)
300 TIGR02405 trehalos_R_Ecol treh 50.9 9.3 0.00024 18.5 1.7 45 21-67 1-45 (311)
301 COG3602 Uncharacterized protei 50.9 8.1 0.00021 18.9 1.4 34 145-178 12-48 (134)
302 cd06171 Sigma70_r4 Sigma70, re 50.6 19 0.00048 16.5 5.1 27 16-42 21-47 (55)
303 pfam06322 Phage_NinH Phage Nin 50.0 19 0.00049 16.4 3.3 28 15-43 11-38 (64)
304 cd04767 HTH_HspR-like_MBC Heli 49.8 20 0.0005 16.4 5.0 50 23-72 3-63 (120)
305 PRK10572 DNA-binding transcrip 49.6 20 0.0005 16.4 5.3 13 151-163 71-83 (290)
306 COG4109 Predicted transcriptio 49.5 14 0.00035 17.4 2.4 40 3-42 1-40 (432)
307 pfam00392 GntR Bacterial regul 49.2 20 0.00051 16.3 4.5 35 7-41 3-44 (64)
308 pfam11740 KfrA_N Plasmid repli 49.1 20 0.00051 16.3 5.2 37 5-42 2-41 (120)
309 PRK09647 RNA polymerase sigma 48.9 20 0.00051 16.3 5.2 49 16-73 168-216 (222)
310 PRK00513 minC septum formation 48.1 21 0.00053 16.2 3.8 47 141-187 161-208 (214)
311 cd04777 HTH_MerR-like_sg1 Heli 47.9 21 0.00053 16.2 3.1 54 22-75 1-64 (107)
312 PRK12680 transcriptional regul 47.0 22 0.00055 16.1 5.7 30 11-41 7-36 (327)
313 PRK12547 RNA polymerase sigma 47.0 22 0.00055 16.1 4.1 19 20-38 127-145 (164)
314 pfam05579 Peptidase_S32 Equine 46.5 22 0.00056 16.1 5.6 51 133-185 83-135 (426)
315 TIGR02147 Fsuc_second hypothet 46.4 20 0.00052 16.3 2.9 46 20-70 26-73 (281)
316 cd07377 WHTH_GntR Winged helix 46.0 22 0.00057 16.0 4.9 36 6-41 3-45 (66)
317 smart00550 Zalpha Z-DNA-bindin 45.9 22 0.00057 16.0 4.6 38 4-41 2-42 (68)
318 PRK11052 malQ 4-alpha-glucanot 45.8 17 0.00044 16.7 2.4 42 24-71 6-47 (694)
319 COG2521 Predicted archaeal met 45.0 23 0.00059 15.9 6.9 32 181-215 159-190 (287)
320 PRK01381 Trp operon repressor; 44.6 19 0.00048 16.5 2.5 36 4-40 33-74 (99)
321 pfam04182 B-block_TFIIIC B-blo 44.5 18 0.00047 16.6 2.4 32 8-40 6-37 (73)
322 pfam07900 DUF1670 Protein of u 44.2 24 0.00061 15.8 4.7 20 22-41 106-125 (220)
323 PRK09645 RNA polymerase sigma 44.1 24 0.00061 15.8 5.4 44 16-68 127-170 (171)
324 COG3355 Predicted transcriptio 44.1 24 0.00061 15.8 4.4 32 11-42 31-63 (126)
325 TIGR01481 ccpA catabolite cont 44.0 5.1 0.00013 20.2 -0.5 47 22-73 3-52 (332)
326 pfam06163 DUF977 Bacterial pro 43.2 25 0.00063 15.8 4.8 40 3-42 4-47 (127)
327 COG2452 Predicted site-specifi 42.9 25 0.00063 15.7 3.5 26 21-46 1-26 (193)
328 pfam10668 Phage_terminase Phag 42.8 17 0.00042 16.9 2.0 23 21-43 22-44 (60)
329 PRK10360 DNA-binding transcrip 42.7 25 0.00064 15.7 4.3 23 20-42 151-173 (196)
330 PRK13869 plasmid-partitioning 42.7 25 0.00064 15.7 8.3 57 9-66 26-100 (405)
331 PRK12684 transcriptional regul 42.0 26 0.00065 15.6 5.7 24 18-41 13-36 (313)
332 smart00531 TFIIE Transcription 42.0 26 0.00065 15.6 3.7 30 12-41 6-35 (147)
333 PRK11640 putative transcriptio 41.9 26 0.00065 15.6 6.7 54 4-67 1-58 (191)
334 pfam08965 DUF1870 Domain of un 41.9 26 0.00066 15.6 4.7 35 13-47 5-41 (117)
335 PRK04435 hypothetical protein; 41.8 24 0.00062 15.8 2.7 35 9-44 21-56 (146)
336 PRK12516 RNA polymerase sigma 41.5 26 0.00066 15.6 3.1 26 15-40 129-154 (190)
337 COG1595 RpoE DNA-directed RNA 40.8 27 0.00068 15.5 3.7 28 16-43 138-165 (182)
338 COG4977 Transcriptional regula 40.7 27 0.00068 15.5 5.0 40 5-44 218-259 (328)
339 cd04779 HTH_MerR-like_sg4 Heli 40.7 27 0.00068 15.5 4.0 54 23-76 2-66 (134)
340 pfam04539 Sigma70_r3 Sigma-70 40.6 27 0.00069 15.5 5.2 38 6-43 3-42 (78)
341 CHL00180 rbcR LysR transcripti 40.6 27 0.00069 15.5 6.1 36 3-41 4-39 (307)
342 PRK09801 transcriptional activ 40.0 28 0.0007 15.4 4.1 32 7-41 9-40 (310)
343 PRK10086 DNA-binding transcrip 39.5 28 0.00071 15.4 6.3 23 18-41 26-48 (311)
344 KOG0844 consensus 38.5 21 0.00053 16.2 1.9 45 2-46 186-233 (408)
345 PRK05932 RNA polymerase factor 38.0 29 0.00075 15.2 3.0 18 23-40 147-164 (461)
346 PHA01083 hypothetical protein 38.0 30 0.00075 15.2 4.2 56 13-72 5-61 (153)
347 pfam05930 Phage_AlpA Prophage 37.9 30 0.00075 15.2 3.7 24 22-45 4-27 (51)
348 PRK12679 cbl transcriptional r 37.8 30 0.00076 15.2 5.8 24 18-41 13-36 (316)
349 pfam06971 Put_DNA-bind_N Putat 37.1 30 0.00078 15.1 3.1 28 12-40 16-46 (49)
350 PRK12532 RNA polymerase sigma 36.9 31 0.00078 15.1 3.1 18 21-38 152-169 (195)
351 TIGR03453 partition_RepA plasm 36.6 31 0.00079 15.1 6.7 58 8-65 10-84 (387)
352 COG2344 AT-rich DNA-binding pr 36.1 32 0.00081 15.0 2.7 59 13-71 22-85 (211)
353 smart00529 HTH_DTXR Helix-turn 36.0 30 0.00075 15.2 2.4 19 24-42 2-20 (96)
354 TIGR03001 Sig-70_gmx1 RNA poly 35.9 28 0.00071 15.4 2.2 24 20-43 181-204 (249)
355 pfam10078 DUF2316 Uncharacteri 35.6 32 0.00082 15.0 5.4 41 3-43 2-45 (89)
356 PRK04280 arginine repressor; P 35.6 32 0.00082 15.0 4.3 34 10-43 7-46 (149)
357 COG2345 Predicted transcriptio 35.6 32 0.00082 15.0 4.0 31 11-41 14-45 (218)
358 TIGR02431 pcaR_pcaU beta-ketoa 35.4 31 0.00078 15.1 2.4 25 17-41 20-44 (252)
359 COG3598 RepA RecA-family ATPas 35.2 33 0.00083 15.0 3.1 27 4-30 137-163 (402)
360 pfam00126 HTH_1 Bacterial regu 35.1 33 0.00083 14.9 5.6 43 11-71 5-47 (60)
361 PRK10632 putative DNA-binding 35.0 33 0.00084 14.9 5.7 23 18-41 14-36 (309)
362 PRK09639 RNA polymerase sigma 34.8 33 0.00084 14.9 3.5 22 20-41 126-147 (166)
363 COG2197 CitB Response regulato 34.7 33 0.00085 14.9 3.1 25 19-43 161-185 (211)
364 pfam05339 DUF739 Protein of un 34.3 34 0.00086 14.9 4.9 51 17-73 13-63 (69)
365 KOG0400 consensus 34.0 34 0.00087 14.8 3.3 53 3-70 27-83 (151)
366 PRK13866 plasmid partitioning 33.8 34 0.00088 14.8 3.6 30 15-44 173-202 (336)
367 PRK09644 RNA polymerase sigma 33.5 35 0.00088 14.8 3.1 23 18-40 121-143 (165)
368 PRK12469 RNA polymerase factor 33.5 35 0.00089 14.8 2.6 13 195-207 286-299 (475)
369 pfam02787 CPSase_L_D3 Carbamoy 32.8 36 0.00091 14.7 4.9 37 5-43 9-45 (122)
370 smart00342 HTH_ARAC helix_turn 32.6 36 0.00091 14.7 3.0 22 22-43 2-23 (84)
371 PRK09637 RNA polymerase sigma 32.6 36 0.00092 14.7 3.3 26 16-41 117-142 (181)
372 TIGR02047 CadR-PbrR Cd(II)/Pb( 32.5 31 0.00079 15.1 2.0 56 23-78 2-69 (127)
373 TIGR02177 PorB_KorB 2-oxoacid: 32.3 9.4 0.00024 18.4 -0.7 53 9-63 12-69 (302)
374 TIGR02305 HpaG-N-term 4-hydrox 32.2 36 0.00093 14.6 3.0 28 150-177 168-198 (206)
375 PRK10837 putative DNA-binding 31.9 37 0.00094 14.6 6.3 35 4-41 3-37 (291)
376 PHA01748 hypothetical protein 31.8 37 0.00094 14.6 3.2 26 6-31 10-35 (60)
377 PRK12520 RNA polymerase sigma 31.4 38 0.00096 14.6 5.1 21 20-40 146-166 (191)
378 cd05726 Ig4_Robo Fhird immunog 31.2 34 0.00086 14.9 2.0 26 175-200 44-69 (90)
379 PRK12511 RNA polymerase sigma 31.0 38 0.00097 14.5 2.5 19 20-38 126-144 (182)
380 TIGR02983 SigE-fam_strep RNA p 30.9 38 0.00097 14.5 3.2 35 6-40 104-148 (165)
381 KOG1575 consensus 30.9 38 0.00098 14.5 3.3 21 21-41 57-79 (336)
382 cd04778 HTH_MerR-like_sg2 Heli 30.8 38 0.00098 14.5 3.5 25 22-46 2-26 (219)
383 PRK11922 RNA polymerase sigma 30.8 38 0.00098 14.5 3.3 27 15-41 159-185 (231)
384 PRK09791 putative DNA-binding 30.7 39 0.00098 14.5 6.2 32 9-42 9-40 (302)
385 PRK12517 RNA polymerase sigma 30.6 39 0.00099 14.5 3.1 19 20-38 143-161 (188)
386 pfam05043 Mga Mga helix-turn-h 30.6 39 0.00099 14.5 5.0 46 11-69 20-65 (87)
387 PRK11924 RNA polymerase sigma 30.6 39 0.00099 14.5 3.9 22 20-41 140-161 (180)
388 PRK09483 response regulator; P 30.4 39 0.001 14.4 6.0 17 22-38 164-180 (216)
389 pfam06242 DUF1013 Protein of u 30.4 39 0.001 14.4 4.7 45 11-55 72-121 (141)
390 TIGR01369 CPSaseII_lrg carbamo 29.9 40 0.001 14.4 3.8 60 16-79 497-562 (1089)
391 PRK10094 DNA-binding transcrip 29.7 40 0.001 14.4 6.1 36 3-41 1-36 (308)
392 PRK11235 bifunctional antitoxi 29.7 40 0.001 14.4 3.7 26 6-31 9-34 (80)
393 KOG1168 consensus 29.4 15 0.00038 17.1 -0.0 34 10-43 223-265 (385)
394 PRK12538 RNA polymerase sigma 29.4 41 0.001 14.3 3.6 25 17-41 183-207 (233)
395 KOG4120 consensus 29.0 39 0.001 14.4 2.0 20 139-158 382-401 (426)
396 PRK12546 RNA polymerase sigma 28.9 41 0.0011 14.3 3.1 25 16-40 124-148 (188)
397 PRK09258 3-oxoacyl-(acyl carri 28.7 31 0.00078 15.1 1.4 64 3-72 14-78 (339)
398 TIGR03339 phn_lysR aminoethylp 28.4 42 0.0011 14.2 5.3 27 13-41 5-31 (279)
399 pfam07453 NUMOD1 NUMOD1 domain 28.3 34 0.00086 14.9 1.6 19 23-41 18-36 (37)
400 TIGR02980 SigBFG RNA polymeras 28.1 43 0.0011 14.2 3.5 32 7-38 91-124 (229)
401 PRK11139 DNA-binding transcrip 28.1 43 0.0011 14.2 5.7 22 19-41 19-40 (295)
402 TIGR01032 rplT_bact ribosomal 27.5 44 0.0011 14.1 2.7 31 9-39 60-91 (114)
403 PRK13702 replication protein; 27.4 44 0.0011 14.1 3.3 21 10-30 53-73 (82)
404 pfam10502 Peptidase_S26 Peptid 27.3 44 0.0011 14.1 5.6 30 188-219 100-134 (138)
405 TIGR02044 CueR Cu(I)-responsiv 27.1 44 0.0011 14.1 2.6 52 22-73 1-64 (127)
406 TIGR00673 cynS cyanate hydrata 26.9 45 0.0011 14.1 7.0 64 9-77 14-77 (156)
407 TIGR01203 HGPRTase hypoxanthin 26.9 45 0.0011 14.1 2.5 19 3-21 2-20 (183)
408 COG4860 Uncharacterized protei 26.8 45 0.0011 14.1 3.4 10 23-32 39-48 (170)
409 PRK11414 putative DNA-binding 26.5 46 0.0012 14.0 4.2 36 6-41 13-54 (221)
410 PRK10082 putative DNA-binding 26.4 46 0.0012 14.0 6.1 36 3-41 10-45 (303)
411 PRK13348 chromosome replicatio 26.3 46 0.0012 14.0 6.2 36 3-41 1-36 (294)
412 pfam09312 SurA_N SurA N-termin 25.8 47 0.0012 13.9 5.7 18 54-71 86-103 (118)
413 TIGR02224 recomb_XerC tyrosine 25.7 47 0.0012 13.9 3.6 66 3-68 49-130 (313)
414 PRK12543 RNA polymerase sigma 25.4 48 0.0012 13.9 4.9 25 16-40 140-164 (190)
415 TIGR02764 spore_ybaN_pdaB poly 25.0 49 0.0012 13.8 1.9 31 1-38 75-105 (198)
416 PRK12542 RNA polymerase sigma 24.9 49 0.0012 13.8 3.4 24 17-40 134-157 (185)
417 PRK08311 putative RNA polymera 24.9 49 0.0012 13.8 4.3 13 61-73 140-152 (237)
418 COG0376 KatG Catalase (peroxid 24.8 49 0.0012 13.8 2.0 73 4-77 446-537 (730)
419 PRK13502 transcriptional activ 24.7 49 0.0013 13.8 4.3 27 137-165 48-74 (282)
420 PRK10421 DNA-binding transcrip 24.6 49 0.0013 13.8 4.5 36 6-41 4-46 (253)
421 PRK12524 RNA polymerase sigma 24.4 50 0.0013 13.8 3.7 12 1-12 8-19 (196)
422 PRK05602 RNA polymerase sigma 24.4 50 0.0013 13.8 3.7 12 1-12 2-13 (186)
423 COG1846 MarR Transcriptional r 24.3 50 0.0013 13.8 4.7 31 11-41 26-56 (126)
424 PRK12544 RNA polymerase sigma 24.2 50 0.0013 13.7 3.2 19 20-38 164-182 (207)
425 TIGR02225 recomb_XerD tyrosine 24.2 50 0.0013 13.7 2.8 26 5-31 44-69 (305)
426 pfam06323 Phage_antiter_Q Phag 24.0 51 0.0013 13.7 4.2 20 21-40 167-186 (230)
427 COG2186 FadR Transcriptional r 23.8 51 0.0013 13.7 4.3 36 5-40 11-53 (241)
428 pfam07506 RepB RepB plasmid pa 23.6 52 0.0013 13.7 5.2 29 13-42 14-42 (185)
429 PRK12702 mannosyl-3-phosphogly 23.6 52 0.0013 13.7 5.6 41 5-45 99-147 (302)
430 pfam08784 RPA_C Replication pr 23.5 52 0.0013 13.7 3.2 35 6-40 49-85 (103)
431 pfam02002 TFIIE_alpha TFIIE al 23.0 53 0.0013 13.6 3.2 35 7-41 13-47 (105)
432 PRK05294 carB carbamoyl phosph 22.9 53 0.0014 13.6 4.5 34 7-42 429-462 (1063)
433 smart00345 HTH_GNTR helix_turn 22.9 53 0.0014 13.6 3.8 19 23-41 22-40 (60)
434 PRK12683 transcriptional regul 22.8 53 0.0014 13.6 5.6 23 19-41 14-36 (308)
435 smart00526 H15 Domain in histo 22.8 48 0.0012 13.9 1.5 25 7-31 9-33 (66)
436 pfam01316 Arg_repressor Argini 22.7 54 0.0014 13.6 4.4 36 8-43 5-46 (70)
437 PRK04158 transcriptional repre 22.7 54 0.0014 13.6 3.1 10 151-160 136-145 (256)
438 COG0361 InfA Translation initi 22.6 54 0.0014 13.5 3.3 26 150-175 46-72 (75)
439 PRK13501 transcriptional activ 22.6 54 0.0014 13.5 4.6 25 139-165 50-74 (290)
440 TIGR03418 chol_sulf_TF putativ 22.6 54 0.0014 13.5 4.1 22 19-41 14-35 (291)
441 smart00497 IENR1 Intron encode 22.6 52 0.0013 13.6 1.7 22 23-44 19-40 (53)
442 PRK12522 RNA polymerase sigma 22.5 54 0.0014 13.5 3.1 19 20-38 134-152 (173)
443 pfam10723 RepB-RCR_reg Replica 22.3 55 0.0014 13.5 3.3 23 9-31 52-74 (85)
444 pfam09012 FeoC FeoC like trans 22.2 55 0.0014 13.5 4.0 31 11-41 3-34 (68)
445 TIGR00589 ogt methylated-DNA-[ 21.8 56 0.0014 13.4 2.1 26 5-32 3-30 (80)
446 pfam10771 DUF2582 Protein of u 21.8 56 0.0014 13.4 4.2 28 13-40 13-41 (65)
447 COG3905 Predicted transcriptio 21.7 56 0.0014 13.4 3.1 31 1-31 2-35 (83)
448 pfam00325 Crp Bacterial regula 21.5 57 0.0014 13.4 2.3 22 21-42 2-23 (32)
449 TIGR01149 mtrG tetrahydrometha 21.5 57 0.0014 13.4 1.9 26 7-32 17-42 (72)
450 pfam00816 Histone_HNS H-NS his 21.4 57 0.0014 13.4 3.3 18 10-27 26-43 (91)
451 PRK09390 fixJ response regulat 21.3 57 0.0015 13.4 3.9 17 6-22 12-28 (202)
452 PRK04841 transcriptional regul 21.3 57 0.0015 13.4 4.3 12 31-42 41-53 (903)
453 cd05793 S1_IF1A S1_IF1A: Trans 21.2 53 0.0014 13.6 1.5 26 151-176 39-65 (77)
454 smart00657 RPOL4c DNA-directed 21.1 58 0.0015 13.3 5.2 59 4-63 51-109 (118)
455 TIGR00004 TIGR00004 endoribonu 21.0 58 0.0015 13.3 2.4 17 55-71 55-71 (129)
456 PRK03635 chromosome replicatio 21.0 58 0.0015 13.3 6.2 22 19-41 15-36 (295)
457 PRK08931 5'-methylthioadenosin 20.9 47 0.0012 13.9 1.2 49 136-185 82-137 (289)
458 KOG2251 consensus 20.7 59 0.0015 13.3 3.9 44 2-46 42-89 (228)
459 pfam04760 IF2_N Translation in 20.6 59 0.0015 13.3 4.8 47 21-67 3-51 (52)
460 pfam02196 RBD Raf-like Ras-bin 20.6 59 0.0015 13.3 2.7 22 7-28 21-42 (71)
461 PRK13503 transcriptional activ 20.2 60 0.0015 13.2 5.3 26 138-165 46-71 (278)
462 cd04456 S1_IF1A_like S1_IF1A_l 20.2 36 0.00093 14.6 0.5 28 151-178 39-68 (78)
463 PRK00082 hrcA heat-inducible t 20.2 60 0.0015 13.2 4.9 41 1-41 1-47 (339)
464 pfam04936 DUF658 Protein of un 20.1 61 0.0015 13.2 2.9 28 23-50 16-43 (134)
No 1
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=99.96 E-value=3.8e-28 Score=202.35 Aligned_cols=209 Identities=34% Similarity=0.510 Sum_probs=162.4
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 75589999999999996499988999982899879889975157887557798999998732187521000011112444
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRT 82 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~~~~~ 82 (223)
++.|..++..++.+..+...+.+.++++.|..+++.+..++.......+|+.+............+.+....... .
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~ 76 (214)
T COG2932 1 MLSHDSGGRAIDALAERGKASSSGLARKEGLDPTSFNLSKRASADVSARWLSTGSGEKVLEAAGAPTDLTAGDAS----E 76 (214)
T ss_pred CCCHHHCCCHHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCC----C
T ss_conf 940230443567777540332234667635687851044430044401022341132355222453221344344----6
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCEEEEECC
Q ss_conf 54422122024310113452221112544464035643721135454200368559999628332421487868999368
Q gi|254780444|r 83 TEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSA 162 (223)
Q Consensus 83 ~~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~l~V~GDSM~P~i~~Gd~vlVd~~ 162 (223)
.+ .....+......++..+.+...+.+.+.+..+++.|...... .+. |+++|.||||+|+|++||+++||++
T Consensus 77 ~~-~~~~~~~~~~a~~G~~~~~~~~~~~~~~~~~~~~~p~~~~~~------~~~-~~i~V~GDSMeP~~~~Gd~ilVd~~ 148 (214)
T COG2932 77 NP-VVPLIPVSGAAGAGADGFFDENGFPVGFGWDEIERPPGIDPD------SGV-FALRVTGDSMEPTYEDGDTLLVDPG 148 (214)
T ss_pred CC-CCCCEEEEEECCCCCCCCCCCCCCEECCCCCCCCCCCCCCCC------CCE-EEEEEECCCCCCCCCCCCEEEEECC
T ss_conf 75-545345331035677753267761421144410056555776------663-8999967766630159999999789
Q ss_pred CCCCCCCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCC-CCEEECHHH-EEEEEEEEEEEC
Q ss_conf 9740588899997179689999999779879999685898-875854786-599977998529
Q gi|254780444|r 163 IQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCY-PVDTVEMSD-IEWIARILWASQ 223 (223)
Q Consensus 163 ~~~~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y-~~~~i~~~~-i~iigrVvw~~~ 223 (223)
.+...||++|++..+++++||+|++++++.+.|.|+||+| |++.+..++ |+|||||||+++
T Consensus 149 ~~~~~gd~v~v~~~g~~~~VK~l~~~~~~~~~l~S~N~~~~~~~~~~~~~~v~iIgrVv~~~~ 211 (214)
T COG2932 149 VNTRRGDRVYVETDGGELYVKKLQREPGGLLRLVSLNPDYYPDEIFSEDDDVEIIGRVVWVSR 211 (214)
T ss_pred CCEEECCEEEEEEECCEEEEEEEEEECCCEEEEEECCCCCCCCCCCCCCCEEEEEEEEEEEEE
T ss_conf 842519999999959948899999957987999968988887333574240799999988667
No 2
>PRK00215 LexA repressor; Validated
Probab=99.92 E-value=3.2e-23 Score=170.46 Aligned_cols=190 Identities=16% Similarity=0.207 Sum_probs=132.2
Q ss_pred CCC--HHHHHHHHHHHHHHCCCCH--HHHHHHHCCC-HHHHHHHHHC-CCCCCC-CCCCHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 755--8999999999999649998--8999982899-8798899751-578875-5779899999873218752100001
Q gi|254780444|r 3 SFS--HKKIWEAIDRMAERHNLTP--SGLARKAGLD-PTSFNKSKRF-GIEGRN-RWPSTESIFKILAATNETICQLLDL 75 (223)
Q Consensus 3 ~~~--~~~i~~~i~~l~~~~gls~--~~lA~~~Gv~-~~ti~~~~~~-~~~g~~-r~p~~~~l~kia~~~~v~~~~l~~~ 75 (223)
||| +.+|+++|.+-.++.|.+| .++|+.+|++ ++|+.++-+. ...|.. |.|+...-.++. ..
T Consensus 1 mLT~kQ~~il~fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~~Le~kG~i~r~~~~~R~i~i~-----------~~ 69 (204)
T PRK00215 1 MLTARQQEILDFIKDRIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGRSRAIEVL-----------PA 69 (204)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCEECCCCCCCEEEEE-----------CC
T ss_conf 9898999999999999997488998999999809998189999999998797887069997338971-----------57
Q ss_pred CCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCCCC-CCCCCCC
Q ss_conf 111244454422122024310113452221112544464035643721135454200368559999628332-4214878
Q gi|254780444|r 76 PFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSM-LPLYRKG 154 (223)
Q Consensus 76 ~~~~~~~~~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~l~V~GDSM-~P~i~~G 154 (223)
... ..........+|+++...||...... ....+.+.+|.... ..++.|+++|+|||| ++.|.+|
T Consensus 70 ~~~-~~~~~~~~~~iPi~G~IaAG~pi~a~------e~~~~~i~vp~~~~-------~~~~~F~LrV~GdSMi~~~I~dG 135 (204)
T PRK00215 70 EAA-DEDAAEEALGLPLVGRVAAGEPILAE------EHIEDHFPLPPSLF-------GPGEDFLLRVRGDSMIDAGILDG 135 (204)
T ss_pred CCC-CCCCCCCCCCCCEEEEECCCCCCCCC------CCCCCCEECCHHHC-------CCCCEEEEEECCCCCCCCCCCCC
T ss_conf 665-44456665226546676589976131------03034371687677-------87676999963787665798999
Q ss_pred CEEEEECCCCCCCCCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCEEECHHHEEEEEEEE
Q ss_conf 68999368974058889999717968999999977987999968589887585478659997799
Q gi|254780444|r 155 DILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARIL 219 (223)
Q Consensus 155 d~vlVd~~~~~~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~~~~i~iigrVv 219 (223)
|+|+|+++..+.+|++|++.. ++++++||+.+. ++.+.|.|.||+|+|+.++.++++|+|+||
T Consensus 136 D~viV~~~~~~~~G~Ivva~i-~~e~tlKr~~~~-~~~i~L~p~N~~y~pi~~~~~~~~I~G~vv 198 (204)
T PRK00215 136 DLVIVRKQQTARNGQIVVALI-DDEATVKRFRRE-GGHIRLLPENPAYEPIIVDPDDVTIEGKVV 198 (204)
T ss_pred CEEEEECCCCCCCCCEEEEEE-CCCCEEEEEEEE-CCEEEEECCCCCCCCEEECCCCEEEEEEEE
T ss_conf 999995789688996999997-377589999997-999999848999998772778379999999
No 3
>PRK12423 LexA repressor; Provisional
Probab=99.91 E-value=2.5e-22 Score=164.71 Aligned_cols=187 Identities=18% Similarity=0.163 Sum_probs=129.2
Q ss_pred CCCCC--HHHHHHHHHHHHHHCCCCHH--HHHHHHCCC-HHHHHHHHH-CCCCCCC-CCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 97755--89999999999996499988--999982899-879889975-1578875-57798999998732187521000
Q gi|254780444|r 1 MTSFS--HKKIWEAIDRMAERHNLTPS--GLARKAGLD-PTSFNKSKR-FGIEGRN-RWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 1 ~~~~~--~~~i~~~i~~l~~~~gls~~--~lA~~~Gv~-~~ti~~~~~-~~~~g~~-r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
|+.|| +++|+++|..-.+++|.+|+ ++|+.+|++ ++++..+-+ -...|.. |.++...-.++ .
T Consensus 1 M~~LT~kQ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~~L~~kG~i~r~~~~~R~i~l-----------~ 69 (202)
T PRK12423 1 MDTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPNQARGIRL-----------P 69 (202)
T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCEECCCCCCEEEEE-----------C
T ss_conf 95208999999999999999629898899999982999867899999999988799706999537993-----------6
Q ss_pred CCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCCCCC-CCCC
Q ss_conf 011112444544221220243101134522211125444640356437211354542003685599996283324-2148
Q gi|254780444|r 74 DLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSML-PLYR 152 (223)
Q Consensus 74 ~~~~~~~~~~~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~l~V~GDSM~-P~i~ 152 (223)
..........+|+++...||...... ....+.+..+.... .....|+++|+||||. ..|.
T Consensus 70 ------~~~~~~~~~~iPv~G~IaAG~Pi~a~------~~~~~~~~~~~~~~-------~~~~~f~LrV~GdSMi~~gI~ 130 (202)
T PRK12423 70 ------GGAGRPELLELPVLGRVAAGAPIGAD------LGIHRQLWLDRSLF-------SRTPDYLLQVQGDSMIDDGIL 130 (202)
T ss_pred ------CCCCCCCCCCCCEEEEECCCCCCCHH------HCCCCEEECCHHHC-------CCCCCEEEEECCCCCCCCCCC
T ss_conf ------87787654105568887379970321------15565072798991-------889868999888865448968
Q ss_pred CCCEEEEECCCCCCCCCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCEEECHH-HEEEEEEEE
Q ss_conf 7868999368974058889999717968999999977987999968589887585478-659997799
Q gi|254780444|r 153 KGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMS-DIEWIARIL 219 (223)
Q Consensus 153 ~Gd~vlVd~~~~~~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~~~-~i~iigrVv 219 (223)
+||+|+|+++..+.+||+|+|.. +|++++||+.+. ++.++|.+.||+|+|+.+.++ +++|+|+||
T Consensus 131 dGD~viV~~~~~~~~GdIVvA~i-dgE~TlKr~~~~-~~~i~L~p~N~~~~pI~~~~~~~~~I~G~vv 196 (202)
T PRK12423 131 DGDLVGVHRSPEARDGQIVVARL-DGEVTIKRLERG-ADRIRLLPRNPAYAPIVVAADQDFAIEGVFC 196 (202)
T ss_pred CCCEEEEECCCCCCCCCEEEEEE-CCEEEEEEEEEE-CCEEEEECCCCCCCCEEECCCCCEEEEEEEE
T ss_conf 99999996368789996999998-992899999998-9999998789999987827999089999999
No 4
>PHA00361 cI Repressor
Probab=99.89 E-value=1.7e-22 Score=165.69 Aligned_cols=148 Identities=21% Similarity=0.260 Sum_probs=118.0
Q ss_pred HHHHHCCCCCCCCCCCCCCCC-----CCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCC
Q ss_conf 987321875210000111124-----445442212202431011345222111254446403564372113545420036
Q gi|254780444|r 60 KILAATNETICQLLDLPFSDG-----RTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQ 134 (223)
Q Consensus 60 kia~~~~v~~~~l~~~~~~~~-----~~~~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~ 134 (223)
|+|++|+++++||+.+..... .......+.+|++++.+||.+....+ .+..+...++++.+.. .+
T Consensus 1 ~lA~~Lg~s~~~Ll~g~~~~~~~~~~~~~~~~~~~vPvis~VqAG~w~e~~~-~~~~~~~~~~~~~~~~---------~~ 70 (165)
T PHA00361 1 KLAKALGTSVDDLLQEDLSIIANVKVSITPKPVGLVPVLSWVQAGMWSEIVE-TFQDGDAEEWVPCPVK---------AG 70 (165)
T ss_pred CHHHHHCCCHHHHHCCCCCCCCCCCEEECCCCCCEECEECHHHCCCCHHHCC-CCCCCCCCEEEECCCC---------CC
T ss_conf 9568669899998557556787751033266365766648714599722044-4686776368835666---------68
Q ss_pred CCEEEEEECCCCCCC----CCCCCCEEEEECCCCCCCCCEEEEEEEC-CCEEEEEEEEECCCEEEEEECCCCCCCEEECH
Q ss_conf 855999962833242----1487868999368974058889999717-96899999997798799996858988758547
Q gi|254780444|r 135 TQDTRHKTQDTSMLP----LYRKGDILILNSAIQVNCGDRLLIKPRT-GDIVAKVLISRRGRSIDLMSLNCCYPVDTVEM 209 (223)
Q Consensus 135 ~~~~~l~V~GDSM~P----~i~~Gd~vlVd~~~~~~~g~~v~~~~~~-~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~~ 209 (223)
+++|+|+|+||||.| .|++||+|+||++.++.+|++|+|...+ +++++|||.+. ++...|.++||+||++.++
T Consensus 71 ~~~F~L~V~GdSM~~p~g~~~~~Gd~iiVdp~~~~~~G~~VvA~~~~~~eaT~K~l~~d-~~~~~L~plNp~yp~I~~~- 148 (165)
T PHA00361 71 ERTFWLEVEGDSMTAPTGLSFPEGDSILVDPEVEAEPGDLVIARLEGASEATFKKLIID-GGAKYLKPLNPQYPYIPIN- 148 (165)
T ss_pred CCEEEEEEECCCCCCCCCCCCCCCCEEEECCCCCCCCCCEEEEEECCCCCEEEEEEEEE-CCEEEEEECCCCCCCCCCC-
T ss_conf 98899999667678875687389999998278757889999999689983489999995-9909998589998958069-
Q ss_pred HHEEEEEEEE
Q ss_conf 8659997799
Q gi|254780444|r 210 SDIEWIARIL 219 (223)
Q Consensus 210 ~~i~iigrVv 219 (223)
++++|||.||
T Consensus 149 ~~~~IiGvVV 158 (165)
T PHA00361 149 GDCSIIGVVI 158 (165)
T ss_pred CCCEEEEEEE
T ss_conf 9839999999
No 5
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=99.88 E-value=3e-21 Score=157.71 Aligned_cols=185 Identities=15% Similarity=0.105 Sum_probs=135.4
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCC--CCCCCCCCCCEE
Q ss_conf 999649998899998289987988997515788755779899999873218752100001111244--454422122024
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGR--TTEKKEKEIPLL 93 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~~~~--~~~~~~~~ip~~ 93 (223)
+.++.++++.++++..|.+| |+..|.++.+. ++...+.+.++++...-............ ........+|++
T Consensus 7 rq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~-----~s~~~~~~~l~~L~~~g~i~~~~~~~r~i~~~~~~~~~~vPv~ 80 (201)
T COG1974 7 RQKELLDFIRSLIKETGYPP-SIREIGDALGL-----ASPSAIHSHLKALERKGYIRRDPTKARAIRILQLTEITGVPVL 80 (201)
T ss_pred HHHHHHHHHHHHHHHHCCCC-HHHHHHHHHCC-----CCHHHHHHHHHHHHCCCCEEECCCCCCCEECCCCCCCCCCCEE
T ss_conf 89998999999999728993-08999875178-----9848999999997308858745898743011244642047546
Q ss_pred EECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCCCCC-CCCCCCCEEEEECCCCCCCCCEEE
Q ss_conf 3101134522211125444640356437211354542003685599996283324-214878689993689740588899
Q gi|254780444|r 94 YFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSML-PLYRKGDILILNSAIQVNCGDRLL 172 (223)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~l~V~GDSM~-P~i~~Gd~vlVd~~~~~~~g~~v~ 172 (223)
+..+++.+... . ....+.++++..... .+..+|+++|.||||. +.|.+||+|+||++..+.+||+|+
T Consensus 81 g~v~Ag~~~~a--~----~~~e~~~~l~~~~~~------~~~~~f~L~V~GdSM~~~gi~dGDlvvV~~~~~a~~GdiVv 148 (201)
T COG1974 81 GRVAAGGPISA--I----EDIEEKIDLPPYLVK------PPSATFFLRVSGDSMIDAGILDGDLVVVDPTEDAENGDIVV 148 (201)
T ss_pred EEECCCCCCCC--H----HHHHCCCCCCHHHHC------CCCCEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCCEEE
T ss_conf 76507897451--1----211023027878818------88770899945885002778889899983888777997899
Q ss_pred EEEECCCEEEEEEEEECCCEEEEEECCCCCCCEEECHHHEEEEEEEE
Q ss_conf 99717968999999977987999968589887585478659997799
Q gi|254780444|r 173 IKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARIL 219 (223)
Q Consensus 173 ~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~~~~i~iigrVv 219 (223)
|...|++.++|||++. ++.+.|.+.||.|+++.++.+.++|+|.||
T Consensus 149 A~i~g~e~TvKrl~~~-g~~i~L~p~Np~~~~i~~~~~~~~I~G~vv 194 (201)
T COG1974 149 ALIDGEEATVKRLYRD-GNQILLKPENPAYPPIPVDADSVTILGKVV 194 (201)
T ss_pred EECCCCCEEEEEEEEE-CCEEEEEECCCCCCCCCCCCCCEEEEEEEE
T ss_conf 9838981789999981-987999817988898025865358999999
No 6
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=99.70 E-value=1.2e-16 Score=127.80 Aligned_cols=81 Identities=22% Similarity=0.372 Sum_probs=74.0
Q ss_pred EEEEECCCCCCCCCCCCCEEEEECCCCCCCCCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCEEECHHHEEEEEE
Q ss_conf 99996283324214878689993689740588899997179689999999779879999685898875854786599977
Q gi|254780444|r 138 TRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIAR 217 (223)
Q Consensus 138 ~~l~V~GDSM~P~i~~Gd~vlVd~~~~~~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~~~~i~iigr 217 (223)
|+++|.||||+|+|++||+|+||++.+..+|+++++... ++.+|||+.+..++.+.|.|+||.|+++.++.++++++|+
T Consensus 1 ~~l~v~GdSM~P~i~~Gd~vivd~~~~~~~g~i~vv~~~-~~~~iKrl~~~~~~~~~L~s~N~~y~~~~~~~~~~~~~~i 79 (81)
T cd06529 1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGDIVVARLD-GELTVKRLQRRGGGRLRLISDNPAYPPIEIDEEELEIVGV 79 (81)
T ss_pred CEEEEECCCCCCCCCCCCEEEEECCCCCCCCCEEEEEEC-CCCEEEEEEECCCCEEEEEECCCCCCCEECCCCCEEEEEE
T ss_conf 989996774771406999999937750479989999975-9806999999189639999799998988308021899999
Q ss_pred EE
Q ss_conf 99
Q gi|254780444|r 218 IL 219 (223)
Q Consensus 218 Vv 219 (223)
|.
T Consensus 80 vg 81 (81)
T cd06529 80 VG 81 (81)
T ss_pred EC
T ss_conf 89
No 7
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=99.70 E-value=2.9e-16 Score=125.39 Aligned_cols=123 Identities=19% Similarity=0.233 Sum_probs=90.1
Q ss_pred CCCCCCCCEEEE-CCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCCCC-CCCCCCCCEEEEEC
Q ss_conf 442212202431-0113452221112544464035643721135454200368559999628332-42148786899936
Q gi|254780444|r 84 EKKEKEIPLLYF-PPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSM-LPLYRKGDILILNS 161 (223)
Q Consensus 84 ~~~~~~ip~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~l~V~GDSM-~P~i~~Gd~vlVd~ 161 (223)
......+|++.. .+||.... +. ....+.+.++.... ..+...|+++|+|||| +..|.+||+++||+
T Consensus 9 ~~e~v~iPl~~~~vaAGfPsp---A~---d~~e~~i~l~~~li------~~p~~tF~lrV~GdSMi~agI~dGDiliVdr 76 (139)
T PRK10276 9 LREIVTLPLFSDLVQCGFPSP---AA---DYVEQRIDLNELLI------QHPSATYFVKASGDSMIDAGISDGDLLIVDS 76 (139)
T ss_pred CCCEEECCCCCCEEECCCCCC---CH---HCCCCCCCCCHHHH------CCCCCEEEEEEECCCCCCCCCCCCCEEEEEE
T ss_conf 576598686788061839898---13---24646206298881------6999879999726873448889989999940
Q ss_pred CCCCCCCCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCEEECHH-HEEEEEEEEEE
Q ss_conf 8974058889999717968999999977987999968589887585478-65999779985
Q gi|254780444|r 162 AIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMS-DIEWIARILWA 221 (223)
Q Consensus 162 ~~~~~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~~~-~i~iigrVvw~ 221 (223)
+.++.+|++|++.. +|+.++|||++. +.+.|.|.||+|+|+.++.+ +++|.|.|+++
T Consensus 77 ~~~~~~GdIVva~i-dge~tvKrl~~~--~~~~L~p~N~~y~pi~i~~~d~~~I~GvV~~v 134 (139)
T PRK10276 77 SITASHGDIVIAAV-DGEFTVKKLQLR--PTVQLIPMNSAYSPITIGSEDTLDVFGVVTHI 134 (139)
T ss_pred CCCCCCCCEEEEEE-CCEEEEEEEEEC--CCCEECCCCCCCCCEECCCCCCEEEEEEEEEE
T ss_conf 59877899999998-998899999988--98169049999997685999967999999999
No 8
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=99.58 E-value=1.1e-14 Score=115.22 Aligned_cols=81 Identities=17% Similarity=0.304 Sum_probs=72.4
Q ss_pred EEEEECCCCCCCCCCCCCEEEEECCCC-CCCCCEEEEEEECCCEEEEEEEEECC-CEEEEEECCCCCCCEEECH-HHEEE
Q ss_conf 999962833242148786899936897-40588899997179689999999779-8799996858988758547-86599
Q gi|254780444|r 138 TRHKTQDTSMLPLYRKGDILILNSAIQ-VNCGDRLLIKPRTGDIVAKVLISRRG-RSIDLMSLNCCYPVDTVEM-SDIEW 214 (223)
Q Consensus 138 ~~l~V~GDSM~P~i~~Gd~vlVd~~~~-~~~g~~v~~~~~~~~~~iKrl~~~~~-~~~~l~s~Np~y~~~~i~~-~~i~i 214 (223)
++++|.||||+|+|.+||+|+||+... ...|+++++...+++.++||+.+..+ +.+.|.|+|++|++..+.. ++..+
T Consensus 1 ~~~~v~gdSM~P~i~~Gd~v~vd~~~~~~~~Gdiv~~~~~~~~~~iKrl~~~~~~~~~~l~~dN~~~~~~~~~~~~~~~~ 80 (84)
T cd06462 1 FALRVEGDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPGGELTVKRVIGLPGEGHYFLLGDNPNSPDSRIDGPPELDI 80 (84)
T ss_pred CEEEEECCCCCCHHHCCCEEEEECCCCCCCCCCEEEEEECCCEEEEEEEEEECCCCCEEEECCCCCCCCCCCCCCCCEEE
T ss_conf 97996567771046489899997356657899699999789939999999888999899979899998812489997299
Q ss_pred EEEE
Q ss_conf 9779
Q gi|254780444|r 215 IARI 218 (223)
Q Consensus 215 igrV 218 (223)
+|+|
T Consensus 81 ~g~v 84 (84)
T cd06462 81 VGVV 84 (84)
T ss_pred EEEC
T ss_conf 9989
No 9
>pfam00717 Peptidase_S24 Peptidase S24-like.
Probab=99.53 E-value=3.1e-14 Score=112.26 Aligned_cols=67 Identities=25% Similarity=0.358 Sum_probs=60.3
Q ss_pred EECCCCCCCCCCCCCEEEEECCCCCCCCCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCEEEC
Q ss_conf 96283324214878689993689740588899997179689999999779879999685898875854
Q gi|254780444|r 141 KTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVE 208 (223)
Q Consensus 141 ~V~GDSM~P~i~~Gd~vlVd~~~~~~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~ 208 (223)
+|.||||+|+|++||+|+|+++.+..+|++|++...+++.+|||+.+.+++ +.|.|.||.|+|+.++
T Consensus 1 ~V~GdSM~p~i~~Gd~viv~~~~~~~~Gdivv~~~~~~~~~iKrl~~~~~~-~~l~~~N~~y~~i~i~ 67 (67)
T pfam00717 1 RVPGDSMEPTIPDGDLLLVDKTSEPKRGDIVVARLPGEEAYVKRLIGLPGD-IILLPSNPEYPPIYIN 67 (67)
T ss_pred CCCCCCCCCCCCCCCEEEEEECCCCCCCCEEEEEECCCCEEEEEEEEECCE-EEEEECCCCCCCEECC
T ss_conf 971788755714999999983464546959999989995699999965992-9998196798589539
No 10
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=99.31 E-value=6.5e-12 Score=97.20 Aligned_cols=74 Identities=19% Similarity=0.202 Sum_probs=65.2
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 5589999999999996499988999982899879889975157887557798999998732187521000011112444
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRT 82 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~~~~~ 82 (223)
|.++.|+++|..+|+++||||++||+++||+.+||++|++|... |+.+.|.++|++++|+++||+.+.....+.
T Consensus 1 m~~~tiG~Ri~~~R~~~glTQ~eLA~~~Gvs~~tVs~wE~g~~~-----P~~~~L~~LA~~L~vs~~wLL~G~~d~~~~ 74 (135)
T PRK09706 1 MKNETLGQRIRYRRKQLKLSQRALAKAVGVSHVSISQWERDETE-----PAGKNLFALAQALQCSPTWLLFGDEDKQPT 74 (135)
T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCCHHHHCCCCCCCCCC
T ss_conf 97130999999999985999999999969889999999828988-----899999999999890999984888778998
No 11
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.21 E-value=5.1e-10 Score=84.96 Aligned_cols=65 Identities=12% Similarity=0.249 Sum_probs=59.8
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 9999999999964999889999828998798899751578875577989999987321875210000111
Q gi|254780444|r 8 KIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPF 77 (223)
Q Consensus 8 ~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~ 77 (223)
.|+.+|++||+++|||..+||+++|++.+++++.+|+... |++.+|.|||+++++++.+|.....
T Consensus 7 ~iG~rIr~lR~~~glTL~eLA~~sGvS~s~LSqIErg~~~-----PSl~tL~kIa~aL~v~l~~lf~~~~ 71 (185)
T PRK09943 7 APGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVS-----PAISTLQKLLKVYGLSLSEFFSEPE 71 (185)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCCHHHHHCCCC
T ss_conf 4889999999985998999998879699999999879999-----9999999999984999999827745
No 12
>PHA01976 helix-turn-helix protein
Probab=99.16 E-value=9.4e-11 Score=89.71 Aligned_cols=64 Identities=13% Similarity=0.077 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 999999999964999889999828998798899751578875577989999987321875210000111
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPF 77 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~ 77 (223)
..++|.+||+++||||.+||+++||+.++|++|+.|... |+.++|.+++++++|+++||++...
T Consensus 3 F~~RL~~lR~~~g~sQ~eLA~~lGVs~~~is~wE~g~~~-----P~~d~L~~la~~~~VS~D~LlGr~~ 66 (67)
T PHA01976 3 FAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRL-----PNLKTLLRLADALGVTLDWLCGRCG 66 (67)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCCHHHHHCCCC
T ss_conf 899999999986999999999949989999999878989-----9989999999997978999926789
No 13
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease; InterPro: IPR014124 Members of this protein family are predicted proteases that are encoded adjacent to the genes for a nickel-type superoxide dismutase (IPR014123 from INTERPRO). This family of predicted peptidases belong to MEROPS peptidase subfamily S26A (signal peptidase I), which have a Ser/Lys catalytic dyad..
Probab=98.79 E-value=1.7e-08 Score=75.14 Aligned_cols=81 Identities=16% Similarity=0.210 Sum_probs=61.9
Q ss_pred EEECCCCCCCCCCCCCEEEEEC---CCCCCC-CCEEEEEEEC--CCEEEEEEEEECCCEEEEEECCCCC--CCEEEC-HH
Q ss_conf 9962833242148786899936---897405-8889999717--9689999999779879999685898--875854-78
Q gi|254780444|r 140 HKTQDTSMLPLYRKGDILILNS---AIQVNC-GDRLLIKPRT--GDIVAKVLISRRGRSIDLMSLNCCY--PVDTVE-MS 210 (223)
Q Consensus 140 l~V~GDSM~P~i~~Gd~vlVd~---~~~~~~-g~~v~~~~~~--~~~~iKrl~~~~~~~~~l~s~Np~y--~~~~i~-~~ 210 (223)
++|+||||.|+|.++|.|+|.| ..+... |.+++++-.- +.+.||||.-..++.+++.-|||+- +.+.+- ..
T Consensus 1 ~kV~G~SM~P~L~~~D~~~V~P~~~~~r~~~~G~v~v~~HP~~p~~~~iKRL~~~~~nG~~~LGDnp~AStDSR~~G~v~ 80 (90)
T TIGR02754 1 LKVTGESMSPTLKPGDRILVRPLLKIARVPPIGEVVVVRHPLKPSLLIIKRLAAVDDNGLFLLGDNPKASTDSRQLGPVP 80 (90)
T ss_pred CEECCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEECCCCCCEEEEEEEEEECCCCCEEECCCCCCCCCCHHHCCCC
T ss_conf 94433215761398886988301102348778808998569899747898613231788388567377876712105888
Q ss_pred HEEEEEEEEE
Q ss_conf 6599977998
Q gi|254780444|r 211 DIEWIARILW 220 (223)
Q Consensus 211 ~i~iigrVvw 220 (223)
.-.+||+|.|
T Consensus 81 ~~~L~G~v~~ 90 (90)
T TIGR02754 81 RELLLGKVLA 90 (90)
T ss_pred CHHEEEEEEC
T ss_conf 2025447859
No 14
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=98.73 E-value=2.5e-08 Score=74.02 Aligned_cols=64 Identities=16% Similarity=0.203 Sum_probs=57.6
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 999999999649998899998289987988997515788755779899999873218752100001111
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFS 78 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~ 78 (223)
-.+|.+|++|+|+|+++||+++|+|.+.+++.++|.++ |++++|.+||+++.+++..|++..+-
T Consensus 7 ftNv~RLr~ErGmT~~eLAe~AGIS~s~LSqIE~Gk~N-----PSL~tLe~IA~AL~VPL~~Lle~~dl 70 (119)
T PRK13890 7 FTNVLRLLDERHMTKKELSDRSGVSISFLSDLTTGKAN-----PSLKVMEDIAQALETPLPLLLESTDL 70 (119)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCCHHHHHHHCCC
T ss_conf 88799999985997999998829889999999779989-----87999999999987977998762358
No 15
>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=98.70 E-value=4.8e-08 Score=72.18 Aligned_cols=58 Identities=17% Similarity=0.157 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf 999999999999649998899998289987988997515788755779899999873218752
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETI 69 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~ 69 (223)
++|+.+|+..|+++||||++||+++|++.++|++.|+|.. .|+.+++.++++++|+.+
T Consensus 1 ~~lG~~Ir~~Rk~~glTQ~~LA~~aGvs~~~Is~iE~G~~-----~~~l~~l~~i~~aLGi~l 58 (58)
T TIGR03070 1 KQIGALVRARRKALGLTQADLADLAGVGLRFIRDIEKGKP-----TVRLDKVLRVLEALGLEL 58 (58)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC-----CCCHHHHHHHHHHHCCCC
T ss_conf 9588999999999499899999881998999999978999-----888999999999808989
No 16
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=98.63 E-value=7.4e-08 Score=70.94 Aligned_cols=56 Identities=23% Similarity=0.344 Sum_probs=51.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 9999999649998899998289987988997515788755779899999873218752100
Q gi|254780444|r 12 AIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 12 ~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
+|+.+|+++|+||.+||+++|++++++++|++|... |+.+.+.+++++++++++++
T Consensus 1 rlr~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~-----p~~~~l~~ia~~l~~~~~~l 56 (56)
T smart00530 1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-----PSLETLKKLAKALGVSLDEL 56 (56)
T ss_pred CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCCHHHC
T ss_conf 989999772999999999989599999999979989-----99999999999988889879
No 17
>TIGR00498 lexA LexA repressor; InterPro: IPR006200 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of proteins are serine peptidases belong to MEROPS peptidase S24 (LexA family, clan SF). The family contains the LexA proteins. LexA represses around 20 genes of the cellular SOS response to DNA damage in Escherichia coli . Damage to cellular DNA results in inactivation of LexA, allowing transcription of the genes involved in DNA repair. In E. coli, this derepression of the DNA repair system is mediated by RecA, which binds to LexA upon interaction with single-stranded DNA. This results in inactivation of LexA by proteolytic self cleavage, disrupting the DNA-binding capabilities of LexA. LexA consists of around 200 amino acids, of which the first 90 form the DNA-binding domain. The remaining residues form the protease domain, Ser-119 and Lys-156 being the active residues. The crystal structures of the wild type and several mutant forms of LexA reveal two distinct conformations: one compatible with cleavage, and the other in which the cleavage site is approximately 20 A from the catalytic centre. It is suggested that recA activates the self-cleavage of LexA and related proteins through selective stabilisation of the cleavable conformation .; GO: 0008992 repressor LexA activity, 0006508 proteolysis.
Probab=98.63 E-value=2.1e-07 Score=67.99 Aligned_cols=207 Identities=16% Similarity=0.203 Sum_probs=124.8
Q ss_pred CCCCC--HHHHHHHHHHHHHHCCCCH--HHHHHHHCCCHHH-HHH-HHHCCCCCCC-CCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 97755--8999999999999649998--8999982899879-889-9751578875-57798999998732187521000
Q gi|254780444|r 1 MTSFS--HKKIWEAIDRMAERHNLTP--SGLARKAGLDPTS-FNK-SKRFGIEGRN-RWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 1 ~~~~~--~~~i~~~i~~l~~~~gls~--~~lA~~~Gv~~~t-i~~-~~~~~~~g~~-r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
|+.+| ..++...+....++.|..+ .+++++.|+..+. +.. .+.-...|.. +.++.....++.+-.........
T Consensus 1 ~~~l~~~~~~~~~~~~~~~~~~g~pp~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~gp 80 (227)
T TIGR00498 1 LKPLTERQREVLDLLKAHIESTGYPPSVREIARALGLTSPSAAEEHLKALERKGYIERDPGKPRALRILDNEEEDEPEGP 80 (227)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHCCCEEECCCCCCEEEECCCCCHHHCCCH
T ss_conf 94024788999999998765148870178898873355730478898887644741223775311211011000000230
Q ss_pred CCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCCCCCC-CCC
Q ss_conf 0111124445442212202431011345222111254446403564372113545420036855999962833242-148
Q gi|254780444|r 74 DLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLP-LYR 152 (223)
Q Consensus 74 ~~~~~~~~~~~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~l~V~GDSM~P-~i~ 152 (223)
................+|+.+...++..... .....+....+... +..+...|.+++.|+||.. .+.
T Consensus 81 ~~~~~~~~~~~p~p~~~p~~g~~~~g~p~~~------~~~~~~~~~~~~~~------~~~~~~~~~l~~~g~~~~~~~~~ 148 (227)
T TIGR00498 81 AVLTEVAGDVLPEPTFVPLIGRVAAGEPLLA------EEHLEDYFPLPESL------LKPPGAVFLLKVLGDSLVDAGIL 148 (227)
T ss_pred HHHHHHHHHHCCCCCHHHHHHCCCCCCCHHH------HHHHHHHHCCCHHH------CCCCCCEEEEEECCCHHHHHHHC
T ss_conf 5677766531377420011100025762011------33223332044223------27875225665414202232211
Q ss_pred CCCEEEEECCC---CCCCCCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCEEECHHH--EEEEEEEEE
Q ss_conf 78689993689---740588899997179689999999779879999685898875854786--599977998
Q gi|254780444|r 153 KGDILILNSAI---QVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSD--IEWIARILW 220 (223)
Q Consensus 153 ~Gd~vlVd~~~---~~~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~~~~--i~iigrVvw 220 (223)
+||++++.... ...+|+.+.+...+++.++|++.+ .+..++|.+.|+.+++..+..++ +.+.|.++-
T Consensus 149 ~gd~~~~~~~~g~~~~~~g~~~~~~~~~~~~~~~~~~~-~g~~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~g 220 (227)
T TIGR00498 149 DGDLLLVRSQKGEEDAENGEIVAARIKDGEVTVKRFYK-EGTKVELKPENPEFDPIVLNAEDQNVEILGKVVG 220 (227)
T ss_pred CCCEEEEECCCCCCCCCCCCEEEEEECCCCHHHHHHHC-CCCEEEEEECCCCCCCCEECCCCCCEEEHHHEEE
T ss_conf 44344764045510003673688862365011232320-5876898655755575010132223000110000
No 18
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=98.62 E-value=6.4e-08 Score=71.36 Aligned_cols=55 Identities=24% Similarity=0.299 Sum_probs=50.1
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 999999649998899998289987988997515788755779899999873218752100
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
|+++|+++|+||.+||+++|++++++++|++|.. .|+.+.+.+++++++++++++
T Consensus 1 ir~~R~~~g~tq~~lA~~~gis~~~is~~E~g~~-----~p~~~~l~~ia~~l~v~~~~l 55 (55)
T pfam01381 1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-----EPSLETLKKLAEALGVSLDEL 55 (55)
T ss_pred CHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC-----CCCHHHHHHHHHHHCCCHHHC
T ss_conf 9898978299899999998969999999987999-----999999999999978979879
No 19
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=98.52 E-value=4.7e-07 Score=65.75 Aligned_cols=65 Identities=18% Similarity=0.265 Sum_probs=56.2
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 7755899999999999964999889999828998798899751578875577989999987321875210
Q gi|254780444|r 2 TSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 2 ~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
+-.|-+++..+|+.+|+++||||+++|+++|+.++||++.+++.. .+++++|.||+.++++.+.-
T Consensus 6 ki~sp~qLa~~Lr~~Rk~~gLsQ~~lA~~vGi~Q~TiS~~E~~p~-----~~~leTLFkiL~aL~Lel~i 70 (88)
T PRK09726 6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPD-----NTTLTTFFKILQSLELSMTL 70 (88)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC-----CCCHHHHHHHHHHCCCEEEE
T ss_conf 028999999999999998598799999981974999999975998-----78699999999967876887
No 20
>TIGR02227 sigpep_I_bact signal peptidase I; InterPro: IPR000223 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S26 (signal peptidase I family, clan SF), subfamily S26A. At least 3 eubacterial leader peptidases are known: murein prelipoprotein peptidase, which cleaves the leader peptide from a component of the bacterial outer membrane; type IV prepilin leader peptidase; and the serine-dependent leader peptidase 1, which has the more general role of cleaving the leader peptide from a variety of secreted proteins and proteins directed to the periplasm and periplasmic membrane . Leader peptidase 1 is similar to the eukaryotic signal peptidase, although the bacterial protein is monomeric, while the eukaryotic protein is multimeric . Mitochondria contain a similar two-subunit serine protease that removes leader peptides from nuclear- and mitochondrial-encoded proteins, which localise in the inner mitochondrial space . The catalytic residues of a number of these peptides have been identified as a serine/lysine dyad .; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0016020 membrane.
Probab=98.42 E-value=1.3e-06 Score=62.93 Aligned_cols=60 Identities=23% Similarity=0.369 Sum_probs=51.7
Q ss_pred EE-EEECCCCCCCCCCCCCEEEEEC-----------------CCCCCCCCEEEEEEEC--CC-EEEEEEEEECCCEEEEE
Q ss_conf 99-9962833242148786899936-----------------8974058889999717--96-89999999779879999
Q gi|254780444|r 138 TR-HKTQDTSMLPLYRKGDILILNS-----------------AIQVNCGDRLLIKPRT--GD-IVAKVLISRRGRSIDLM 196 (223)
Q Consensus 138 ~~-l~V~GDSM~P~i~~Gd~vlVd~-----------------~~~~~~g~~v~~~~~~--~~-~~iKrl~~~~~~~~~l~ 196 (223)
.. +.|.|.||+|||++||.|+|.+ ...+..||+|++...+ .. .+|||+.-.+|+.+++.
T Consensus 21 ~~~~~v~g~SM~PTL~~gD~~lv~K~~y~r~~lp~~~~~~~~~~~~~rgDivVF~~~~~~~~~~yiKRviglPGD~v~~~ 100 (203)
T TIGR02227 21 FPVYKVPGGSMEPTLKEGDRILVNKFAYGRLKLPFTHKLLFKTSDPKRGDIVVFKAPDDPDNRIYIKRVIGLPGDKVEIK 100 (203)
T ss_pred EEEEEECCCCCCHHHCCCCEEEEEEECCCEEEEECCEEEEEEECCCEECCEEEEECCCCCCCCEEEEEEEECCCCEEEEE
T ss_conf 78898088975532237988999981264456302100035605750040899953899889616789996588889998
Q ss_pred E
Q ss_conf 6
Q gi|254780444|r 197 S 197 (223)
Q Consensus 197 s 197 (223)
-
T Consensus 101 ~ 101 (203)
T TIGR02227 101 D 101 (203)
T ss_pred E
T ss_conf 0
No 21
>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=98.39 E-value=8.5e-07 Score=64.08 Aligned_cols=57 Identities=23% Similarity=0.307 Sum_probs=51.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 99999999649998899998289987988997515788755779899999873218752100
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
.+|..+|+++|+|+.+||+++|++++++++|++|.. .|+.+.+.++++++++++.++
T Consensus 2 ~~l~~~r~~~~ls~~~lA~~~gis~~~l~~~e~g~~-----~p~~~~l~~la~~~~~~~~~l 58 (58)
T cd00093 2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKR-----NPSLETLEKLAKALGVSLDEL 58 (58)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCC-----CCCHHHHHHHHHHHCCCHHHC
T ss_conf 899999997599999995714999999999987998-----999999999999938989879
No 22
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=98.35 E-value=1.2e-06 Score=63.07 Aligned_cols=75 Identities=17% Similarity=0.233 Sum_probs=54.6
Q ss_pred EEEECCCCCCCCCCCCCEEEEECCC----CCCCCCEEEEEEEC--CCEEEEEEEEECCCEEEEEECCC--CCCCEEECH-
Q ss_conf 9996283324214878689993689----74058889999717--96899999997798799996858--988758547-
Q gi|254780444|r 139 RHKTQDTSMLPLYRKGDILILNSAI----QVNCGDRLLIKPRT--GDIVAKVLISRRGRSIDLMSLNC--CYPVDTVEM- 209 (223)
Q Consensus 139 ~l~V~GDSM~P~i~~Gd~vlVd~~~----~~~~g~~v~~~~~~--~~~~iKrl~~~~~~~~~l~s~Np--~y~~~~i~~- 209 (223)
.+.|.|.||+|+|.+||++++++.. ....||+|++...+ +..++||+.. +++..||+ ...+..+-.
T Consensus 2 ~~~V~g~SM~Pt~~~Gd~v~v~~~~~~~~~~~~GDivv~~~p~~~~~~~ikRVi~-----~~~~GDN~~ns~Dsr~~g~v 76 (85)
T cd06530 2 PVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG-----YFVLGDNRNNSLDSRYWGPV 76 (85)
T ss_pred CEEECCCCCCCCCCCCCEEEEEECCCCCCCCCCCCEEEEECCCCCCCEEEECCCE-----EEEEECCCCCCCCCCCCCCC
T ss_conf 9695688880603089899999613565777778699996799999759974327-----89873596768645714767
Q ss_pred HHEEEEEEE
Q ss_conf 865999779
Q gi|254780444|r 210 SDIEWIARI 218 (223)
Q Consensus 210 ~~i~iigrV 218 (223)
..-.++|||
T Consensus 77 ~~~~i~Gkv 85 (85)
T cd06530 77 PEDDIVGKV 85 (85)
T ss_pred CHHHEEEEC
T ss_conf 789939959
No 23
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=98.32 E-value=1.3e-06 Score=62.85 Aligned_cols=59 Identities=22% Similarity=0.288 Sum_probs=52.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 9999999649998899998289987988997515788755779899999873218752100001
Q gi|254780444|r 12 AIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDL 75 (223)
Q Consensus 12 ~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~ 75 (223)
.|+.+|+++|+||++||+++||+.+|+..++++.-+ |+++...++|.+++.+++++.-.
T Consensus 5 k~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~-----Psl~La~kia~~f~~~iedIF~~ 63 (68)
T COG1476 5 KLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYN-----PSLELALKIARVFGKTIEDIFQL 63 (68)
T ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHCCCCC-----CHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 999999982858999999919579999999917988-----30999999999939979999865
No 24
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=98.32 E-value=2.1e-06 Score=61.51 Aligned_cols=66 Identities=14% Similarity=0.109 Sum_probs=60.1
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 99999999999649998899998289987988997515788755779899999873218752100001111
Q gi|254780444|r 8 KIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFS 78 (223)
Q Consensus 8 ~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~ 78 (223)
.+++++.++|+++|+|..+||+.+|||..++.+.+.|.++ |+...|.++|.++++++.+|......
T Consensus 28 ~lg~rvr~~R~~rg~sr~~la~~sgvS~r~la~lE~G~gN-----~si~~L~~iA~Al~~~l~~l~~~~~~ 93 (304)
T PRK08154 28 ALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGN-----VSILLLRRVARALGCPLADLLGDEDT 93 (304)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCCHHHHHCCCCC
T ss_conf 9999999999975998999998729989999988258888-----51999999999959989998178888
No 25
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=98.11 E-value=6.1e-06 Score=58.54 Aligned_cols=54 Identities=22% Similarity=0.359 Sum_probs=45.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf 99999999649998899998289987988997515788755779899999873218752
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETI 69 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~ 69 (223)
+-|++.|++.|+||++||+++|++|+.|-+.+.|.-+ |.+.++.++++++...-
T Consensus 8 edlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vd-----PrlSt~k~Il~aL~e~e 61 (187)
T COG3620 8 EDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVD-----PRLSTVKRILEALEEAE 61 (187)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHHHHH
T ss_conf 9999999875977899998708648889998638879-----30899999999999854
No 26
>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=98.01 E-value=1.5e-05 Score=56.02 Aligned_cols=62 Identities=15% Similarity=0.089 Sum_probs=53.1
Q ss_pred HHHHHHHHCCCC-HHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 999999964999-88999982899879889975157887557798999998732187521000011112
Q gi|254780444|r 12 AIDRMAERHNLT-PSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSD 79 (223)
Q Consensus 12 ~i~~l~~~~gls-~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~~ 79 (223)
.|+|+++..|.+ +++||+.+|++++|++.|++.+. ...+.+.+++...|++++||..+..++
T Consensus 2 vi~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R~~------~P~e~iv~~~~~tGvsl~WL~~G~G~~ 64 (65)
T pfam07022 2 VIERLMKAYGFKSRSELADHLGVSKSTLSTWYKRDS------FPAEWVIRCALETGVSLDWLATGDGEL 64 (65)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCC------CCHHHHHHHHHHHCCCHHHHHCCCCCC
T ss_conf 899999996888699999996988888999998699------989999999999882999997089999
No 27
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=97.84 E-value=8.2e-05 Score=51.23 Aligned_cols=66 Identities=17% Similarity=0.122 Sum_probs=56.0
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 99999999999964999889999828998798899751578875577989999987321875210000111
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPF 77 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~ 77 (223)
++..++|...|+++||||.+||.+++.+.+.|.+|+++... |+.+...++...|++.+.+......
T Consensus 78 edY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~-----P~~~~akkLEk~LgIkL~e~~~~~~ 143 (165)
T COG1813 78 EDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEAT-----PNIKVAKKLEKLLGIKLVEKVDEEE 143 (165)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC-----CCHHHHHHHHHHHCCEEEEECCCCC
T ss_conf 77999999999982888999999965469999999841367-----5588999999985855220035554
No 28
>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=97.62 E-value=0.0001 Score=50.63 Aligned_cols=58 Identities=14% Similarity=0.157 Sum_probs=48.0
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 999996499988999982899879889975157887557798999998732187521000011
Q gi|254780444|r 14 DRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLP 76 (223)
Q Consensus 14 ~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~ 76 (223)
..-++..|+|.++||+.+||++++||+.-++.+ ..+.++..|+++++|.+.+.++...
T Consensus 13 eEfL~PLg~s~~~LA~~LgVsr~~~sriv~~~~-----~iT~dmALRL~~~lG~sp~~WLnlQ 70 (81)
T TIGR02607 13 EEFLEPLGLSVRALAKALGVSRSTLSRIVNGRR-----GITADMALRLAKALGTSPEFWLNLQ 70 (81)
T ss_pred HHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCC-----CCCHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 775210470689999870999788888874489-----9888899999997389876899877
No 29
>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=97.58 E-value=0.00012 Score=50.21 Aligned_cols=62 Identities=13% Similarity=0.185 Sum_probs=54.5
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 99999964999889999828998798899751578875577989999987321875210000111
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPF 77 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~ 77 (223)
|.++|+.+|+|-.+||.++||.|+.|...++....|. -.+++|.+.|+++++.+-|-+=...
T Consensus 30 vR~~R~ALGms~~QLA~RlGV~p~Rv~~~E~~E~~G~---VTL~tlr~aAEAl~C~FVYafVP~~ 91 (150)
T TIGR02612 30 VRAIRKALGMSGAQLAARLGVTPQRVEAIEKSELSGA---VTLKTLRKAAEALDCTFVYAFVPKT 91 (150)
T ss_pred HHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHCCC---HHHHHHHHHHHHHCCEEEEECCCCC
T ss_conf 6889877251578876652897377999888875553---5588899999985984434018860
No 30
>PRK08359 transcription factor; Validated
Probab=97.58 E-value=0.00038 Score=46.90 Aligned_cols=61 Identities=15% Similarity=0.162 Sum_probs=51.8
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC
Q ss_conf 999999999964999889999828998798899751578875577989999987321875210000
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLD 74 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~ 74 (223)
-.+.|...|+++||||.+||++++.+.+.|.+.++|... |..+...|+-.+|++++-+-..
T Consensus 84 Y~~~Ir~ARE~~GlSqeeLA~ki~ek~nvI~kiE~G~l~-----P~~~~akKLEk~L~IkL~E~~e 144 (175)
T PRK08359 84 YAERVYEAIRKSGLSYEELSHKVGLSVNDLRRIAHGEYT-----PTIEEARKLERFFKIKLIERVE 144 (175)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHCCCCC-----CCHHHHHHHHHHHCEEEEEECC
T ss_conf 999999999985999999999972229999999838879-----9989999999984906885146
No 31
>PRK06424 transcription factor; Provisional
Probab=97.57 E-value=0.00035 Score=47.12 Aligned_cols=59 Identities=17% Similarity=0.131 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 9999999999964999889999828998798899751578875577989999987321875210
Q gi|254780444|r 8 KIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 8 ~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
+-.+.|...|+++||||.+||.+++.+.+.|.+.++|... |..+...|+-.+|++++-+
T Consensus 84 Dy~~~Ir~ARE~~GlsqeeLA~ki~ek~svI~kiE~G~l~-----P~~~~~kKLEk~L~I~L~E 142 (144)
T PRK06424 84 DYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLL-----PDIKTARKLEKILGITLIE 142 (144)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCEEEE
T ss_conf 7999999999984999999999965449999999838989-----9989999999984967663
No 32
>PRK04140 hypothetical protein; Provisional
Probab=97.56 E-value=0.0003 Score=47.55 Aligned_cols=61 Identities=20% Similarity=0.322 Sum_probs=52.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 999999999649998899998289987988997515788755779899999873218752100001
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDL 75 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~ 75 (223)
++.|+++|+++|+|-.+||..+|||.-|+++|++|..+ .+.+...|+.+.++.++-.-...
T Consensus 127 g~~Lr~~Re~~g~SlG~LA~~LGVSRrtv~~YE~g~~~-----~sievA~kLeeif~~~i~~~Idi 187 (319)
T PRK04140 127 GDLLRELREKLGLSLGELASELGVSRRTISKYENGGMN-----ASIEVAIKLEEILDEPLTKPIDI 187 (319)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC-----CCHHHHHHHHHHHCCCCCCCCCC
T ss_conf 79999999981988889999849869999999706886-----64999999999838732355202
No 33
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=97.39 E-value=0.00019 Score=48.87 Aligned_cols=59 Identities=24% Similarity=0.350 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf 9999999999996499988999982899879889975157887557798999998732187521
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~ 70 (223)
++.+++|++-|+..++||.+||+.+|++|+-|+.|+. |+.+.|+...+.|+-+++ +.++
T Consensus 26 ~~pge~lrKWR~~F~iSQ~elA~~l~vSpSVISDYE~----GRRk~Pg~~~vkk~V~AL-IeID 84 (241)
T COG1709 26 EDPGETLRKWREIFNVSQTELARELGVSPSVISDYES----GRRKSPGIAFVKKFVEAL-IEID 84 (241)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCCCEEEHHHC----CCCCCCCHHHHHHHHHHH-HHHH
T ss_conf 7825899999998182499999872899100312112----575686178999999999-8666
No 34
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=97.25 E-value=0.00065 Score=45.42 Aligned_cols=37 Identities=19% Similarity=0.224 Sum_probs=33.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC
Q ss_conf 9999999964999889999828998798899751578
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIE 47 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~ 47 (223)
..|+++|++.||||..||+.+|++-+|+++|++|...
T Consensus 47 ~eIk~iRe~~~lSq~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 47 TEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHCCCCC
T ss_conf 9999999982888999999988879999999817858
No 35
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=97.25 E-value=0.0009 Score=44.48 Aligned_cols=65 Identities=18% Similarity=0.188 Sum_probs=55.2
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 999999999649998899998289987988997515788755779899999873218752100001111
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFS 78 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~ 78 (223)
.-+++.++.+++++..+||+.+|++.+++++.+ .||-+...+++|.+|+.++.+.+.+++.....
T Consensus 4 ~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~----~gk~k~I~~~tL~~iC~~LeCqpgDiley~~d 68 (73)
T COG3655 4 AVRLDVMLADRKISLKELAEAIGISEANLSKLK----TGKVKAIRLSTLEKICKALECQPGDILEYVPD 68 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH----CCCCCEEEHHHHHHHHHHCCCCHHHEEEEECC
T ss_conf 376799999975017789999843698999997----28866044899999999838984054577168
No 36
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=97.23 E-value=0.0013 Score=43.46 Aligned_cols=55 Identities=18% Similarity=0.312 Sum_probs=47.5
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf 5899999999999964999889999828998798899751578875577989999987321
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~ 65 (223)
+.|+-++-+++++.|+||+++++|+++|+.++|+.+.-+| +.|+.++|.+++...
T Consensus 13 s~E~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G------~dpr~~tl~~I~kti 67 (170)
T COG4800 13 SGEDFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG------SDPRYDTLTRIFKTI 67 (170)
T ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHC------CCCCHHHHHHHHHHH
T ss_conf 4007999999999981999899988709989999999817------996577899999999
No 37
>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=97.18 E-value=0.00096 Score=44.30 Aligned_cols=55 Identities=29% Similarity=0.378 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf 99999999996499988999982899879889975157887557798999998732187521
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~ 70 (223)
|..||=-.++.+|+| +||+++|++.-++.+..++.++ |+.+++.|+.++||+.+-
T Consensus 35 ~~~ALG~iArArGMt--qlA~~tGlsREsLYkALs~~Gn-----P~f~T~lkV~~ALG~~L~ 89 (91)
T TIGR02684 35 IAAALGVIARARGMT--QLAKKTGLSRESLYKALSGGGN-----PTFDTILKVTKALGLKLT 89 (91)
T ss_pred HHHHHHHHHHHCCHH--HHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHCCCEEE
T ss_conf 999988998651657--8999828767887887356889-----566888999984086020
No 38
>TIGR02228 sigpep_I_arch signal peptidase I; InterPro: IPR001733 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S26 (signal peptidase I family, clan SF), subfamily S26B. Eukaryotic microsomal signal peptidase is involved in the removal of signal peptides from secretory proteins as they pass into the endoplasmic reticulum lumen . The peptidase is more complex than its mitochondrial and bacterial counterparts, containing a number of subunits, ranging from two in the chicken oviduct peptidase, to five in the dog pancreas protein . They share sequence similarity with the bacterial leader peptidases (family S26A), although activity here is mediated by a serine/histidine dyad rather than a serine/lysine dyad . Archaeal signal peptidases also belong to this group. ; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0006508 proteolysis, 0016020 membrane.
Probab=97.18 E-value=0.0016 Score=42.94 Aligned_cols=75 Identities=20% Similarity=0.302 Sum_probs=52.2
Q ss_pred ECCCCCCCCCCCCCEEEEEC---CCCCCCCCEEEEEEECC----CEEEEEEEE------ECCCEEEE--EECCCCCCC--
Q ss_conf 62833242148786899936---89740588899997179----689999999------77987999--968589887--
Q gi|254780444|r 142 TQDTSMLPLYRKGDILILNS---AIQVNCGDRLLIKPRTG----DIVAKVLIS------RRGRSIDL--MSLNCCYPV-- 204 (223)
Q Consensus 142 V~GDSM~P~i~~Gd~vlVd~---~~~~~~g~~v~~~~~~~----~~~iKrl~~------~~~~~~~l--~s~Np~y~~-- 204 (223)
|-+.||||.|+.||+++++. -.+.+.||+++....+. ...+=|+.. ..++...+ +-||...||
T Consensus 42 VlSgSMEP~f~~Gd~~~~~~~~~~~~~~~GDvI~y~~~~~~WyG~~v~HRv~~~~yiyi~~~~~~~fiTKGDnN~~pDqr 121 (175)
T TIGR02228 42 VLSGSMEPTFNTGDLILVTGKVDPEDIQVGDVIVYKSEGKRWYGTPVIHRVIEIKYIYINSGGELGFITKGDNNPAPDQR 121 (175)
T ss_pred EEEEEECCEEECCEEEEEECCCCHHHCCCCCEEEEEECCCCCCCEEEEEEEEEEEEEEEECCCEEEEEEECCCCCCCCCC
T ss_conf 98554306252130999804217666301567999246995235389999998899999659878999425678655842
Q ss_pred -E-EECHHHEEEEEEE
Q ss_conf -5-8547865999779
Q gi|254780444|r 205 -D-TVEMSDIEWIARI 218 (223)
Q Consensus 205 -~-~i~~~~i~iigrV 218 (223)
. .++.+ .+||++
T Consensus 122 v~~p~~~~--NviG~~ 135 (175)
T TIGR02228 122 VIEPVPSE--NVIGKY 135 (175)
T ss_pred EEEEECCC--CEEEEE
T ss_conf 35001158--547650
No 39
>KOG1568 consensus
Probab=97.13 E-value=0.0046 Score=39.91 Aligned_cols=83 Identities=18% Similarity=0.154 Sum_probs=56.0
Q ss_pred EEEEEECCCCCCCCCCCC------CEEEEECC----CCCCCCCEEEEEEECC--CEEEEEEEEE----------------
Q ss_conf 599996283324214878------68999368----9740588899997179--6899999997----------------
Q gi|254780444|r 137 DTRHKTQDTSMLPLYRKG------DILILNSA----IQVNCGDRLLIKPRTG--DIVAKVLISR---------------- 188 (223)
Q Consensus 137 ~~~l~V~GDSM~P~i~~G------d~vlVd~~----~~~~~g~~v~~~~~~~--~~~iKrl~~~---------------- 188 (223)
....+|.|+||.|+++++ |+|++++- .+...||+|++....+ ...|||+.-.
T Consensus 31 ~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~~k~~~v~ 110 (174)
T KOG1568 31 VHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTEDEKEEPVV 110 (174)
T ss_pred EEEEEEECCCCCCCCCCCCCCCCCCEEEEEEECCCCCEECCCCEEEEECCCCHHHEEEEEEECCCCCEECCCCCCCCCEE
T ss_conf 78767854767875188766553548999850333430346878999589992152355151356647515888777354
Q ss_pred -CCCEEEEEECCCC--CCCEEECH-HHEEEEEEEE
Q ss_conf -7987999968589--88758547-8659997799
Q gi|254780444|r 189 -RGRSIDLMSLNCC--YPVDTVEM-SDIEWIARIL 219 (223)
Q Consensus 189 -~~~~~~l~s~Np~--y~~~~i~~-~~i~iigrVv 219 (223)
+.|+.+...+|+. |...+|-+ +-=-|+||++
T Consensus 111 vpkghcWVegDn~~hs~DSntFGPVS~gli~grai 145 (174)
T KOG1568 111 VPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAI 145 (174)
T ss_pred CCCCCEEEECCCCCCCCCCCCCCCCCHHHEEEEEE
T ss_conf 68984789648755334467547733421242589
No 40
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=97.06 E-value=0.0011 Score=44.02 Aligned_cols=63 Identities=14% Similarity=0.076 Sum_probs=50.4
Q ss_pred HHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 9999-9999996499988999982899879889975157887557798999998732187521000011
Q gi|254780444|r 9 IWEA-IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLP 76 (223)
Q Consensus 9 i~~~-i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~ 76 (223)
.++. -+.+++..|+|+++||+.+||.+.+|+...+|.. ..+.++..++++++|.+++.++...
T Consensus 10 PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~-----~iT~dmAlrL~k~fGtspefWlNlQ 73 (104)
T COG3093 10 PGEILREEFLEPLGLTQTELAEALGVTRNTISELINGRR-----AITADMALRLAKVFGTSPEFWLNLQ 73 (104)
T ss_pred CHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHCCCC-----CCCHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 418899998452169899999993998999999983776-----7899999999999299899999999
No 41
>KOG3398 consensus
Probab=97.06 E-value=0.0016 Score=42.83 Aligned_cols=60 Identities=15% Similarity=0.170 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 99999999999964999889999828998798899751578875577989999987321875210
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
.+++.+|...|.+.||||.+||.+..=.|+-|..|++|.+. |+-.-|.|+-.++|+-+.+
T Consensus 72 ~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAI-----pNqqil~kmEraLgvKlrg 131 (135)
T KOG3398 72 LEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAI-----PNQQILSKMERALGVKLRG 131 (135)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCC-----CHHHHHHHHHHHHCEECCC
T ss_conf 78999999988863754889999960286136557503567-----4199999999985311246
No 42
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=96.98 E-value=0.0013 Score=43.54 Aligned_cols=58 Identities=17% Similarity=0.174 Sum_probs=36.5
Q ss_pred EEEEECCCCCCCCCCCCCEEEEECCCCC----CCCCEEEEEEECCCEEEEEEEEECCCEEEE
Q ss_conf 9999628332421487868999368974----058889999717968999999977987999
Q gi|254780444|r 138 TRHKTQDTSMLPLYRKGDILILNSAIQV----NCGDRLLIKPRTGDIVAKVLISRRGRSIDL 195 (223)
Q Consensus 138 ~~l~V~GDSM~P~i~~Gd~vlVd~~~~~----~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l 195 (223)
..+.|.|+||+|+++.||+++|+..... ..++.+..........+||..-..++.+..
T Consensus 32 ~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~~~~~~~~~~kr~~~~~GD~i~~ 93 (166)
T COG0681 32 EPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVLPAVVEGDLIKRVIGLRGDIVVF 93 (166)
T ss_pred EEEEEECCCCCCCCCCCCEEEEECCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCEEEE
T ss_conf 88998089874567778899996655676645654200144223340403246799888997
No 43
>PRK10861 lsignal peptidase I; Provisional
Probab=96.90 E-value=0.002 Score=42.23 Aligned_cols=57 Identities=18% Similarity=0.208 Sum_probs=41.6
Q ss_pred EEEECCCCCCCCCCCCCEEEEECC----------------CCCCCCCEEEEEEECC--CEEEEEEEEECCCEEEE
Q ss_conf 999628332421487868999368----------------9740588899997179--68999999977987999
Q gi|254780444|r 139 RHKTQDTSMLPLYRKGDILILNSA----------------IQVNCGDRLLIKPRTG--DIVAKVLISRRGRSIDL 195 (223)
Q Consensus 139 ~l~V~GDSM~P~i~~Gd~vlVd~~----------------~~~~~g~~v~~~~~~~--~~~iKrl~~~~~~~~~l 195 (223)
.+++---||+|++.-||.|+|++- .+++.||+||+....+ .-+|||+.-.+|+.+.+
T Consensus 84 PF~IPSgSM~PTLlvGDfIlVnKf~YG~r~P~~~~~ii~~~~PkRGDVVVF~yP~d~~~dYIKRvIGLPGD~I~y 158 (324)
T PRK10861 84 PFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTY 158 (324)
T ss_pred CEECCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEECCCCCCCCCEEEE
T ss_conf 702786434342355888999812046677766751245799988999999589999876441045569877974
No 44
>PRK10072 putative transcriptional regulator; Provisional
Probab=96.88 E-value=0.0019 Score=42.45 Aligned_cols=35 Identities=11% Similarity=0.213 Sum_probs=31.6
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC
Q ss_conf 99999964999889999828998798899751578
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIE 47 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~ 47 (223)
++++|+..|++|+++|+.+|+|..|+..|+.+..+
T Consensus 38 vkaIR~~tgl~q~eFA~~lGvSv~tvksWEq~Rr~ 72 (96)
T PRK10072 38 FEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC
T ss_conf 99999880999999999977779999999967878
No 45
>KOG0171 consensus
Probab=96.77 E-value=0.0024 Score=41.77 Aligned_cols=55 Identities=18% Similarity=0.274 Sum_probs=39.8
Q ss_pred EEEECCCCCCCCCCCCCEEEE-E----CCCCCCCCCEEEEEEEC--CCEEEEEEEEECCCEE
Q ss_conf 999628332421487868999-3----68974058889999717--9689999999779879
Q gi|254780444|r 139 RHKTQDTSMLPLYRKGDILIL-N----SAIQVNCGDRLLIKPRT--GDIVAKVLISRRGRSI 193 (223)
Q Consensus 139 ~l~V~GDSM~P~i~~Gd~vlV-d----~~~~~~~g~~v~~~~~~--~~~~iKrl~~~~~~~~ 193 (223)
...+.|.||+|++.+++.++. + ...+...||+|++.... .+..|||+.-.+|+.+
T Consensus 35 ~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD~v 96 (176)
T KOG0171 35 FVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGDLV 96 (176)
T ss_pred EEECCCCCCCCEECCCCCEEEHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHEEECCCCCEE
T ss_conf 06625887575362798688633545764589877789994899803422110321488628
No 46
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=96.69 E-value=0.0051 Score=39.62 Aligned_cols=57 Identities=21% Similarity=0.177 Sum_probs=49.9
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 99999999964999889999828998798899751578875577989999987321875210
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
++.|+.+|+++|+|-..||.-+|+|.-|+++|++|..+ |+++...|+-+.++..+-.
T Consensus 127 ge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~-----~sleva~kLeei~g~~iv~ 183 (313)
T COG1395 127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSD-----ASLEVALKLEEIFGEDIVK 183 (313)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCCCCCC-----CCHHHHHHHHHHHCCHHHC
T ss_conf 29999999980867878898838468889876247777-----3299999999985622203
No 47
>KOG3342 consensus
Probab=96.66 E-value=0.0028 Score=41.29 Aligned_cols=81 Identities=21% Similarity=0.257 Sum_probs=52.7
Q ss_pred EEEECCCCCCCCCCCCCEEEEE-CC-CCCCCCCEEEEEEECCCE-----EEEEEEEECCCE-EEEEECCCC------CCC
Q ss_conf 9996283324214878689993-68-974058889999717968-----999999977987-999968589------887
Q gi|254780444|r 139 RHKTQDTSMLPLYRKGDILILN-SA-IQVNCGDRLLIKPRTGDI-----VAKVLISRRGRS-IDLMSLNCC------YPV 204 (223)
Q Consensus 139 ~l~V~GDSM~P~i~~Gd~vlVd-~~-~~~~~g~~v~~~~~~~~~-----~iKrl~~~~~~~-~~l~s~Np~------y~~ 204 (223)
.+-|-..||||.|+.||+++.. .. ...+-||++++...+-+. ++|...+..+.. +.-.-||.. |++
T Consensus 50 iVVVLSgSMePaF~RGDlLfL~N~~~~p~~vGdivVf~vegR~IPiVHRviK~he~~~~~~~~LTKGDNN~~dD~~Ly~~ 129 (180)
T KOG3342 50 IVVVLSGSMEPAFHRGDLLFLTNRNEDPIRVGDIVVFKVEGREIPIVHRVIKQHEKSNGHIKFLTKGDNNAVDDRGLYAQ 129 (180)
T ss_pred EEEEECCCCCCCCCCCCEEEEECCCCCCCEECCEEEEEECCCCCCHHHHHHHHHCCCCCCEEEEECCCCCCCCCHHHCCC
T ss_conf 89997388675512574899855889964005489998889247511788998626788578974277876661320556
Q ss_pred EEECHHHEEEEEEEE
Q ss_conf 585478659997799
Q gi|254780444|r 205 DTVEMSDIEWIARIL 219 (223)
Q Consensus 205 ~~i~~~~i~iigrVv 219 (223)
-..=.+.-+|+||+.
T Consensus 130 gq~~L~r~~Ivg~~~ 144 (180)
T KOG3342 130 GQNWLERKDIVGRVR 144 (180)
T ss_pred CCCCEEHHHEEEEEE
T ss_conf 554222301324776
No 48
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=96.62 E-value=0.0061 Score=39.08 Aligned_cols=66 Identities=12% Similarity=0.075 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHC-----CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 9999999999964999889999828-----9987988997515788755779899999873218752100001111
Q gi|254780444|r 8 KIWEAIDRMAERHNLTPSGLARKAG-----LDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFS 78 (223)
Q Consensus 8 ~i~~~i~~l~~~~gls~~~lA~~~G-----v~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~ 78 (223)
...++|..+|+.+|+.|.+|++++. ++.+.+|+|.+|... |..+.+.-+|+.++++.+||++...+
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (518)
T PRK13355 5 TQAERLVQLMNSRGLKQEDLVHAAEARGVKVGKSHISQYVRGKTG-----PRSDKLPFLASELGVSEGWLLGGESE 75 (518)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCCHHHHCCCCCC
T ss_conf 089999999987699689999999981755047888777338864-----42117999999968897886079976
No 49
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=96.06 E-value=0.015 Score=36.53 Aligned_cols=54 Identities=22% Similarity=0.365 Sum_probs=43.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 99999996499988999982899879889975157887557798999998732187521000
Q gi|254780444|r 12 AIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 12 ~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
-|.+.++++|+|-.+|++.+|+++.|+.+-.. ..+|+.|.+ ||+++|+++.++-
T Consensus 12 dI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~------rp~pkgEri--IA~algv~P~eIW 65 (82)
T COG3423 12 DIIAALKKKGTSLAALSREAGLSSSTLANALD------RPWPKGERI--IADALGVPPEEIW 65 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHC------CCCCHHHHH--HHHHHCCCHHHHC
T ss_conf 99999998564299999880878789999874------788718899--9999589888818
No 50
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=96.02 E-value=0.016 Score=36.36 Aligned_cols=53 Identities=19% Similarity=0.296 Sum_probs=42.0
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 9999996499988999982899879889975157887557798999998732187521000
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
|.+.++++|+|-++|++..|++.+|+.+-.. ..||+.|.+ ||+++|+.+.++-
T Consensus 13 IiAAL~KrG~sLa~Lsr~aGls~sTL~nAL~------rpwPKgE~i--IA~aLGv~P~eIW 65 (90)
T PRK10344 13 IIAGLRKKGTSMAAESRRNGLSSSTLANALS------RPWPKGEMI--IAKALGTDPWVIW 65 (90)
T ss_pred HHHHHHHCCCCHHHHHHHCCCCHHHHHHHHC------CCCCHHHHH--HHHHHCCCHHHCC
T ss_conf 9999998688699999990998688999874------899567999--9999787988809
No 51
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=95.65 E-value=0.054 Score=32.97 Aligned_cols=61 Identities=25% Similarity=0.364 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 99999999996499988999982899879889975157887557798999998732187521000
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
+..+++.+++..|+|+.++|.+.|++..++++|+++... .|....+..++..+++...++.
T Consensus 2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~----~~~~~~~~~~~~~~~~~~~~~~ 62 (120)
T COG1396 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSE----SPSLELLARLAAALGVSLDELL 62 (120)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC----CCCHHHHHHHHHHHCCCHHHHH
T ss_conf 789999999986999999998939889999999807877----8469999999999697899884
No 52
>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=95.61 E-value=0.026 Score=35.06 Aligned_cols=41 Identities=22% Similarity=0.457 Sum_probs=34.9
Q ss_pred CCCCC--HHHHHHHHHHHHHHCCCCHH--HHHHHHCC-CHHHHHHH
Q ss_conf 97755--89999999999996499988--99998289-98798899
Q gi|254780444|r 1 MTSFS--HKKIWEAIDRMAERHNLTPS--GLARKAGL-DPTSFNKS 41 (223)
Q Consensus 1 ~~~~~--~~~i~~~i~~l~~~~gls~~--~lA~~~Gv-~~~ti~~~ 41 (223)
|+.|| +.+|+++|....++.|.+|+ ++|+.+|+ |++++...
T Consensus 1 M~~LT~rQ~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~ 46 (65)
T pfam01726 1 MKPLTERQREVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEH 46 (65)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 9633799999999999999982889879999999389980999999
No 53
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=95.57 E-value=0.034 Score=34.30 Aligned_cols=74 Identities=9% Similarity=-0.026 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCC-CHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf 9999999999964999889999828998798899751578875577-9899999873218752100001111244
Q gi|254780444|r 8 KIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWP-STESIFKILAATNETICQLLDLPFSDGR 81 (223)
Q Consensus 8 ~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p-~~~~l~kia~~~~v~~~~l~~~~~~~~~ 81 (223)
.+++.++..|+++|||..++|.++.|.+.++...+.+.-+.-|-.. ...-|.+.|++++++.+.+.........
T Consensus 3 ~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l~~~~~~~~~ 77 (284)
T COG1426 3 TLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDELLQAFEDEKP 77 (284)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCC
T ss_conf 778999999998499999999885775999999866770106415767899999999968998999998641045
No 54
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria..
Probab=95.50 E-value=0.029 Score=34.76 Aligned_cols=62 Identities=16% Similarity=0.181 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 9999999999996499988999982899879889975157887557798999998732187521000
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
|+-..-|.+-|+++|||+.+||+++-...++|++.++..-+ |..+.+.++-..|.+.|.+-.
T Consensus 82 Edyg~iIR~eREKRgwS~E~LAkki~eK~S~i~kiE~~e~e-----P~~k~~~kLEkllkIkL~E~~ 143 (169)
T TIGR00270 82 EDYGRIIREEREKRGWSREELAKKIKEKASVIKKIEREELE-----PEEKVVKKLEKLLKIKLLEKV 143 (169)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC-----CCHHHHHHHHHHHCCCCCCCC
T ss_conf 43225422000146878789999874106788887540379-----888999998888350100235
No 55
>PHA00542 putative Cro-like protein
Probab=95.42 E-value=0.043 Score=33.61 Aligned_cols=44 Identities=14% Similarity=0.247 Sum_probs=32.1
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHH
Q ss_conf 9999996499988999982899879889975157887557798999998
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKI 61 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~ki 61 (223)
+++|+ ..|+||+++|..+|+++++|++.- .|+-+.|....+.++
T Consensus 24 V~aLi-~~G~tQ~qI~~~tgv~QpsisRil----sGk~kDpR~s~v~~L 67 (82)
T PHA00542 24 VCALI-RAGWSQEQIADATDVSQPTICRIY----SGRHKDPRYSVVEKL 67 (82)
T ss_pred HHHHH-HCCCCHHHHHHHHCCCCHHHHHHH----CCCCCCCCCHHHHHH
T ss_conf 99999-822569999986087703689998----088789720699999
No 56
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=95.12 E-value=0.061 Score=32.65 Aligned_cols=56 Identities=29% Similarity=0.353 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 999999999964999889999828998798899751578875577989999987321875210
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
|.+++......+| .+++|+++|++...+.+.-+..++ |...++.++++++|.-+.-
T Consensus 39 i~~alg~var~~G--MsqvA~~aGlsRe~LYkaLS~~GN-----Ptf~Til~V~kAlG~rl~~ 94 (100)
T COG3636 39 IAAALGVVARSRG--MSQVARKAGLSREGLYKALSPGGN-----PTFDTILAVLKALGLRLSA 94 (100)
T ss_pred HHHHHHHHHHHCC--HHHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHCCCEEEC
T ss_conf 9999999998657--899999949669999998478999-----7589999999980865421
No 57
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=94.72 E-value=0.071 Score=32.21 Aligned_cols=38 Identities=18% Similarity=0.250 Sum_probs=28.5
Q ss_pred HHHHHHHH-----HHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 99999999-----9999649998899998289987988997515
Q gi|254780444|r 7 KKIWEAID-----RMAERHNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 7 ~~i~~~i~-----~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
+.++-+|. .|++ .|+||.+.|+.+|++|+.+|+|-++.
T Consensus 4 ~~vlPaiRa~lA~~L~e-eG~Sq~~iA~LLGltqaAVS~Yls~k 46 (119)
T COG2522 4 EEVLPAIRALLAKELIE-EGLSQYRIAKLLGLTQAAVSQYLSGK 46 (119)
T ss_pred HHHHHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHCCC
T ss_conf 88879899999999999-58869999999688899999997367
No 58
>pfam08667 BetR BetR domain. This family includes an N-terminal helix-turn-helix domain.
Probab=94.71 E-value=0.14 Score=30.24 Aligned_cols=66 Identities=14% Similarity=0.076 Sum_probs=52.4
Q ss_pred HHHHHHHHHHHHCCCCH----HHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 99999999999649998----899998289987988997515788755779899999873218752100001111
Q gi|254780444|r 8 KIWEAIDRMAERHNLTP----SGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFS 78 (223)
Q Consensus 8 ~i~~~i~~l~~~~gls~----~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~ 78 (223)
-|.++|..|+.+.|+.+ +.+++-+|+|-+..++=.+|... =.++.|.|++.++|++...|.+..+.
T Consensus 5 ~ia~rvr~lL~r~GI~kRqh~s~is~iL~LSfS~a~RKLkG~sp-----W~l~Ql~kVA~~fg~~~a~L~~~~~~ 74 (146)
T pfam08667 5 IVAERVRKLLTRTGIAERQHNTTIANILGLSFSQAYRKLKGSIP-----WNLAQLQKVAQYFGVPAAILLIYYED 74 (146)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCCHHHHHCCCHH
T ss_conf 99999999998639975677889999978748988787358997-----44999999999959799999275022
No 59
>PRK10856 hypothetical protein; Provisional
Probab=94.65 E-value=0.15 Score=30.13 Aligned_cols=69 Identities=10% Similarity=-0.086 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCC-CCCHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 9999999999649998899998289987988997515788755-77989999987321875210000111
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNR-WPSTESIFKILAATNETICQLLDLPF 77 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r-~p~~~~l~kia~~~~v~~~~l~~~~~ 77 (223)
++..|++.|+++|||..++|+++-+++..|..+|.+.-+.-+- ..-..-|...|+.++++.+.++....
T Consensus 15 ~G~~Lr~ARE~~GlSi~dvA~~LkL~~~~ieALE~dd~~~Lp~~tF~RGylRsYAr~LglD~~~ll~~~~ 84 (332)
T PRK10856 15 TGVRLRQAREQLGLSQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELLPGLE 84 (332)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHC
T ss_conf 8799999999859999999987089899999985782210870364799999999997889799654210
No 60
>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=94.59 E-value=0.11 Score=30.97 Aligned_cols=46 Identities=22% Similarity=0.258 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCC
Q ss_conf 77558999999999999649998899998289987988997515788
Q gi|254780444|r 2 TSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEG 48 (223)
Q Consensus 2 ~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g 48 (223)
..+|.|...++++... +.|.|.+++|+..||+++++.+|++.-..|
T Consensus 5 rrys~efK~~~V~~~~-~~g~sv~~var~~gi~~~~l~~W~k~~~~g 50 (75)
T pfam01527 5 RRYSEEFKARAVKESL-EPGASVSELAREHGVSPATLYKWRKKYRGG 50 (75)
T ss_pred CCCCHHHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHCC
T ss_conf 8899999999999998-099849999999895999999999998468
No 61
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=94.47 E-value=0.056 Score=32.88 Aligned_cols=64 Identities=17% Similarity=0.158 Sum_probs=50.6
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf 75589999999999996499988999982899879889975157887557798999998732187521
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~ 70 (223)
+.++-.++.+|..++++++++|++.|..+||+++.+|..-++ +-...+..+|.-.+...+...+
T Consensus 23 m~ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~g----k~~~fs~dkLvtml~~~g~ei~ 86 (91)
T COG5606 23 MKIRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARG----KIQDFSIDKLVTMLARAGQEID 86 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHC----CHHHHHHHHHHHHHHHCCCCCC
T ss_conf 999999999999999997877999999838887318899836----1457669999999997598552
No 62
>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=94.28 E-value=0.11 Score=30.96 Aligned_cols=38 Identities=18% Similarity=0.326 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 7755899999999999964999889999828998798899
Q gi|254780444|r 2 TSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 2 ~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
..||.+++-++ .+|+ +.|.|.+++|+..||+.+||.++
T Consensus 4 ~~lt~~q~~~a-r~l~-~~G~~~~~iA~~~GVsr~Tiyr~ 41 (42)
T cd00569 4 PKLTPEQIEEA-RRLL-AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCCHHHHHHH-HHHH-HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 86999999999-9999-97898999999979799999865
No 63
>PRK08099 nicotinamide-nucleotide adenylyltransferase; Provisional
Probab=94.03 E-value=0.18 Score=29.58 Aligned_cols=144 Identities=12% Similarity=0.015 Sum_probs=78.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCC-CCCCCCC
Q ss_conf 999999996499988999982899879889975157887557798999998732187521000011112444-5442212
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRT-TEKKEKE 89 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~~~~~-~~~~~~~ 89 (223)
..|+..+++.|++..+.|..+|+....+++.. ++|.+.|+..+|.++-.+++.....-....+-.... .+.....
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~k~iGvifGkF~PlH~GH 80 (411)
T PRK08099 5 DYLKTAIKQQGCTLQQVADASGMTKGYLSQLL----NAKIKSPSAQKLEALHRFLGLEFPRRMKKIGVVFGKFYPLHTGH 80 (411)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCHHHHHHHHH----HCCCCCCCHHHHHHHHHHHCCCCHHHCCCCCEEEEEECCCCCCH
T ss_conf 89999999848829887654234099999986----25248943789999999958864022202337987640542428
Q ss_pred CCEEEECCC---------CCCCCCCCCCCCCCCCCE-EEECCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCEEEE
Q ss_conf 202431011---------345222111254446403-5643721135454200368559999628332421487868999
Q gi|254780444|r 90 IPLLYFPPS---------GSGGFFDSGVFPTGNKWN-TVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILIL 159 (223)
Q Consensus 90 ip~~~~~~~---------~~~~~~~~~~~~~~~~~~-~~~~p~~~~~~~~~~~~~~~~~~l~V~GDSM~P~i~~Gd~vlV 159 (223)
+-.+..+.. +....- +......++.- ...+.....+..-.|....+..+....-|+|.| +++|.-...
T Consensus 81 i~~I~~A~~~~D~L~Vvv~~d~~r-d~~l~~~s~m~~~~t~~dR~Rwl~q~f~d~~~I~v~~l~E~~ip~-yp~gW~~W~ 158 (411)
T PRK08099 81 IYLIQRACSQVDELHIIMGYDDTR-DRKLFEDSAMSQQPTVQDRLRWLLQTFKYQKNIRIHAFNEEGMEP-YPHGWDVWS 158 (411)
T ss_pred HHHHHHHHHCCCEEEEEEEECCCC-CCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCC-CCCCHHHHH
T ss_conf 999999973178589999407985-400033446544567899999999995447670899835679988-998668999
Q ss_pred E
Q ss_conf 3
Q gi|254780444|r 160 N 160 (223)
Q Consensus 160 d 160 (223)
+
T Consensus 159 ~ 159 (411)
T PRK08099 159 N 159 (411)
T ss_pred H
T ss_conf 9
No 64
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=93.90 E-value=0.21 Score=29.18 Aligned_cols=43 Identities=21% Similarity=0.329 Sum_probs=29.9
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 977558999999999999649998899998289987988997515
Q gi|254780444|r 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 1 ~~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
|.+|=.++..+-| +| +++|+||+++|+.+|.|.+.|+-.++..
T Consensus 1 ~~s~Lt~~q~~vL-~l-R~~G~tQ~eIA~~lgTSraNvs~iEk~A 43 (139)
T PRK03975 1 MDSFLTERQIEVL-RL-RKRGLTQQEIADILGTSRANISIIEKRA 43 (139)
T ss_pred CCCHHHHHHHHHH-HH-HHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9325689999999-99-9828979999999773288999999999
No 65
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=93.64 E-value=0.17 Score=29.78 Aligned_cols=72 Identities=11% Similarity=0.052 Sum_probs=45.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC-CCCC----CCCC---CCHHHHHHHHHHCCCCCCCCCC
Q ss_conf 755899999999999964999889999828998798899751-5788----7557---7989999987321875210000
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRF-GIEG----RNRW---PSTESIFKILAATNETICQLLD 74 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~-~~~g----~~r~---p~~~~l~kia~~~~v~~~~l~~ 74 (223)
...+++....+.+|-=..|+||+++|+++|+|..+++++-.. ...| +... ...+.-.++-+.++..-.+...
T Consensus 8 ~~~~~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~~a~VVp 87 (321)
T COG2390 8 LMEEERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLKEAIVVP 87 (321)
T ss_pred CHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEC
T ss_conf 12689999999999984688799999883988999999999999879389996798765399999999965997699974
No 66
>PRK09526 lacI lac repressor; Reviewed
Probab=93.34 E-value=0.12 Score=30.66 Aligned_cols=53 Identities=15% Similarity=0.082 Sum_probs=35.5
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 9964999889999828998798899751578875577989999987321875210
Q gi|254780444|r 17 AERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 17 ~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
|+++..|-.++|+++|||.+|+|+..++... -+.-..+.+.++++-+|-.++.
T Consensus 1 m~~k~~TikDIA~~agVS~sTVSrvLn~~~~--vs~~tr~rV~~~a~elgY~pn~ 53 (342)
T PRK09526 1 MKSKPVTLYDVARYAGVSYQTVSRVLNQASH--VSAKTREKVEAAMAELNYVPNR 53 (342)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHCCCCCH
T ss_conf 9989976999999989699999999789799--9999999999999983999788
No 67
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=93.27 E-value=0.21 Score=29.10 Aligned_cols=58 Identities=22% Similarity=0.216 Sum_probs=45.4
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 9999999996499988999982899879889975157887557798999998732187521000
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
.++|+.+|+..|+|+++||...| |.+-+|+.-+ | .|...++.+.|+..-+|++.+-+.
T Consensus 62 ve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~----~-rraLTle~ikkL~q~~gIpa~~lI 119 (120)
T COG5499 62 VEVIRTLMDQYGLTLADLANEIG-SKSRVSNILS----G-RRALTLEHIKKLHQRFGIPADVLI 119 (120)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHC-CHHHHHHHHH----H-HHHHHHHHHHHHHHHHCCCHHHHC
T ss_conf 89999999993871888899867-6188999973----2-067669999999998695888753
No 68
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=93.23 E-value=0.2 Score=29.27 Aligned_cols=43 Identities=19% Similarity=0.295 Sum_probs=36.1
Q ss_pred CCCCCHHHHHHHHHHHHHHCC---CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 977558999999999999649---9988999982899879889975
Q gi|254780444|r 1 MTSFSHKKIWEAIDRMAERHN---LTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 1 ~~~~~~~~i~~~i~~l~~~~g---ls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
|..||.++|..+==+|+.+.| +|...||+++|++++++..+..
T Consensus 1 ~a~Lsre~Iv~aAl~Lld~~Gl~alSMRrLA~~LgV~~~sLY~Hv~ 46 (205)
T PRK13756 1 MSRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVK 46 (205)
T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHHHHHCC
T ss_conf 9978999999999999982380006699999994899317898738
No 69
>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=93.17 E-value=0.22 Score=29.02 Aligned_cols=41 Identities=20% Similarity=0.267 Sum_probs=35.0
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 7755899999999999964999889999828998798899751
Q gi|254780444|r 2 TSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 2 ~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
.+||-++=.+.|+++ +.|-|.++||+..|+..+|++.|.+.
T Consensus 5 ~~LTl~eKi~iI~~~--e~G~s~~~lar~~gi~~STl~~I~Kn 45 (53)
T pfam04218 5 TSLTLREKIEVIQRS--EEGESKASLARRFNVPRSTLRDILKN 45 (53)
T ss_pred EEECHHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 141699999999999--85896889999969879799999980
No 70
>PRK02866 cyanate hydratase; Validated
Probab=93.03 E-value=0.66 Score=25.92 Aligned_cols=65 Identities=14% Similarity=0.044 Sum_probs=50.9
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 5589999999999996499988999982899879889975157887557798999998732187521000
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
+++.++-+.|-+...++|||=+++|+.+|+++.-+.....|-.. .+.+...++++.++.+-+...
T Consensus 1 m~r~~lte~i~~aK~~kgltw~~ia~~~G~s~v~~aaa~lGQ~~-----~~~e~A~~l~~~L~L~~~~~~ 65 (147)
T PRK02866 1 MKREELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMT-----LPAEEAEKVAELLGLDEDAVA 65 (147)
T ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC-----CCHHHHHHHHHHCCCCHHHHH
T ss_conf 98899999999999984998999998949899999999846778-----999999999997499999999
No 71
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=92.97 E-value=0.18 Score=29.55 Aligned_cols=52 Identities=10% Similarity=-0.022 Sum_probs=35.7
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 964999889999828998798899751578875577989999987321875210
Q gi|254780444|r 18 ERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 18 ~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
+++.+|.+++|+++|||.+|+|+.-++... -+.-..+.+.++++.+|-.+..
T Consensus 3 ~~kkvTi~dIA~~aGVS~aTVSrvLn~~~~--Vs~eTr~rV~~aa~elgY~pn~ 54 (342)
T PRK10014 3 TAKKITIHDVALAAGVSVSTVSLVLSGKGR--ISTATGERVNQAIEELGFVRNR 54 (342)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHCCCCCH
T ss_conf 999887999999989699999999779899--9999999999999994899786
No 72
>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=92.32 E-value=0.18 Score=29.66 Aligned_cols=41 Identities=22% Similarity=0.245 Sum_probs=28.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC------CCHHHHHHHH
Q ss_conf 9988999982899879889975157887557------7989999987
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRNRW------PSTESIFKIL 62 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~------p~~~~l~kia 62 (223)
||.++.|+.+||+++|+.+|.+...-.-.|. ...+.+.+++
T Consensus 1 lt~~e~A~~lgVs~~TlrrW~~~G~i~~~rt~~GhRry~~~dl~~ll 47 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERLL 47 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCEEECCCCCEEECHHHHHHHH
T ss_conf 98899999979899999999987994315889987761899999985
No 73
>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=91.79 E-value=0.36 Score=27.66 Aligned_cols=40 Identities=18% Similarity=0.258 Sum_probs=33.9
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 58999999999999649998899998289987988997515
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
|++++.+||++++... +|....|++-||+.+|+.+..++.
T Consensus 1 tee~l~~Al~av~~g~-~S~~kAa~~ygIP~sTL~~r~~g~ 40 (45)
T pfam05225 1 TEEDLAEALEAVRNGK-MSLRKAARKYGIPRSTLWRRLRGK 40 (45)
T ss_pred CHHHHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHHCCC
T ss_conf 9789999999999199-679999999789858999997563
No 74
>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=91.65 E-value=0.41 Score=27.25 Aligned_cols=37 Identities=16% Similarity=0.357 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 9999999999649998899998289987988997515
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
+.+-|+..+..++++|.+++..+|+|++.+++|-+.+
T Consensus 116 v~~~Ik~~m~~h~ipQ~~vv~~TGlnQS~lSq~LnkG 152 (177)
T pfam04814 116 VAKMIKSYMQQHNIPQREVVDATGLNQSHLSQHLNKG 152 (177)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHCC
T ss_conf 9999999998768846678761065599999999668
No 75
>PRK09492 treR trehalose repressor; Provisional
Probab=91.29 E-value=0.37 Score=27.59 Aligned_cols=51 Identities=12% Similarity=0.111 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 49998899998289987988997515788755779899999873218752100
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
+.+|-.++|+++|||.+|+|+.-++... -+.-..+.+.++++-+|-.++..
T Consensus 3 kkvTikDIA~~aGVS~aTVSrvLn~~~~--vs~eTr~rV~~~a~elgY~Pn~~ 53 (315)
T PRK09492 3 NKLTIKDIARLSGVGKSTVSRVLNNEPK--VSPRTRERVEAVINQHGFSPSKS 53 (315)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 9887999999989799999999789899--99999999999999969980778
No 76
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=91.04 E-value=0.32 Score=27.99 Aligned_cols=47 Identities=13% Similarity=0.064 Sum_probs=30.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf 98899998289987988997515788755779899999873218752
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETI 69 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~ 69 (223)
|-.++|+++|||.+|+|+.-++....+-+.-..+.+.++++-+|-.+
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 77
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=91.00 E-value=0.52 Score=26.61 Aligned_cols=42 Identities=24% Similarity=0.251 Sum_probs=31.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf 9999999964999889999828998798899751578875577989999987321
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~ 65 (223)
+|| +|..-.||+|.+-|.+.|||.+|+++.-. +.-.|+|+++
T Consensus 43 EAi-RL~D~egl~QeeaA~~MgVSR~Tf~ril~------------~ARkKvA~aL 84 (100)
T pfam02001 43 EAI-RLVDYEDYTQEEAAKLMGISRRTVWRLLT------------SARKKIADAL 84 (100)
T ss_pred HHH-HHHHHCCCCHHHHHHHCCCCHHHHHHHHH------------HHHHHHHHHH
T ss_conf 999-98736079899999884976999999999------------9999999998
No 78
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=90.62 E-value=1.4 Score=23.78 Aligned_cols=41 Identities=15% Similarity=0.288 Sum_probs=29.5
Q ss_pred CCCCC--HHHHHHHH-HHHHHHCCC-CHHHHHHHHCCCHHHHHHH
Q ss_conf 97755--89999999-999996499-9889999828998798899
Q gi|254780444|r 1 MTSFS--HKKIWEAI-DRMAERHNL-TPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 1 ~~~~~--~~~i~~~i-~~l~~~~gl-s~~~lA~~~Gv~~~ti~~~ 41 (223)
|++|| +.+|+.+| +..+++.+. --.+.|..++.++.|+.+-
T Consensus 1 ~~~LT~~QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNq 45 (294)
T COG2524 1 MKELTSSQKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQ 45 (294)
T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHH
T ss_conf 964218899999999999985378855599999874596169999
No 79
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=90.54 E-value=0.69 Score=25.79 Aligned_cols=50 Identities=16% Similarity=0.109 Sum_probs=33.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCH---HHHHHHHHHCCCCCCCCC
Q ss_conf 9988999982899879889975157887557798---999998732187521000
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPST---ESIFKILAATNETICQLL 73 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~---~~l~kia~~~~v~~~~l~ 73 (223)
+|-.+.|+++|||.+|+|+.-+|... ++..+. +.+.++++.+|-.++...
T Consensus 1 vTikDVA~~AGVS~aTVSrvLNg~~~--~~~Vs~~Tr~rV~~aa~eLgY~Pn~~A 53 (330)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGKAK--QYRISDKTVEKVMAVVREHNYHPNAVA 53 (330)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCC--CCCCCHHHHHHHHHHHHHHCCCCCHHH
T ss_conf 97899999979799899888389998--887699999999999999689948889
No 80
>PRK09480 slmA nucleoid occlusion protein; Provisional
Probab=90.46 E-value=1.2 Score=24.23 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHH
Q ss_conf 89999999999996499---98899998289987988997
Q gi|254780444|r 6 HKKIWEAIDRMAERHNL---TPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gl---s~~~lA~~~Gv~~~ti~~~~ 42 (223)
+++|.+++-++.++.|. |-++||+++|||+.++.++.
T Consensus 12 r~~Il~a~~~ll~~~~~~~iTt~~iA~~~gvs~aalYrHF 51 (194)
T PRK09480 12 REQILQTLAQMLESPPGERITTAKLAARVGVSEAALYRHF 51 (194)
T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf 9999999999986279764229999989099789999975
No 81
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=90.31 E-value=0.6 Score=26.19 Aligned_cols=37 Identities=27% Similarity=0.191 Sum_probs=25.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 988999982899879889975157887557798999998732
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAA 64 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~ 64 (223)
|-.++|+++|+|.+|+|+..++... .+.++-.++.++
T Consensus 1 Ti~DIA~~agVS~~TVSr~ln~~~~-----vs~~tr~rI~~~ 37 (46)
T pfam00356 1 TIKDVARLAGVSKATVSRVLNNPER-----VSEETREKVEAA 37 (46)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHH
T ss_conf 9999999989799999999879798-----999999999999
No 82
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=89.75 E-value=0.82 Score=25.31 Aligned_cols=42 Identities=24% Similarity=0.244 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHHHHHHCCC-CHHHHHHHHCCCHHHHHHHH
Q ss_conf 9775589999999999996499-98899998289987988997
Q gi|254780444|r 1 MTSFSHKKIWEAIDRMAERHNL-TPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 1 ~~~~~~~~i~~~i~~l~~~~gl-s~~~lA~~~Gv~~~ti~~~~ 42 (223)
|-+=+-|+-+++|-.|.++.|. +-+++|+.+||+++|++..-
T Consensus 1 M~T~s~EdYLe~Iy~L~~~~~~vr~~dIA~~L~Vs~~SVs~mi 43 (142)
T PRK03902 1 MPTPSMEDYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMV 43 (142)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 9894299999999999825897129999999789953399999
No 83
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=89.66 E-value=0.78 Score=25.45 Aligned_cols=55 Identities=9% Similarity=0.109 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf 999999999964999889999828------99879889975157887557798999998732187521
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAG------LDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~G------v~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~ 70 (223)
.....+..|-..|+||.+.+.++| .|++||.+.++-. .+..++.|+-.++..|+.
T Consensus 12 Fa~~fk~rRi~LG~TQ~dVG~aL~~l~g~~~SQttIcRFE~l~-------LS~kn~~kLkPiL~~WL~ 72 (75)
T smart00352 12 FAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQ-------LSFKNMCKLKPLLEKWLE 72 (75)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC-------CCHHHHHHHHHHHHHHHH
T ss_conf 9999999898737759999999998618643146888988605-------479889988999999987
No 84
>PRK04217 hypothetical protein; Provisional
Probab=89.52 E-value=0.8 Score=25.38 Aligned_cols=42 Identities=17% Similarity=0.261 Sum_probs=31.8
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf 9999999964999889999828998798899751578875577989999987321
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~ 65 (223)
+|| +|..-.||+|.+-|.+.|||.+|+++.-. +.-.|+|+++
T Consensus 49 Eai-RL~D~egl~qeeaA~~M~VSR~Tf~ril~------------~AR~KvA~aL 90 (110)
T PRK04217 49 EAL-RLVDYEGLTQEEAGKRMGVSRGTVWRALT------------SARKKVAQML 90 (110)
T ss_pred HHH-HHHHHCCCCHHHHHHHCCCCHHHHHHHHH------------HHHHHHHHHH
T ss_conf 999-98736079899999884976999999999------------9999999998
No 85
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=89.30 E-value=0.62 Score=26.09 Aligned_cols=40 Identities=13% Similarity=0.220 Sum_probs=36.5
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9775589999999999996499988999982899879889
Q gi|254780444|r 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 1 ~~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|++-..||...-++.|.++.-++-.+||+..|+|..||.+
T Consensus 1 ~~~kkeeR~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRR 40 (252)
T PRK10681 1 METRREERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRR 40 (252)
T ss_pred CCCCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9846999999999999986979999999887979989987
No 86
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=89.26 E-value=0.78 Score=25.45 Aligned_cols=39 Identities=13% Similarity=0.249 Sum_probs=32.6
Q ss_pred CHHHHHHHHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 589999999999996499---988999982899879889975
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNL---TPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gl---s~~~lA~~~Gv~~~ti~~~~~ 43 (223)
|+++|.++--++-.++|. |-+++|+++||+..+|..+.+
T Consensus 12 tR~~Il~AA~~lFaekGy~~ttl~dIA~~AGVS~GaiY~HF~ 53 (216)
T PRK10668 12 TRQHILDVALRLFSQQGVSATSLADIAKAAGVTRGAIYWHFK 53 (216)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 999999999999998493518899999996898579998759
No 87
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=89.24 E-value=0.84 Score=25.24 Aligned_cols=48 Identities=15% Similarity=0.132 Sum_probs=31.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 99889999828998798899751578875577989999987321875210
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
.|-.++|+++|||.+|+|+.-++... -+.-..+.+.+.++.+|-.++.
T Consensus 2 vTi~DVA~~AGVS~aTVSrvLn~~~~--Vs~eTr~rV~~aa~eLgY~Pn~ 49 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNSAL--VSPDTREAVMKAVSELGYRPNA 49 (346)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHCCCCCH
T ss_conf 97899999989799999999779499--9999999999999994998488
No 88
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=89.14 E-value=0.68 Score=25.84 Aligned_cols=16 Identities=19% Similarity=0.331 Sum_probs=11.8
Q ss_pred CCCCCCCEEEEECCCC
Q ss_conf 2148786899936897
Q gi|254780444|r 149 PLYRKGDILILNSAIQ 164 (223)
Q Consensus 149 P~i~~Gd~vlVd~~~~ 164 (223)
=.+.+||++++|.+.+
T Consensus 92 ~~l~pGd~~l~D~~~P 107 (303)
T PRK09685 92 VELAAGDITLIDASRP 107 (303)
T ss_pred EEECCCEEEEEECCCC
T ss_conf 9973986999988987
No 89
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=88.92 E-value=1.9 Score=22.93 Aligned_cols=36 Identities=14% Similarity=0.272 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHCC------------CCHHHHHHHHCCCHHHHHHH
Q ss_conf 8999999999999649------------99889999828998798899
Q gi|254780444|r 6 HKKIWEAIDRMAERHN------------LTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~g------------ls~~~lA~~~Gv~~~ti~~~ 41 (223)
.++|.+.|-.|.++.| +|+.+||..+|+++.|+++.
T Consensus 157 ~~Rla~~Ll~L~~~~g~~~~~~~~i~l~lt~~dLA~~lG~trEtVsR~ 204 (235)
T PRK11161 157 EERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRL 204 (235)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCEEEECCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999999999983877888877982378999998878989999999
No 90
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=88.80 E-value=0.9 Score=25.06 Aligned_cols=48 Identities=13% Similarity=0.046 Sum_probs=32.5
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 98899998289987988997515788755779899999873218752100
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
|-.++|+++|||.+|+|+.-++... -+.-..+.+.+.++.+|-.++..
T Consensus 3 TIkDIA~~AGVS~sTVSrvLN~~~~--Vs~~Tr~rV~~aa~eLgY~Pn~~ 50 (342)
T PRK10727 3 TIKDVARLAGVSVATVSRVINNSPK--ASEASRLAVHSAMESLSYHPNAN 50 (342)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 8899999979699999999779799--99999999999999939985888
No 91
>PRK11050 manganese transport regulator MntR; Provisional
Probab=88.46 E-value=0.87 Score=25.14 Aligned_cols=37 Identities=14% Similarity=0.141 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHCCCC-HHHHHHHHCCCHHHHHHHH
Q ss_conf 899999999999964999-8899998289987988997
Q gi|254780444|r 6 HKKIWEAIDRMAERHNLT-PSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gls-~~~lA~~~Gv~~~ti~~~~ 42 (223)
-|+-++.|..|.++.|.. ..++|+.+||+++|+++.-
T Consensus 38 ~EDYlE~I~~L~~~~G~aR~~DIA~~LgVs~pSVt~ml 75 (155)
T PRK11050 38 IEDYVELIADLIAEVGEARQVDIAARLGVSQPTVAKML 75 (155)
T ss_pred HHHHHHHHHHHHHCCCCEEHHHHHHHHCCCCHHHHHHH
T ss_conf 99999999999982695649999989099933199999
No 92
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=88.43 E-value=0.96 Score=24.88 Aligned_cols=47 Identities=11% Similarity=0.032 Sum_probs=30.1
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 9889999828998798899751578875577989999987321875210
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
|..++|+++|||.+|+|+..++... -+.-..+++.++++.+|--++.
T Consensus 2 TikDVA~~AGVS~sTVSrvln~~~~--Vs~eTr~rV~~a~~elgY~pn~ 48 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNGSPY--VSEETREKVLAAIKELGYRPNA 48 (333)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHCCCCCH
T ss_conf 6899999968999898898779998--7999999999999997899898
No 93
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=88.35 E-value=0.8 Score=25.37 Aligned_cols=32 Identities=13% Similarity=0.240 Sum_probs=27.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999999964999889999828998798899
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
|..|..|.++-++||++||+.+|+.++|+++.
T Consensus 43 ~~vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ 74 (144)
T PRK11512 43 FKVLCSIRCAACITPVELKKVLSVDLGALTRM 74 (144)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999869979999999978888789999
No 94
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=88.22 E-value=1 Score=24.66 Aligned_cols=48 Identities=13% Similarity=0.078 Sum_probs=31.4
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 98899998289987988997515788755779899999873218752100
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
|-.++|+++|+|.+|+|+..++... -+....+.+.++++.+|-.++..
T Consensus 2 Ti~dvA~~aGVS~sTVSr~ln~~~~--Vs~~tr~rV~~~a~~lgY~pn~~ 49 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNGNGR--VSEETREKVLAAMEELGYIPNRV 49 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 8999999989599999999779998--99999999999999978998999
No 95
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=88.21 E-value=0.34 Score=27.80 Aligned_cols=49 Identities=24% Similarity=0.153 Sum_probs=31.8
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCC--CCCCCCC
Q ss_conf 649998899998289987988997515788755779899999873218--7521000
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN--ETICQLL 73 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~--v~~~~l~ 73 (223)
-.| .|+++|+++||+++++|+|-++...+-+ +....|..+.. |+..+|.
T Consensus 11 vvg-~q~a~a~LLgvsp~~vnQw~~g~r~~~a-----~r~~aIerAt~g~Vs~~elr 61 (96)
T COG4197 11 VVG-GQKALARLLGVSPPSVNQWIKGRRQVAA-----ERALAIERATSGQVSREELR 61 (96)
T ss_pred HHC-CHHHHHHHHCCCCHHHHHHHHHEEECCC-----CCCHHHHHHHCCCCCHHHHC
T ss_conf 970-3899999972681478877652010475-----53328999853771599976
No 96
>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=88.09 E-value=0.52 Score=26.58 Aligned_cols=25 Identities=28% Similarity=0.320 Sum_probs=21.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 9988999982899879889975157
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGI 46 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~ 46 (223)
+|+.+||..+|++.++||+|-|..+
T Consensus 1 mT~eELa~~~G~srQtINkwaRkeG 25 (122)
T pfam07037 1 MTPEELAELTGYSRQTINRWVRKEG 25 (122)
T ss_pred CCHHHHHHHHCCHHHHHHHHHHHCC
T ss_conf 9878998874712999999999738
No 97
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=87.96 E-value=1.1 Score=24.47 Aligned_cols=48 Identities=13% Similarity=0.082 Sum_probs=31.5
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 98899998289987988997515788755779899999873218752100
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
|-.++|+++|||.+|+|+.-++.. +-+.-..+.+.++++.+|-.++..
T Consensus 11 TikDIA~~aGVS~sTVSrvLn~~~--~Vs~~Tr~rV~~aa~eLgY~pn~~ 58 (341)
T PRK11041 11 TMKDVALKAGVSTATVSRALMNPE--KVSQSTRNRVEQAVLEVGYSPQSL 58 (341)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCC--CCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 899999997979999999978989--999999999999999819983888
No 98
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=87.85 E-value=0.92 Score=25.00 Aligned_cols=32 Identities=16% Similarity=0.449 Sum_probs=26.2
Q ss_pred HHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999999999-64999889999828998798899
Q gi|254780444|r 10 WEAIDRMAE-RHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 10 ~~~i~~l~~-~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
|..|-.|.+ .-|+||++||+.+|+.++|+++.
T Consensus 34 ~~~L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ 66 (144)
T PRK03573 34 WVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRT 66 (144)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999997398989999999979878369999
No 99
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=87.84 E-value=1 Score=24.73 Aligned_cols=39 Identities=13% Similarity=0.317 Sum_probs=29.8
Q ss_pred CCCCHHHH-HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 77558999-9999999996499988999982899879889
Q gi|254780444|r 2 TSFSHKKI-WEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 2 ~~~~~~~i-~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
..+.-+++ ..-|+.|.+...+|-++||+++|+|++|+.+
T Consensus 3 ~~~klD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~stv~~ 42 (153)
T PRK11179 3 ENYQIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHV 42 (153)
T ss_pred CCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 6576789999999999984899999999998929999999
No 100
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=87.77 E-value=1.1 Score=24.39 Aligned_cols=48 Identities=10% Similarity=0.104 Sum_probs=31.4
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 98899998289987988997515788755779899999873218752100
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
|-.+.|+++|||.+|+|+.-++... -+.-..+++.++++.+|-.++..
T Consensus 3 TikDIA~~AGVS~aTVSrvLn~~~~--Vs~~Tr~rV~~aa~eLgY~pn~~ 50 (335)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINKTRF--VAEETRNAVWAAIKELHYSPSAV 50 (335)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 8899999979899999999689699--89999999999999829997877
No 101
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=87.75 E-value=0.44 Score=27.10 Aligned_cols=29 Identities=17% Similarity=0.153 Sum_probs=25.3
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 99649998899998289987988997515
Q gi|254780444|r 17 AERHNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 17 ~~~~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
++++||||+++|+.+|.+...+|..++..
T Consensus 19 lRekG~tQ~eIA~~L~TTraNvSaIEkrA 47 (143)
T COG1356 19 LREKGLTQSEIARILKTTRANVSAIEKRA 47 (143)
T ss_pred HHHCCCCHHHHHHHHCCCCCCHHHHHHHH
T ss_conf 26405648999999754510179999999
No 102
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=87.50 E-value=1.2 Score=24.36 Aligned_cols=42 Identities=24% Similarity=0.307 Sum_probs=31.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf 9999999964999889999828998798899751578875577989999987321
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~ 65 (223)
+|| +|..-.||+|.+.|.+.|||++|+.+.-+ ....|+++++
T Consensus 40 EAl-RLvD~~~l~QeeAA~rMgISr~Tfwr~l~------------sAR~KvA~aL 81 (99)
T COG1342 40 EAL-RLVDYEGLTQEEAALRMGISRQTFWRLLT------------SARKKVADAL 81 (99)
T ss_pred HHH-HHHHHHHCCHHHHHHHHCCCHHHHHHHHH------------HHHHHHHHHH
T ss_conf 899-98868610578999984642999999999------------9999999998
No 103
>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=87.22 E-value=0.56 Score=26.40 Aligned_cols=40 Identities=8% Similarity=0.184 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 5589999999999996499988999982899879889975157
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGI 46 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~ 46 (223)
||..|+- =|. ++++||+|+++|+.+|.+.+-+|-.++..-
T Consensus 7 LTe~Q~k-VL~--lR~kGl~Q~eIAk~LkTtRaNvS~iEkrA~ 46 (142)
T TIGR00721 7 LTERQIK-VLE--LREKGLKQKEIAKILKTTRANVSIIEKRAL 46 (142)
T ss_pred CHHHHHH-HHH--HHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 4065689-999--863388878898772672013789888744
No 104
>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=87.14 E-value=1.1 Score=24.43 Aligned_cols=33 Identities=27% Similarity=0.366 Sum_probs=27.9
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999999649998899998289987988997
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+..|..+.++-|+|+++||+.++++++++++.-
T Consensus 6 ~~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i 38 (59)
T pfam01047 6 FHILRILYEHGPLTVSELAEKLGVDRSTVTRVL 38 (59)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999994699299999999885865499999
No 105
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=86.87 E-value=1.3 Score=23.96 Aligned_cols=33 Identities=21% Similarity=0.392 Sum_probs=27.8
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999999649998899998289987988997
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
|..|..|..+-|+|+++||+.++++++++++.-
T Consensus 13 ~~vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v 45 (101)
T smart00347 13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVL 45 (101)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999997699799999999896887999999
No 106
>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=86.69 E-value=1.1 Score=24.46 Aligned_cols=34 Identities=12% Similarity=0.347 Sum_probs=27.6
Q ss_pred HHHHHHH---HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 8999999---9999996499988999982899879889
Q gi|254780444|r 6 HKKIWEA---IDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 6 ~~~i~~~---i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
++++..+ +.+|++. .+||.|+|.+.|+|-++|+|
T Consensus 39 r~dl~~R~~I~~~LL~~-~~~QREi~~~lG~SiA~ITR 75 (95)
T TIGR01321 39 REDLGSRVRIVEELLEG-EMSQREIAEKLGVSIATITR 75 (95)
T ss_pred HHHHHHHHHHHHHHHCC-CCCHHHHHHHHCCCHHHHHH
T ss_conf 99998799999999614-89747888863761667878
No 107
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=86.68 E-value=1.4 Score=23.84 Aligned_cols=40 Identities=10% Similarity=0.013 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 5589999999999996499---988999982899879889975
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNL---TPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gl---s~~~lA~~~Gv~~~ti~~~~~ 43 (223)
-|+++|..+=-++-.++|. |-+++|+++||+..+|..+..
T Consensus 11 ~TR~~Il~AA~~lFae~G~~~tTl~~IA~~AGVt~GaiY~HF~ 53 (213)
T PRK09975 11 KTRQELIETAIAQFALRGVANTTLNDIADAANVTRGAIYWHFE 53 (213)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 9999999999999998594558899999996898489998779
No 108
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=86.63 E-value=1.1 Score=24.39 Aligned_cols=38 Identities=11% Similarity=0.252 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 75589999999999996499988999982899879889
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|+..+|...-++.|.++.-++.++||+..|||..||.+
T Consensus 1 m~~~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRR 38 (253)
T COG1349 1 MLKEERHQKILELLKEKGKVSVEELAELFGVSEMTIRR 38 (253)
T ss_pred CCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 97778999999999985969799999885978999986
No 109
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=86.55 E-value=1.1 Score=24.38 Aligned_cols=38 Identities=8% Similarity=0.166 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 75589999999999996499988999982899879889
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|++.|+...-++.|.++.-++-.+||+..|||..||.+
T Consensus 1 M~~~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRR 38 (252)
T PRK10906 1 MKQTQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRR 38 (252)
T ss_pred CCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 98799999999999986989999999987969989988
No 110
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=86.46 E-value=0.91 Score=25.02 Aligned_cols=40 Identities=23% Similarity=0.481 Sum_probs=30.9
Q ss_pred CCHHHHHH-HHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 55899999-99999996499---988999982899879889975
Q gi|254780444|r 4 FSHKKIWE-AIDRMAERHNL---TPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 4 ~~~~~i~~-~i~~l~~~~gl---s~~~lA~~~Gv~~~ti~~~~~ 43 (223)
-|++.|.. |+..|..++|+ |-.++|+.+|++|+++.++..
T Consensus 11 ~TR~~lldAAl~~l~~~~gf~~lslreiar~aGv~~~afYrHF~ 54 (203)
T PRK11202 11 KTRRALIDAAFSQLSAERSFSSLSLREVAREAGIAPTSFYRHFK 54 (203)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCHHHHHCC
T ss_conf 99999999999998604893306799999984899751888759
No 111
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=86.31 E-value=2.4 Score=22.30 Aligned_cols=42 Identities=26% Similarity=0.312 Sum_probs=30.8
Q ss_pred CCHHHHHHH-HHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 558999999-9999996--49998899998289987988997515
Q gi|254780444|r 4 FSHKKIWEA-IDRMAER--HNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 4 ~~~~~i~~~-i~~l~~~--~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
|+|+++... |+-+-++ ..+|..+||+.+|+|+.++++..+..
T Consensus 1 m~~~~~i~~~~~yI~~h~~~~i~l~~lA~~~~~S~~~l~r~Fk~~ 45 (107)
T PRK10219 1 MSHQKIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 988999999999999866999999999989893999999999999
No 112
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=86.07 E-value=1.9 Score=22.89 Aligned_cols=30 Identities=27% Similarity=0.310 Sum_probs=26.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 999999996499988999982899879889
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
..|...+++.+.+++.-|+.+|++.+|+.+
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 113
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=85.64 E-value=2.9 Score=21.73 Aligned_cols=62 Identities=15% Similarity=0.146 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHC------------CCCHHHHHHHHCCCHHHHHHH----HHCC----CCCCCCCCCHHHHHHHHHHC
Q ss_conf 899999999999964------------999889999828998798899----7515----78875577989999987321
Q gi|254780444|r 6 HKKIWEAIDRMAERH------------NLTPSGLARKAGLDPTSFNKS----KRFG----IEGRNRWPSTESIFKILAAT 65 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~------------gls~~~lA~~~Gv~~~ti~~~----~~~~----~~g~~r~p~~~~l~kia~~~ 65 (223)
..++...|-+|.+.. .+|+.+||..+|.+..|+|+. ++.+ ..++-.-...+.|.++|+.-
T Consensus 118 ~~RlA~~Ll~L~~~~~~~~~~~~~i~l~lT~~eLA~~iGttREtVsR~L~~l~~~GlI~~~~~~I~I~D~~~L~~lAe~~ 197 (201)
T PRK13918 118 RARIAGELLELKDTALATQLDSGETMIYATHDELAAAVGSVRETVTKVVGELSREGVIRSGYGKIQLLDLKALKELAESR 197 (201)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCEEEEECHHHHHHHHHHC
T ss_conf 99999999999986087778995488057999999885986899999999999889889679989992899999998744
Q ss_pred CC
Q ss_conf 87
Q gi|254780444|r 66 NE 67 (223)
Q Consensus 66 ~v 67 (223)
|.
T Consensus 198 g~ 199 (201)
T PRK13918 198 GQ 199 (201)
T ss_pred CC
T ss_conf 79
No 114
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=85.62 E-value=1.3 Score=23.94 Aligned_cols=38 Identities=11% Similarity=0.085 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 75589999999999996499988999982899879889
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|+..||...-++.|.++.-++-.+||+..|||..||.+
T Consensus 1 M~~~eR~~~Il~~L~~~g~v~v~eLa~~l~VS~~TIRR 38 (256)
T PRK10434 1 MKPRQRQAAILEYLQKQGKCSVEELAQYFDTTGTTIRK 38 (256)
T ss_pred CCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 98899999999999986979999999987969989998
No 115
>pfam00157 Pou Pou domain - N-terminal to homeobox domain.
Probab=85.61 E-value=1.9 Score=22.94 Aligned_cols=55 Identities=9% Similarity=0.097 Sum_probs=40.0
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 99999999964999889999828------998798899751578875577989999987321875210
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAG------LDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~G------v~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
....+..|-..|+||.+...+.| .|+++|.+.++-. .+..++.|+-.++..|+.+
T Consensus 13 a~~fk~rRi~LG~TQ~dVg~al~~l~G~~~SQttIcRFE~l~-------Ls~kn~~kLkP~L~~WL~e 73 (75)
T pfam00157 13 AKEFKQRRIKLGYTQADVGLALGALYGPVFSQTTICRFEALQ-------LSFKNMCKLKPLLEKWLEE 73 (75)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC-------CCHHHHHHHHHHHHHHHHH
T ss_conf 999999898737759999999998708654235888888504-------4799899889999999874
No 116
>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=85.60 E-value=1.6 Score=23.47 Aligned_cols=38 Identities=18% Similarity=0.342 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHH
Q ss_conf 58999999999999649-998899998289987988997
Q gi|254780444|r 5 SHKKIWEAIDRMAERHN-LTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~g-ls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+-|+-+++|-.|.++.| .+.++||+++|++++|++..-
T Consensus 3 s~EdYLk~Iy~l~~~~~~v~~~~iA~~L~Vs~~SVt~ml 41 (58)
T pfam01325 3 STEDYLETIYTLSEEKGVVKTKDLAERLNVSPSTVSEML 41 (58)
T ss_pred CHHHHHHHHHHHHCCCCCEEHHHHHHHHCCCCHHHHHHH
T ss_conf 189999999998826996129999999599925299999
No 117
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=85.48 E-value=1 Score=24.69 Aligned_cols=29 Identities=21% Similarity=0.126 Sum_probs=23.2
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHCCCC
Q ss_conf 964999889999828998798899751578
Q gi|254780444|r 18 ERHNLTPSGLARKAGLDPTSFNKSKRFGIE 47 (223)
Q Consensus 18 ~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~ 47 (223)
+-.| |++.||+++||++++|++|.....+
T Consensus 8 ~~FG-sk~klA~aLgIs~~aVsqWge~IPE 36 (75)
T PRK09744 8 AFFG-SKTKLANAAGVRLASVAAWGELVPE 36 (75)
T ss_pred HHHC-CHHHHHHHHCCCHHHHHHHHHHCCH
T ss_conf 9961-2999999949987999887401606
No 118
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=85.33 E-value=0.84 Score=25.25 Aligned_cols=17 Identities=12% Similarity=0.018 Sum_probs=8.3
Q ss_pred CCCCCHHHHHHHHHHCC
Q ss_conf 55779899999873218
Q gi|254780444|r 50 NRWPSTESIFKILAATN 66 (223)
Q Consensus 50 ~r~p~~~~l~kia~~~~ 66 (223)
|+...-.+|.++.+.+.
T Consensus 152 PkGi~~~Tl~~i~~~~~ 168 (224)
T COG4565 152 PKGLDELTLQKVREALK 168 (224)
T ss_pred CCCCCHHHHHHHHHHHH
T ss_conf 87767999999999986
No 119
>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=85.26 E-value=2.4 Score=22.29 Aligned_cols=37 Identities=16% Similarity=0.231 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHCC--------CCHHHHHHHHCCCHHHHHHHH
Q ss_conf 8999999999999649--------998899998289987988997
Q gi|254780444|r 6 HKKIWEAIDRMAERHN--------LTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~g--------ls~~~lA~~~Gv~~~ti~~~~ 42 (223)
.+++.+.|-.|.++.| +|+.++|+.+|++..|+|+..
T Consensus 2 ~~Rla~~Ll~l~~~~g~~~~~~l~ltr~eiA~~lG~t~eTVsR~l 46 (67)
T cd00092 2 KERLASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTL 46 (67)
T ss_pred HHHHHHHHHHHHHHHCCCCEEECCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 689999999999975899666617799999999789099999999
No 120
>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=85.18 E-value=2 Score=22.84 Aligned_cols=42 Identities=21% Similarity=0.298 Sum_probs=33.0
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHH
Q ss_conf 99999964999889999828998798899751578875577989
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTE 56 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~ 56 (223)
++.|..-..++..+.|+.+|++.|++-+..|..+ -+|||...
T Consensus 7 ~~dl~~~F~lpi~~AA~~Lgv~~T~LKk~CR~~g--I~RWP~RK 48 (52)
T pfam02042 7 LEDLSKYFHLPIKEAAKELGVCLTVLKKICRQLG--IPRWPHRK 48 (52)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHCC--CCCCCHHH
T ss_conf 9999998187599999996877999999999879--98785787
No 121
>KOG3802 consensus
Probab=85.12 E-value=0.96 Score=24.88 Aligned_cols=58 Identities=9% Similarity=0.087 Sum_probs=44.7
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC
Q ss_conf 99999999964999889999828------998798899751578875577989999987321875210000
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAG------LDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLD 74 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~G------v~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~ 74 (223)
....+..|-++|+||.+.--++| .|+|||.|.|.-. .+.++++|+--.|..|+++...
T Consensus 212 AK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALq-------LSFKNMCKLKPLL~KWLeEAes 275 (398)
T KOG3802 212 AKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQ-------LSFKNMCKLKPLLEKWLEEAES 275 (398)
T ss_pred HHHHHHHEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHC-------CCHHHHHHHHHHHHHHHHHHHC
T ss_conf 999876500036442678889876507644302666767625-------4778776637999999999860
No 122
>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=84.91 E-value=2 Score=22.88 Aligned_cols=39 Identities=23% Similarity=0.319 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 7755899999999999964999889999828998798899
Q gi|254780444|r 2 TSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 2 ~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+.|+++.-..-+..|++. ++|.+++|+.+|++++++++.
T Consensus 2 ~~l~~~~r~~Il~~L~~~-~~~~~eia~~l~is~~~vs~h 40 (78)
T cd00090 2 KALSDPTRLRILRLLLEG-PLTVSELAERLGLSQSTVSRH 40 (78)
T ss_pred CCCCCHHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHH
T ss_conf 712799999999999848-906999987778487899999
No 123
>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=84.86 E-value=2.2 Score=22.50 Aligned_cols=34 Identities=9% Similarity=0.068 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 899999999999964999889999828998798899751
Q gi|254780444|r 6 HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
+++|.+++ +.|.|..+.|+..+|+..|+.+|.+.
T Consensus 8 R~rVl~~v-----e~G~S~~eaA~~F~Is~~Tv~rWlkr 41 (120)
T pfam01710 8 RKKVIDYI-----ESGGSITEASKVFQIGRATIYRWLKR 41 (120)
T ss_pred HHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 99999999-----86999999999937029999999855
No 124
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=84.80 E-value=2.3 Score=22.46 Aligned_cols=54 Identities=11% Similarity=0.223 Sum_probs=37.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC------CCHHH-----HHHHHHHCCCCCCCCCCC
Q ss_conf 9988999982899879889975157887557------79899-----999873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRNRW------PSTES-----IFKILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~------p~~~~-----l~kia~~~~v~~~~l~~~ 75 (223)
||-+++|+++|++..||..|++.+--...|. -+.+. +.+.+..+|.++++....
T Consensus 2 mtIgelA~~~gvs~~tiRyYE~~GLl~p~R~~~gyR~Y~~~~l~rl~~I~~~r~lGfsL~eI~~l 66 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEA 66 (139)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 97899999988788999999987884666789887704989999999999999859989999999
No 125
>PRK10870 transcriptional repressor MprA; Provisional
Probab=84.56 E-value=1.2 Score=24.24 Aligned_cols=38 Identities=21% Similarity=0.316 Sum_probs=23.6
Q ss_pred CCHHHHHHHHHHHHHHCCC-------------------CHHHHHHHHCCCHHHHHHH
Q ss_conf 5589999999999996499-------------------9889999828998798899
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNL-------------------TPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gl-------------------s~~~lA~~~Gv~~~ti~~~ 41 (223)
..+.++.++++++++++|| +|++||+++|++++++++.
T Consensus 35 ~v~~~l~~~~n~~L~~~GLs~~~f~vL~~L~~~~~~~l~PseLa~~l~~s~a~iTr~ 91 (176)
T PRK10870 35 HMQSKLLENRNKMLKAQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRI 91 (176)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999999998998829988899999999718999859899999977871019999
No 126
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=84.36 E-value=1.7 Score=23.21 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 755899999999999964999889999828998798899
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
|++.||...-++.|.++.-++-++||+..|||..||.+-
T Consensus 1 M~~~eR~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRRD 39 (251)
T PRK13509 1 MNEAQRHQILLDMLAQLGFVTVEKVIERLGISPATARRD 39 (251)
T ss_pred CCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHH
T ss_conf 988999999999999869898999999989699899983
No 127
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=84.30 E-value=1.9 Score=23.03 Aligned_cols=46 Identities=15% Similarity=0.055 Sum_probs=29.7
Q ss_pred HHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 899998289987988997515788755779899999873218752100
Q gi|254780444|r 25 SGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 25 ~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
.++|+++|||.+|+|+.-++... -+.-..+.+.++++.+|-.++..
T Consensus 2 kDIA~~AGVS~sTVSrvLn~~~~--Vs~~tr~rV~~aa~elgY~pn~~ 47 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVINKDRF--VSEAITAKVEAAIKELNYAPSAL 47 (327)
T ss_pred HHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 68987869899999999789599--99999999999999829986888
No 128
>PRK00767 transcriptional regulator BetI; Validated
Probab=84.06 E-value=2.7 Score=21.99 Aligned_cols=38 Identities=21% Similarity=0.241 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 89999999999996499---988999982899879889975
Q gi|254780444|r 6 HKKIWEAIDRMAERHNL---TPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gl---s~~~lA~~~Gv~~~ti~~~~~ 43 (223)
+++|.++--++..+.|+ |-.+.|+.+|+|+.+++.|..
T Consensus 11 R~~i~~Aa~~~i~~~G~~~~t~~~IA~~AGvs~g~v~~yF~ 51 (197)
T PRK00767 11 RQQLIDATLRSIGEVGLLDTTIAQIARRAGVSSGIISHYFG 51 (197)
T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 99999999999998593528899999995998999999908
No 129
>PRK11753 cAMP-regulatory protein; Provisional
Probab=83.65 E-value=3.2 Score=21.47 Aligned_cols=19 Identities=16% Similarity=0.286 Sum_probs=9.3
Q ss_pred CCHHHHHHHHCCCHHHHHH
Q ss_conf 9988999982899879889
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~ 40 (223)
+|+.+||..+|+++.|+++
T Consensus 169 lt~~eLA~~lG~sretvsR 187 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGR 187 (211)
T ss_pred CCHHHHHHHHCCCHHHHHH
T ss_conf 6999999886998999999
No 130
>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=83.19 E-value=1.8 Score=23.14 Aligned_cols=40 Identities=15% Similarity=0.094 Sum_probs=25.9
Q ss_pred HHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHH---HHHCCCCC
Q ss_conf 8999982899879889975157887557798999998---73218752
Q gi|254780444|r 25 SGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKI---LAATNETI 69 (223)
Q Consensus 25 ~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~ki---a~~~~v~~ 69 (223)
.++|+++|+|++|+++..++... .+-++..++ ++.+|..+
T Consensus 1 ~diA~~~gvS~~TVSr~ln~~~~-----Vs~~tr~~I~~~~~elgY~~ 43 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGKPR-----VSEETRERVLAAAEELGYRP 43 (52)
T ss_pred CHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHHHHCCCC
T ss_conf 92888878599999999879898-----99999999999999988897
No 131
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=83.14 E-value=1.7 Score=23.22 Aligned_cols=29 Identities=21% Similarity=0.536 Sum_probs=24.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 99999996499988999982899879889
Q gi|254780444|r 12 AIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 12 ~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
-|+.|.+.-.+|.++||+++|+|++|+.+
T Consensus 8 Il~~L~~n~R~s~~~iA~~lg~S~~tv~~ 36 (108)
T smart00344 8 ILEELQKDARISLAELAKKVGLSPSTVHN 36 (108)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 99999982899999999998939999999
No 132
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=83.06 E-value=2.5 Score=22.21 Aligned_cols=37 Identities=19% Similarity=0.391 Sum_probs=27.7
Q ss_pred CCHHHH-HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 558999-9999999996499988999982899879889
Q gi|254780444|r 4 FSHKKI-WEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 4 ~~~~~i-~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
..=+++ ..-|+.|.+....|+++||+++|+|++++.+
T Consensus 4 ~~lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~ 41 (154)
T COG1522 4 MKLDDIDRRILRLLQEDARISNAELAERVGLSPSTVLR 41 (154)
T ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 55379999999999972765799999997979899999
No 133
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=82.99 E-value=3.8 Score=21.00 Aligned_cols=43 Identities=19% Similarity=0.155 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCC
Q ss_conf 999889999828998798899751578875577989999987321875
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNET 68 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~ 68 (223)
-+|..+|++.+|+..+.+++|-+|..- |+.+...++.+.+.-.
T Consensus 23 ~~tykELs~~~gip~s~L~RYv~g~vl-----Ps~e~A~~i~~~l~~~ 65 (238)
T PRK08558 23 TYTYEELSSILGLPESVLSRYVNGHVL-----PSVERAREIVEKLKPY 65 (238)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHHHH
T ss_conf 268999998879799998505348878-----7589999999984211
No 134
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=82.90 E-value=3 Score=21.63 Aligned_cols=40 Identities=18% Similarity=0.238 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHH
Q ss_conf 7558999999999999649-998899998289987988997
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHN-LTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~g-ls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+.+-++-+.+|..+.++.| ...+++|+.++|+|+|++...
T Consensus 5 s~~~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml 45 (154)
T COG1321 5 SETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEML 45 (154)
T ss_pred CHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 21689999999999843687519999998589927899999
No 135
>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=82.75 E-value=3.5 Score=21.20 Aligned_cols=55 Identities=16% Similarity=0.260 Sum_probs=37.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC------CCCCCCCCHHH-----HHHHHHHCCCCCCCCCCCC
Q ss_conf 9988999982899879889975157------88755779899-----9998732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGI------EGRNRWPSTES-----IFKILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~------~g~~r~p~~~~-----l~kia~~~~v~~~~l~~~~ 76 (223)
||-+++|+++|++..||.-|++.+- ++.-|.-+.+. +.+.+..+|.++.++....
T Consensus 1 mtIgelA~~~gvs~~TiRyYE~~GLl~~~~r~~gyR~Y~~~~l~rl~~I~~~r~lGfsL~EI~~ll 66 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAML 66 (120)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 968999999886889898999649806544699841588999999999999999599999999988
No 136
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=82.67 E-value=1.6 Score=23.49 Aligned_cols=61 Identities=5% Similarity=0.002 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC-----CCCCCCCCCHHHHHHHHHHCC
Q ss_conf 77558999999999999649998899998289987988997515-----788755779899999873218
Q gi|254780444|r 2 TSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFG-----IEGRNRWPSTESIFKILAATN 66 (223)
Q Consensus 2 ~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~-----~~g~~r~p~~~~l~kia~~~~ 66 (223)
|-++-+++.++|++.++.+. .|+..-.++|..+-++.... ...-|+..+..+|.++.+++.
T Consensus 107 KPf~~erl~~~L~~y~~~~~----~l~~~~~~~Q~~iD~~~~~~~~~~~~~~lpKGl~~~Tl~~v~~~l~ 172 (225)
T PRK10046 107 KPIAYERLGQTLTRFRQRKH----MLESIDSASQKQIDEMFNAYARGEPKDELPTGIDPLTLNAVRKLFK 172 (225)
T ss_pred CCCCHHHHHHHHHHHHHHHH----HHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 89999999999999999999----8635776899999999623356888565899999899999999997
No 137
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=82.60 E-value=1.8 Score=23.03 Aligned_cols=30 Identities=17% Similarity=0.436 Sum_probs=26.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 999999996499988999982899879889
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
.-|+.|.+...+|.++||+++|+|++++.+
T Consensus 18 ~IL~~Lq~daR~s~~eLA~~vglS~stv~~ 47 (164)
T PRK11169 18 NILNELQKDGRISNVELSKRVGLSPTPCLE 47 (164)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999984899999999998929999999
No 138
>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=82.28 E-value=0.97 Score=24.84 Aligned_cols=53 Identities=19% Similarity=0.328 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHCC------CCCCCCCCCHH-----HHHHHHHHCCCCCCCCC
Q ss_conf 9998899998289987988997515------78875577989-----99998732187521000
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNKSKRFG------IEGRNRWPSTE-----SIFKILAATNETICQLL 73 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~~~~~~------~~g~~r~p~~~-----~l~kia~~~~v~~~~l~ 73 (223)
.||..+||+++||.-+.+..||.-+ ..|+-|=.+-+ .+.|+|...|+++.++.
T Consensus 1 ~lTvG~lA~R~GVAVSALHFYE~KGLI~S~Rn~GnQRRy~Rd~LRRVa~Ik~AQ~vGipL~~I~ 64 (142)
T TIGR01950 1 ELTVGELAKRAGVAVSALHFYESKGLIHSVRNAGNQRRYKRDVLRRVAVIKVAQRVGIPLAEIA 64 (142)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 9861016556557888776541035610113688834232001115674332332589888999
No 139
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=82.14 E-value=1.8 Score=23.08 Aligned_cols=41 Identities=17% Similarity=0.369 Sum_probs=30.8
Q ss_pred HHHHHH--HHHHHHHHCCCCHHHHHHHHCCCHHHHHH-HHHCCCC
Q ss_conf 899999--99999996499988999982899879889-9751578
Q gi|254780444|r 6 HKKIWE--AIDRMAERHNLTPSGLARKAGLDPTSFNK-SKRFGIE 47 (223)
Q Consensus 6 ~~~i~~--~i~~l~~~~gls~~~lA~~~Gv~~~ti~~-~~~~~~~ 47 (223)
|=.+.+ .|+++. +.|+|-.++|+.+|..++||++ .+|+...
T Consensus 7 hLT~~eR~~I~~l~-~~~~S~reIA~~LgRh~sTIsRElkRn~~~ 50 (318)
T COG2826 7 HLTLFERYEIERLL-KAKMSIREIAKQLNRHHSTISRELKRNRTR 50 (318)
T ss_pred HCCHHHHHHHHHHH-HCCCCHHHHHHHHCCCCCHHHHHHHCCCCC
T ss_conf 46888899999999-859989999998576862042798668752
No 140
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=81.75 E-value=2.2 Score=22.55 Aligned_cols=38 Identities=8% Similarity=0.204 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 7558999999999999649998899998289987988997
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
.++.++ ++.+.+|.++ |.+..++|+..|++.+||.++.
T Consensus 5 kl~~~~-~~~v~~L~~~-G~~i~~IA~~~~vsrsTvYRyl 42 (45)
T pfam02796 5 KLNEED-INEVITLLEE-GISIKQIAKIFGISRSTVYRYL 42 (45)
T ss_pred CCCHHH-HHHHHHHHHC-CCCHHHHHHHHCCHHHHHHHHC
T ss_conf 038999-9999999987-9949999999860088887644
No 141
>PRK09775 hypothetical protein; Provisional
Probab=81.48 E-value=2.6 Score=22.08 Aligned_cols=33 Identities=12% Similarity=0.281 Sum_probs=28.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 999999996499988999982899879889975
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
+.|..|+.+--++.++||.++|||++|+|+.-+
T Consensus 2 ~~l~~Ll~~Gp~~a~eLa~~lgvSqpTlSR~l~ 34 (443)
T PRK09775 2 SLLTTLLLQGPLSAAELAQRLGISQATLSRLLA 34 (443)
T ss_pred CHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 268999973993599999986888888999998
No 142
>PHA00675 hypothetical protein
Probab=81.44 E-value=3.8 Score=20.98 Aligned_cols=36 Identities=19% Similarity=0.093 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999999999649998899998289987988997
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+...++|..|++..||+...||.+..++.+||-++.
T Consensus 25 d~~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtIAkIC 60 (78)
T PHA00675 25 DAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKIC 60 (78)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 899999999998728438999999727568999998
No 143
>PRK07773 replicative DNA helicase; Validated
Probab=81.13 E-value=4.4 Score=20.57 Aligned_cols=52 Identities=21% Similarity=0.300 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCC
Q ss_conf 999999999999649998899998289987988997515788755779899999873218
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN 66 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~ 66 (223)
.++|+.+.+.+.+.|+|..+|++++|+.....+-|+ +.++.+.+.+++++++
T Consensus 710 ~evw~~Vr~a~~~~g~t~r~~~~~~g~~~~g~~~~k--------~~~SR~Rl~~~A~~l~ 761 (868)
T PRK07773 710 KKVWKQVRPRLQAKQMTTRQLHEPIGTSYCGSTLWK--------HSPSRERAHRVAARIQ 761 (868)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHC--------CCCCHHHHHHHHHHHC
T ss_conf 899999999998606548999987254546401320--------3422778999998747
No 144
>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=81.02 E-value=4.5 Score=20.54 Aligned_cols=54 Identities=24% Similarity=0.273 Sum_probs=36.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC-------CCCCCCHHHH-----HHHHHHCCCCCCCCCCC
Q ss_conf 998899998289987988997515788-------7557798999-----99873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEG-------RNRWPSTESI-----FKILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g-------~~r~p~~~~l-----~kia~~~~v~~~~l~~~ 75 (223)
+|-+++|+++|++..||..|++.+.-. .-|.-+.+.+ .+.+..+|.+++++...
T Consensus 1 m~IgevA~~~gvs~~TlRyYE~~GLl~~~~R~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~l 66 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAEL 66 (126)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 978999999893989999999869988763189996017799999999999999879989999999
No 145
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=80.86 E-value=3.9 Score=20.92 Aligned_cols=54 Identities=13% Similarity=0.144 Sum_probs=36.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC-C------CCCHHH-----HHHHHHHCCCCCCCCCCC
Q ss_conf 99889999828998798899751578875-5------779899-----999873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRN-R------WPSTES-----IFKILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~-r------~p~~~~-----l~kia~~~~v~~~~l~~~ 75 (223)
|+-++||+++|++..||.-|++.+--..+ | .-+.+. ..+-+..+|.++++....
T Consensus 1 M~IgelAk~tGv~~~TIRyYE~~GLl~~~~R~~~GyR~Y~~~~l~rL~fI~~ar~lGfsL~EI~~L 66 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGEL 66 (135)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 968999999896999999999838977343289992177899999999999998879999999999
No 146
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=79.98 E-value=4.2 Score=20.69 Aligned_cols=39 Identities=10% Similarity=0.199 Sum_probs=27.1
Q ss_pred CCHHHHH---HHHH--HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 5589999---9999--9999649998899998289987988997
Q gi|254780444|r 4 FSHKKIW---EAID--RMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 4 ~~~~~i~---~~i~--~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+|.+++- .+++ +.+-+.|.|+.++|..+|+|-+||++--
T Consensus 27 ~T~~E~~ala~R~~va~~LL~~~~syreI~~~~g~S~aTItRvs 70 (88)
T pfam01371 27 LTPDEREALAQRLRIAKELLRGELSQREIAQELGASIATITRGS 70 (88)
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999999999999999789989999998598523147889
No 147
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=79.89 E-value=3 Score=21.64 Aligned_cols=37 Identities=14% Similarity=0.263 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 5589999999999996499988999982899879889
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|+.||...-++.|.++.-++-.+||+..|||..||.+
T Consensus 1 Lk~eR~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRR 37 (240)
T PRK10411 1 MKAARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRR 37 (240)
T ss_pred CHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9489999999999986979999999988959989998
No 148
>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=79.86 E-value=3.4 Score=21.28 Aligned_cols=59 Identities=15% Similarity=0.326 Sum_probs=44.0
Q ss_pred HHHHHHH-HHCCCCHHH-HHHHHCCCHHHHHHHHHCCCCCCCCCCC--HHHHHHHHHHCCCCCCCC
Q ss_conf 9999999-964999889-9998289987988997515788755779--899999873218752100
Q gi|254780444|r 11 EAIDRMA-ERHNLTPSG-LARKAGLDPTSFNKSKRFGIEGRNRWPS--TESIFKILAATNETICQL 72 (223)
Q Consensus 11 ~~i~~l~-~~~gls~~~-lA~~~Gv~~~ti~~~~~~~~~g~~r~p~--~~~l~kia~~~~v~~~~l 72 (223)
++||++. .=.-+..++ |.+.+||+..|++|+++... .|.+. -+.|+|++.+...-.+-+
T Consensus 26 ~~ld~~aG~~~~~~k~esl~~~~gi~~atl~RR~~~~~---krl~~eES~RlaR~ArV~~~A~D~f 88 (138)
T TIGR02293 26 EVLDRLAGHYLAIGKAESLLKATGIPKATLQRRKKADN---KRLSSEESDRLARVARVLKAAVDVF 88 (138)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCC---CCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 78998876423887458999984463544788750679---8688212479999999999999652
No 149
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=79.85 E-value=3.4 Score=21.29 Aligned_cols=40 Identities=10% Similarity=0.063 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 7558999999999999649998899998289987988997
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
.|+++.=..-+..|.++..++..+|++.+|++++++|+.-
T Consensus 10 aLaD~tRl~Il~lL~~~gelcV~eL~~~l~~sQs~vS~HL 49 (106)
T PRK10141 10 ILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHL 49 (106)
T ss_pred HHCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9088999999999987499569999988699888999999
No 150
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=79.78 E-value=2.9 Score=21.76 Aligned_cols=39 Identities=5% Similarity=0.035 Sum_probs=28.4
Q ss_pred HHHHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 89999999-9999964999889999828998798899751
Q gi|254780444|r 6 HKKIWEAI-DRMAERHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 6 ~~~i~~~i-~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
+++|...| +.--+-..+|-++||+++|+|++||.|..+.
T Consensus 31 Ek~IA~yIL~~~~~v~~~si~eLA~~~~vS~aTVvRf~kk 70 (293)
T PRK11337 31 ESRVVDWLLKPGNLSCATALKDVAEALAVSEAMIVKVAKL 70 (293)
T ss_pred HHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999982989997666999998959988899999999
No 151
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=79.54 E-value=3 Score=21.63 Aligned_cols=25 Identities=28% Similarity=0.550 Sum_probs=21.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 9988999982899879889975157
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGI 46 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~ 46 (223)
.|-+++|+++|+++.||..|++.+.
T Consensus 1 ytI~eva~~~gvs~~tlR~ye~~gL 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
T ss_conf 9588999998939999999999799
No 152
>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=79.31 E-value=5.1 Score=20.19 Aligned_cols=56 Identities=16% Similarity=0.252 Sum_probs=34.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC------CCCCCCCHHHHHH------HHHHCCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578------8755779899999------87321875210000111
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE------GRNRWPSTESIFK------ILAATNETICQLLDLPF 77 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~------g~~r~p~~~~l~k------ia~~~~v~~~~l~~~~~ 77 (223)
.|-+++|+++|+++.|+.-|++.+-- +.-|.-+.+.+.+ +..++|.++.+.....+
T Consensus 1 ytIgevA~~~Gvs~~tlRyYE~~GLl~P~R~~~gyR~Y~~~dl~rL~~I~~l~~~lGfsL~eIk~lL~ 68 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLE 68 (96)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHC
T ss_conf 94889999989799999999987998998699998235999999999999999957998999999981
No 153
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=79.16 E-value=5 Score=20.23 Aligned_cols=39 Identities=18% Similarity=0.279 Sum_probs=29.9
Q ss_pred CHHHHHHHHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 589999999999996499---988999982899879889975
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNL---TPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gl---s~~~lA~~~Gv~~~ti~~~~~ 43 (223)
+.++|..+--.+..++|+ |-.++|+++|++.+++.++..
T Consensus 13 ~~~~ii~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~f~ 54 (201)
T COG1309 13 RRERILDAALRLFAEKGYAATTVDEIAKAAGVSKGTLYRHFP 54 (201)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 599999999999986593228999999887949789998878
No 154
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=78.77 E-value=3.2 Score=21.53 Aligned_cols=40 Identities=20% Similarity=0.120 Sum_probs=27.8
Q ss_pred HHHHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 899999999-9999649998899998289987988997515
Q gi|254780444|r 6 HKKIWEAID-RMAERHNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 6 ~~~i~~~i~-~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
.++|.+.|- ---+-..+|.++||+++|+|++||.|.-+.-
T Consensus 18 Ek~iA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkL 58 (284)
T PRK11302 18 ERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSL 58 (284)
T ss_pred HHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999999809899976669999989699888999999995
No 155
>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=78.39 E-value=1.3 Score=23.97 Aligned_cols=30 Identities=40% Similarity=0.545 Sum_probs=22.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999999649998899998289987988997
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+|| .|.+=.|+||.++|.++|+|-|+. +++
T Consensus 107 ~a~-~L~el~G~sQ~e~A~kLGlSlSGa-KSR 136 (170)
T TIGR02959 107 EAI-RLTELEGLSQKEIAEKLGLSLSGA-KSR 136 (170)
T ss_pred HHH-HHHHCCCCCHHHHHHHCCCCCCCH-HHH
T ss_conf 898-887507998279987617533515-678
No 156
>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=78.34 E-value=3.5 Score=21.22 Aligned_cols=24 Identities=13% Similarity=0.146 Sum_probs=20.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 998899998289987988997515
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
.|-+++|+.+||++.|+.-|++..
T Consensus 1 YtI~eva~~~Gv~~~tLRyyEk~~ 24 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEF 24 (67)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 978999999886878999998737
No 157
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=78.22 E-value=2.4 Score=22.33 Aligned_cols=29 Identities=10% Similarity=-0.159 Sum_probs=21.4
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 99649998899998289987988997515
Q gi|254780444|r 17 AERHNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 17 ~~~~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
+-=.|+|+.++|...|++.+++..|++..
T Consensus 118 ~~~~g~t~~EIA~~~gis~~~Vk~~~r~A 146 (154)
T PRK06759 118 RFFVGKTMGEIALETEMTYYQVRWIYRQA 146 (154)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99969989999999898999999999999
No 158
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=77.86 E-value=2.2 Score=22.60 Aligned_cols=49 Identities=14% Similarity=0.107 Sum_probs=28.3
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCC-----C-CCCHHHHHHHHHHCCCCCCC
Q ss_conf 9889999828998798899751578875-----5-77989999987321875210
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRN-----R-WPSTESIFKILAATNETICQ 71 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~-----r-~p~~~~l~kia~~~~v~~~~ 71 (223)
.-+..|.++||||.||.+|.+.-...-. . ...-+.|..++++-..-++.
T Consensus 2 kT~~vAk~LGVspkTVQRWvKq~ni~~~rNE~GHy~Ft~e~l~~lLk~~~~q~~q 56 (178)
T PRK13182 2 KTPFVAKKLGVSPKTVQRWVKQLNLPIERNEYGHYIFTEDDLDQLLKYHRSQIEQ 56 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEEECHHHHHHHHHHHHHHHHC
T ss_conf 7178899939992999999999589955365544332498999999999998605
No 159
>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=77.79 E-value=5.6 Score=19.90 Aligned_cols=40 Identities=15% Similarity=0.155 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 5589999999999996499---988999982899879889975
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNL---TPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gl---s~~~lA~~~Gv~~~ti~~~~~ 43 (223)
.-+++|.+|--++..++|+ |-.+.|+.+|+|..++..+..
T Consensus 8 ~RR~~il~Aa~~~i~~~G~~~~t~~~IA~~AGvS~G~v~~yF~ 50 (189)
T TIGR03384 8 IRRAELIDATIESIGERGSLDVTIAQIARRAGVSSGIISHYFG 50 (189)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 7999999999999998493528899999996999999999838
No 160
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=77.71 E-value=3.6 Score=21.17 Aligned_cols=31 Identities=13% Similarity=0.357 Sum_probs=24.9
Q ss_pred HHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999999649-99889999828998798899
Q gi|254780444|r 11 EAIDRMAERHN-LTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 11 ~~i~~l~~~~g-ls~~~lA~~~Gv~~~ti~~~ 41 (223)
.-|+.|++..+ +|.++||+.+|||..||.+.
T Consensus 4 ~il~~L~~~~~~vt~~~La~~l~VSr~TV~rd 35 (55)
T pfam08279 4 QILELLLQAREPISGQELAEKLGVSRRTIRRD 35 (55)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999997699918999999969889999999
No 161
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=77.53 E-value=2.5 Score=22.15 Aligned_cols=40 Identities=13% Similarity=0.252 Sum_probs=28.8
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 97755899999999999964999889999828998798899
Q gi|254780444|r 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 1 ~~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
|.|-.+|.+..-|++. ...|+.|+++.+.+|+|.+|++--
T Consensus 1 ~~M~~reklir~Lk~a-~~~GI~Q~eIeel~GlSKStvSEa 40 (321)
T COG3888 1 MLMSLREKLIRELKRA-GPEGIDQTEIEELMGLSKSTVSEA 40 (321)
T ss_pred CCCCHHHHHHHHHHHC-CCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9521789999999862-877765878898857456479999
No 162
>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=77.26 E-value=4.1 Score=20.82 Aligned_cols=26 Identities=19% Similarity=0.287 Sum_probs=23.4
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 64999889999828998798899751
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
=+|++++++|+.+|++..||..|++.
T Consensus 11 ~qg~~~~eIA~~Lg~~~~tVysWk~r 36 (58)
T pfam06056 11 WQGYRPAEIAQELGLKARTVYSWKDR 36 (58)
T ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHH
T ss_conf 96898999999978993145658652
No 163
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=77.20 E-value=5.8 Score=19.79 Aligned_cols=41 Identities=22% Similarity=0.129 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHC
Q ss_conf 7558999999999999649998899998289-98798899751
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGL-DPTSFNKSKRF 44 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv-~~~ti~~~~~~ 44 (223)
.+|.|.=. .|-++..+.|.|.+++|+..|| +++++.+|.+.
T Consensus 7 ~~s~EfK~-~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 7 KYSPEFKL-EAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred CCCHHHHH-HHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 48999999-9999998178359999999487753789999999
No 164
>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=77.06 E-value=5.9 Score=19.77 Aligned_cols=61 Identities=15% Similarity=0.132 Sum_probs=41.8
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHH-HCCCHHHHHHHHHCCCCCCCC----CCCHHHHHHHHHHCCC
Q ss_conf 558999999999999649998899998-289987988997515788755----7798999998732187
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARK-AGLDPTSFNKSKRFGIEGRNR----WPSTESIFKILAATNE 67 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~-~Gv~~~ti~~~~~~~~~g~~r----~p~~~~l~kia~~~~v 67 (223)
+--.+|...|...+++++++|+-||+. +|.++.|++..-+ +.||- .-+.+...++.+-++.
T Consensus 3 ldT~~i~~~i~~eL~~~~I~Q~~Fa~~vL~rsQGtlSdLL~---~PKPW~~l~~~gr~~y~RM~~wL~~ 68 (81)
T pfam02376 3 LDTAEIARRIKEELKRANISQALFAEVVLGRSQGSLSDLLR---RPKPWNKLLLKGREPFRRMQNFLSL 68 (81)
T ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHH---CCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 88999999999999994976999999997318378999881---8997788508506989999999868
No 165
>PRK09413 insertion sequence 2 OrfA protein; Reviewed
Probab=77.04 E-value=3.8 Score=20.97 Aligned_cols=33 Identities=21% Similarity=0.187 Sum_probs=28.0
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCC
Q ss_conf 996499988999982899879889975157887
Q gi|254780444|r 17 AERHNLTPSGLARKAGLDPTSFNKSKRFGIEGR 49 (223)
Q Consensus 17 ~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~ 49 (223)
--+-|.|.++.||+.|++++.+.+|++.-.+|.
T Consensus 25 s~ePG~sVs~VARrHGi~~~qlf~WRr~~~eG~ 57 (121)
T PRK09413 25 SFEPGMTVSLVARQHGVAASQLFLWRKQYQEGS 57 (121)
T ss_pred HHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf 956998499999994998999999999986212
No 166
>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=76.96 E-value=4 Score=20.89 Aligned_cols=40 Identities=25% Similarity=0.203 Sum_probs=27.8
Q ss_pred HHHHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 8999999-999999649998899998289987988997515
Q gi|254780444|r 6 HKKIWEA-IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 6 ~~~i~~~-i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
..+|... ++..-+-..+|-.+||+++|+|++||.|.-+.-
T Consensus 18 e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kkl 58 (106)
T pfam01418 18 EKKIADYILASPDNAIHLSIAELAKAAGVSEASVVRFCRKL 58 (106)
T ss_pred HHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999999929999988339999989699899999999995
No 167
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=76.46 E-value=3.8 Score=20.98 Aligned_cols=28 Identities=21% Similarity=0.311 Sum_probs=23.3
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999964999889999828998798899
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
|..|+ +..++.++||+.+|++++++++.
T Consensus 3 l~~L~-~~~~~~~ela~~l~is~~tvs~H 30 (66)
T smart00418 3 LKLLA-EGELCVCELAEILGLSQSTVSHH 30 (66)
T ss_pred HHHHH-CCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 88977-39966999999988298888799
No 168
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=76.46 E-value=6.1 Score=19.66 Aligned_cols=16 Identities=0% Similarity=-0.062 Sum_probs=8.3
Q ss_pred CCCCCHHHHHHHHHHC
Q ss_conf 5577989999987321
Q gi|254780444|r 50 NRWPSTESIFKILAAT 65 (223)
Q Consensus 50 ~r~p~~~~l~kia~~~ 65 (223)
|+..+..+|.++.+++
T Consensus 156 PKGl~~~TL~~i~~~l 171 (239)
T PRK10430 156 PKGLTPQTLRTLCQWI 171 (239)
T ss_pred CCCCCHHHHHHHHHHH
T ss_conf 9999999999999999
No 169
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR; InterPro: IPR014075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents members of the SufR cyanobacterial protein family of transcriptional regulators that control the SUF system. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus..
Probab=76.39 E-value=3.4 Score=21.32 Aligned_cols=36 Identities=14% Similarity=0.305 Sum_probs=29.1
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 589999999999996499988999982899879889975
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
|-++|++. |+++--.|..+||..++|||+.|.+.-|
T Consensus 2 TK~~IL~~---LL~~Gq~sA~~lA~~L~iSpQAvRrHLK 37 (215)
T TIGR02702 2 TKEDILEY---LLKEGQASALALAEELAISPQAVRRHLK 37 (215)
T ss_pred CHHHHHHH---HHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 57899999---8860048899999972788678876543
No 170
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=76.36 E-value=5.9 Score=19.76 Aligned_cols=36 Identities=22% Similarity=0.303 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999999999996-49998899998289987988997
Q gi|254780444|r 7 KKIWEAIDRMAER-HNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 7 ~~i~~~i~~l~~~-~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
++-.+-|+.+.++ .++|.+++|+.+|++.+|+.+.-
T Consensus 5 ~ral~IL~~l~~~~~~~sl~eia~~~~l~ksT~~RlL 41 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLL 41 (91)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999999728999899999999890999999999
No 171
>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=76.34 E-value=4.2 Score=20.74 Aligned_cols=31 Identities=23% Similarity=0.457 Sum_probs=24.6
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 999999649998899998289987988997515
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
|....+++| |...|+.+|+.++.|++.-|-.
T Consensus 5 L~dyv~~~G--Q~kaA~~lGV~Q~AISKAlrag 35 (58)
T pfam09048 5 LSDYVEEHG--QAKAAKDLGVNQSAISKALRAG 35 (58)
T ss_pred HHHHHHHHC--HHHHHHHCCCCHHHHHHHHHCC
T ss_conf 899999976--5989998297589999999648
No 172
>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=76.33 E-value=6.2 Score=19.64 Aligned_cols=54 Identities=17% Similarity=0.076 Sum_probs=36.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC-CCCCCC------CHHHH-----HHHHHHCCCCCCCCCCC
Q ss_conf 99889999828998798899751578-875577------98999-----99873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE-GRNRWP------STESI-----FKILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~-g~~r~p------~~~~l-----~kia~~~~v~~~~l~~~ 75 (223)
+|-+++|+++|++..||..|++.+-- .-.|.+ +.+.+ .+-+..+|.+++++...
T Consensus 1 ytIgelA~~~Gvs~~TiRyYe~~GLl~~~~Rt~~GyR~Y~~~~l~rL~fI~~~r~~G~sl~eI~~l 66 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARL 66 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 958899999788948998999878989988899988135999999999999999879999999999
No 173
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=76.33 E-value=4.3 Score=20.64 Aligned_cols=39 Identities=21% Similarity=0.227 Sum_probs=28.2
Q ss_pred HHHHHHHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 89999999999-9964999889999828998798899751
Q gi|254780444|r 6 HKKIWEAIDRM-AERHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 6 ~~~i~~~i~~l-~~~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
+++|...|-.- -+-..+|.++||+++|+|++||.|.-+.
T Consensus 18 Ek~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTVvRf~kk 57 (282)
T PRK11557 18 DRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQK 57 (282)
T ss_pred HHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999980989997656999998969998899999999
No 174
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=76.27 E-value=5.8 Score=19.83 Aligned_cols=35 Identities=23% Similarity=0.351 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999999999649-998899998289987988997
Q gi|254780444|r 8 KIWEAIDRMAERHN-LTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 8 ~i~~~i~~l~~~~g-ls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+-..-|+.|.+..+ ++.++||+++|++++|+.++-
T Consensus 5 ral~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL 40 (246)
T COG1414 5 RALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLL 40 (246)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999999718888879999998791988999999
No 175
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=76.19 E-value=5.6 Score=19.89 Aligned_cols=46 Identities=11% Similarity=0.176 Sum_probs=30.0
Q ss_pred HHHHHHH---HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCH
Q ss_conf 8999999---9999996499988999982899879889975157887557798
Q gi|254780444|r 6 HKKIWEA---IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPST 55 (223)
Q Consensus 6 ~~~i~~~---i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~ 55 (223)
++.++.+ +.+|+. ..+||.+++.+.|++-+||.+ |...-|...|..
T Consensus 43 Real~~Rv~Iv~eLL~-ge~sQREi~~~LgvsiAtITR---GSN~LK~~~~~~ 91 (103)
T COG2973 43 REALGTRVRIVEELLR-GELSQREIAQKLGVSIATITR---GSNSLKTADPEF 91 (103)
T ss_pred HHHHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHCC---CHHHHCCCCHHH
T ss_conf 9999999999999995-635399999985862565504---444423598789
No 176
>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=76.00 E-value=3.3 Score=21.42 Aligned_cols=24 Identities=13% Similarity=0.156 Sum_probs=21.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 999889999828998798899751
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
.+|+++||...|||+.||.+|-+.
T Consensus 2 ~vnk~elA~~~gVS~~tv~~W~~~ 25 (164)
T pfam07471 2 EVNKKQLAEIFGVSIRTIDNWQSQ 25 (164)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 678999999969888899999985
No 177
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=75.93 E-value=6.3 Score=19.57 Aligned_cols=58 Identities=19% Similarity=0.154 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC-----------CCCCCCCCCHHHHHHHHHHC
Q ss_conf 99999999999649998899998289987988997515-----------78875577989999987321
Q gi|254780444|r 8 KIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFG-----------IEGRNRWPSTESIFKILAAT 65 (223)
Q Consensus 8 ~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~-----------~~g~~r~p~~~~l~kia~~~ 65 (223)
+...++=.+-.-.|+|..++|.+.|++.+|+.+|.+.- +.|+|+..+.+.+.-+++.+
T Consensus 8 ~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~ 76 (138)
T COG3415 8 DLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERL 76 (138)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf 999999999997685499999996922999999998733353315676689997325889999999997
No 178
>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=75.63 E-value=4.7 Score=20.43 Aligned_cols=54 Identities=17% Similarity=0.265 Sum_probs=34.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC-CC------CCCCHHHH-----HHHHHHCCCCCCCCCCC
Q ss_conf 998899998289987988997515788-75------57798999-----99873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEG-RN------RWPSTESI-----FKILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g-~~------r~p~~~~l-----~kia~~~~v~~~~l~~~ 75 (223)
+|-+++|+++|+++.||..|++.+--. .. |.-+.+.+ .+.+..+|.++.++...
T Consensus 1 mtIgelAk~~gvs~~tlRyYE~~GLl~p~r~~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~ 66 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATV 66 (108)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 968999999897999999999779829987799985467999999999999999969999999999
No 179
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=75.24 E-value=4 Score=20.85 Aligned_cols=28 Identities=7% Similarity=0.128 Sum_probs=21.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999649998899998289987988997
Q gi|254780444|r 15 RMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 15 ~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
.|..-.|+|..++|+.+|+|.+||.++-
T Consensus 129 ~L~~~eGls~~EIA~~LgiS~~tVk~~l 156 (172)
T PRK12523 129 LYNRLDGMGHAEIAERLGVSVSRVRQYL 156 (172)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999939999999999893999999999
No 180
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=74.98 E-value=4.9 Score=20.27 Aligned_cols=39 Identities=28% Similarity=0.333 Sum_probs=26.3
Q ss_pred HHHHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 89999999-9999964999889999828998798899751
Q gi|254780444|r 6 HKKIWEAI-DRMAERHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 6 ~~~i~~~i-~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
..+|+..| +.--+-.-+|.++||+.+|||++||.|.-+.
T Consensus 20 er~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~k 59 (281)
T COG1737 20 ERKIADYILANPDEVALLSIAELAERAGVSPATVVRFARK 59 (281)
T ss_pred HHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999993967885614999998819988899999998
No 181
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=74.95 E-value=6.7 Score=19.41 Aligned_cols=33 Identities=6% Similarity=0.014 Sum_probs=25.9
Q ss_pred HHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999999996-49998899998289987988997
Q gi|254780444|r 10 WEAIDRMAER-HNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 10 ~~~i~~l~~~-~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+.-|+.+.+. .++|.++||+++|++.+|+.++-
T Consensus 28 l~IL~~la~~~~~ltl~eia~~lglpksT~~RlL 61 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLL 61 (271)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999747999799999999791999999999
No 182
>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=74.93 E-value=2.5 Score=22.23 Aligned_cols=51 Identities=14% Similarity=0.060 Sum_probs=33.6
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCC-CCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 98899998289987988997515788-7557798999998732187521000
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEG-RNRWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g-~~r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
|-+++||.+|||.||.|-.-||.++- |-+.-..+++..+++..+-.++-..
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 183
>PRK06930 positive control sigma-like factor; Validated
Probab=74.91 E-value=6.4 Score=19.54 Aligned_cols=28 Identities=14% Similarity=0.091 Sum_probs=20.0
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999649998899998289987988997
Q gi|254780444|r 15 RMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 15 ~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
-|....|+|.++.|..+|++.+|+...-
T Consensus 124 ll~~~~glsy~EIA~~L~Is~~tV~~~l 151 (170)
T PRK06930 124 LMHRGYGLSYSEIAAYLNIKKSTVQSMI 151 (170)
T ss_pred HHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 8897618889999999798899999999
No 184
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=74.51 E-value=6.7 Score=19.40 Aligned_cols=32 Identities=19% Similarity=0.162 Sum_probs=25.5
Q ss_pred HHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999999-649998899998289987988997
Q gi|254780444|r 11 EAIDRMAE-RHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 11 ~~i~~l~~-~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
.-|+.+.. +.++|.++||+++|++++|+.++-
T Consensus 15 ~ILe~l~~~~~~lslsela~~lglpksTv~RlL 47 (264)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLL 47 (264)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999987417999799999999790999999999
No 185
>pfam00376 MerR MerR family regulatory protein.
Probab=74.26 E-value=5.2 Score=20.12 Aligned_cols=25 Identities=20% Similarity=0.410 Sum_probs=21.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCC
Q ss_conf 9889999828998798899751578
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIE 47 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~ 47 (223)
|.+++|+++||+..||..|++.+.-
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 186
>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=74.25 E-value=4.8 Score=20.37 Aligned_cols=26 Identities=27% Similarity=0.489 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
Q ss_conf 99889999828998798899751578
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE 47 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~ 47 (223)
.+.++||+++|++..||..|++.+--
T Consensus 1 Yri~ElA~~~Gvs~~tiR~YE~~GLl 26 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGLI 26 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
T ss_conf 97899999989699999999996999
No 187
>PRK11642 exoribonuclease R; Provisional
Probab=74.10 E-value=7 Score=19.28 Aligned_cols=69 Identities=4% Similarity=-0.131 Sum_probs=40.5
Q ss_pred EECCCCCCCCCCCCCEEEEECCCCC----CCCCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCC-CCEEECHHH
Q ss_conf 9628332421487868999368974----0588899997179689999999779879999685898-875854786
Q gi|254780444|r 141 KTQDTSMLPLYRKGDILILNSAIQV----NCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCY-PVDTVEMSD 211 (223)
Q Consensus 141 ~V~GDSM~P~i~~Gd~vlVd~~~~~----~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y-~~~~i~~~~ 211 (223)
.+....|.-. -+||.|+|...... ..|.++-+.-.....++-++.... +...++++++.. .++.++.++
T Consensus 109 fI~~~~l~~a-~~GDrVlvr~~~~~r~gr~Eg~Vv~IleR~~~~ivG~~~~~~-~~~~v~P~d~ri~~~I~i~~~~ 182 (813)
T PRK11642 109 YLSSEQMKTC-IHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDA-GVGFVVPDDSRLSFDILIPPEQ 182 (813)
T ss_pred EECHHHHCCC-CCCCEEEEEEECCCCCCCCCEEEEEEEECCCCEEEEEEEEEC-CEEEEECCCCCCCCCEEECCCC
T ss_conf 0084674326-799999999824778898617999999518878999999808-7589935888877408955500
No 188
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=74.02 E-value=5.2 Score=20.11 Aligned_cols=34 Identities=15% Similarity=0.188 Sum_probs=24.6
Q ss_pred HHHHHHHHHHCC---CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 999999999649---9988999982899879889975
Q gi|254780444|r 10 WEAIDRMAERHN---LTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 10 ~~~i~~l~~~~g---ls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
.++=.+|..++| +|-.++|+++|++++++..+..
T Consensus 2 l~aA~~l~~~~G~~~~s~~~Ia~~agvs~~~iy~~F~ 38 (47)
T pfam00440 2 LDAALELFAEKGYDATTVREIAKEAGVSKGALYRHFP 38 (47)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 9999999998691507799999997969889998876
No 189
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=73.73 E-value=6.1 Score=19.68 Aligned_cols=42 Identities=10% Similarity=0.149 Sum_probs=35.7
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 977558999999999999649998899998289987988997
Q gi|254780444|r 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 1 ~~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
|.|..=+++..-|..|+....+|..+||+..|||.-||.+-.
T Consensus 2 ~~~~ka~RL~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RDi 43 (311)
T COG2378 2 RLMRKAERLLQIIQILRAKETVTAAELADEFEVSVRTIYRDI 43 (311)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHH
T ss_conf 305489999999999985760459999987298899999999
No 190
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=73.58 E-value=7.2 Score=19.19 Aligned_cols=35 Identities=20% Similarity=0.376 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999999996-49998899998289987988997
Q gi|254780444|r 8 KIWEAIDRMAER-HNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 8 ~i~~~i~~l~~~-~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+-.+-|+.+..+ .+++-+++|+.+|++++|+.++-
T Consensus 4 r~l~iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL 39 (52)
T pfam09339 4 RALAILEALAEAPGGLSLTEIARRTGLPKSTAHRLL 39 (52)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999998628999899999999891999999999
No 191
>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=73.37 E-value=4.6 Score=20.44 Aligned_cols=23 Identities=26% Similarity=0.400 Sum_probs=20.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 99889999828998798899751
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
.|-+++|+.+|+++.|+..|++.
T Consensus 1 YtI~eva~~~gv~~~tLR~wE~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 97899999988298999999985
No 192
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=73.12 E-value=4 Score=20.89 Aligned_cols=24 Identities=25% Similarity=0.375 Sum_probs=21.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 998899998289987988997515
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
.|-+++|+.+|+++.||..|++.+
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 193
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=73.07 E-value=3.3 Score=21.37 Aligned_cols=34 Identities=21% Similarity=0.208 Sum_probs=31.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 9999999964999889999828998798899751
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
.-+++.++-.|++|..+|+.+|+++++++++.+|
T Consensus 9 k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g 42 (297)
T COG2842 9 KKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNG 42 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCC
T ss_conf 9999999861666999998736684457878437
No 194
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=73.02 E-value=4.2 Score=20.74 Aligned_cols=24 Identities=21% Similarity=0.432 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 499988999982899879889975
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
++.|..+||+.+|++++|++..-|
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 195
>PRK11886 biotin--protein ligase; Provisional
Probab=73.01 E-value=7.5 Score=19.11 Aligned_cols=38 Identities=16% Similarity=0.215 Sum_probs=31.9
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 58999999999999649998899998289987988997
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
|++.+..-|+.|.+..=+|-.+||+.+|+|.++|.+.-
T Consensus 2 ~~~~~~~lL~~L~~g~~~SGe~la~~LgvSR~aVwK~i 39 (319)
T PRK11886 2 TYEKMLQLLSLLADGDFHSGEQLAEELGISRAAIWKHI 39 (319)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 17899999999737992969999998798899999999
No 196
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=72.93 E-value=6.1 Score=19.67 Aligned_cols=36 Identities=11% Similarity=0.258 Sum_probs=28.9
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 589999999999996499988999982899879889
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|.||...-++.|.++.-++-.+||+..|||..||.+
T Consensus 15 t~ER~~~Il~~L~~~g~v~v~eLae~~~VS~~TIRR 50 (269)
T PRK09802 15 TSERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRN 50 (269)
T ss_pred CHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 099999999999986989999999987969889998
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=72.68 E-value=6.3 Score=19.59 Aligned_cols=55 Identities=16% Similarity=0.212 Sum_probs=33.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC-------CCCCHHHH-----HHHHH-HCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578875-------57798999-----99873-2187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRN-------RWPSTESI-----FKILA-ATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~-------r~p~~~~l-----~kia~-~~~v~~~~l~~~~ 76 (223)
++-++||+++|++..||.-|++.+--..+ |.-+-+.+ .+-+. .+|.++.++....
T Consensus 1 M~IgelA~~tGvs~~TIRyYe~~GLL~p~~R~~~g~r~Y~~~~v~rL~~Ir~l~~~lG~sL~eIr~lL 68 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVL 68 (95)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 97899999989789999999997899987769998715499999999999999993699999999998
No 198
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator; InterPro: IPR014290 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents proteins belonging to the Rtf2 family of transcriptional regulators and are found, typically, as the first gene of the SUF operon. They are found only in a subset of the genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role..
Probab=72.49 E-value=1.9 Score=22.94 Aligned_cols=26 Identities=23% Similarity=0.433 Sum_probs=22.1
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99649998899998289987988997
Q gi|254780444|r 17 AERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 17 ~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
.++.-+|.++||+.+|++.+|+++.-
T Consensus 21 ~~~~~ySAA~lA~~tgL~~pTvsK~L 46 (130)
T TIGR02944 21 ADEQTYSAAELAEQTGLEAPTVSKIL 46 (130)
T ss_pred CCCCHHHHHHHHHHCCCCCCHHHHHH
T ss_conf 89970068887864598860478998
No 199
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=72.46 E-value=7.7 Score=19.03 Aligned_cols=55 Identities=20% Similarity=0.300 Sum_probs=35.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC-------CCCCHHH-----HHHHHHHCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578875-------5779899-----9998732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRN-------RWPSTES-----IFKILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~-------r~p~~~~-----l~kia~~~~v~~~~l~~~~ 76 (223)
++-+++|+.+||++.|+..|++.+.-..+ |--+.+. +.+.+...|+++..+....
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~sL~eI~~~l 67 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELL 67 (124)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9599999997969999999999089997635899976319999999999999998699899999999
No 200
>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=71.62 E-value=4.5 Score=20.52 Aligned_cols=55 Identities=16% Similarity=0.208 Sum_probs=36.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC-CC-------CCCCCHHHHH-----HHHHHCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578-87-------5577989999-----98732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE-GR-------NRWPSTESIF-----KILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~-g~-------~r~p~~~~l~-----kia~~~~v~~~~l~~~~ 76 (223)
+|-+++|+++|+++.|+.-|++-+-- .. -|.-+.+.+. +.+..+|.++.++....
T Consensus 1 ~tIgevAk~~gvs~~TlRyYE~~GLl~P~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sL~eI~~~l 68 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEIL 68 (108)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEECCCCCCEEECHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 97899999989599999999985998854156999844377889899999999999799999999998
No 201
>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=71.58 E-value=6.6 Score=19.44 Aligned_cols=56 Identities=16% Similarity=0.124 Sum_probs=36.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC------CCCCCCHHHHH-----HHHHHCCCCCCCCCCCCC
Q ss_conf 998899998289987988997515788------75577989999-----987321875210000111
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEG------RNRWPSTESIF-----KILAATNETICQLLDLPF 77 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g------~~r~p~~~~l~-----kia~~~~v~~~~l~~~~~ 77 (223)
+|-+++|+.+|+++.|+..|++.+.-. .-|.-+.+.+. +.+...|.++.++.....
T Consensus 1 ysI~eva~~~gvs~~tlR~Ye~~GLl~p~r~~~g~R~Y~~~~i~~l~~I~~lr~~G~sl~~I~~~l~ 67 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLD 67 (100)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 9788999998959999999987699998835899742569999999999999997999999999983
No 202
>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=71.04 E-value=4.1 Score=20.76 Aligned_cols=24 Identities=13% Similarity=0.218 Sum_probs=21.5
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 649998899998289987988997
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
..|++++++|+++|-+++-|+++-
T Consensus 1 ~~G~kk~~IAk~LGks~s~VS~hl 24 (93)
T pfam08535 1 AKGVKQAEIAKKLGKSKSFVSQHL 24 (93)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 998779999999788988999999
No 203
>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=70.63 E-value=4.8 Score=20.35 Aligned_cols=55 Identities=18% Similarity=0.289 Sum_probs=36.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC-------CCCCCCCHHHHH-----HHHHHCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578-------875577989999-----98732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE-------GRNRWPSTESIF-----KILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~-------g~~r~p~~~~l~-----kia~~~~v~~~~l~~~~ 76 (223)
+|-+++|+.+|+++.|+..|++.+-- +.-|.-+.+.+. +.+..+|.++.++....
T Consensus 1 ~tIge~Ak~~gvs~~tlRyYe~~GLl~p~~~~~ngyR~Y~~~~~~~l~~I~~lr~~G~~L~eIk~~l 67 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELL 67 (96)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9789999998869999999984399798724999985179999999999999999799999999999
No 204
>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=70.62 E-value=8.4 Score=18.76 Aligned_cols=39 Identities=21% Similarity=0.134 Sum_probs=30.0
Q ss_pred CHHHHHHHHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 589999999999996499---988999982899879889975
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNL---TPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gl---s~~~lA~~~Gv~~~ti~~~~~ 43 (223)
|++.|+++=-.+-.++|+ |-.++|+++|++++++..|..
T Consensus 9 ~r~~il~aa~~~f~~~G~~g~~~~~Ia~~ag~~k~~i~yyF~ 50 (202)
T TIGR03613 9 KRKAILSAALDTFSRFGFHGTSLEQIAELAGVSKTNLLYYFP 50 (202)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 999999999999998495648899999985998889999858
No 205
>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=70.60 E-value=8.4 Score=18.76 Aligned_cols=52 Identities=13% Similarity=0.185 Sum_probs=32.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC-------CCCCCCHHHHHHHH-----HHCCCCCCCCC
Q ss_conf 998899998289987988997515788-------75577989999987-----32187521000
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEG-------RNRWPSTESIFKIL-----AATNETICQLL 73 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g-------~~r~p~~~~l~kia-----~~~~v~~~~l~ 73 (223)
+|-+++|+.+|+++.++..|++...-. .-|.-+.+.+.++. ...|.++....
T Consensus 2 ~tIgeva~~~gvs~~tLRyye~~gli~p~~~~~~g~R~Ys~~dl~~l~~I~~l~~~G~sl~~i~ 65 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAV 65 (88)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 6789999998959999999999499899876999821479999999999999999799899999
No 206
>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=70.26 E-value=5.6 Score=19.91 Aligned_cols=40 Identities=23% Similarity=0.205 Sum_probs=26.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC-------CCCCCCCCHHHHHHH
Q ss_conf 9988999982899879889975157-------887557798999998
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGI-------EGRNRWPSTESIFKI 61 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~-------~g~~r~p~~~~l~ki 61 (223)
.|-+++|+.+||++.|+.-|++..+ ++.-|.-+.+.+.++
T Consensus 1 ysI~eva~~~Gv~~~tLR~wE~~~~l~~p~R~~~g~R~Ys~~di~~l 47 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREFGLLKPQRSDGGHRLFNDADIDRI 47 (68)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 97889999988794575898870589998679999965499999999
No 207
>pfam01402 RHH_1 Ribbon-helix-helix protein, copG family. The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement. The helix-turn-helix-like structure is involved in dimerization and not DNA binding as might have been expected.
Probab=69.76 E-value=6.5 Score=19.48 Aligned_cols=26 Identities=31% Similarity=0.520 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 89999999999996499988999982
Q gi|254780444|r 6 HKKIWEAIDRMAERHNLTPSGLARKA 31 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gls~~~lA~~~ 31 (223)
-++..+.|+.++++.|+|.|++-+.+
T Consensus 7 ~~~~~~~L~ela~~~g~S~S~~ir~a 32 (35)
T pfam01402 7 DEELAERLDELAKKRGLSRSELIREA 32 (35)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 49999999999997488689999998
No 208
>COG1438 ArgR Arginine repressor [Transcription]
Probab=69.61 E-value=8.8 Score=18.62 Aligned_cols=41 Identities=10% Similarity=0.196 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHHHCCC-CHHHHHHHHC-----CCHHHHHHHHH
Q ss_conf 75589999999999996499-9889999828-----99879889975
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNL-TPSGLARKAG-----LDPTSFNKSKR 43 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gl-s~~~lA~~~G-----v~~~ti~~~~~ 43 (223)
|++.++-.+.|+++..+..+ ||.+|.+.+- ++|+|+||.-+
T Consensus 1 ~~kk~~R~~~Ik~iI~~~~i~TQ~Elv~~L~~~Gi~vTQaTvSRDlk 47 (150)
T COG1438 1 MMKKEERLELIKEIITEEKISTQEELVELLQEEGIEVTQATVSRDLK 47 (150)
T ss_pred CCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCEEEHHHHHHHHH
T ss_conf 98478999999999986777789999999998297586398787799
No 209
>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=69.55 E-value=8.9 Score=18.62 Aligned_cols=50 Identities=18% Similarity=0.274 Sum_probs=31.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC------CCCCCCCCHHHHH------HHHHHCCCCCCC
Q ss_conf 9988999982899879889975157------8875577989999------987321875210
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGI------EGRNRWPSTESIF------KILAATNETICQ 71 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~------~g~~r~p~~~~l~------kia~~~~v~~~~ 71 (223)
.+-++.|+.+|+++.|+..|++.+- .|.-|.-+.+.+. ++....|.++..
T Consensus 2 Y~IgevA~l~Gv~~~tLR~yEr~gli~P~Rt~gG~R~Ys~~Dl~~L~~I~~L~~~~G~~l~g 63 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLGLVSPARTNGGGRRYSNNDLELLRQVQRLSQDEGFNLAG 63 (98)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf 35899999979899999999993897866189999434999999999999999958988999
No 210
>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=69.53 E-value=5.3 Score=20.05 Aligned_cols=55 Identities=11% Similarity=0.122 Sum_probs=36.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCC-------CCCCCHHH-----HHHHHHHCCCCCCCCCCCC
Q ss_conf 9988999982899879889975157887-------55779899-----9998732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGR-------NRWPSTES-----IFKILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~-------~r~p~~~~-----l~kia~~~~v~~~~l~~~~ 76 (223)
++-+++|+++|++..|+..|++.+--.. -|.-+.+. +.+.+..+|.++.++....
T Consensus 1 M~Ige~Ak~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~~~~l~~I~~~r~~G~sL~eI~~ll 67 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELL 67 (127)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9789999998959999999998589898651999984251999999999999998799899999998
No 211
>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=69.24 E-value=5.5 Score=19.98 Aligned_cols=55 Identities=16% Similarity=0.215 Sum_probs=36.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC-------CCCCHHH-----HHHHHHHCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578875-------5779899-----9998732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRN-------RWPSTES-----IFKILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~-------r~p~~~~-----l~kia~~~~v~~~~l~~~~ 76 (223)
++-+++|+++|+++.|+.-|++.+--... |.-+.+. ..+-+..+|.+++++....
T Consensus 1 M~Ige~A~~~gvs~~TlRyYe~~GLl~p~~r~~~GyR~Y~~~~~~~l~~I~~~r~~G~sL~eIr~ll 67 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEIL 67 (133)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9689999998978999999998599988622899945132999999999999998699999999999
No 212
>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=69.21 E-value=9 Score=18.57 Aligned_cols=35 Identities=20% Similarity=0.317 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 7558999999999999649998899998289987988997
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+|+-.+|..+| +.|.|..++|+.+|++-..|.++.
T Consensus 55 ~lspreIQarI-----RaGas~eevA~~~g~~~~rVerfa 89 (169)
T pfam11268 55 TLSPREIQARI-----RAGASAEEVAEAAGVPEERVERFE 89 (169)
T ss_pred CCCHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHCC
T ss_conf 88989999998-----879999999999599999987422
No 213
>PRK05066 arginine repressor; Provisional
Probab=69.09 E-value=8.2 Score=18.84 Aligned_cols=40 Identities=5% Similarity=0.231 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHHHHCCC-CHHHHHHHH---C---CCHHHHHHHHH
Q ss_conf 5589999999999996499-988999982---8---99879889975
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNL-TPSGLARKA---G---LDPTSFNKSKR 43 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gl-s~~~lA~~~---G---v~~~ti~~~~~ 43 (223)
-+.++..++|++|.+++.+ ||.+|++.+ | |+|+|+||--+
T Consensus 5 ~k~~~~~~aIk~lI~~~~I~tQeeL~~~L~~~G~~~VTQATvSRDlk 51 (156)
T PRK05066 5 AKQEELVKAFKALLKEEKFGSQGEIVTALQEQGFDNINQSKVSRMLT 51 (156)
T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 64699999999998518966799999999973986120888887899
No 214
>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=68.98 E-value=8.1 Score=18.87 Aligned_cols=55 Identities=22% Similarity=0.228 Sum_probs=35.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC------CCCCCCCHHHHH-----HHHHHCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578------875577989999-----98732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE------GRNRWPSTESIF-----KILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~------g~~r~p~~~~l~-----kia~~~~v~~~~l~~~~ 76 (223)
++-+++|+++|++..|+..|++.+-- +.-|.-+.+.+. +.+..+|.++.+.....
T Consensus 2 ~~Ige~A~~~gvs~~TlRyYe~~GLl~~~R~~ngyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l 67 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACL 67 (102)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 809999999897999999999869989881999995069999999999999999799899999998
No 215
>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=68.81 E-value=5.6 Score=19.92 Aligned_cols=55 Identities=16% Similarity=0.253 Sum_probs=36.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC-------CCCCCCCHHHH-----HHHHHHCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578-------87557798999-----998732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE-------GRNRWPSTESI-----FKILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~-------g~~r~p~~~~l-----~kia~~~~v~~~~l~~~~ 76 (223)
++-+++|+++|++..||..|++.+-- +.-|.-+.+.+ .+.+..+|.++.++....
T Consensus 1 m~IgelA~~~gvs~~tlRyYE~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~~r~~GfsL~eI~~ll 67 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALL 67 (126)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9689999998949999999998499898705899984278999999999999998799899999997
No 216
>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=68.03 E-value=8.6 Score=18.69 Aligned_cols=53 Identities=17% Similarity=0.258 Sum_probs=33.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC------CCCCCCCHHH---HHH---HHHHCCCCCCCCCC
Q ss_conf 99889999828998798899751578------8755779899---999---87321875210000
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE------GRNRWPSTES---IFK---ILAATNETICQLLD 74 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~------g~~r~p~~~~---l~k---ia~~~~v~~~~l~~ 74 (223)
.|-+++|+.+|+++.|+..|++.+-- +.-|.-+.+. |.. +++.+|.++.....
T Consensus 2 YtIgevA~~~Gvs~~tLR~yE~~GLl~P~R~~~g~R~Ys~~di~~l~~I~~L~~~~G~sl~~I~~ 66 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKR 66 (91)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf 65899999989299999999985997988399999744799999999999999986998999999
No 217
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=68.02 E-value=9.5 Score=18.41 Aligned_cols=45 Identities=22% Similarity=0.107 Sum_probs=30.1
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCC
Q ss_conf 999964999889999828998798899751578875577989999987321875
Q gi|254780444|r 15 RMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNET 68 (223)
Q Consensus 15 ~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~ 68 (223)
.|..-.|+|..++|..+|+|.+|+...-.. ....|.+.+++-+-+
T Consensus 133 ~L~~~eg~s~~EIAe~LgiS~~tVk~~l~r---------Al~~LR~~Le~~~~~ 177 (183)
T PRK07037 133 EMVRLRGETLQDIARELNVSQTLVNFMIRD---------ALRHCRKCLDACARG 177 (183)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHH---------HHHHHHHHHHHHCCC
T ss_conf 989873989999999989299999999999---------999999999876135
No 218
>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=67.90 E-value=6 Score=19.72 Aligned_cols=54 Identities=19% Similarity=0.322 Sum_probs=35.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC-CCC------CCCHHH-----HHHHHHHCCCCCCCCCCC
Q ss_conf 998899998289987988997515788-755------779899-----999873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEG-RNR------WPSTES-----IFKILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g-~~r------~p~~~~-----l~kia~~~~v~~~~l~~~ 75 (223)
|+-+++|+++|++..|+..|++.+.-. ..| .-+.+. +.+.+..+|.++.++...
T Consensus 1 m~Ige~A~~~gvs~~tlR~Ye~~GLl~~~~R~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~l 66 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIREL 66 (123)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEECCCCCEEEHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 968999999895999999999818987514679995621377878899999999869999999999
No 219
>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=67.53 E-value=9.8 Score=18.35 Aligned_cols=30 Identities=17% Similarity=0.246 Sum_probs=23.7
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9999996499988999982899879889975
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
|..|+ +.-++.++||+.+|++++++++.-+
T Consensus 8 l~~L~-~~~~~v~el~~~l~~sq~~vS~HL~ 37 (47)
T pfam01022 8 LYLLS-EGELCVCELAEILGLSQSTVSHHLK 37 (47)
T ss_pred HHHHH-CCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99998-0899699999998958869999999
No 220
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=67.27 E-value=9.9 Score=18.32 Aligned_cols=31 Identities=10% Similarity=0.271 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999999999964999889999828998798899
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.+...++++++. |-+.-|+++|++|+++|+.
T Consensus 26 LL~~F~al~e~~--svtrAA~~L~vSQpAvS~a 56 (314)
T PRK09508 26 LLTVFDAVMQEQ--NITRAAHNLGMSQPAVSNA 56 (314)
T ss_pred HHHHHHHHHHCC--CHHHHHHHHCCCHHHHHHH
T ss_conf 899999999829--9999999978986699999
No 221
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=67.15 E-value=9.9 Score=18.30 Aligned_cols=47 Identities=9% Similarity=0.145 Sum_probs=30.6
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 99964999889999828998798899751578875577989999987321875210
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
|+--.|+|..++|..+|++..|+...-.. ....|.+.++..|+..+|
T Consensus 142 l~~~e~~s~~EIA~~lgis~~tV~~~l~R---------Ar~~Lr~~L~~~g~~~g~ 188 (189)
T PRK12515 142 LVYYHEKSVEEVGEIVGIPESTVKTRMFY---------ARKKLAELLKAAGVERGW 188 (189)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHH---------HHHHHHHHHHHHCCCCCC
T ss_conf 99984999999999989299999999999---------999999999972833589
No 222
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=66.88 E-value=6.3 Score=19.58 Aligned_cols=22 Identities=23% Similarity=0.317 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 4999889999828998798899
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.-+|+.+||..+|+++.|+++.
T Consensus 7 l~lt~~~iA~~lG~tretvsR~ 28 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRT 28 (48)
T ss_pred ECCCHHHHHHHHCCCHHHHHHH
T ss_conf 3379999999979979999999
No 223
>PRK01905 DNA-binding protein Fis; Provisional
Probab=66.79 E-value=8.4 Score=18.76 Aligned_cols=28 Identities=18% Similarity=0.232 Sum_probs=25.0
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999996499988999982899879889
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|...++..+-+|+..|+.+|++..|+.+
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 224
>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=66.74 E-value=8.7 Score=18.66 Aligned_cols=30 Identities=10% Similarity=0.161 Sum_probs=25.6
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 999964999889999828998798899751
Q gi|254780444|r 15 RMAERHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 15 ~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
+.+++.|+++..++.++|++.+++|++..-
T Consensus 171 ~~l~~~g~~r~~I~~aL~vdks~lSrml~V 200 (325)
T TIGR03454 171 QRLEDRGFDRDTIMAALSVDKTELSRMISV 200 (325)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999984999999999988899999999999
No 225
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=66.60 E-value=7.7 Score=19.01 Aligned_cols=56 Identities=20% Similarity=0.232 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCCCCCC-C------CCCCHHH-----HHHHHHHCCCCCCCCCCC
Q ss_conf 499988999982899879889975157887-5------5779899-----999873218752100001
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKSKRFGIEGR-N------RWPSTES-----IFKILAATNETICQLLDL 75 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~-~------r~p~~~~-----l~kia~~~~v~~~~l~~~ 75 (223)
.+++-++||+++|++..||..|++.+.-.. . |.-+.+. ..+-+..+|.++++....
T Consensus 6 ~~m~IgelAk~~gvs~~tIRyYE~~GLl~~~~R~~~gyR~Y~~~~v~rL~fI~~~r~lGfsL~eI~~L 73 (144)
T PRK13752 6 ENLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAEL 73 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 23829999999789845667987259979877799998247999999999999999879989999999
No 226
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=66.29 E-value=10 Score=18.19 Aligned_cols=35 Identities=6% Similarity=0.206 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 5589999999999996499988999982899879889
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|+.|+ +++|....+.+| |-.++|+..|+|++|+..
T Consensus 34 L~~E~-l~Fi~~fi~~~G-nlke~~~~lgiSYpTvR~ 68 (113)
T pfam09862 34 LTPEQ-LEFVELFIKCRG-NIKEVEKELGISYPTVRN 68 (113)
T ss_pred CCHHH-HHHHHHHHHHCC-CHHHHHHHHCCCCHHHHH
T ss_conf 89999-999999999168-899999997888188999
No 227
>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=66.01 E-value=6.9 Score=19.32 Aligned_cols=55 Identities=15% Similarity=0.221 Sum_probs=36.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCC-CCCC------CHHH-----HHHHHHHCCCCCCCCCCCC
Q ss_conf 9988999982899879889975157887-5577------9899-----9998732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGR-NRWP------STES-----IFKILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~-~r~p------~~~~-----l~kia~~~~v~~~~l~~~~ 76 (223)
++-++||+++|++..||..|++.+--.. .|.. +.+. +.+-+..+|.+++++....
T Consensus 1 M~IgelA~~~gvs~~tlR~YE~~GLl~p~~r~~nGyR~Y~~~~i~~l~~I~~~r~lGfsL~eI~~ll 67 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLL 67 (131)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9789999998878899999997799898776999975349999999999999999699999999986
No 228
>pfam08822 DUF1804 Protein of unknown function (DUF1804). This family of bacterial protein is uncharacterized.
Probab=65.99 E-value=10 Score=18.16 Aligned_cols=39 Identities=26% Similarity=0.204 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 999999999996499988999982899879889975157
Q gi|254780444|r 8 KIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGI 46 (223)
Q Consensus 8 ~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~ 46 (223)
+...++.++---.++|-...|.++||+.+|..+|++...
T Consensus 6 e~r~~vR~~Yv~~~~~Le~aA~~~gV~~~TArrWK~~Ak 44 (165)
T pfam08822 6 ETRDAVRRLYVFDRLTLEVAAAKAGVSYSTARRWKREAK 44 (165)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 999999999996678799999880998888999999888
No 229
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=65.89 E-value=10 Score=18.15 Aligned_cols=25 Identities=20% Similarity=0.311 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 4999889999828998798899751
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
.++|-++||+.+|+|++|..+|-..
T Consensus 18 ~~~t~~ela~~l~~S~qta~R~l~~ 42 (214)
T COG1339 18 VKVTSSELAKRLGVSSQTAARKLKE 42 (214)
T ss_pred CCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf 6020899998857470778899886
No 230
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=65.71 E-value=11 Score=18.12 Aligned_cols=20 Identities=20% Similarity=0.424 Sum_probs=13.9
Q ss_pred CCHHHHHHHHCCCHHHHHHH
Q ss_conf 99889999828998798899
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~ 41 (223)
+|+.+||..+|+++.|+++.
T Consensus 174 ~t~~~lA~~lG~tretvsR~ 193 (236)
T PRK09392 174 YEKRTLASYLGMTPENLSRA 193 (236)
T ss_pred CCHHHHHHHHCCCHHHHHHH
T ss_conf 78999999878989999999
No 231
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=65.71 E-value=11 Score=18.12 Aligned_cols=37 Identities=24% Similarity=0.357 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9999999999996--499988999982899879889975
Q gi|254780444|r 7 KKIWEAIDRMAER--HNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 7 ~~i~~~i~~l~~~--~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
++|..+++.+.++ .-+|-.+||+.+|+|+-++++..+
T Consensus 216 ~~l~~~~~~i~~~l~~~ls~~~lA~~~~~S~R~l~R~Fk 254 (320)
T PRK09393 216 DRLGPLIDWMRAHLAQPHTVASLAARAAMSPRTFLRRFE 254 (320)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 589999999996111478899999997879879998997
No 232
>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=65.43 E-value=4.1 Score=20.76 Aligned_cols=38 Identities=21% Similarity=0.253 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf 49998899998289987988997515788755779899999873
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILA 63 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~ 63 (223)
.=+.|..+|+.+|+..+.||+|+.+= .|....|..+++
T Consensus 22 a~~gq~~~A~~~Gv~es~ISRwK~~~------~~~~smllAvLE 59 (91)
T pfam05269 22 AMLGQRKTAEAVGVDESQISRWKRDW------IPKFSMLLAVLE 59 (91)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHH------HHHHHHHHHHHH
T ss_conf 99843668999688899863444306------999999999999
No 233
>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=65.37 E-value=11 Score=18.08 Aligned_cols=55 Identities=16% Similarity=0.181 Sum_probs=36.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC------CCCCCCHHHH-----HHHHHHCCCCCCCCCCCC
Q ss_conf 998899998289987988997515788------7557798999-----998732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEG------RNRWPSTESI-----FKILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g------~~r~p~~~~l-----~kia~~~~v~~~~l~~~~ 76 (223)
+|-+++|+++|++..|+.-|++.+--. .-|.-+.+.+ .+.+..+|.++.++....
T Consensus 2 ~~Ige~a~~~gis~~tlRyYe~~GLl~~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sL~eIk~lL 67 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCL 67 (102)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 878999999894999999999879999873999996378999999999999999699999999998
No 234
>PRK13832 plasmid partitioning protein; Provisional
Probab=65.27 E-value=11 Score=18.07 Aligned_cols=39 Identities=21% Similarity=0.296 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 5589999999999996499988999982899879889975
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
|+--+.|.+|.+| .+.|+|..++|.++++++-.|.+.+.
T Consensus 102 mnpvDqWRaierl-valGwTeeaIa~ALal~vrqiRkLrL 140 (518)
T PRK13832 102 LNPVDQWRAIERL-VALGWTEEAIAVALALPVRQIRKLRL 140 (518)
T ss_pred CCHHHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9869999999999-98499889999996689999999999
No 235
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.06 E-value=6.1 Score=19.68 Aligned_cols=25 Identities=16% Similarity=0.377 Sum_probs=19.4
Q ss_pred CCCCCHHHHH---HHHHHHHHHCCCCHHH
Q ss_conf 9775589999---9999999964999889
Q gi|254780444|r 1 MTSFSHKKIW---EAIDRMAERHNLTPSG 26 (223)
Q Consensus 1 ~~~~~~~~i~---~~i~~l~~~~gls~~~ 26 (223)
|-+|||++-. ++|+.||.+ |+|-.+
T Consensus 5 lp~LtHeqQQ~AVE~Iq~lMae-GmSsGE 32 (60)
T COG3140 5 LPSLTHEQQQKAVERIQELMAE-GMSSGE 32 (60)
T ss_pred CCCCCHHHHHHHHHHHHHHHHC-CCCCHH
T ss_conf 5555679999999999999981-144006
No 236
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=64.06 E-value=9.7 Score=18.37 Aligned_cols=27 Identities=30% Similarity=0.332 Sum_probs=15.2
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999964999889999828998798899
Q gi|254780444|r 15 RMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 15 ~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.|+.-.|+|..++|..+|+|..|+...
T Consensus 129 ~L~~~egls~~EIA~~lgiS~~tVk~~ 155 (172)
T PRK09651 129 LLSQLDGLTYSEIAHKLGVSISSVKKY 155 (172)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999883999999999989399999999
No 237
>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=63.76 E-value=7.6 Score=19.05 Aligned_cols=53 Identities=15% Similarity=0.121 Sum_probs=34.0
Q ss_pred HHHHHHHHCCCHHHHHHHHHCCC-CCCCCCCCH------HHHH-----HHHHHCCCCCCCCCCCC
Q ss_conf 88999982899879889975157-887557798------9999-----98732187521000011
Q gi|254780444|r 24 PSGLARKAGLDPTSFNKSKRFGI-EGRNRWPST------ESIF-----KILAATNETICQLLDLP 76 (223)
Q Consensus 24 ~~~lA~~~Gv~~~ti~~~~~~~~-~g~~r~p~~------~~l~-----kia~~~~v~~~~l~~~~ 76 (223)
-.+||++++|++.|+.-|++.+- +.-.|+-+. +..+ .-|+.+|.+++++..+-
T Consensus 4 IGeLAklc~V~~DTlRfYEK~gl~~p~~RtdsGYRlYtd~d~~rlRFIl~AK~lGftLdeI~eLL 68 (132)
T TIGR02043 4 IGELAKLCDVTADTLRFYEKNGLLKPAERTDSGYRLYTDEDLKRLRFILKAKELGFTLDEIKELL 68 (132)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 02247661798433347767743055667787653417756898889998877468788878763
No 238
>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=63.72 E-value=12 Score=17.88 Aligned_cols=54 Identities=17% Similarity=0.208 Sum_probs=33.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC------CCCCHHHH-----HHHHHHCCCCCCCCCCC
Q ss_conf 99889999828998798899751578875------57798999-----99873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRN------RWPSTESI-----FKILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~------r~p~~~~l-----~kia~~~~v~~~~l~~~ 75 (223)
+.-+++|+++|++..|+..|++.+--.-. |.-+.+.+ .+.+..+|.++.++...
T Consensus 1 M~Ige~a~~~gvs~~tlRyYe~~GLl~p~r~~~gyR~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~ 65 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREF 65 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 96899999989799999999984899998089987005999999999999999969999999999
No 239
>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=63.48 E-value=8.2 Score=18.84 Aligned_cols=53 Identities=23% Similarity=0.241 Sum_probs=34.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC-------CCCCCCHHHH-----HHHHHHCCCCCCCCCC
Q ss_conf 998899998289987988997515788-------7557798999-----9987321875210000
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEG-------RNRWPSTESI-----FKILAATNETICQLLD 74 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g-------~~r~p~~~~l-----~kia~~~~v~~~~l~~ 74 (223)
.|-+++|+++||+..|+.-|++-+.-. .-|.-+.+.+ .+.+..+|.+++++..
T Consensus 1 ytIgelA~~~gvs~~tlRyYe~~GLl~~~~r~~~gyR~Y~~~~v~rl~~I~~lr~lG~sL~eI~~ 65 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKE 65 (113)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf 97889999989599999999983897998408998862349898999979759987998999999
No 240
>PRK11569 transcriptional repressor IclR; Provisional
Probab=63.20 E-value=12 Score=17.82 Aligned_cols=32 Identities=22% Similarity=0.373 Sum_probs=25.4
Q ss_pred HHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999999999-64999889999828998798899
Q gi|254780444|r 10 WEAIDRMAE-RHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 10 ~~~i~~l~~-~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+.-|+.+.. +.++|-++||+++|++.+|+.++
T Consensus 31 l~IL~~la~~~~~lsl~eia~~lglpksT~~Rl 63 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRL 63 (274)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999963899989999999879199999999
No 241
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=63.19 E-value=12 Score=17.82 Aligned_cols=24 Identities=25% Similarity=0.207 Sum_probs=21.4
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 964999889999828998798899
Q gi|254780444|r 18 ERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 18 ~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.+.|+|-++-|+++++||+++|+-
T Consensus 13 a~~~~n~t~AA~~L~iSQPavS~q 36 (324)
T PRK12681 13 VNHNLNVSATAESLYTSQPGISKQ 36 (324)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 976999999999978977799999
No 242
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=63.14 E-value=12 Score=17.82 Aligned_cols=35 Identities=20% Similarity=0.402 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHCCC-------CHHHHHHHHCCCHHHHHHH
Q ss_conf 9999999999996499-------9889999828998798899
Q gi|254780444|r 7 KKIWEAIDRMAERHNL-------TPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gl-------s~~~lA~~~Gv~~~ti~~~ 41 (223)
+||...|...+...-| |-.+||..+||||.|+++-
T Consensus 14 ~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~ra 55 (125)
T COG1725 14 EQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRA 55 (125)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999999998088688888975999999819898899999
No 243
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=62.70 E-value=12 Score=17.77 Aligned_cols=10 Identities=30% Similarity=0.531 Sum_probs=5.1
Q ss_pred CCCCCCEEEE
Q ss_conf 1487868999
Q gi|254780444|r 150 LYRKGDILIL 159 (223)
Q Consensus 150 ~i~~Gd~vlV 159 (223)
+|+.|+.|+-
T Consensus 36 sfkKGe~If~ 45 (224)
T PRK09391 36 SYKKGEEIYG 45 (224)
T ss_pred CCCCCCEEEC
T ss_conf 3889898899
No 244
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator; InterPro: IPR011794 This entry represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix .; GO: 0003677 DNA binding, 0045340 mercury ion binding, 0045449 regulation of transcription, 0046689 response to mercury ion.
Probab=62.68 E-value=3.3 Score=21.39 Aligned_cols=54 Identities=19% Similarity=0.199 Sum_probs=35.4
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCC-------CHHHHHH-----HHHHCCCCCCCCCCCC
Q ss_conf 9889999828998798899751578875577-------9899999-----8732187521000011
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRNRWP-------STESIFK-----ILAATNETICQLLDLP 76 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p-------~~~~l~k-----ia~~~~v~~~~l~~~~ 76 (223)
|-|+||+++|||--||.-|+|-+.-..|.-| +.+++.+ =+..||-|++++..+.
T Consensus 1 tIg~LA~~~GVNvETiRyYeRkGLl~eP~k~~~GyR~Y~~~~v~R~rFIKR~QeLGFsL~EI~~LL 66 (126)
T TIGR02051 1 TIGELAKAAGVNVETIRYYERKGLLPEPDKPEGGYRRYPEETVKRVRFIKRAQELGFSLEEIGKLL 66 (126)
T ss_pred CHHHHHHHCCCCEEEEEHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHC
T ss_conf 901136666897012210010077888899887714078654436455442000379788999870
No 245
>pfam10654 DUF2481 Protein of unknown function (DUF2481). This is a hypothetical protein family homologous to Lmo2305 in Bacteriophage A118 systems.
Probab=62.53 E-value=11 Score=17.95 Aligned_cols=35 Identities=17% Similarity=0.131 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 9999999999649998899998289987988997515
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
|.+.++ +.+.|||..++|+-.+||.+++-++.+..
T Consensus 70 i~Efv~--LRhAGlt~~aIAD~F~iS~s~~~nft~~n 104 (126)
T pfam10654 70 IIEFVE--LRHAGLTGYAIADHFKVSKSVVFNFTRRN 104 (126)
T ss_pred HHHHHH--HHHCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999--88558860799999747799999999961
No 246
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=62.43 E-value=12 Score=17.73 Aligned_cols=35 Identities=9% Similarity=0.095 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 899999999999964999889999828998798899
Q gi|254780444|r 6 HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
-+++.+.-..| ++.|||..++|+-+.+|+.|++=+
T Consensus 4 i~eLi~kA~eL-~~~Gls~geIAdELnvS~eT~~WL 38 (201)
T PRK02277 4 IEELIEKALEL-RSEGLSTGEIADELNVSRETATWL 38 (201)
T ss_pred HHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 89999999999-986997666355540269999999
No 247
>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=62.41 E-value=9.6 Score=18.41 Aligned_cols=28 Identities=11% Similarity=0.235 Sum_probs=23.6
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9996499988999982899879889975
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
|+--.|+|..++|+.+|+|.+++++..+
T Consensus 15 l~y~~~~t~~EIA~~lgis~~~V~~~~~ 42 (50)
T pfam04545 15 LRFGEGLTLEEIGERLGISRERVRQIEK 42 (50)
T ss_pred HHCCCCCHHHHHHHHHCCCHHHHHHHHH
T ss_conf 8706882499999998979999999999
No 248
>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=62.38 E-value=8.9 Score=18.61 Aligned_cols=55 Identities=15% Similarity=0.242 Sum_probs=36.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC-------CCCCCCCHHHHH-----HHHHHCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578-------875577989999-----98732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE-------GRNRWPSTESIF-----KILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~-------g~~r~p~~~~l~-----kia~~~~v~~~~l~~~~ 76 (223)
.+-+++|+.+||+..|+.-|++-+-- +.=|.-+.+.+. +.+..+|.++.++....
T Consensus 1 y~Ige~Ak~~gvs~~TLRyYe~~GLl~p~~~~~ngYR~Y~~~~~~~l~~I~~~r~lG~sL~eI~~~~ 67 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYL 67 (97)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9789999998969999999996699898613999984279999999999999999699999999998
No 249
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=62.13 E-value=11 Score=17.91 Aligned_cols=30 Identities=17% Similarity=0.173 Sum_probs=26.5
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 996499988999982899879889975157
Q gi|254780444|r 17 AERHNLTPSGLARKAGLDPTSFNKSKRFGI 46 (223)
Q Consensus 17 ~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~ 46 (223)
|.+.|.|.+++|+-.|.+.+|+.++-++..
T Consensus 57 rekag~Ti~EIAeelG~TeqTir~hlkget 86 (182)
T COG1318 57 REKAGMTISEIAEELGRTEQTVRNHLKGET 86 (182)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHCCH
T ss_conf 987037499999996877999999975140
No 250
>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=62.07 E-value=12 Score=17.69 Aligned_cols=54 Identities=17% Similarity=0.211 Sum_probs=35.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC------CCCCCCCHHHH-----HHHHHHCCCCCCCCCCC
Q ss_conf 99889999828998798899751578------87557798999-----99873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE------GRNRWPSTESI-----FKILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~------g~~r~p~~~~l-----~kia~~~~v~~~~l~~~ 75 (223)
+.-+++|+++|++..||.-|++.+-- +.-|.-+.+.+ .+.+..+|.++.++...
T Consensus 1 M~IgevAk~~gvs~~TlRyYE~~GLl~~~~r~~~yR~Y~~~~l~~l~~I~~~r~~GfsL~eI~~l 65 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAI 65 (116)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 96899999989699999999986999987577773322899999999999999979999999999
No 251
>PRK00430 fis DNA-binding protein Fis; Provisional
Probab=61.97 E-value=12 Score=17.77 Aligned_cols=28 Identities=14% Similarity=0.192 Sum_probs=24.9
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999996499988999982899879889
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|+..++..+-+|+..|+.+|++..|+.+
T Consensus 63 l~~vL~~t~gNqskAA~~LGInR~TLRk 90 (98)
T PRK00430 63 LDMVMQYTRGNQTRAALMLGINRGTLRK 90 (98)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999999669599999997877889999
No 252
>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=61.65 E-value=9.6 Score=18.39 Aligned_cols=26 Identities=15% Similarity=0.155 Sum_probs=22.7
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 64999889999828998798899751
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
-.|+|..++|..+|+++.|+..+.+.
T Consensus 13 ~~G~s~~eIA~~L~is~~TV~~~~~~ 38 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 80799999999989789999999999
No 253
>pfam09824 ArsR ArsR transcriptional regulator. Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=61.61 E-value=13 Score=17.64 Aligned_cols=28 Identities=29% Similarity=0.417 Sum_probs=11.5
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999996499988999982899879889
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|.+++++-+.|.+.++|+.|++|..|..
T Consensus 113 i~~~i~~g~~si~dlsr~lg~sp~~ikg 140 (160)
T pfam09824 113 IEAEVEAGNTSIGDLTRDLGISPTFIKA 140 (160)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999984991388989882878899999
No 254
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=61.54 E-value=10 Score=18.23 Aligned_cols=28 Identities=14% Similarity=0.344 Sum_probs=22.5
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999996499988999982899879889
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
++.|.++.-++-++||+..++|..|+.+
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 255
>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=61.45 E-value=9.8 Score=18.33 Aligned_cols=37 Identities=24% Similarity=0.481 Sum_probs=22.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHC-CCHHHH-HHHHHCCCCC
Q ss_conf 9999999964999889999828-998798-8997515788
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAG-LDPTSF-NKSKRFGIEG 48 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~G-v~~~ti-~~~~~~~~~g 48 (223)
+.|++|=. .|+|.|++|+.+| |+...| .+..|-+..+
T Consensus 9 e~LkkLW~-eGlSaSqIA~~LGgvTRNAVIGKaHRLgLs~ 47 (162)
T pfam07750 9 ELLKKLWL-EGLSASQIAAQLGGVSRNAVIGKVHRLGLSG 47 (162)
T ss_pred HHHHHHHH-CCCCHHHHHHHHCCCCCCCEEEHHHHCCCCC
T ss_conf 99999998-5365999999976554000000224225565
No 256
>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=61.32 E-value=9.4 Score=18.46 Aligned_cols=57 Identities=21% Similarity=0.241 Sum_probs=36.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC-------CCCCCCHHHH-----HHHHHHCCCCCCCCCCCCCC
Q ss_conf 998899998289987988997515788-------7557798999-----99873218752100001111
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEG-------RNRWPSTESI-----FKILAATNETICQLLDLPFS 78 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g-------~~r~p~~~~l-----~kia~~~~v~~~~l~~~~~~ 78 (223)
+|-+++|+.+|++..|+..|++.+--. .-|.-+.+.+ .+.+..+|.++.+....-+.
T Consensus 2 ~tI~e~Ak~~gvs~~TLRyYe~~GLl~P~~r~~nGYR~Ys~~dl~rL~~I~~lr~lG~sL~eIk~~L~~ 70 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQ 70 (172)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 978999999894988999999887989988499987077999999999999999879999999999839
No 257
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=61.14 E-value=13 Score=17.59 Aligned_cols=38 Identities=16% Similarity=0.114 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHHHHHCCC--CHHHHHHHHCCCHHHHHHHH
Q ss_conf 589999999999996499--98899998289987988997
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNL--TPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gl--s~~~lA~~~Gv~~~ti~~~~ 42 (223)
|+++|.++=-++-.++|+ |-.++|.++|+|..+|..|.
T Consensus 14 tr~~ll~aA~~~F~~~G~~attr~Ia~~Ag~~~~~i~yyF 53 (224)
T PRK11552 14 AKQQLIAAALAQFGEYGLHATTRDIAAQAGQNIAAITYYF 53 (224)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHC
T ss_conf 9999999999999884914009999998399999998873
No 258
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=60.82 E-value=13 Score=17.55 Aligned_cols=33 Identities=15% Similarity=0.356 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999999999996499988999982899879889
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
+|..+-|+ |+++..+|+.+||+.+|||.=||.+
T Consensus 4 ~Rq~~il~-lL~~~~lt~~eLA~~L~VS~RTIR~ 36 (585)
T PRK09863 4 ERELKIVD-LLEQQDRSGGELAQQLGVSRRTIVR 36 (585)
T ss_pred HHHHHHHH-HHHCCCCCHHHHHHHCCCCCHHHHH
T ss_conf 79999999-9975999989999874997117899
No 259
>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=60.80 E-value=9.7 Score=18.37 Aligned_cols=55 Identities=15% Similarity=0.220 Sum_probs=36.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC-------CCCCCCCHHHH-----HHHHHHCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578-------87557798999-----998732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE-------GRNRWPSTESI-----FKILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~-------g~~r~p~~~~l-----~kia~~~~v~~~~l~~~~ 76 (223)
.|-+++|+.+||+..|+..|++.+-- +.-|.-+.+.+ .+.+..+|.++.++....
T Consensus 1 ytIge~a~~~gvs~~tlRyYe~~GLl~p~~~~~~gyR~Y~~~~i~~l~~I~~lr~~G~~l~eI~~~l 67 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELL 67 (103)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEECCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9788999998969999999985389788614899986568999999999999999799999999998
No 260
>PRK13749 transcriptional regulator MerD; Provisional
Probab=60.78 E-value=13 Score=17.55 Aligned_cols=55 Identities=16% Similarity=0.053 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHCCCC-CCCCCC------CHHHH-----HHHHHHCCCCCCCCCCC
Q ss_conf 999889999828998798899751578-875577------98999-----99873218752100001
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNKSKRFGIE-GRNRWP------STESI-----FKILAATNETICQLLDL 75 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~~~~~~~~-g~~r~p------~~~~l-----~kia~~~~v~~~~l~~~ 75 (223)
.+|-++||+.+|||-.||..|++.+.- ...|+. ....+ .+-+..+|.+++.+...
T Consensus 3 aytIg~LA~~aGVsv~tIR~Y~~~GLL~p~~Rt~gGyRlyd~~~l~RL~FIR~a~elGf~LdeI~~L 69 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARL 69 (121)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 4209999999599735548898768989988899884367899999999999999908989999999
No 261
>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=60.71 E-value=6 Score=19.74 Aligned_cols=32 Identities=16% Similarity=0.203 Sum_probs=20.7
Q ss_pred CCCCCEEEEECCCCCCCCCEEEEEEECCCEEEEEEE
Q ss_conf 487868999368974058889999717968999999
Q gi|254780444|r 151 YRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLI 186 (223)
Q Consensus 151 i~~Gd~vlVd~~~~~~~g~~v~~~~~~~~~~iKrl~ 186 (223)
|..-|+-+. +.....+|+.+|+.+.+| +|.|+
T Consensus 180 f~~fDY~lf-~~LA~~SgN~iY~LILNg---lKglY 211 (275)
T TIGR02812 180 FTEFDYQLF-RGLAFASGNPIYGLILNG---LKGLY 211 (275)
T ss_pred HHHHHHHHH-HHHEECCCCCEEEEHCCH---HHHHH
T ss_conf 769889998-741001378233302001---01455
No 262
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=60.61 E-value=8.5 Score=18.73 Aligned_cols=26 Identities=23% Similarity=0.402 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 49998899998289987988997515
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
.|+--.++|.+.|++|.||..|++..
T Consensus 18 ~gmk~~dIAeklGvspntiksWKrr~ 43 (279)
T COG5484 18 KGMKLKDIAEKLGVSPNTIKSWKRRD 43 (279)
T ss_pred HHCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 43419999999689868888778740
No 263
>PRK09954 hypothetical protein; Provisional
Probab=60.53 E-value=13 Score=17.52 Aligned_cols=33 Identities=9% Similarity=0.126 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 899999999999964999889999828998798899
Q gi|254780444|r 6 HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+++|++-| ++.-=+||++||+++|++.+++...
T Consensus 5 e~~il~~i---~~~p~i~q~ela~~lgisrs~va~h 37 (362)
T PRK09954 5 EKEILAIL---RRNPLIQQNEIADILQISRSRVAAH 37 (362)
T ss_pred HHHHHHHH---HHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999---8789958999999979879999999
No 264
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=60.00 E-value=11 Score=18.11 Aligned_cols=26 Identities=8% Similarity=0.102 Sum_probs=22.5
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 64999889999828998798899751
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
-.|+|..++|+.+|+++.|+..+.+.
T Consensus 16 ~~G~s~~eIA~~L~is~~TV~~h~~~ 41 (58)
T pfam00196 16 AAGKSNKEIADILGISEKTVKVHRSN 41 (58)
T ss_pred HHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 80799999999978889999999999
No 265
>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=59.90 E-value=10 Score=18.16 Aligned_cols=54 Identities=20% Similarity=0.175 Sum_probs=34.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC-----CCCCCCCCHHHHH-----HHHHHCCCCCCCCCCC
Q ss_conf 9988999982899879889975157-----8875577989999-----9873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGI-----EGRNRWPSTESIF-----KILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~-----~g~~r~p~~~~l~-----kia~~~~v~~~~l~~~ 75 (223)
.|-+++|+++|++..||.-|++.+- .+.-|.-+.+.+. +-+..+|.++.++...
T Consensus 1 ytIge~A~~~gvs~~tlRyYe~~GLl~p~r~~g~R~Y~~~~~~~l~~I~~~r~~G~sL~eI~~~ 64 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQTRVYSRRDRARLKLILRGKRLGFSLEEIREL 64 (118)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 9588999998979999999998699875557986860899999999999999829989999999
No 266
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=59.87 E-value=11 Score=17.90 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=18.6
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99964999889999828998798899
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
|..-.|+|..++|..+|+|.+|+...
T Consensus 116 L~~~egls~~EIA~~lgis~~tVk~~ 141 (159)
T PRK12527 116 LRKLEGLSHQQIAEHLGISRSLVEKH 141 (159)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 89873979999999989199999999
No 267
>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=59.81 E-value=10 Score=18.16 Aligned_cols=54 Identities=15% Similarity=0.209 Sum_probs=34.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCC-CC------CCCHHHH-----HHHHHHCCCCCCCCCCC
Q ss_conf 9988999982899879889975157887-55------7798999-----99873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGR-NR------WPSTESI-----FKILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~-~r------~p~~~~l-----~kia~~~~v~~~~l~~~ 75 (223)
+.-+++|+++|++..|+..|++.+.-.. .| .-+.+.+ .+.+..+|.++.++...
T Consensus 1 M~Ige~a~~~gvs~~tlRyYE~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~GfsL~eI~~l 66 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTL 66 (127)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEECCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 968999999894999999999858988753479995436399999999999998649879999999
No 268
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=59.35 E-value=11 Score=18.06 Aligned_cols=55 Identities=13% Similarity=0.132 Sum_probs=35.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC-CCCCC------CHH-----HHHHHHHHCCCCCCCCCCCC
Q ss_conf 998899998289987988997515788-75577------989-----99998732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEG-RNRWP------STE-----SIFKILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g-~~r~p------~~~-----~l~kia~~~~v~~~~l~~~~ 76 (223)
++-+++|+++|++..||..|++.+.-. ..|.. +.+ ...+-+..+|.++.+.....
T Consensus 2 ~~Ige~A~~~gvs~~tiRyYE~~GLl~~~~R~~~gyR~Y~~~~v~rL~fI~~~r~lGfsL~eI~~ll 68 (140)
T PRK09514 2 YRIGELAKLCEVTPDTLRFYEKQGLMDPSVRTESGYRLYTEQDLQRLRFILRAKQLGFTLEEIRELL 68 (140)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 8699999998968999999998699986511899802067109999999999999399999999998
No 269
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=59.30 E-value=11 Score=18.03 Aligned_cols=25 Identities=16% Similarity=0.291 Sum_probs=22.2
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 6499988999982899879889975
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
-.|+|..++|+.+|+++.|+..+.+
T Consensus 16 ~~G~s~~eIA~~L~is~~TV~~~~~ 40 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred HHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 8179999999898978989999999
No 270
>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=59.27 E-value=14 Score=17.38 Aligned_cols=28 Identities=11% Similarity=0.114 Sum_probs=22.8
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999649998899998289987988997
Q gi|254780444|r 15 RMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 15 ~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
.|..-.|+|..++|+.+|++.+|+...-
T Consensus 20 ~l~~~~~~s~~eIA~~lg~s~~tVk~~l 47 (54)
T pfam08281 20 LLRYLEGLSYAEIAELLGISEGTVKSRL 47 (54)
T ss_pred HHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 8799878599999999894999999999
No 271
>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=59.24 E-value=14 Score=17.38 Aligned_cols=37 Identities=11% Similarity=0.052 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 55899999999999964999889999828998798899
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
||..++.-. -.|.+.-..|.+++|+.+|++.+++.+.
T Consensus 6 ls~~E~~vY-~~Ll~~g~~t~~eia~~~~i~r~~vY~~ 42 (68)
T pfam01978 6 LSEYEAKVY-LALLKLGPATADEIAEESGVPRSKVYEV 42 (68)
T ss_pred CCHHHHHHH-HHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 899999999-9999819988999999959889899999
No 272
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=58.99 E-value=14 Score=17.35 Aligned_cols=38 Identities=13% Similarity=0.286 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 5589999999999996499988999982899879889975
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
+|.-+|++-|- +.+-...|+++|+++|++++.++.+.+
T Consensus 10 ~t~fqIL~ei~--~~qp~v~q~eIA~~lgiT~QaVsehiK 47 (260)
T COG1497 10 LTRFQILSEIA--VRQPRVKQKEIAKKLGITLQAVSEHIK 47 (260)
T ss_pred CHHHHHHHHHH--HHCCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 15989999999--758877888999870987999999999
No 273
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=58.91 E-value=14 Score=17.34 Aligned_cols=45 Identities=18% Similarity=0.149 Sum_probs=27.9
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf 999649998899998289987988997515788755779899999873218752
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETI 69 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~ 69 (223)
|+.-.|+|..++|+.+|++..|+...-.. ....|.+.++.-|+.+
T Consensus 117 L~~~egls~~EIA~~l~is~~tVk~~l~R---------Ar~~Lr~~Le~~gi~~ 161 (161)
T PRK09047 117 LRYWEDMDVAETAAAMGCSEGSVKTHCSR---------ATHTLAKALEAKGITL 161 (161)
T ss_pred HHHHHCCCHHHHHHHHCCCHHHHHHHHHH---------HHHHHHHHHHHCCCCC
T ss_conf 99998779999999989699999999999---------9999999999869839
No 274
>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=58.84 E-value=11 Score=18.01 Aligned_cols=55 Identities=15% Similarity=0.162 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHCCC-CHHHHHHHH-----C-CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCC-CCCCCCC
Q ss_conf 999999999996499-988999982-----8-9987988997515788755779899999873218-7521000
Q gi|254780444|r 8 KIWEAIDRMAERHNL-TPSGLARKA-----G-LDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN-ETICQLL 73 (223)
Q Consensus 8 ~i~~~i~~l~~~~gl-s~~~lA~~~-----G-v~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~-v~~~~l~ 73 (223)
+..++|++...+.++ ||.||...+ - ++|+|+||+-+.. .+.|+.+.-+ ...+-|.
T Consensus 2 ~R~~~Ik~Ii~~e~~~tQ~El~~~L~~~G~~nvTQaTvSRDL~el-----------~lvK~~~~~gG~~~Y~L~ 64 (155)
T TIGR01529 2 ERQEAIKEIITEEKISTQEELVALLKKEGVKNVTQATVSRDLREL-----------GLVKVRDEKGGSYVYSLP 64 (155)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCEECCCCHHHHHHHH-----------CCEECCCCCCCEEEEEEC
T ss_conf 479999999874376798899999986597511234067878752-----------204223699744899860
No 275
>LOAD_arc_metj consensus
Probab=58.74 E-value=14 Score=17.39 Aligned_cols=26 Identities=27% Similarity=0.479 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 89999999999996499988999982
Q gi|254780444|r 6 HKKIWEAIDRMAERHNLTPSGLARKA 31 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gls~~~lA~~~ 31 (223)
-+++++.++.++++.|.|.|++-+.+
T Consensus 9 ~~~~~~~l~~~~~~~g~s~Se~ir~a 34 (43)
T LOAD_arc_metj 9 PDELYEALEELAAERGRSRSELIREA 34 (43)
T ss_pred CHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 68999999999998384488999999
No 276
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity..
Probab=58.65 E-value=11 Score=17.89 Aligned_cols=33 Identities=9% Similarity=0.257 Sum_probs=26.1
Q ss_pred HHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999999649-998899998289987988997
Q gi|254780444|r 10 WEAIDRMAERHN-LTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 10 ~~~i~~l~~~~g-ls~~~lA~~~Gv~~~ti~~~~ 42 (223)
.+=|..|.++.| .+-..+|+.+|.|.+|+++.-
T Consensus 172 ~~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~~~~ 205 (231)
T TIGR01884 172 LKVLEALKAEKGEKSVKNIAKKLGKSLSTISRHL 205 (231)
T ss_pred HHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHH
T ss_conf 9999998507880528779988578887999999
No 277
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=58.55 E-value=9.9 Score=18.30 Aligned_cols=28 Identities=18% Similarity=0.120 Sum_probs=24.0
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHH
Q ss_conf 9999999996499988999982899879
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAGLDPTS 37 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~Gv~~~t 37 (223)
.+.|.+-++..|+|.|++-|.+|++++-
T Consensus 22 ~~~I~~~A~~aGLSvS~yLR~~~lgy~i 49 (114)
T PRK13877 22 KAEIEANAAAAGLSVARYLRDVGQGYQI 49 (114)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHCCCCC
T ss_conf 9999999999599899999997689978
No 278
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=58.02 E-value=14 Score=17.25 Aligned_cols=30 Identities=13% Similarity=0.290 Sum_probs=23.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999999964999889999828998798899
Q gi|254780444|r 12 AIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 12 ~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
-|+-|..+-+++..++|.++|++++|++.-
T Consensus 28 Il~lL~~k~plNvneiAe~lgLpqst~s~~ 57 (308)
T COG4189 28 ILQLLHRKGPLNVNEIAEALGLPQSTMSAN 57 (308)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999998717987899998858865666655
No 279
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=57.52 E-value=15 Score=17.19 Aligned_cols=38 Identities=8% Similarity=0.068 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHHHHCCCC-------HHHHHHHHCCCHHHHHHH
Q ss_conf 55899999999999964999-------889999828998798899
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLT-------PSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls-------~~~lA~~~Gv~~~ti~~~ 41 (223)
...++|.+.|..++-+..|. -.+||...|||.+++..-
T Consensus 9 r~yeqV~~~Lr~~I~~G~l~PGdrLP~EreLAe~lgVSRt~VREA 53 (257)
T PRK10225 9 RPYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREA 53 (257)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 099999999999998289999793952999999979887899999
No 280
>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=56.85 E-value=12 Score=17.68 Aligned_cols=55 Identities=18% Similarity=0.238 Sum_probs=35.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC-------CCCCCCCHHHH-----HHHHHHCCCCCCCCCCCC
Q ss_conf 99889999828998798899751578-------87557798999-----998732187521000011
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE-------GRNRWPSTESI-----FKILAATNETICQLLDLP 76 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~-------g~~r~p~~~~l-----~kia~~~~v~~~~l~~~~ 76 (223)
++-+++|+++||+..|+.-|++.+-- +.-|.-+.+.+ .+.+..+|.++.++....
T Consensus 1 y~Ige~Ak~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l 67 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRAL 67 (96)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9488999998959999999997399898887999882189999999999999999799999999998
No 281
>PRK05114 hypothetical protein; Provisional
Probab=56.75 E-value=13 Score=17.56 Aligned_cols=26 Identities=15% Similarity=0.362 Sum_probs=19.4
Q ss_pred CCCCCHHHHH---HHHHHHHHHCCCCHHHH
Q ss_conf 9775589999---99999999649998899
Q gi|254780444|r 1 MTSFSHKKIW---EAIDRMAERHNLTPSGL 27 (223)
Q Consensus 1 ~~~~~~~~i~---~~i~~l~~~~gls~~~l 27 (223)
|-+|||++-. ++|+.||.+ |+|-.+.
T Consensus 5 lp~LtHeqQQ~AvErIq~LM~~-GmssgeA 33 (60)
T PRK05114 5 LPSLTHEQQQKAVERIQELMAQ-GMSSGEA 33 (60)
T ss_pred CCCCCHHHHHHHHHHHHHHHHC-CCCHHHH
T ss_conf 8776879999999999999980-4467789
No 282
>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=56.55 E-value=15 Score=17.09 Aligned_cols=24 Identities=21% Similarity=0.196 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 998899998289987988997515
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
||..|.|+.+||+.+|+.++-..+
T Consensus 2 lTv~EaA~yLgv~~~t~~~l~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKSTVYRLIEEG 25 (49)
T ss_pred CCHHHHHHHCCCCHHHHHHHHHCC
T ss_conf 877889977199905789999718
No 283
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=56.35 E-value=15 Score=17.07 Aligned_cols=35 Identities=14% Similarity=0.194 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 999999999964999889999828998798899751
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
|...|+.=.. ..+|-.+||+.+|+|+.++++..+.
T Consensus 14 i~~yI~~n~~-~~lsl~~lA~~~~~S~~~l~r~Fk~ 48 (127)
T PRK11511 14 ILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999998658-9999999999989599999999999
No 284
>pfam03701 UPF0181 Uncharacterized protein family (UPF0181). This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH.
Probab=56.13 E-value=14 Score=17.43 Aligned_cols=26 Identities=15% Similarity=0.358 Sum_probs=19.4
Q ss_pred CCCCCHHHHH---HHHHHHHHHCCCCHHHH
Q ss_conf 9775589999---99999999649998899
Q gi|254780444|r 1 MTSFSHKKIW---EAIDRMAERHNLTPSGL 27 (223)
Q Consensus 1 ~~~~~~~~i~---~~i~~l~~~~gls~~~l 27 (223)
|-+|||++-. ++|+.||.+ |+|-.+.
T Consensus 5 lp~LtHeeQQ~AvErIq~LMaq-GmSsgeA 33 (52)
T pfam03701 5 LPSLTHEEQQEAVERIQELMAQ-GMSSGEA 33 (52)
T ss_pred CCCCCHHHHHHHHHHHHHHHHC-CCCHHHH
T ss_conf 7666879999999999999980-4558899
No 285
>PRK08402 replication factor A; Reviewed
Probab=55.79 E-value=16 Score=17.01 Aligned_cols=55 Identities=9% Similarity=0.097 Sum_probs=33.2
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf 9775589999999999996499988999982899879889975157887557798999998732187521
Q gi|254780444|r 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70 (223)
Q Consensus 1 ~~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~ 70 (223)
|+-||.++|.+.| +++.|+|..++.++. ++..+..+.+ ....+.-+|+-+|+.+.
T Consensus 1 m~vltkEeIiekI---~~e~G~S~eEIeekI-------~ei~ee~gIS-----E~gAalllAeeLGV~L~ 55 (357)
T PRK08402 1 MVVLTKEEIIERI---ERETGLSREEIEEEI-------REIMEEDGIS-----EHAAALLLAERLGVDLI 55 (357)
T ss_pred CCCCCHHHHHHHH---HHHHCCCHHHHHHHH-------HHHHHHCCCC-----HHHHHHHHHHHHCCCCC
T ss_conf 9412299999999---987288899999999-------9999862877-----67899999998588655
No 286
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=55.70 E-value=16 Score=17.00 Aligned_cols=38 Identities=13% Similarity=0.094 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 97755899999999999964999889999828998798899
Q gi|254780444|r 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 1 ~~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
|..|+=.++.-. .+..+. | |-++-|+.+|++|+++|+.
T Consensus 1 m~~m~LrqL~~F-~aVa~~-g-sft~AA~~L~isQpavS~~ 38 (309)
T PRK11013 1 MAAVSLRHIEIF-HAVMTA-G-SLTEAARLLHTSQPTVSRE 38 (309)
T ss_pred CCCCCHHHHHHH-HHHHHC-C-CHHHHHHHHCCCHHHHHHH
T ss_conf 998888999999-999980-9-9999999988888899999
No 287
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=54.60 E-value=16 Score=17.04 Aligned_cols=28 Identities=14% Similarity=0.334 Sum_probs=22.9
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999996499988999982899879889
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
++.|.++.-++-.+||+..++|..|+.+
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 288
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=54.41 E-value=17 Score=16.87 Aligned_cols=24 Identities=21% Similarity=0.221 Sum_probs=20.8
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 964999889999828998798899
Q gi|254780444|r 18 ERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 18 ~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
-+.|.|-++.|++++++|+++|+.
T Consensus 13 v~~~~Sft~AA~~L~isQ~avS~~ 36 (309)
T PRK12682 13 VRRNLNLTEAAKALHTSQPGVSKA 36 (309)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 986999999999978987899999
No 289
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=54.16 E-value=8.2 Score=18.82 Aligned_cols=36 Identities=17% Similarity=0.149 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 589999999999996499988999982899879889
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
++++-..-.+.+.+.-=+|-.+||++.|||-+||.-
T Consensus 5 K~eRq~~L~~~i~~nPF~TDeeLa~~f~VSiqTIRL 40 (185)
T PRK04424 5 KKERQELLQETIEENPFITDEELAEKFGVSIQTIRL 40 (185)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHCCCEEEEEEE
T ss_conf 799999999999868998779999860957778882
No 290
>pfam10000 DUF2241 Uncharacterized protein conserved in bacteria (DUF2241). This domain, found in various hypothetical bacterial proteins, has no known function.
Probab=53.73 E-value=17 Score=16.80 Aligned_cols=17 Identities=24% Similarity=0.382 Sum_probs=14.5
Q ss_pred CCCCCCCCCCCEEEEEC
Q ss_conf 33242148786899936
Q gi|254780444|r 145 TSMLPLYRKGDILILNS 161 (223)
Q Consensus 145 DSM~P~i~~Gd~vlVd~ 161 (223)
-||.|.+.+|++|++--
T Consensus 12 ~~m~P~L~~~~yVF~t~ 28 (72)
T pfam10000 12 ASMSPELDDGEYVFCTV 28 (72)
T ss_pred HHCCCEECCCCEEEEEE
T ss_conf 65993778996899996
No 291
>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=53.39 E-value=17 Score=16.76 Aligned_cols=23 Identities=17% Similarity=0.176 Sum_probs=20.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 99889999828998798899751
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
.|-+++|+.+|+++.|+.-|++.
T Consensus 1 ysIgEva~~~gv~~~tLRywE~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 97889999989499999999987
No 292
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=53.00 E-value=17 Score=16.72 Aligned_cols=22 Identities=14% Similarity=0.199 Sum_probs=10.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9998899998289987988997
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
|+|-.++|+++++|..|+..++
T Consensus 165 G~snkeIA~~L~iS~~TV~~h~ 186 (216)
T PRK10840 165 GFLVTEIAKKLNRSIKTISSQK 186 (216)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999989698999999999
No 293
>KOG0775 consensus
Probab=52.83 E-value=8.7 Score=18.67 Aligned_cols=23 Identities=22% Similarity=0.111 Sum_probs=19.1
Q ss_pred HHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 88999982899879889975157
Q gi|254780444|r 24 PSGLARKAGLDPTSFNKSKRFGI 46 (223)
Q Consensus 24 ~~~lA~~~Gv~~~ti~~~~~~~~ 46 (223)
..+||+++|++.+-+++|.+...
T Consensus 206 KReLA~aTgLt~tQVsNWFKNRR 228 (304)
T KOG0775 206 KRELAEATGLTITQVSNWFKNRR 228 (304)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 89999871886300215542035
No 294
>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=52.54 E-value=12 Score=17.80 Aligned_cols=26 Identities=15% Similarity=0.241 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 49998899998289987988997515
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
.-|+..++|..+|+..+|||+..++.
T Consensus 48 ~PLtlk~iA~~l~lh~STVSRav~~K 73 (160)
T pfam04552 48 RPLTLREVAEALGMHESTVSRATTNK 73 (160)
T ss_pred CCCCHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 57619999988099810699999613
No 295
>pfam06892 Phage_CP76 Phage regulatory protein CII (CP76). This family consists of several phage regulatory protein CII (CP76) sequences which are thought to be DNA binding proteins which are involved in the establishment of lysogeny.
Probab=51.72 E-value=18 Score=16.59 Aligned_cols=58 Identities=21% Similarity=0.241 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCC
Q ss_conf 899999999999964999889999828998798899751578875577989999987321875
Q gi|254780444|r 6 HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNET 68 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~ 68 (223)
|.-.-+|-.+.+..+ +-++||+++|++++++.+-- +.+ .|+..+...|..|.++.+-.
T Consensus 7 q~hfd~ACraFA~~h--nl~~lA~~~Gm~~~~LRNkL--NP~-qpH~Lt~~el~~it~~t~d~ 64 (163)
T pfam06892 7 QPHFDEACRAFADSH--NLAELAERAGMNGQMLRNKL--NPE-QPHQLTVPELVLITKATGDY 64 (163)
T ss_pred CHHHHHHHHHHHHHC--CHHHHHHHCCCCHHHHHHCC--CCC-CCCCCCHHHHHHHHHCCCCH
T ss_conf 345899999999880--19999998099889998524--988-98827899999998612765
No 296
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=51.38 E-value=18 Score=16.56 Aligned_cols=67 Identities=13% Similarity=-0.019 Sum_probs=46.9
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 589999999999996499988999982899879889975157887557798999998732187521000011
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLP 76 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~ 76 (223)
...+|-.+|=..-+++|||=++||+.+|.+...+....-+-. ..+.+...+++++++.+-+.+..+.
T Consensus 5 ~i~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygq~-----~~~~~ear~v~e~L~L~~~~v~~L~ 71 (151)
T COG1513 5 IILDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQA-----ALPADEARAVGEALDLDEDAILLLQ 71 (151)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHC-----CCCHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 589999999997875499699997550833999999997620-----2899999999998199878899842
No 297
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=51.13 E-value=19 Score=16.53 Aligned_cols=23 Identities=9% Similarity=0.115 Sum_probs=12.1
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 64999889999828998798899
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
-.|+|.+++|+.+|++.+|+...
T Consensus 134 ~~~~s~~EIA~~l~is~~tVk~~ 156 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSR 156 (175)
T ss_pred HHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 92999999999989599999999
No 298
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=51.12 E-value=19 Score=16.53 Aligned_cols=11 Identities=18% Similarity=0.166 Sum_probs=4.2
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999996
Q gi|254780444|r 9 IWEAIDRMAER 19 (223)
Q Consensus 9 i~~~i~~l~~~ 19 (223)
+.+.|..+.++
T Consensus 12 vr~gl~~ll~~ 22 (204)
T PRK09958 12 AIAAIRNLLIK 22 (204)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999986
No 299
>TIGR01455 glmM phosphoglucosamine mutase; InterPro: IPR006352 This family describes GlmM, phosphoglucosamine mutase, also designated MrsA and YhbF in Escherichia coli , UreC in Helicobacter pylori , and femR315 or FemD in Staphlococcus aureus . It converts glucosamine-6-phosphate to glucosamine-1-phosphate as part of the pathway toward UDP-N-acetylglucosamine for peptidoglycan and lipopolysaccharides..
Probab=51.04 E-value=11 Score=17.99 Aligned_cols=36 Identities=17% Similarity=0.153 Sum_probs=16.1
Q ss_pred HHHHHHHHH--HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 899999999--999964999889999828998798899
Q gi|254780444|r 6 HKKIWEAID--RMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 6 ~~~i~~~i~--~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.+=|.+||+ +.+++.|.|-|+|+...-..|+++.+-
T Consensus 343 GDGivsALqvl~~m~~~G~~LSeL~~~~~~~PQ~L~NV 380 (450)
T TIGR01455 343 GDGIVSALQVLTIMKKSGSSLSELASELTKYPQVLVNV 380 (450)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHCCCCCCCEEEEE
T ss_conf 07999999999999862897899951874278207888
No 300
>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=50.94 E-value=9.3 Score=18.47 Aligned_cols=45 Identities=16% Similarity=0.185 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf 99988999982899879889975157887557798999998732187
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNE 67 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v 67 (223)
.||-.++||.+||+.+|+||--++... -+.-..|.+..+.+-.|-
T Consensus 1 kLTIkDIArLagVgKSTVSRVLnNe~~--V~~~tRERVE~viq~~gF 45 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNNESK--VSIETRERVEAVIQQSGF 45 (311)
T ss_pred CCHHHHHHHHHCCCCEEEEEEEECCCC--CCCHHHHHHHHHHHHCCC
T ss_conf 961777697708862023315616888--872033688888751588
No 301
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.90 E-value=8.1 Score=18.86 Aligned_cols=34 Identities=24% Similarity=0.200 Sum_probs=19.9
Q ss_pred CCCCCCCCCCCEEEEECC---CCCCCCCEEEEEEECC
Q ss_conf 332421487868999368---9740588899997179
Q gi|254780444|r 145 TSMLPLYRKGDILILNSA---IQVNCGDRLLIKPRTG 178 (223)
Q Consensus 145 DSM~P~i~~Gd~vlVd~~---~~~~~g~~v~~~~~~~ 178 (223)
-||.|.+.+||+|+.-.. ....+-+.+.-+...+
T Consensus 12 ~smtPeL~~G~yVfcT~~~ga~~~~~lePla~FRE~E 48 (134)
T COG3602 12 ASMTPELLDGDYVFCTVAPGALQPKNLEPLATFRERE 48 (134)
T ss_pred HHCCCCCCCCCEEEEEECCCCCCCCCCCHHHHHCCCC
T ss_conf 9659100589669998447767976777476620246
No 302
>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=50.56 E-value=19 Score=16.48 Aligned_cols=27 Identities=11% Similarity=0.172 Sum_probs=22.4
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999649998899998289987988997
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
|.--.|+|..++|..+|++.+|+....
T Consensus 21 l~y~~~~s~~EIa~~lgis~~tVk~~l 47 (55)
T cd06171 21 LRFGEGLSYEEIAEILGISRSTVRQRL 47 (55)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999809999999999895999999999
No 303
>pfam06322 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=49.95 E-value=19 Score=16.42 Aligned_cols=28 Identities=14% Similarity=0.186 Sum_probs=22.8
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 99996499988999982899879889975
Q gi|254780444|r 15 RMAERHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 15 ~l~~~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
-|.+.+| +|++.||.++.+..|+.+|-.
T Consensus 11 lLi~~~G-N~teVaR~L~c~R~TVrkY~~ 38 (64)
T pfam06322 11 MLIETYG-NQTEVARRLNCSRNTVRKYAE 38 (64)
T ss_pred HHHHHHC-CHHHHHHHHCCHHHHHHHHHC
T ss_conf 9999707-799997885110888998723
No 304
>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=49.77 E-value=20 Score=16.40 Aligned_cols=50 Identities=18% Similarity=0.240 Sum_probs=32.3
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCC-----CCCCCCCHHH------HHHHHHHCCCCCCCC
Q ss_conf 9889999828998798899751578-----8755779899------999873218752100
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIE-----GRNRWPSTES------IFKILAATNETICQL 72 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~-----g~~r~p~~~~------l~kia~~~~v~~~~l 72 (223)
+-+++|+.+||++.|+..|++.+.- +.-|.-+.+. +.++++.+|.++...
T Consensus 3 ~Ig~vA~l~gv~~~TLR~YEr~GLi~P~R~~G~RlYs~~Di~rLrfIkrL~~e~G~nlagI 63 (120)
T cd04767 3 PIGVVAELLNIHPETLRIWERHGLIKPARRNGQRLYSNNDLKRLRFIKKLINEKGLNIAGV 63 (120)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 4899999978688999999985896888889822779999999999999999759689999
No 305
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=49.57 E-value=20 Score=16.38 Aligned_cols=13 Identities=31% Similarity=0.659 Sum_probs=7.5
Q ss_pred CCCCCEEEEECCC
Q ss_conf 4878689993689
Q gi|254780444|r 151 YRKGDILILNSAI 163 (223)
Q Consensus 151 i~~Gd~vlVd~~~ 163 (223)
+..||.+++-|+.
T Consensus 71 l~~Gd~fLi~Pg~ 83 (290)
T PRK10572 71 CRPGDLLLFPPGA 83 (290)
T ss_pred ECCCCEEEECCCC
T ss_conf 6699889988999
No 306
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=49.53 E-value=14 Score=17.42 Aligned_cols=40 Identities=13% Similarity=0.249 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 7558999999999999649998899998289987988997
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
|-+||+|+..|+.|.--..+|...+|+.+++|..|-.+.-
T Consensus 1 msKHeqIL~Yie~L~vG~kISVR~Ia~~l~VSeGTAYRAI 40 (432)
T COG4109 1 MSKHEQILNYIESLEVGKKISVRGIAKHLKVSEGTAYRAI 40 (432)
T ss_pred CCCHHHHHHHHHHCCCCCEEEHHHHHHHCCCCCCHHHHHH
T ss_conf 9717899999971656656666776643776633588888
No 307
>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=49.16 E-value=20 Score=16.34 Aligned_cols=35 Identities=14% Similarity=0.265 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHCCC-------CHHHHHHHHCCCHHHHHHH
Q ss_conf 9999999999996499-------9889999828998798899
Q gi|254780444|r 7 KKIWEAIDRMAERHNL-------TPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gl-------s~~~lA~~~Gv~~~ti~~~ 41 (223)
++|.+.|........+ |..+||+..|+|.+|+.+.
T Consensus 3 ~qi~~~i~~~I~~g~~~~G~~LPs~~~La~~~~vSr~tvr~A 44 (64)
T pfam00392 3 EQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREA 44 (64)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCHHHHHHH
T ss_conf 999999999998499999299847999999979699999999
No 308
>pfam11740 KfrA_N Plasmid replication region DNA-binding N-term. The broad host-range plasmid RK2 is able to replicate in and be inherited in a stable manner in diverse Gram-negative bacterial species. It encodes a number of co-ordinately regulated operons including a central control korF1 operon that represses the kfrA operon. The KfrA polypeptide is a site-specific DNA-binding protein whose operator overlaps the kfrA promoter. The N-terminus, containing an helix-turn-helix motif, is essential for function. Downstream from this family is an extended coiled-coil domain containing a heptad repeat segment which is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning.
Probab=49.12 E-value=20 Score=16.33 Aligned_cols=37 Identities=19% Similarity=0.239 Sum_probs=29.9
Q ss_pred CHHHHHHHHHHHHHHCCC--CHHHHHHHHC-CCHHHHHHHH
Q ss_conf 589999999999996499--9889999828-9987988997
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNL--TPSGLARKAG-LDPTSFNKSK 42 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gl--s~~~lA~~~G-v~~~ti~~~~ 42 (223)
|.++|+.+-|+|..+ |. |...+-..+| -|++||+++.
T Consensus 2 t~e~V~~Aad~L~~~-G~~PTv~~VR~~lG~GS~stI~~~L 41 (120)
T pfam11740 2 TKEDVAAAADALLAA-GERPTVDAVREELGTGSPTTISKYL 41 (120)
T ss_pred CHHHHHHHHHHHHHC-CCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 699999999999874-8999599999997797888899999
No 309
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=48.87 E-value=20 Score=16.31 Aligned_cols=49 Identities=14% Similarity=0.126 Sum_probs=28.1
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 9996499988999982899879889975157887557798999998732187521000
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
|+.-.|+|..++|..+|++..|+...-.. ....|.+.+++.+-.-+++.
T Consensus 168 Lr~~eglS~~EIAe~Lgis~gTVKsrl~R---------Ar~~LR~~Lea~~~~~e~~~ 216 (222)
T PRK09647 168 LCDIEGLSYEEIAATLGVKLGTVRSRIHR---------GRQALRAYLAAHAPHGEELA 216 (222)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHH---------HHHHHHHHHHHCCCCCHHHH
T ss_conf 79963999999999989399999999999---------99999999871099721764
No 310
>PRK00513 minC septum formation inhibitor; Reviewed
Probab=48.05 E-value=21 Score=16.23 Aligned_cols=47 Identities=15% Similarity=0.091 Sum_probs=29.6
Q ss_pred EECCCCCCCC-CCCCCEEEEECCCCCCCCCEEEEEEECCCEEEEEEEE
Q ss_conf 9628332421-4878689993689740588899997179689999999
Q gi|254780444|r 141 KTQDTSMLPL-YRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLIS 187 (223)
Q Consensus 141 ~V~GDSM~P~-i~~Gd~vlVd~~~~~~~g~~v~~~~~~~~~~iKrl~~ 187 (223)
.|-..+|+|+ ++=||++.-.|......+..-+|+..++..+|.+++.
T Consensus 161 ~I~A~~l~P~qlrIad~iar~pd~~~~~~~peiA~i~~~~I~ie~~~~ 208 (214)
T PRK00513 161 VIAALQLEPTQLRIADVVARAPEDKEDPNYPEVAYINEGGIVIERLQP 208 (214)
T ss_pred EEEECCCCCCEEEECCEEEECCCCCCCCCCCEEEEEECCEEEEEECCC
T ss_conf 999854787488996365048778877899879999699899998941
No 311
>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=47.88 E-value=21 Score=16.21 Aligned_cols=54 Identities=9% Similarity=0.180 Sum_probs=33.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC-----CCCCCCCHHH-----HHHHHHHCCCCCCCCCCC
Q ss_conf 99889999828998798899751578-----8755779899-----999873218752100001
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIE-----GRNRWPSTES-----IFKILAATNETICQLLDL 75 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~-----g~~r~p~~~~-----l~kia~~~~v~~~~l~~~ 75 (223)
++-++||+++|++..|+.-|++.+-- +.-|.-+... ..+.++.+|.++++.-..
T Consensus 1 m~Ige~Ak~~~vs~~TlRyYe~~GLl~P~~~~g~r~Y~~~d~~~L~~I~~~k~lgfsL~eIk~l 64 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDLGLLIPEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKI 64 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 9689999996998988899998588688768994661999999999999998889989999999
No 312
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=47.02 E-value=22 Score=16.13 Aligned_cols=30 Identities=10% Similarity=0.071 Sum_probs=23.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9999999964999889999828998798899
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+.+.+. .++|+|-++-|+++++||+++|+-
T Consensus 7 r~f~aV-a~~~~n~s~AA~~L~iSQPaVSkq 36 (327)
T PRK12680 7 RYLVAI-ADAELNITLAAARVHATQPGLSKQ 36 (327)
T ss_pred HHHHHH-HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999-965899999999978976799999
No 313
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=46.99 E-value=22 Score=16.12 Aligned_cols=19 Identities=11% Similarity=0.079 Sum_probs=6.7
Q ss_pred CCCCHHHHHHHHCCCHHHH
Q ss_conf 4999889999828998798
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSF 38 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti 38 (223)
.|+|..++|..+|++..|+
T Consensus 127 ~g~s~~EIA~~lgis~~tV 145 (164)
T PRK12547 127 SGFSYEEAAEICGCAVGTI 145 (164)
T ss_pred CCCCHHHHHHHHCCCHHHH
T ss_conf 4999999999989399999
No 314
>pfam05579 Peptidase_S32 Equine arteritis virus serine endopeptidase S32. Serine peptidases involved in processing nidovirus polyprotein.
Probab=46.46 E-value=22 Score=16.07 Aligned_cols=51 Identities=10% Similarity=0.119 Sum_probs=36.2
Q ss_pred CCCCEEEEEECCCCCCCCC-CCCCEEEEECCCCCCCCCEEEEEEECCC-EEEEEE
Q ss_conf 3685599996283324214-8786899936897405888999971796-899999
Q gi|254780444|r 133 IQTQDTRHKTQDTSMLPLY-RKGDILILNSAIQVNCGDRLLIKPRTGD-IVAKVL 185 (223)
Q Consensus 133 ~~~~~~~l~V~GDSM~P~i-~~Gd~vlVd~~~~~~~g~~v~~~~~~~~-~~iKrl 185 (223)
..+-+|++.--|||-.|.| ++|++|-|.++.+ ..|.+.| -+.+|. .-++-+
T Consensus 83 g~~~a~cfT~cGDSGSpVi~e~g~lvGVHTGSn-k~Gsg~v-TTp~G~t~~~~~v 135 (426)
T pfam05579 83 GLGFAFCFTKCGDSGSPVITEDGNLVGVHTGSN-KRGSGMV-TTPSGKTLGMAPV 135 (426)
T ss_pred CCCEEEEECCCCCCCCCCCCCCCCEEEEECCCC-CCCCEEE-ECCCCCCCCCCCE
T ss_conf 574389984678889953778997898862688-7674368-8899836166640
No 315
>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=46.39 E-value=20 Score=16.29 Aligned_cols=46 Identities=15% Similarity=0.075 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHHCCCH--HHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf 4999889999828998--79889975157887557798999998732187521
Q gi|254780444|r 20 HNLTPSGLARKAGLDP--TSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~--~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~ 70 (223)
.-.|-..+|.++|.++ ..+++..+|..+ .+...+.|++++++..=.
T Consensus 26 ~~FS~R~fa~KaGfsS~r~~~~~~~~GK~~-----Lt~~~i~k~~~~l~Lde~ 73 (281)
T TIGR02147 26 RAFSWRSFAEKAGFSSKRSYLKRIIKGKKN-----LTKRMIPKFAEALGLDEK 73 (281)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHH-----HHHHHHHHHHHHHCCCCH
T ss_conf 433089999864889877788899866675-----300035766655246722
No 316
>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=46.04 E-value=22 Score=16.03 Aligned_cols=36 Identities=17% Similarity=0.250 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHCC------C-CHHHHHHHHCCCHHHHHHH
Q ss_conf 8999999999999649------9-9889999828998798899
Q gi|254780444|r 6 HKKIWEAIDRMAERHN------L-TPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~g------l-s~~~lA~~~Gv~~~ti~~~ 41 (223)
+++|.+.|........ | |..+||+..|+|.+|+.+.
T Consensus 3 y~qi~~~i~~~I~~g~~~~G~~LPs~~~La~~~~vSr~tvr~A 45 (66)
T cd07377 3 YEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREA 45 (66)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999999998599999199927999999979888999999
No 317
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=45.90 E-value=22 Score=16.02 Aligned_cols=38 Identities=24% Similarity=0.295 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHHHHHCC---CCHHHHHHHHCCCHHHHHHH
Q ss_conf 558999999999999649---99889999828998798899
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHN---LTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~g---ls~~~lA~~~Gv~~~ti~~~ 41 (223)
++++.+-+.|=.+.++.| .+.-.||+.+|++...+|+.
T Consensus 2 ~~~~~~eqkil~~L~~~g~~~~tA~~lak~lg~~Kk~vN~~ 42 (68)
T smart00550 2 LTQDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRV 42 (68)
T ss_pred CCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHH
T ss_conf 74007999999999974886403999999949989999999
No 318
>PRK11052 malQ 4-alpha-glucanotransferase; Provisional
Probab=45.81 E-value=17 Score=16.75 Aligned_cols=42 Identities=24% Similarity=0.260 Sum_probs=33.7
Q ss_pred HHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 889999828998798899751578875577989999987321875210
Q gi|254780444|r 24 PSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 24 ~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
-.+||++.||.+... ...|+.+..+.+++.+++.++|++...
T Consensus 6 L~~LA~~~GI~~~y~------d~~G~~~~vs~~tl~avL~aLG~~~~~ 47 (694)
T PRK11052 6 LDQAALAAGIAPSYI------NAHGKPQSISAETKRRLLAAMGYRTSA 47 (694)
T ss_pred HHHHHHHCCCCCEEE------CCCCCEEECCHHHHHHHHHHCCCCCCC
T ss_conf 999999809987579------999976978999999999965999999
No 319
>COG2521 Predicted archaeal methyltransferase [General function prediction only]
Probab=44.99 E-value=23 Score=15.93 Aligned_cols=32 Identities=19% Similarity=0.245 Sum_probs=17.0
Q ss_pred EEEEEEEECCCEEEEEECCCCCCCEEECHHHEEEE
Q ss_conf 99999997798799996858988758547865999
Q gi|254780444|r 181 VAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWI 215 (223)
Q Consensus 181 ~iKrl~~~~~~~~~l~s~Np~y~~~~i~~~~i~ii 215 (223)
.|-.+.+. ...++|.++|| |....++. .|+||
T Consensus 159 ~VitvEkd-p~VLeLa~lNP-wSr~l~~~-~i~ii 190 (287)
T COG2521 159 HVITVEKD-PNVLELAKLNP-WSRELFEI-AIKII 190 (287)
T ss_pred EEEEEEEC-CCEEEEECCCC-CCCCCCCC-CCEEE
T ss_conf 89999608-77277413588-98420200-31786
No 320
>PRK01381 Trp operon repressor; Provisional
Probab=44.64 E-value=19 Score=16.51 Aligned_cols=36 Identities=6% Similarity=0.282 Sum_probs=25.2
Q ss_pred CCHHH---HHHH---HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 55899---9999---9999996499988999982899879889
Q gi|254780444|r 4 FSHKK---IWEA---IDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 4 ~~~~~---i~~~---i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
||.++ |..+ ++.|++ -.+||.++|...|++-.||++
T Consensus 33 LTp~Er~al~~R~~I~~~Ll~-ge~sQReIa~~lgvsiAtITR 74 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLR-GELSQREIKQELGVGIATITR 74 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHCCCCEECCC
T ss_conf 899999999999999999994-876499999984974020000
No 321
>pfam04182 B-block_TFIIIC B-block binding subunit of TFIIIC. Yeast transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding.
Probab=44.50 E-value=18 Score=16.55 Aligned_cols=32 Identities=34% Similarity=0.452 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 999999999996499988999982899879889
Q gi|254780444|r 8 KIWEAIDRMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 8 ~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
.+++.|-+- +..|.+|++|++.+|..+-++..
T Consensus 6 ~lL~~Ia~~-r~~Gi~q~dL~k~~~~D~rs~~~ 37 (73)
T pfam04182 6 ELLEEIARS-RYNGITQSDLAKLTGQDPRSVFY 37 (73)
T ss_pred HHHHHHHHC-CCCCCCHHHHHHHHCCCCCCCHH
T ss_conf 999999951-76880189999996899643179
No 322
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=44.17 E-value=24 Score=15.85 Aligned_cols=20 Identities=25% Similarity=0.393 Sum_probs=18.5
Q ss_pred CCHHHHHHHHCCCHHHHHHH
Q ss_conf 99889999828998798899
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~ 41 (223)
||+.+||..+|+|++||++.
T Consensus 106 LT~~Dla~LL~~S~~TI~~~ 125 (220)
T pfam07900 106 LTHADIAILLGVSTTTISRH 125 (220)
T ss_pred EEHHHHHHHHCCCHHHHHHH
T ss_conf 11766999988988899999
No 323
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=44.12 E-value=24 Score=15.84 Aligned_cols=44 Identities=9% Similarity=0.135 Sum_probs=23.6
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCC
Q ss_conf 99964999889999828998798899751578875577989999987321875
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNET 68 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~ 68 (223)
|+--.|+|..++|..+|++..|+...... ..+.|.+.++-.|++
T Consensus 127 l~~~~g~s~~EIA~~l~is~~tVk~~l~r---------a~~~Lr~~L~~~gi~ 170 (171)
T PRK09645 127 RSYYRGWSTAQIAADLGIPEGTVKSRLHY---------AVRALRLTLQEMGVT 170 (171)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHH---------HHHHHHHHHHHCCCC
T ss_conf 99986999999999989299999999999---------999999999970999
No 324
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=44.12 E-value=24 Score=15.84 Aligned_cols=32 Identities=22% Similarity=0.172 Sum_probs=27.1
Q ss_pred HHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999999-9649998899998289987988997
Q gi|254780444|r 11 EAIDRMA-ERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 11 ~~i~~l~-~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+...+|+ ++.++|.-+||..++++.+|++++-
T Consensus 31 ~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl 63 (126)
T COG3355 31 EVYKALLEENGPLTVDELAEILNRSRSTVYRSL 63 (126)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999864699579999999783199999999
No 325
>TIGR01481 ccpA catabolite control protein A; InterPro: IPR006377 Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [e.g. acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription.
Probab=43.96 E-value=5.1 Score=20.17 Aligned_cols=47 Identities=15% Similarity=0.105 Sum_probs=31.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH---CCCCCCCCC
Q ss_conf 9988999982899879889975157887557798999998732---187521000
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAA---TNETICQLL 73 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~---~~v~~~~l~ 73 (223)
+|-.+.||-+|||+.|+||--+|+.+=|| .+-.|++++ |+--++-..
T Consensus 3 VTIYDVArEA~VSMATVSRVVNGN~NVKp-----~TrKKVL~VI~RL~YRPNAVA 52 (332)
T TIGR01481 3 VTIYDVAREAGVSMATVSRVVNGNPNVKP-----ATRKKVLEVIKRLDYRPNAVA 52 (332)
T ss_pred EEEEEHHHHCCCCCEEEEEEECCCCCCCH-----HHHHHHHHHHHHCCCCCCHHH
T ss_conf 22221465248764056424657899756-----763359999965279854453
No 326
>pfam06163 DUF977 Bacterial protein of unknown function (DUF977). This family consists of several hypothetical bacterial proteins from Escherichia coli and Salmonella typhi. The function of this family is unknown.
Probab=43.22 E-value=25 Score=15.75 Aligned_cols=40 Identities=23% Similarity=0.219 Sum_probs=31.8
Q ss_pred CCCH---HHHHHHHHHHHHHCCC-CHHHHHHHHCCCHHHHHHHH
Q ss_conf 7558---9999999999996499-98899998289987988997
Q gi|254780444|r 3 SFSH---KKIWEAIDRMAERHNL-TPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 3 ~~~~---~~i~~~i~~l~~~~gl-s~~~lA~~~Gv~~~ti~~~~ 42 (223)
-+|+ +.|..+|=.|.++.|- |-++|.+.+|++..++.++-
T Consensus 4 ~fT~eeReeik~rIveLVr~~GR~T~~qL~~~tG~~~~s~~~~l 47 (127)
T pfam06163 4 PFTQEEREIIKERIIGLVREQGRITTNQLEAITGAHRTTAEKYL 47 (127)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 78889999999999999998052139999998783399999999
No 327
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=42.87 E-value=25 Score=15.72 Aligned_cols=26 Identities=19% Similarity=0.214 Sum_probs=22.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 99988999982899879889975157
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNKSKRFGI 46 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~~~~~~~ 46 (223)
.+++.+-|...|++..|+.+|.+.+.
T Consensus 1 ~m~~~e~~~~lgis~~Tl~rw~r~G~ 26 (193)
T COG2452 1 LLRPKEACQLLGISYSTLLRWIREGK 26 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHCCC
T ss_conf 98889999983947999999987686
No 328
>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=42.78 E-value=17 Score=16.85 Aligned_cols=23 Identities=17% Similarity=0.247 Sum_probs=20.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 99988999982899879889975
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
.++-.++|..+|++.++|++|+.
T Consensus 22 ~~~l~~IA~~L~vs~~~IrkWKs 44 (60)
T pfam10668 22 TMKLKDIANKLNVSESQIRKWKS 44 (60)
T ss_pred CEEHHHHHHHHCCCHHHHHHCCH
T ss_conf 64499999996879888760311
No 329
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=42.73 E-value=25 Score=15.70 Aligned_cols=23 Identities=17% Similarity=0.429 Sum_probs=10.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 49998899998289987988997
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
.|+|-.++|..+++|+.|+..+.
T Consensus 151 ~G~snkeIA~~L~IS~~TVk~h~ 173 (196)
T PRK10360 151 QGMAVKEIAAELGLSPKTVHVHR 173 (196)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 79999999999699999999999
No 330
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=42.71 E-value=25 Score=15.70 Aligned_cols=57 Identities=19% Similarity=0.257 Sum_probs=38.2
Q ss_pred HHHHHHHHHHH----------CCCCHHHHHHHHCCCHHHHHHHHHCC--------CCCCCCCCCHHHHHHHHHHCC
Q ss_conf 99999999996----------49998899998289987988997515--------788755779899999873218
Q gi|254780444|r 9 IWEAIDRMAER----------HNLTPSGLARKAGLDPTSFNKSKRFG--------IEGRNRWPSTESIFKILAATN 66 (223)
Q Consensus 9 i~~~i~~l~~~----------~gls~~~lA~~~Gv~~~ti~~~~~~~--------~~g~~r~p~~~~l~kia~~~~ 66 (223)
+-..|++++++ +-+|..+.|+.+||+++++.+....+ ..| .|+-+++.+..+=..+.
T Consensus 26 ls~~l~~~r~~~~~P~~~K~lr~fs~~e~a~l~gv~~~~lr~~~~~g~~p~p~~~~~g-rr~ytl~~i~~lR~~l~ 100 (405)
T PRK13869 26 LSSQLQAMSEALFPPTSHKSLRKFTSGEAARLMKISDSTLRKMTLAGEGPQPELASNG-RRFYTLGQINEIRGMLA 100 (405)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCC-CCEECHHHHHHHHHHHH
T ss_conf 9999999998508996656658788899999969699999999865999999878998-54301999999999997
No 331
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=42.01 E-value=26 Score=15.63 Aligned_cols=24 Identities=17% Similarity=0.166 Sum_probs=20.9
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 964999889999828998798899
Q gi|254780444|r 18 ERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 18 ~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.+.|.|-++-|++++++|+++|+-
T Consensus 13 a~~~~sft~AA~~L~iSQpavS~~ 36 (313)
T PRK12684 13 VRQNFNLTEAAKALYTSQPGVSKA 36 (313)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 986999999999978977899999
No 332
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=41.99 E-value=26 Score=15.63 Aligned_cols=30 Identities=20% Similarity=0.312 Sum_probs=26.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999999964999889999828998798899
Q gi|254780444|r 12 AIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 12 ~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
-||+|.++.-++-.+||.++|++...+.+.
T Consensus 6 Vid~L~~~~~v~dedLa~~l~~~~n~vRki 35 (147)
T smart00531 6 VLDALMRNGCVTEEDLAELLGIKQKQLRKI 35 (147)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 229888659707999999979999999999
No 333
>PRK11640 putative transcriptional regulator; Provisional
Probab=41.94 E-value=26 Score=15.63 Aligned_cols=54 Identities=9% Similarity=0.208 Sum_probs=40.3
Q ss_pred CCHHHHHHHHHHHHHHCCCC---HHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHH-HHHHHCCC
Q ss_conf 55899999999999964999---889999828998798899751578875577989999-98732187
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLT---PSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIF-KILAATNE 67 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls---~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~-kia~~~~v 67 (223)
+++|+|+++=.+|--+.|+. .-.+...+||+..|+.++. ||.+.|. ..++....
T Consensus 1 ~kReriL~~A~~LFy~~Gi~atGid~I~~eAgVaK~TLY~hF----------~SKd~LI~a~L~~~~~ 58 (191)
T PRK11640 1 MQREDVLGEALKLLEQQGIANTTLEMVAERVDYPLDELQRFW----------PDKEALLYDALRYLSQ 58 (191)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHC----------CCHHHHHHHHHHHHHH
T ss_conf 938999999999999749420479999999599899999877----------9889999999999767
No 334
>pfam08965 DUF1870 Domain of unknown function (DUF1870). This domain is found in a set of hypothetical bacterial proteins.
Probab=41.86 E-value=26 Score=15.62 Aligned_cols=35 Identities=14% Similarity=0.164 Sum_probs=29.8
Q ss_pred HHHHHHHCCCCHHHHHHHHC--CCHHHHHHHHHCCCC
Q ss_conf 99999964999889999828--998798899751578
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAG--LDPTSFNKSKRFGIE 47 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~G--v~~~ti~~~~~~~~~ 47 (223)
|++||+-.-||..+-|.-.| ++..+..+|++|...
T Consensus 5 LQAlR~if~mti~EaA~~I~~~~~s~~Wq~WE~G~~~ 41 (117)
T pfam08965 5 LQALRKILFLTIVEAAELIGQSVSSRTWQRWEKGDIA 41 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCC
T ss_conf 9999999996499999999468888999999758988
No 335
>PRK04435 hypothetical protein; Provisional
Probab=41.79 E-value=24 Score=15.76 Aligned_cols=35 Identities=14% Similarity=0.336 Sum_probs=25.6
Q ss_pred HHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 99999999996-4999889999828998798899751
Q gi|254780444|r 9 IWEAIDRMAER-HNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 9 i~~~i~~l~~~-~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
+.++ ++|++. ...|-++.++++|+|.+++.+|+-.
T Consensus 21 v~ea-K~LL~~g~~~~i~EAvk~vGISRSafYKYKD~ 56 (146)
T PRK04435 21 VLKA-KELLKSGKVKSITEAVKQVGISRSAFYKYKDY 56 (146)
T ss_pred HHHH-HHHHHCCCCCCHHHHHHHHCCCHHHEECCCCC
T ss_conf 9999-99997389774999999839652101123662
No 336
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=41.52 E-value=26 Score=15.59 Aligned_cols=26 Identities=8% Similarity=0.036 Sum_probs=19.0
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 99996499988999982899879889
Q gi|254780444|r 15 RMAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 15 ~l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
.|..-.|+|..++|..+|++..|+..
T Consensus 129 ~L~~~egls~~EIAe~Lgis~~TVks 154 (190)
T PRK12516 129 ILIGASGFAYEEAAEICGCAVGTIKS 154 (190)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 98998299999999998949999999
No 337
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=40.83 E-value=27 Score=15.52 Aligned_cols=28 Identities=11% Similarity=0.121 Sum_probs=18.9
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9996499988999982899879889975
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
|+.-.|+|+.++|+.+|++.+|+.....
T Consensus 138 l~~~~gls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 138 LRYLEGLSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9998599999999895999999999999
No 338
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=40.75 E-value=27 Score=15.51 Aligned_cols=40 Identities=25% Similarity=0.355 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 589999999999996--4999889999828998798899751
Q gi|254780444|r 5 SHKKIWEAIDRMAER--HNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~--~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
.|+.|.++|+.+... .-+|..+||+.+|+|+=++.+..+.
T Consensus 218 ~~~~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~ 259 (328)
T COG4977 218 RDPRLLRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRA 259 (328)
T ss_pred CCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 887899999999986538868999999968788789999999
No 339
>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=40.69 E-value=27 Score=15.50 Aligned_cols=54 Identities=15% Similarity=0.252 Sum_probs=34.4
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCC------CCCCCCCHHHH-----HHHHHHCCCCCCCCCCCC
Q ss_conf 9889999828998798899751578------87557798999-----998732187521000011
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIE------GRNRWPSTESI-----FKILAATNETICQLLDLP 76 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~------g~~r~p~~~~l-----~kia~~~~v~~~~l~~~~ 76 (223)
+-+++|+.+|++..|+.-|++.+-- +.-|.-+.+.+ .+.+..+|.++.+....-
T Consensus 2 ~IgelA~~~gvs~~TlRyYe~~GLl~p~R~~~gyR~Y~~~~~~rL~~I~~lr~lg~sL~eIk~lL 66 (134)
T cd04779 2 RIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQL 66 (134)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 58899999886889999999779979996999982069999999999999999799899999998
No 340
>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=40.65 E-value=27 Score=15.50 Aligned_cols=38 Identities=18% Similarity=0.249 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHCCC--CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 89999999999996499--988999982899879889975
Q gi|254780444|r 6 HKKIWEAIDRMAERHNL--TPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gl--s~~~lA~~~Gv~~~ti~~~~~ 43 (223)
..+|..+..+|..+.|= |..++|..+|++...+....+
T Consensus 3 i~ki~ka~~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~ 42 (78)
T pfam04539 3 LNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLE 42 (78)
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 7999999999999988899999999996949999999998
No 341
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=40.63 E-value=27 Score=15.50 Aligned_cols=36 Identities=8% Similarity=0.070 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 755899999999999964999889999828998798899
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.||-+++.-. -++. +.| |-++-|++++++|+++|+.
T Consensus 4 ~~tL~qL~~F-~~va-~~g-sft~AA~~L~isQpavS~~ 39 (307)
T CHL00180 4 PFTLDQLRIL-KAIA-SEG-SFKKAAESLYVSQPAVSLQ 39 (307)
T ss_pred CCCHHHHHHH-HHHH-HCC-CHHHHHHHHCCCHHHHHHH
T ss_conf 8489999999-9999-809-9999999988887899999
No 342
>PRK09801 transcriptional activator TtdR; Provisional
Probab=39.96 E-value=28 Score=15.43 Aligned_cols=32 Identities=19% Similarity=0.195 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999999999964999889999828998798899
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+++.-++. ..+.| |-++.|+.+|++++++|+-
T Consensus 9 ~dL~~F~~--Va~~g-Sfs~AA~~L~vs~saVSr~ 40 (310)
T PRK09801 9 KDLQVLVE--IVHSG-SFSAAAATLGQTPAFVTKR 40 (310)
T ss_pred HHHHHHHH--HHHHC-CHHHHHHHHCCCHHHHHHH
T ss_conf 99999999--99809-9999999979598899999
No 343
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=39.54 E-value=28 Score=15.39 Aligned_cols=23 Identities=22% Similarity=0.330 Sum_probs=19.3
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 964999889999828998798899
Q gi|254780444|r 18 ERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 18 ~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.+.| |-+..|+.+|++++++|+.
T Consensus 26 a~~g-Sft~AA~~L~vsqsaVS~~ 48 (311)
T PRK10086 26 ARHQ-SFALAADELSLTPSAVSHR 48 (311)
T ss_pred HHHC-CHHHHHHHHCCCHHHHHHH
T ss_conf 9829-9999999978698999999
No 344
>KOG0844 consensus
Probab=38.53 E-value=21 Score=16.22 Aligned_cols=45 Identities=16% Similarity=0.112 Sum_probs=34.3
Q ss_pred CCCCHHHHHHHHHHHHHHCCCC---HHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 7755899999999999964999---88999982899879889975157
Q gi|254780444|r 2 TSFSHKKIWEAIDRMAERHNLT---PSGLARKAGLDPTSFNKSKRFGI 46 (223)
Q Consensus 2 ~~~~~~~i~~~i~~l~~~~gls---~~~lA~~~Gv~~~ti~~~~~~~~ 46 (223)
|.||+|||..-=++.-+|.=+| .-+||-++.+..+||.-|.++..
T Consensus 186 TAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRR 233 (408)
T KOG0844 186 TAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRR 233 (408)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCEEEHHHHHCH
T ss_conf 665199999999998875224574055677763798430000111010
No 345
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=38.03 E-value=29 Score=15.24 Aligned_cols=18 Identities=6% Similarity=0.093 Sum_probs=9.4
Q ss_pred CHHHHHHHHCCCHHHHHH
Q ss_conf 988999982899879889
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~ 40 (223)
+..++|...|++...+.+
T Consensus 147 ~~~eia~~l~~~~~~ve~ 164 (461)
T PRK05932 147 DLEEIAEELEVELDEVEA 164 (461)
T ss_pred CHHHHHHHHCCCHHHHHH
T ss_conf 999999884979999999
No 346
>PHA01083 hypothetical protein
Probab=37.96 E-value=30 Score=15.23 Aligned_cols=56 Identities=14% Similarity=0.143 Sum_probs=39.9
Q ss_pred HHHHHHHCCCCH-HHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 999999649998-899998289987988997515788755779899999873218752100
Q gi|254780444|r 13 IDRMAERHNLTP-SGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 13 i~~l~~~~gls~-~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
||+.-+.....| .++|-.+|++|+.|+..++|.. +..+.+...=+|+..|..++..
T Consensus 5 ldAYK~aknYvQdKQIAhDlg~~pq~iS~~RkG~R----~Ylsd~eAifLAe~~GiD~E~a 61 (153)
T PHA01083 5 LDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVR----TYISDEEAIFLAESAGIDPEIA 61 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCHH----HHCCHHHHHHHHHHCCCCHHHH
T ss_conf 99999999888899999980999899999981237----6435388999898709988888
No 347
>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=37.92 E-value=30 Score=15.23 Aligned_cols=24 Identities=17% Similarity=0.261 Sum_probs=20.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 998899998289987988997515
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
+...++++.+|++.+||.++.+.+
T Consensus 4 lr~~eV~~~~glsrstiyr~i~~G 27 (51)
T pfam05930 4 LRLKEVEQLTGLSRSTIYRLIKDG 27 (51)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 379999999898999999999879
No 348
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=37.80 E-value=30 Score=15.22 Aligned_cols=24 Identities=8% Similarity=0.115 Sum_probs=21.0
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 964999889999828998798899
Q gi|254780444|r 18 ERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 18 ~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.+.|+|-++.|++++++|+++|+-
T Consensus 13 a~~~~s~t~AAe~L~iSQPavS~q 36 (316)
T PRK12679 13 ARQDYNLTEVANMLFTSQSGVSRH 36 (316)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 986899999999978977899999
No 349
>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=37.12 E-value=30 Score=15.15 Aligned_cols=28 Identities=18% Similarity=0.438 Sum_probs=20.0
Q ss_pred HHHHHHHHCCC---CHHHHHHHHCCCHHHHHH
Q ss_conf 99999996499---988999982899879889
Q gi|254780444|r 12 AIDRMAERHNL---TPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 12 ~i~~l~~~~gl---s~~~lA~~~Gv~~~ti~~ 40 (223)
.++.|.+ .|. |-.+||+.+|++++.|.+
T Consensus 16 ~L~~L~~-~g~~~vSS~eLa~~~gv~~aqiRK 46 (49)
T pfam06971 16 YLEELLE-EGVERVSSKELSEAIGIDAAQIRK 46 (49)
T ss_pred HHHHHHH-CCCCEECHHHHHHHHCCCHHHHHC
T ss_conf 9999998-599049799999997939999614
No 350
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=36.92 E-value=31 Score=15.13 Aligned_cols=18 Identities=6% Similarity=0.458 Sum_probs=7.0
Q ss_pred CCCHHHHHHHHCCCHHHH
Q ss_conf 999889999828998798
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSF 38 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti 38 (223)
|+|..++|..+|++.+|+
T Consensus 152 gls~~EIA~~lgis~~tV 169 (195)
T PRK12532 152 GFSSDEIQQMCGISTSNY 169 (195)
T ss_pred CCCHHHHHHHHCCCHHHH
T ss_conf 999999999989599999
No 351
>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=36.59 E-value=31 Score=15.09 Aligned_cols=58 Identities=16% Similarity=0.201 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHH----------CCCCHHHHHHHHCCCHHHHHHHHHCC-------CCCCCCCCCHHHHHHHHHHC
Q ss_conf 999999999996----------49998899998289987988997515-------78875577989999987321
Q gi|254780444|r 8 KIWEAIDRMAER----------HNLTPSGLARKAGLDPTSFNKSKRFG-------IEGRNRWPSTESIFKILAAT 65 (223)
Q Consensus 8 ~i~~~i~~l~~~----------~gls~~~lA~~~Gv~~~ti~~~~~~~-------~~g~~r~p~~~~l~kia~~~ 65 (223)
++-+.|+++|++ +-+|..+.|+.+|++++++.+....+ ..+..|+-+++.+..+=..+
T Consensus 10 ~ls~~l~~~r~~~~~P~~~K~lr~f~~~e~a~l~gv~~~~lr~~~~~g~~p~p~~~~~grR~ytl~ei~~lR~~l 84 (387)
T TIGR03453 10 ELSSQLQALRERLFPPNAQKTLRRFTSGEAAKLLGVTDSYLRQLSLEGKGPQPEVLANGRRSYTLEQINELRRHL 84 (387)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEEEEHHHHHHHHHHH
T ss_conf 999999999997379965566688888999988496999999998669999987589982584399999999999
No 352
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=36.09 E-value=32 Score=15.04 Aligned_cols=59 Identities=10% Similarity=0.295 Sum_probs=31.3
Q ss_pred HHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHC-CCCCCCCC-CCHHHHHHHH-HHCCCCCCC
Q ss_conf 9999996--4999889999828998798899751-57887557-7989999987-321875210
Q gi|254780444|r 13 IDRMAER--HNLTPSGLARKAGLDPTSFNKSKRF-GIEGRNRW-PSTESIFKIL-AATNETICQ 71 (223)
Q Consensus 13 i~~l~~~--~gls~~~lA~~~Gv~~~ti~~~~~~-~~~g~~r~-p~~~~l~kia-~~~~v~~~~ 71 (223)
+++|.++ .-.|-.+||+++|+++.+|.+=..- +.-||+.. =..+.|.+.+ +.++.+-.|
T Consensus 22 le~l~a~~v~rvsS~els~~~~vdsatIRrDfSYFG~lGkrG~GYnV~~L~~ff~~~Lg~~~~t 85 (211)
T COG2344 22 LERLHASGVERVSSKELSEALGVDSATIRRDFSYFGELGKRGYGYNVKYLRDFFDDLLGQDKTT 85 (211)
T ss_pred HHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCE
T ss_conf 9999872980126899999868999998635678775278877843999999999983877403
No 353
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=35.99 E-value=30 Score=15.23 Aligned_cols=19 Identities=16% Similarity=0.336 Sum_probs=16.1
Q ss_pred HHHHHHHHCCCHHHHHHHH
Q ss_conf 8899998289987988997
Q gi|254780444|r 24 PSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 24 ~~~lA~~~Gv~~~ti~~~~ 42 (223)
.+++|+.+|++++|++..-
T Consensus 2 ~~diA~~L~vs~~sVs~~l 20 (96)
T smart00529 2 TSEIAERLNVSPPTVTQML 20 (96)
T ss_pred HHHHHHHHCCCCHHHHHHH
T ss_conf 7889988499916799999
No 354
>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=35.90 E-value=28 Score=15.42 Aligned_cols=24 Identities=8% Similarity=0.073 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 499988999982899879889975
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
.|||--.++..-+++++||++|-.
T Consensus 181 ~~Ls~~r~g~my~~~~STvsR~~~ 204 (249)
T TIGR03001 181 EGLSMDRLGAMYQVHRSTVSRWVA 204 (249)
T ss_pred CCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 033299998774577507899999
No 355
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=35.65 E-value=32 Score=15.00 Aligned_cols=41 Identities=15% Similarity=0.163 Sum_probs=29.1
Q ss_pred CCCHHHHHHH---HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 7558999999---9999996499988999982899879889975
Q gi|254780444|r 3 SFSHKKIWEA---IDRMAERHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 3 ~~~~~~i~~~---i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
+|+-++-... +++=.+..|+|..++|..+|+++..+.+..+
T Consensus 2 SLn~~Q~~~T~~ELqeNf~~~~ls~~~iA~dL~~s~~~ve~vL~ 45 (89)
T pfam10078 2 SLNIEEMQATRKELQANFELSGLTIEQVAKDLNTTPEKVEALLQ 45 (89)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98899999999999999988389899999894999999999997
No 356
>PRK04280 arginine repressor; Provisional
Probab=35.58 E-value=32 Score=14.99 Aligned_cols=34 Identities=9% Similarity=0.208 Sum_probs=25.7
Q ss_pred HHHHHHHHHHCCC-CHHHHHHHHC-----CCHHHHHHHHH
Q ss_conf 9999999996499-9889999828-----99879889975
Q gi|254780444|r 10 WEAIDRMAERHNL-TPSGLARKAG-----LDPTSFNKSKR 43 (223)
Q Consensus 10 ~~~i~~l~~~~gl-s~~~lA~~~G-----v~~~ti~~~~~ 43 (223)
.+.|.+|.++..+ ||.+|.+.+. ++|+|+||--+
T Consensus 7 ~~~I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATlSRDlk 46 (149)
T PRK04280 7 HIKIREIITNEEIETQDELVDRLREYGFNVTQATVSRDIK 46 (149)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHHHHH
T ss_conf 9999999974897789999999998597553898898799
No 357
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=35.57 E-value=32 Score=14.99 Aligned_cols=31 Identities=19% Similarity=0.374 Sum_probs=24.2
Q ss_pred HHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999999-64999889999828998798899
Q gi|254780444|r 11 EAIDRMAE-RHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 11 ~~i~~l~~-~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+.|..+++ .-+.|..++|+++|+++.++.+.
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~H 45 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRH 45 (218)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999983169824999998859998999999
No 358
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794 Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=35.37 E-value=31 Score=15.14 Aligned_cols=25 Identities=28% Similarity=0.367 Sum_probs=21.8
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9964999889999828998798899
Q gi|254780444|r 17 AERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 17 ~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.++..+|-++.|+++|++..+..+.
T Consensus 20 ~~~~~ltl~~vA~~TGL~RAaARR~ 44 (252)
T TIGR02431 20 EERPRLTLTDVAEATGLTRAAARRF 44 (252)
T ss_pred CCCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf 0378989899998758994798889
No 359
>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]
Probab=35.21 E-value=33 Score=14.95 Aligned_cols=27 Identities=19% Similarity=0.402 Sum_probs=22.8
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 558999999999999649998899998
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARK 30 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~ 30 (223)
+..++|+++++..++..|||+++.+..
T Consensus 137 l~re~~L~Rl~~v~a~mgLsPadvrn~ 163 (402)
T COG3598 137 LYREDILERLEPVRARMGLSPADVRNM 163 (402)
T ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHE
T ss_conf 686889999999998709985763220
No 360
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=35.14 E-value=33 Score=14.95 Aligned_cols=43 Identities=14% Similarity=0.231 Sum_probs=29.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 9999999964999889999828998798899751578875577989999987321875210
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQ 71 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~ 71 (223)
+.+.++.+. | |-+.-|+.++++++++++. +.++-+.+++.+-.
T Consensus 5 ~~f~~v~~~-g-s~~~AA~~l~isqs~vs~~----------------i~~LE~~lg~~Lf~ 47 (60)
T pfam00126 5 RVFVAVAEE-G-SFTAAAERLGLSQPAVSRQ----------------IKRLEEELGVPLFE 47 (60)
T ss_pred HHHHHHHHC-C-CHHHHHHHHCCCHHHHHHH----------------HHHHHHHHCCEEEE
T ss_conf 999999980-9-9999999979898899999----------------99999995997078
No 361
>PRK10632 putative DNA-binding transcriptional regulator; Provisional
Probab=34.97 E-value=33 Score=14.93 Aligned_cols=23 Identities=13% Similarity=0.202 Sum_probs=19.4
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 964999889999828998798899
Q gi|254780444|r 18 ERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 18 ~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.+.| |-++.|+++|++++++|+.
T Consensus 14 ae~g-Sfs~AA~~L~~s~saVSr~ 36 (309)
T PRK10632 14 VEFG-SFTAAARQLQMSVSSISQT 36 (309)
T ss_pred HHCC-CHHHHHHHHCCCHHHHHHH
T ss_conf 9809-9999999979598899999
No 362
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=34.84 E-value=33 Score=14.92 Aligned_cols=22 Identities=18% Similarity=0.341 Sum_probs=14.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 4999889999828998798899
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.|+|..++|..+|++.+|+...
T Consensus 126 ~g~s~~EIA~~l~is~~tVk~~ 147 (166)
T PRK09639 126 SGYSYKEIAQALGIDESSVGTT 147 (166)
T ss_pred HCCCHHHHHHHHCCCHHHHHHH
T ss_conf 3899999999989199999999
No 363
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=34.68 E-value=33 Score=14.90 Aligned_cols=25 Identities=12% Similarity=0.197 Sum_probs=17.6
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 6499988999982899879889975
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
..|+|-.++|+++++|..|+..+..
T Consensus 161 a~G~snkeIA~~L~iS~~TVk~h~~ 185 (211)
T COG2197 161 AEGLSNKEIAEELNLSEKTVKTHVS 185 (211)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 8799889999997878989999999
No 364
>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=34.26 E-value=34 Score=14.86 Aligned_cols=51 Identities=18% Similarity=0.116 Sum_probs=36.4
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 996499988999982899879889975157887557798999998732187521000
Q gi|254780444|r 17 AERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLL 73 (223)
Q Consensus 17 ~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~ 73 (223)
.++.| ||..+|..+|++..|++. +- +++- .-+...+.|..+.++.+.+++.
T Consensus 13 ~Ek~g-tq~~Fa~~lg~se~tlsl-kl---n~~v-~w~q~ei~kai~lL~i~~d~i~ 63 (69)
T pfam05339 13 LEKYG-TQYNFASAIGLSERSLSL-KL---NDKV-IWVANEIEKAIDLLGIPKDDIV 63 (69)
T ss_pred HHHHC-CHHHHHHHHCCCHHHHHH-HH---CCCC-CCCHHHHHHHHHHHCCCHHHHH
T ss_conf 89956-798999995811768889-87---6867-7539999999999689988877
No 365
>KOG0400 consensus
Probab=33.99 E-value=34 Score=14.83 Aligned_cols=53 Identities=23% Similarity=0.389 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHH----HHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf 755899999999999964999889999----82899879889975157887557798999998732187521
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLAR----KAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~----~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~ 70 (223)
.++-+++.+.|-.+.++ ||+++++.- .-|+.+ -|....+++.+|++..|+-++
T Consensus 27 K~~~ddvkeqI~K~akK-GltpsqIGviLRDshGi~q--------------~r~v~G~kI~Rilk~~Gl~Pe 83 (151)
T KOG0400 27 KLTADDVKEQIYKLAKK-GLTPSQIGVILRDSHGIGQ--------------VRFVTGNKILRILKSNGLAPE 83 (151)
T ss_pred HCCHHHHHHHHHHHHHC-CCCHHHCEEEEECCCCCCH--------------HHHHHHHHHHHHHHHCCCCCC
T ss_conf 63889999999999866-9986581266532247544--------------441000699999997699889
No 366
>PRK13866 plasmid partitioning protein RepB; Provisional
Probab=33.80 E-value=34 Score=14.81 Aligned_cols=30 Identities=7% Similarity=0.052 Sum_probs=25.3
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 999964999889999828998798899751
Q gi|254780444|r 15 RMAERHNLTPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 15 ~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
+-+++.|++...+...+++..+.++++..-
T Consensus 173 ~~l~~~g~~r~~i~~aL~~dk~~lS~m~~v 202 (336)
T PRK13866 173 LRLEDAGFDRATIIAALSTDKADLSRYITV 202 (336)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999976998889999967888899999999
No 367
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=33.54 E-value=35 Score=14.78 Aligned_cols=23 Identities=22% Similarity=0.300 Sum_probs=12.7
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 96499988999982899879889
Q gi|254780444|r 18 ERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 18 ~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
.-.|+|..++|..+|++.+|+..
T Consensus 121 ~~~~~s~~EIA~~l~is~~tVk~ 143 (165)
T PRK09644 121 DVHELTYEEAASVLDLKENTYKS 143 (165)
T ss_pred HHHCCCHHHHHHHHCCCHHHHHH
T ss_conf 99888999999998939999999
No 368
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=33.47 E-value=35 Score=14.77 Aligned_cols=13 Identities=23% Similarity=0.444 Sum_probs=4.9
Q ss_pred EEECCCCC-CCEEE
Q ss_conf 99685898-87585
Q gi|254780444|r 195 LMSLNCCY-PVDTV 207 (223)
Q Consensus 195 l~s~Np~y-~~~~i 207 (223)
.+..|+.+ |.+.+
T Consensus 286 ~v~ln~~~~P~l~i 299 (475)
T PRK12469 286 IVTINPAVLPRARV 299 (475)
T ss_pred EEEECCCCCCCHHH
T ss_conf 99846777863021
No 369
>pfam02787 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.
Probab=32.80 E-value=36 Score=14.70 Aligned_cols=37 Identities=16% Similarity=0.344 Sum_probs=28.2
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 589999999999996499988999982899879889975
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
|-++|+.-.++| ++|+|..++.+.+++.+=-+.+.++
T Consensus 9 ~~~Rl~~i~eAl--r~G~sveeI~~~TkID~wFL~~i~~ 45 (122)
T pfam02787 9 TDERIFAIAEAL--RRGYSVEEIHELTKIDPWFLEKIKE 45 (122)
T ss_pred CCHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 935999999999--9599999999988968999999999
No 370
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=32.63 E-value=36 Score=14.69 Aligned_cols=22 Identities=27% Similarity=0.448 Sum_probs=15.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9988999982899879889975
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKR 43 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~ 43 (223)
||-.+||+.+|+|+.++++..+
T Consensus 2 lsl~~lA~~~~~S~~~l~~~f~ 23 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 8999999988909999999999
No 371
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=32.55 E-value=36 Score=14.68 Aligned_cols=26 Identities=23% Similarity=0.346 Sum_probs=19.0
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99964999889999828998798899
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
|+.-.|+|..++|..+|++.+|+...
T Consensus 117 L~~~eg~s~~EIA~~L~is~~tVksr 142 (181)
T PRK09637 117 LTELEGLSQKEIAEKLGLSLSGAKSR 142 (181)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99885999999999989499999999
No 372
>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=32.46 E-value=31 Score=15.11 Aligned_cols=56 Identities=16% Similarity=0.184 Sum_probs=34.9
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCC-------CC--C-CHHHHHHH--HHHCCCCCCCCCCCCCC
Q ss_conf 9889999828998798899751578875-------57--7-98999998--73218752100001111
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRN-------RW--P-STESIFKI--LAATNETICQLLDLPFS 78 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~-------r~--p-~~~~l~ki--a~~~~v~~~~l~~~~~~ 78 (223)
--.+||+++|++=.||..|++.+--+.| |- + -.|.|+=| +..++.+++++-.+..-
T Consensus 2 kIGeLA~~t~v~v~TIRFYE~~gLLPeP~R~~nnYRlYt~~hvErL~FI~~CR~Ldmsl~EIr~L~~l 69 (127)
T TIGR02047 2 KIGELAKKTGVSVETIRFYEKEGLLPEPARADNNYRLYTEEHVERLAFIRNCRTLDMSLAEIRELLRL 69 (127)
T ss_pred CHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 41345455334400224644137853865447795103888999999998316230018999988763
No 373
>TIGR02177 PorB_KorB 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family; InterPro: IPR011896 A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This entry describes the beta subunits, representing mostly pyruvate and 2-ketoisovalerate specific enzymes..
Probab=32.26 E-value=9.4 Score=18.45 Aligned_cols=53 Identities=19% Similarity=0.300 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHH-HHHHHHC----CCCCCCCCCCHHHHHHHHH
Q ss_conf 99999999996499988999982899879-8899751----5788755779899999873
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTS-FNKSKRF----GIEGRNRWPSTESIFKILA 63 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~t-i~~~~~~----~~~g~~r~p~~~~l~kia~ 63 (223)
|++||++.+.|++|.+.+.+--.||..++ ..+|-+. +..||. ...-+=+|+|+
T Consensus 12 IL~AL~~AL~EL~LdP~qvvVVSGIGCS~ktPhY~n~~g~h~LHGRA--~P~A~G~KlAN 69 (302)
T TIGR02177 12 ILSALQKALAELNLDPEQVVVVSGIGCSAKTPHYVNVNGFHGLHGRA--LPVATGIKLAN 69 (302)
T ss_pred HHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCC--CHHHHHHHHCC
T ss_conf 89999999986288985279981313113477300136645233563--10110120108
No 374
>TIGR02305 HpaG-N-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal subunit; InterPro: IPR012686 This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related C-terminal domain (IPR012684 from INTERPRO). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity.
Probab=32.17 E-value=36 Score=14.64 Aligned_cols=28 Identities=29% Similarity=0.546 Sum_probs=21.1
Q ss_pred CCCCCCEEEEE---CCCCCCCCCEEEEEEEC
Q ss_conf 14878689993---68974058889999717
Q gi|254780444|r 150 LYRKGDILILN---SAIQVNCGDRLLIKPRT 177 (223)
Q Consensus 150 ~i~~Gd~vlVd---~~~~~~~g~~v~~~~~~ 177 (223)
||..||++++= ...++..||.|-+...+
T Consensus 168 TL~~GDvll~Gt~~~~~~v~~Gd~V~v~~~~ 198 (206)
T TIGR02305 168 TLEAGDVLLLGTPEERVKVGPGDRVRVEIEG 198 (206)
T ss_pred HCCCCCEEEECCCCCCEECCCCCEEEEEECC
T ss_conf 0276988997067886242788788861016
No 375
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=31.95 E-value=37 Score=14.62 Aligned_cols=35 Identities=3% Similarity=0.074 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 55899999999999964999889999828998798899
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
++=+++.-. .++++. | |-+..|++++++++++|+.
T Consensus 3 m~L~~L~~F-~~va~~-g-sft~AA~~L~isQpavS~~ 37 (291)
T PRK10837 3 ITLRQLEVF-AEVLKS-G-STTQASVMLALSQSAVSAA 37 (291)
T ss_pred CCHHHHHHH-HHHHHC-C-CHHHHHHHHCCCHHHHHHH
T ss_conf 869999999-999980-9-9999999988887899999
No 376
>PHA01748 hypothetical protein
Probab=31.84 E-value=37 Score=14.60 Aligned_cols=26 Identities=35% Similarity=0.446 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 89999999999996499988999982
Q gi|254780444|r 6 HKKIWEAIDRMAERHNLTPSGLARKA 31 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gls~~~lA~~~ 31 (223)
.++++.-+|+.+-++|++.|+.-|++
T Consensus 10 eedll~LLdrYAik~~lnRSEaIRkA 35 (60)
T PHA01748 10 EEDLLLLLDRYAIKHKLNRSEAIRKA 35 (60)
T ss_pred CHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 78999999999999477788999999
No 377
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=31.42 E-value=38 Score=14.56 Aligned_cols=21 Identities=10% Similarity=0.170 Sum_probs=13.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHH
Q ss_conf 499988999982899879889
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~ 40 (223)
.|+|..+.|+.+|+|.+++..
T Consensus 146 ~~ls~~EIA~~l~~s~~tVk~ 166 (191)
T PRK12520 146 LELETEEICKELQITATNLWV 166 (191)
T ss_pred HCCCHHHHHHHHCCCHHHHHH
T ss_conf 389999999998949999999
No 378
>cd05726 Ig4_Robo Fhird immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Ig4_Robo: domain similar to the fhird immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit responsiveness, antagoni
Probab=31.16 E-value=34 Score=14.85 Aligned_cols=26 Identities=19% Similarity=0.142 Sum_probs=16.2
Q ss_pred EECCCEEEEEEEEECCCEEEEEECCC
Q ss_conf 71796899999997798799996858
Q gi|254780444|r 175 PRTGDIVAKVLISRRGRSIDLMSLNC 200 (223)
Q Consensus 175 ~~~~~~~iKrl~~~~~~~~~l~s~Np 200 (223)
..++.++|+.++....|.|.....|.
T Consensus 44 ~~~g~L~I~~v~~~D~G~Y~C~A~N~ 69 (90)
T cd05726 44 SQTGDLTITNVQRSDVGYYICQTLNV 69 (90)
T ss_pred CCCCEEEECCCCHHHCEEEEEEEECC
T ss_conf 89985999707968898999997924
No 379
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=31.04 E-value=38 Score=14.52 Aligned_cols=19 Identities=16% Similarity=0.172 Sum_probs=8.3
Q ss_pred CCCCHHHHHHHHCCCHHHH
Q ss_conf 4999889999828998798
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSF 38 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti 38 (223)
.|+|..++|..+|++..|+
T Consensus 126 egls~~EIAe~Lgis~gTV 144 (182)
T PRK12511 126 EGLSYQEAANVLGIPIGTL 144 (182)
T ss_pred CCCCHHHHHHHHCCCHHHH
T ss_conf 7999999999989399999
No 380
>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=30.94 E-value=38 Score=14.51 Aligned_cols=35 Identities=17% Similarity=0.343 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHH----------CCCCHHHHHHHHCCCHHHHHH
Q ss_conf 89999999999996----------499988999982899879889
Q gi|254780444|r 6 HKKIWEAIDRMAER----------HNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 6 ~~~i~~~i~~l~~~----------~gls~~~lA~~~Gv~~~ti~~ 40 (223)
+..++.||.+|=.. .+||-.+.|..+|+|..|+.-
T Consensus 104 r~~l~~AL~~LP~rQR~vvVLRY~eDlSe~~~A~~LG~SvGTVKS 148 (165)
T TIGR02983 104 RAALARALRRLPARQRAVVVLRYYEDLSEAEVAEVLGISVGTVKS 148 (165)
T ss_pred HHHHHHHHHHCCHHCCEEEEEECCCCCCHHHHHHHHCCCCHHHHH
T ss_conf 999999997356412367232045789868999881999322899
No 381
>KOG1575 consensus
Probab=30.86 E-value=38 Score=14.50 Aligned_cols=21 Identities=10% Similarity=-0.023 Sum_probs=7.3
Q ss_pred CCCHHHHHHHHC--CCHHHHHHH
Q ss_conf 999889999828--998798899
Q gi|254780444|r 21 NLTPSGLARKAG--LDPTSFNKS 41 (223)
Q Consensus 21 gls~~~lA~~~G--v~~~ti~~~ 41 (223)
|++-=+-|+--| .+...+.+|
T Consensus 57 Gin~fDtAe~Yg~~~~E~llg~~ 79 (336)
T KOG1575 57 GINFFDTAEVYGNGQSEELLGEF 79 (336)
T ss_pred CCCEEEHHHHCCCCCCHHHHHHH
T ss_conf 97776325430876438999999
No 382
>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=30.80 E-value=38 Score=14.49 Aligned_cols=25 Identities=24% Similarity=0.276 Sum_probs=20.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 9988999982899879889975157
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGI 46 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~ 46 (223)
++-++||+++|++..||.-|.+.+-
T Consensus 2 y~i~eLa~~~g~~~rtiR~Y~~~GL 26 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAYQDRGL 26 (219)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHCCC
T ss_conf 7599999982998111279887689
No 383
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=30.77 E-value=38 Score=14.49 Aligned_cols=27 Identities=15% Similarity=0.166 Sum_probs=20.6
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999964999889999828998798899
Q gi|254780444|r 15 RMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 15 ~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.|+.-.|+|..++|..+|++..|+...
T Consensus 159 ~L~~~eglS~~EIA~~Lgis~~TVKsr 185 (231)
T PRK11922 159 VLRVVEELSVEETAQALGLPEETVKTR 185 (231)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999993999999999989399999999
No 384
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=30.71 E-value=39 Score=14.48 Aligned_cols=32 Identities=19% Similarity=0.232 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999999999649998899998289987988997
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
-+....++.+. | |-+..|+.++++|+++|+.-
T Consensus 9 qLr~F~av~~~-g-s~s~AA~~L~isQpavS~~I 40 (302)
T PRK09791 9 QIRAFVEVARQ-G-SIRGASRMLNMSQPALSKSI 40 (302)
T ss_pred HHHHHHHHHHC-C-CHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999980-9-99999999789879999999
No 385
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=30.63 E-value=39 Score=14.47 Aligned_cols=19 Identities=11% Similarity=0.184 Sum_probs=8.6
Q ss_pred CCCCHHHHHHHHCCCHHHH
Q ss_conf 4999889999828998798
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSF 38 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti 38 (223)
.|+|..++|..+|++.+|+
T Consensus 143 eg~s~~EIA~~Lgis~~tV 161 (188)
T PRK12517 143 GGFSGEEIAEILDLNKNTV 161 (188)
T ss_pred CCCCHHHHHHHHCCCHHHH
T ss_conf 3999999999989399999
No 386
>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=30.60 E-value=39 Score=14.47 Aligned_cols=46 Identities=13% Similarity=0.166 Sum_probs=36.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf 99999999649998899998289987988997515788755779899999873218752
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETI 69 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~ 69 (223)
.-|+.+..+...|-.++|.+..+|.+|+.+..+ .+.+.++-.+..+
T Consensus 20 ~il~~lf~~~~~s~~~~a~~l~iS~sTl~R~ik-------------~l~~~L~~~~l~i 65 (87)
T pfam05043 20 QLLKFLFFHEFFSLTSLAQKLFISESTLYRLIK-------------KLNKLLKEFDLSI 65 (87)
T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH-------------HHHHHHHHCCEEE
T ss_conf 999999818999899999997889999999999-------------9999999859688
No 387
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.58 E-value=39 Score=14.47 Aligned_cols=22 Identities=14% Similarity=0.220 Sum_probs=9.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 4999889999828998798899
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.|+|..++|+.+|++.+|+...
T Consensus 140 ~g~s~~eIA~~lgis~~tv~~~ 161 (180)
T PRK11924 140 EGLSYQEIADQLGVPLGTVKSR 161 (180)
T ss_pred HCCCHHHHHHHHCCCHHHHHHH
T ss_conf 6859999999989499999999
No 388
>PRK09483 response regulator; Provisional
Probab=30.38 E-value=39 Score=14.45 Aligned_cols=17 Identities=12% Similarity=0.307 Sum_probs=5.3
Q ss_pred CCHHHHHHHHCCCHHHH
Q ss_conf 99889999828998798
Q gi|254780444|r 22 LTPSGLARKAGLDPTSF 38 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti 38 (223)
+|-.++|+.+++|..|+
T Consensus 164 ~snkeIA~~L~iS~~TV 180 (216)
T PRK09483 164 QKVNEISEQLNLSPKTV 180 (216)
T ss_pred CCHHHHHHHHCCCHHHH
T ss_conf 99999999969899999
No 389
>pfam06242 DUF1013 Protein of unknown function (DUF1013). Family of uncharacterized proteins found in Proteobacteria.
Probab=30.38 E-value=39 Score=14.45 Aligned_cols=45 Identities=18% Similarity=0.238 Sum_probs=32.4
Q ss_pred HHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHCC----CCCCCCCCCH
Q ss_conf 999999996-49998899998289987988997515----7887557798
Q gi|254780444|r 11 EAIDRMAER-HNLTPSGLARKAGLDPTSFNKSKRFG----IEGRNRWPST 55 (223)
Q Consensus 11 ~~i~~l~~~-~gls~~~lA~~~Gv~~~ti~~~~~~~----~~g~~r~p~~ 55 (223)
.||-+|.+. -.|+-+++++.+|....||...+... .+-+|+.|-+
T Consensus 72 dAI~WLiknhPeL~D~QI~kLiGTTK~TI~~IR~rthWN~~Ni~p~dPV~ 121 (141)
T pfam06242 72 DAIAWLLRNHPELSDAQISKLIGTTKTTIEAIRDRSHWNSANIKPRDPVT 121 (141)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCCE
T ss_conf 99999997167024878888747757889998635744445778699823
No 390
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=29.90 E-value=40 Score=14.39 Aligned_cols=60 Identities=12% Similarity=0.022 Sum_probs=34.9
Q ss_pred HHHHCCCCHHHHHHHHCCCHHH------HHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 9996499988999982899879------889975157887557798999998732187521000011112
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTS------FNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSD 79 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~t------i~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~~~ 79 (223)
.+|++|.|-.++|+.++++..+ |.+.|+..+. .|..+.+==.|.-+..-..|+.......
T Consensus 497 ~aK~lGFSD~~iA~~~~~~~~~~~~~~~vR~~R~~~gi----~Pv~K~vDTcAAEF~A~TpY~YSTY~~e 562 (1089)
T TIGR01369 497 KAKKLGFSDAQIARLVNVTEAESIEELEVRKLRKELGI----IPVYKRVDTCAAEFEAKTPYLYSTYEGE 562 (1089)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHCCCHHHHHHHHHHCCC----EEEEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf 98641888789999868974442006899999984697----4778775232120201568852577666
No 391
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=29.72 E-value=40 Score=14.38 Aligned_cols=36 Identities=11% Similarity=0.100 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 755899999999999964999889999828998798899
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
||.-+++.-.+. . .+.| |-+.-|++++++++++|+.
T Consensus 1 MmDl~~Lr~F~a-V-ae~g-Sfs~AA~~L~isqsavS~~ 36 (308)
T PRK10094 1 MFDPETLRTFIA-V-AETG-SFSKAAERLCKTTATISYR 36 (308)
T ss_pred CCCHHHHHHHHH-H-HHCC-CHHHHHHHHCCCHHHHHHH
T ss_conf 989899999999-9-9819-9999999978987899999
No 392
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=29.70 E-value=40 Score=14.37 Aligned_cols=26 Identities=19% Similarity=0.183 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 89999999999996499988999982
Q gi|254780444|r 6 HKKIWEAIDRMAERHNLTPSGLARKA 31 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gls~~~lA~~~ 31 (223)
-+++.++=.+..++.|+|||++-|..
T Consensus 9 D~~LK~~A~avL~~lGltpS~avr~~ 34 (80)
T PRK11235 9 DDELKARAYAVLEKLGVTPSEALRLL 34 (80)
T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 68889999999999199989999999
No 393
>KOG1168 consensus
Probab=29.39 E-value=15 Score=17.14 Aligned_cols=34 Identities=9% Similarity=0.151 Sum_probs=19.8
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHC---------CCHHHHHHHHH
Q ss_conf 99999999964999889999828---------99879889975
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARKAG---------LDPTSFNKSKR 43 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~~G---------v~~~ti~~~~~ 43 (223)
.++.+..|-+.|+||++..+++. ++++||-+.+.
T Consensus 223 AErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFES 265 (385)
T KOG1168 223 AERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFES 265 (385)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEE
T ss_conf 9998754543064277778898727688755323121332100
No 394
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=29.38 E-value=41 Score=14.34 Aligned_cols=25 Identities=8% Similarity=0.097 Sum_probs=14.4
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9964999889999828998798899
Q gi|254780444|r 17 AERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 17 ~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+.-.|+|..++|..+|++.+|+...
T Consensus 183 ~~~egls~~EIA~~Lgis~~TVKsr 207 (233)
T PRK12538 183 SYHENMSNGEIAEVMDTTVAAVESL 207 (233)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9984999999999989299999999
No 395
>KOG4120 consensus
Probab=29.01 E-value=39 Score=14.43 Aligned_cols=20 Identities=10% Similarity=0.099 Sum_probs=10.0
Q ss_pred EEEECCCCCCCCCCCCCEEE
Q ss_conf 99962833242148786899
Q gi|254780444|r 139 RHKTQDTSMLPLYRKGDILI 158 (223)
Q Consensus 139 ~l~V~GDSM~P~i~~Gd~vl 158 (223)
...++|+||.|.|++|.+..
T Consensus 382 s~elr~e~~~~~ipn~q~~t 401 (426)
T KOG4120 382 SVELRGESAFSGIPNGQWMT 401 (426)
T ss_pred EHHCCCCCCCCCCCCCCCHH
T ss_conf 01003533367898852032
No 396
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=28.85 E-value=41 Score=14.28 Aligned_cols=25 Identities=8% Similarity=0.134 Sum_probs=16.2
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9996499988999982899879889
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|..-.|+|..++|..+|++..|+..
T Consensus 124 L~~~egls~~EIAe~Lgis~gTVKs 148 (188)
T PRK12546 124 LVGASGFSYEEAAEMCGVAVGTVKS 148 (188)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 7998298999999998939999999
No 397
>PRK09258 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed
Probab=28.71 E-value=31 Score=15.13 Aligned_cols=64 Identities=17% Similarity=0.192 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCC-CCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 7558999999999999649998899998289987988997515788-755779899999873218752100
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEG-RNRWPSTESIFKILAATNETICQL 72 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g-~~r~p~~~~l~kia~~~~v~~~~l 72 (223)
..|+++|-+.|+.+-++.++.+..+.+++||.. |+-..++ .......+...+.++..++.++++
T Consensus 14 ~vtn~el~~~~~~~~~~~~~~~~~i~~~tGI~~------Rr~a~~~e~~sdma~~Aa~~AL~~agi~p~dI 78 (339)
T PRK09258 14 VVTSSEIESRLAPLYQRLRIPMGQLEALTGIRE------RRWWPKGHQLSDGATEAARKALAEAGIDASDI 78 (339)
T ss_pred CCCHHHHHHHHCCCHHHHCCCCCHHHHCCCCEE------EEECCCCCCHHHHHHHHHHHHHHHCCCCHHHC
T ss_conf 174899997753304542587113233467303------53679999889999999999999759998999
No 398
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=28.38 E-value=42 Score=14.23 Aligned_cols=27 Identities=15% Similarity=0.230 Sum_probs=20.5
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999964999889999828998798899
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
..++.+. | |-+.-|+++|++|+++|+.
T Consensus 5 F~~va~~-g-s~s~AA~~L~isQpavS~~ 31 (279)
T TIGR03339 5 FHAVARC-G-SFTRAAERLGLSQPTVTDQ 31 (279)
T ss_pred HHHHHHH-C-CHHHHHHHHCCCHHHHHHH
T ss_conf 9999980-9-9999999988888999999
No 399
>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=28.25 E-value=34 Score=14.87 Aligned_cols=19 Identities=26% Similarity=0.354 Sum_probs=14.9
Q ss_pred CHHHHHHHHCCCHHHHHHH
Q ss_conf 9889999828998798899
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~ 41 (223)
|.+++|+.+|++..+|+++
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 400
>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=28.10 E-value=43 Score=14.20 Aligned_cols=32 Identities=22% Similarity=0.394 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHCCCCHH--HHHHHHCCCHHHH
Q ss_conf 9999999999996499988--9999828998798
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPS--GLARKAGLDPTSF 38 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~--~lA~~~Gv~~~ti 38 (223)
-+|..+.+.|.+++|=+|+ +||..+||++--|
T Consensus 91 ~~~~~a~eeL~~~lgR~Pt~~EiAe~L~~s~EEv 124 (229)
T TIGR02980 91 LKINKATEELTQRLGRSPTVAEIAEELGVSEEEV 124 (229)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHH
T ss_conf 9999999999998288988789998858899999
No 401
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=28.06 E-value=43 Score=14.19 Aligned_cols=22 Identities=14% Similarity=0.114 Sum_probs=18.8
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 64999889999828998798899
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+.| |-+.-|++++++++++|+-
T Consensus 19 ~~g-S~s~AA~~L~~sqsaVS~~ 40 (295)
T PRK11139 19 RHL-SFTRAAEELFVTQAAVSHQ 40 (295)
T ss_pred HHC-CHHHHHHHHCCCHHHHHHH
T ss_conf 839-9999999988698899999
No 402
>TIGR01032 rplT_bact ribosomal protein L20; InterPro: IPR005812 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This family covers bacterial ribosomal protein L20 and its chloroplast equivalent.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=27.53 E-value=44 Score=14.13 Aligned_cols=31 Identities=23% Similarity=0.363 Sum_probs=22.2
Q ss_pred HH-HHHHHHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf 99-99999999649998899998289987988
Q gi|254780444|r 9 IW-EAIDRMAERHNLTPSGLARKAGLDPTSFN 39 (223)
Q Consensus 9 i~-~~i~~l~~~~gls~~~lA~~~Gv~~~ti~ 39 (223)
+| .+|.+...++|||.|.|=..+-.+-=.|+
T Consensus 60 LWI~RINAA~R~~GlsYS~fin~LK~A~I~iN 91 (114)
T TIGR01032 60 LWITRINAAAREHGLSYSRFINGLKKANIEIN 91 (114)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC
T ss_conf 89999999987458848998757987482314
No 403
>PRK13702 replication protein; Provisional
Probab=27.45 E-value=44 Score=14.12 Aligned_cols=21 Identities=19% Similarity=0.292 Sum_probs=13.8
Q ss_pred HHHHHHHHHHCCCCHHHHHHH
Q ss_conf 999999999649998899998
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGLARK 30 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~lA~~ 30 (223)
..-+..|.++-|+||+++-.+
T Consensus 53 K~~l~e~C~~~GlTQAe~ie~ 73 (82)
T PRK13702 53 KDKLLELCEEEGLTQAEMIEK 73 (82)
T ss_pred HHHHHHHHHHCCCCHHHHHHH
T ss_conf 999999998838649999999
No 404
>pfam10502 Peptidase_S26 Peptidase S26. This is a family of serine endopeptidases which function in the processing of newly-synthesized secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes.
Probab=27.33 E-value=44 Score=14.11 Aligned_cols=30 Identities=20% Similarity=0.114 Sum_probs=18.6
Q ss_pred ECCCEEEEEECC-C-CCCCEEE---CHHHEEEEEEEE
Q ss_conf 779879999685-8-9887585---478659997799
Q gi|254780444|r 188 RRGRSIDLMSLN-C-CYPVDTV---EMSDIEWIARIL 219 (223)
Q Consensus 188 ~~~~~~~l~s~N-p-~y~~~~i---~~~~i~iigrVv 219 (223)
.+.+++.+.++| + ++....+ +.+ .|+||++
T Consensus 100 vp~g~~fvlgdn~~~S~DSRy~G~V~~~--~I~G~a~ 134 (138)
T pfam10502 100 LPEGELFLMSVTSPDSFDSRYFGPVPAS--AIIGRAR 134 (138)
T ss_pred ECCCEEEEECCCCCCCCCCCCEEECCHH--HEEEEEE
T ss_conf 1899899976999987545418135779--9699999
No 405
>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=27.08 E-value=44 Score=14.08 Aligned_cols=52 Identities=12% Similarity=0.065 Sum_probs=33.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC-CCCC-----------CCHHHHHHHHHHCCCCCCCCC
Q ss_conf 998899998289987988997515788-7557-----------798999998732187521000
Q gi|254780444|r 22 LTPSGLARKAGLDPTSFNKSKRFGIEG-RNRW-----------PSTESIFKILAATNETICQLL 73 (223)
Q Consensus 22 ls~~~lA~~~Gv~~~ti~~~~~~~~~g-~~r~-----------p~~~~l~kia~~~~v~~~~l~ 73 (223)
++-++.|+++|++.-+|.-||+-+-.. -.|+ ...=.|..=|..+|-++++.-
T Consensus 1 mNIg~~AK~tglssK~IR~YE~kGLi~Pp~Rse~GYR~Y~~~h~~~L~li~raR~~GFSLeEc~ 64 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKSIRYYEEKGLIPPPLRSEGGYRTYTDKHVDELRLISRARSVGFSLEECK 64 (127)
T ss_pred CCHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf 9767775014772688988776326799886888885638767888899999987189889999
No 406
>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=26.94 E-value=45 Score=14.06 Aligned_cols=64 Identities=9% Similarity=0.001 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 999999999964999889999828998798899751578875577989999987321875210000111
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPF 77 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~~~~ 77 (223)
|-.+|=..-+++|||=+++++++|.++..+....-|-.. .+.+...+++..++.+=+.+..+..
T Consensus 14 l~~~lle~Kk~kgltfad~~~~lG~~ev~~aa~~ygqa~-----a~~dea~~v~~~L~L~ed~~~eL~~ 77 (156)
T TIGR00673 14 LAKKLLEAKKKKGLTFADVEDKLGKAEVYVAAVLYGQAA-----ADADEAKKVAELLDLEEDEVAELKD 77 (156)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHC-----CCHHHHHHHHHHCCCCHHHHHHHHC
T ss_conf 899999988735997899865318759999999984206-----8888999999870998113466540
No 407
>TIGR01203 HGPRTase hypoxanthine phosphoribosyltransferase; InterPro: IPR005904 Phosphoribosyltransferases (PRT) are enzymes that catalyze the synthesis of beta-n-5'-monophosphates from phosphoribosylpyrophosphate (PRPP) and an enzyme specific amine. A number of PRT's are involved in the biosynthesis of purine, pyrimidine, and pyridine nucleotides, or in the salvage of purines and pyrimidines. Purine nucleotides are synthesized both via the de novo pathway and via the salvage pathway and are vital for cell functions and cell proliferation through DNA and RNA syntheses and ATP energy supply. This entry presents hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC), which belongs to phosphoribosyltransferase family and is involved in purine salvage.; GO: 0004422 hypoxanthine phosphoribosyltransferase activity, 0006166 purine ribonucleoside salvage, 0005737 cytoplasm.
Probab=26.87 E-value=45 Score=14.06 Aligned_cols=19 Identities=21% Similarity=0.254 Sum_probs=15.4
Q ss_pred CCCHHHHHHHHHHHHHHCC
Q ss_conf 7558999999999999649
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHN 21 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~g 21 (223)
.+++++|+++|++|+++-.
T Consensus 2 li~~~~i~~r~~eLa~~I~ 20 (183)
T TIGR01203 2 LISEEQIKARIAELAKQIT 20 (183)
T ss_pred CCCHHHHHHHHHHHHHHHH
T ss_conf 2678999999999999999
No 408
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.82 E-value=45 Score=14.05 Aligned_cols=10 Identities=30% Similarity=0.401 Sum_probs=3.6
Q ss_pred CHHHHHHHHC
Q ss_conf 9889999828
Q gi|254780444|r 23 TPSGLARKAG 32 (223)
Q Consensus 23 s~~~lA~~~G 32 (223)
|..++-.+.|
T Consensus 39 T~~eiee~iG 48 (170)
T COG4860 39 TLPEIEEKIG 48 (170)
T ss_pred EHHHHHHHHC
T ss_conf 4899999965
No 409
>PRK11414 putative DNA-binding transcriptional regulator; Provisional
Probab=26.48 E-value=46 Score=14.01 Aligned_cols=36 Identities=14% Similarity=0.190 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHH
Q ss_conf 8999999999999649------99889999828998798899
Q gi|254780444|r 6 HKKIWEAIDRMAERHN------LTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~g------ls~~~lA~~~Gv~~~ti~~~ 41 (223)
.++|-+.|...+-.-. |+..+||+..|||.+.|.--
T Consensus 13 ~~qV~~~Lr~~I~~G~l~PG~~L~e~~La~~lgVSRtPVREA 54 (221)
T PRK11414 13 TLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREA 54 (221)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999999999839989959718999999979990689999
No 410
>PRK10082 putative DNA-binding transcriptional regulator; Provisional
Probab=26.37 E-value=46 Score=14.00 Aligned_cols=36 Identities=11% Similarity=0.250 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 755899999999999964999889999828998798899
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
.|.-+++..++. +. +.| |=+..|++++++|+++|+.
T Consensus 10 nmelr~L~~F~~-Va-e~g-SFs~AA~~L~itQpavS~~ 45 (303)
T PRK10082 10 NIETKWLYDFLT-LE-KCR-NFSQAAVSRNVSQPAFSRR 45 (303)
T ss_pred CCCHHHHHHHHH-HH-HCC-CHHHHHHHHCCCHHHHHHH
T ss_conf 662999999999-99-809-9999999978981599999
No 411
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=26.29 E-value=46 Score=13.99 Aligned_cols=36 Identities=8% Similarity=0.080 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 755899999999999964999889999828998798899
Q gi|254780444|r 3 SFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
||.-+++.-.+ +. .+.| |-++-|+++|++++++|+.
T Consensus 1 mmd~~~L~~F~-aV-a~~G-sfs~AA~~L~~sqsavS~~ 36 (294)
T PRK13348 1 MLDYKQLEALA-AV-VETG-SFERAARRLHVTRSAVSQR 36 (294)
T ss_pred CCCHHHHHHHH-HH-HHCC-CHHHHHHHHCCCHHHHHHH
T ss_conf 98989999999-99-9809-9999999978887899999
No 412
>pfam09312 SurA_N SurA N-terminal domain. This domain is found at the N-terminus of the chaperone SurA. It is a helical domain of unknown function. The C-terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment.
Probab=25.83 E-value=47 Score=13.94 Aligned_cols=18 Identities=17% Similarity=0.135 Sum_probs=8.2
Q ss_pred CHHHHHHHHHHCCCCCCC
Q ss_conf 989999987321875210
Q gi|254780444|r 54 STESIFKILAATNETICQ 71 (223)
Q Consensus 54 ~~~~l~kia~~~~v~~~~ 71 (223)
+.+.+.+.+..-|++++.
T Consensus 86 s~~~~~~~L~~~G~~~~~ 103 (118)
T pfam09312 86 TLDQLRAALAADGLSYDE 103 (118)
T ss_pred CHHHHHHHHHHCCCCHHH
T ss_conf 999999999984999999
No 413
>TIGR02224 recomb_XerC tyrosine recombinase XerC; InterPro: IPR011931 The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This entry represents XerC, which is closely related to the other chromosomal protein XerD (IPR011932 from INTERPRO). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. XerC and XerD interact with cell division protein FtsK .; GO: 0003677 DNA binding, 0006310 DNA recombination, 0007049 cell cycle, 0007059 chromosome segregation, 0015074 DNA integration, 0051301 cell division.
Probab=25.66 E-value=47 Score=13.92 Aligned_cols=66 Identities=18% Similarity=0.241 Sum_probs=43.0
Q ss_pred CCCHHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHCC-C--------------CCCCCCCCHHHHHHHHHHCC
Q ss_conf 75589999999999996-49998899998289987988997515-7--------------88755779899999873218
Q gi|254780444|r 3 SFSHKKIWEAIDRMAER-HNLTPSGLARKAGLDPTSFNKSKRFG-I--------------EGRNRWPSTESIFKILAATN 66 (223)
Q Consensus 3 ~~~~~~i~~~i~~l~~~-~gls~~~lA~~~Gv~~~ti~~~~~~~-~--------------~g~~r~p~~~~l~kia~~~~ 66 (223)
.++..+|...|-+|.++ .|+|.+-+||++--=.+-..-+.+.+ . ..=|+..+.+.+.++++...
T Consensus 49 ~~~~~d~R~~la~l~~~~~g~s~rS~~R~LSalRsFy~~L~~~~~~~~nPa~~~~~PK~~~~LP~~L~~~~~~~ll~~~~ 128 (313)
T TIGR02224 49 EVTAADLRSFLAELHAKERGLSRRSLARKLSALRSFYRFLLRRGLIDANPAAGVRAPKKPKKLPKFLSEDEMEALLDAPE 128 (313)
T ss_pred HCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCC
T ss_conf 24889999999999846578767689999999999999998728740223887226754467998889899999960123
Q ss_pred CC
Q ss_conf 75
Q gi|254780444|r 67 ET 68 (223)
Q Consensus 67 v~ 68 (223)
..
T Consensus 129 ~~ 130 (313)
T TIGR02224 129 ED 130 (313)
T ss_pred CC
T ss_conf 46
No 414
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=25.42 E-value=48 Score=13.89 Aligned_cols=25 Identities=8% Similarity=0.110 Sum_probs=15.0
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9996499988999982899879889
Q gi|254780444|r 16 MAERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 16 l~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|+--.|+|..++|..+|++..|+..
T Consensus 140 L~~~~g~s~~EIA~~l~is~~tVk~ 164 (190)
T PRK12543 140 LRYLHDYSQEEVAQILHIPIGTVKS 164 (190)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9998599999999998939999999
No 415
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB; InterPro: IPR014132 This entry describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reduced sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterised polysaccharide deacetylase; the exact function this protein family is unknown..
Probab=24.98 E-value=49 Score=13.83 Aligned_cols=31 Identities=19% Similarity=0.269 Sum_probs=13.7
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHH
Q ss_conf 97755899999999999964999889999828998798
Q gi|254780444|r 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSF 38 (223)
Q Consensus 1 ~~~~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti 38 (223)
|++|..|+|.+-| -.+|..|.+.+|..++-+
T Consensus 75 ~~~l~~E~ikkd~-------~~a~~~i~~~~g~~p~Ll 105 (198)
T TIGR02764 75 YTTLEDEKIKKDL-------LRAQEIIEKLTGKKPTLL 105 (198)
T ss_pred CCCCCHHHHHHHH-------HHHHHHHHHHCCCCEEEE
T ss_conf 1258764899999-------998888865105550165
No 416
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=24.92 E-value=49 Score=13.83 Aligned_cols=24 Identities=21% Similarity=0.199 Sum_probs=14.6
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 996499988999982899879889
Q gi|254780444|r 17 AERHNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 17 ~~~~gls~~~lA~~~Gv~~~ti~~ 40 (223)
+--.|+|..++|..+|++..|+..
T Consensus 134 ~~~~gls~~EIA~~L~is~~tVk~ 157 (185)
T PRK12542 134 KVFYNLTYQEISSVMGITEANVRK 157 (185)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 998399999999998929999999
No 417
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=24.89 E-value=49 Score=13.82 Aligned_cols=13 Identities=23% Similarity=0.094 Sum_probs=5.2
Q ss_pred HHHHCCCCCCCCC
Q ss_conf 8732187521000
Q gi|254780444|r 61 ILAATNETICQLL 73 (223)
Q Consensus 61 ia~~~~v~~~~l~ 73 (223)
.+.-+|+++.+|.
T Consensus 140 ~L~eygIsf~dLv 152 (237)
T PRK08311 140 ELKEFGITFEDLV 152 (237)
T ss_pred HHHHCCCCHHHHH
T ss_conf 9999397599997
No 418
>COG0376 KatG Catalase (peroxidase I) [Inorganic ion transport and metabolism]
Probab=24.82 E-value=49 Score=13.82 Aligned_cols=73 Identities=29% Similarity=0.361 Sum_probs=44.8
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH-HHCCCCC-CCC------CCC--HHHHHHHHH-------HCC
Q ss_conf 55899999999999964999889999828998798899-7515788-755------779--899999873-------218
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS-KRFGIEG-RNR------WPS--TESIFKILA-------ATN 66 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~-~~~~~~g-~~r------~p~--~~~l~kia~-------~~~ 66 (223)
|+.++| ++|++-+-..|||.++|-.-+.-|.+|+..+ +||+.+| +.| |+. -..|+|++. .++
T Consensus 446 l~d~di-~~lK~~IlasgLsvs~lVstAWaSAsTfRgsDkRGGaNGaRirLaPqkdWevN~P~~l~kvl~~le~iq~~fn 524 (730)
T COG0376 446 LVDADI-AALKAKILASGLSVSQLVSTAWASASTFRGSDKRGGANGARIRLAPQKDWEVNQPAELAKVLAVLEKIQKEFN 524 (730)
T ss_pred CCHHHH-HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 207789-9999999873587999999988753001477655776763276055556777898999999999999999865
Q ss_pred --CCCCCCCCCCC
Q ss_conf --75210000111
Q gi|254780444|r 67 --ETICQLLDLPF 77 (223)
Q Consensus 67 --v~~~~l~~~~~ 77 (223)
+|+.+|+-+..
T Consensus 525 kkvSlADlIVL~G 537 (730)
T COG0376 525 KKVSLADLIVLGG 537 (730)
T ss_pred CCCCHHHHEEECC
T ss_conf 6620557102145
No 419
>PRK13502 transcriptional activator RhaR; Provisional
Probab=24.75 E-value=49 Score=13.81 Aligned_cols=27 Identities=11% Similarity=0.251 Sum_probs=18.9
Q ss_pred EEEEEECCCCCCCCCCCCCEEEEECCCCC
Q ss_conf 59999628332421487868999368974
Q gi|254780444|r 137 DTRHKTQDTSMLPLYRKGDILILNSAIQV 165 (223)
Q Consensus 137 ~~~l~V~GDSM~P~i~~Gd~vlVd~~~~~ 165 (223)
.....|+|.+.. +..||+++|.|+...
T Consensus 48 ~g~~~i~~~~y~--l~~Gdl~lI~p~~~H 74 (282)
T PRK13502 48 NGLHVLNERPYR--ITRGDLFYIRAEDKH 74 (282)
T ss_pred EEEEEECCEEEE--ECCCEEEEECCCCEE
T ss_conf 299999999999--529989999999858
No 420
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=24.62 E-value=49 Score=13.79 Aligned_cols=36 Identities=19% Similarity=0.362 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHCCC-------CHHHHHHHHCCCHHHHHHH
Q ss_conf 89999999999996499-------9889999828998798899
Q gi|254780444|r 6 HKKIWEAIDRMAERHNL-------TPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gl-------s~~~lA~~~Gv~~~ti~~~ 41 (223)
.++|.+.|..++....| +..+||...|||.+++.--
T Consensus 4 ~e~V~e~Lr~~I~~g~l~pG~~LP~E~eLae~~GVSRt~VREA 46 (253)
T PRK10421 4 SDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREA 46 (253)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999999998199998595933999999979698999999
No 421
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=24.43 E-value=50 Score=13.77 Aligned_cols=12 Identities=8% Similarity=0.205 Sum_probs=5.7
Q ss_pred CCCCCHHHHHHH
Q ss_conf 977558999999
Q gi|254780444|r 1 MTSFSHKKIWEA 12 (223)
Q Consensus 1 ~~~~~~~~i~~~ 12 (223)
|+.+|-++++.+
T Consensus 8 ~~~~sD~~Lv~~ 19 (196)
T PRK12524 8 LSDVSDEALLVL 19 (196)
T ss_pred CCCCCHHHHHHH
T ss_conf 688999999999
No 422
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=24.42 E-value=50 Score=13.77 Aligned_cols=12 Identities=8% Similarity=0.105 Sum_probs=5.4
Q ss_pred CCCCCHHHHHHH
Q ss_conf 977558999999
Q gi|254780444|r 1 MTSFSHKKIWEA 12 (223)
Q Consensus 1 ~~~~~~~~i~~~ 12 (223)
|...|-++++.+
T Consensus 2 M~~~sD~eLi~~ 13 (186)
T PRK05602 2 MDADPDAELMAR 13 (186)
T ss_pred CCCCCHHHHHHH
T ss_conf 998429999999
No 423
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=24.33 E-value=50 Score=13.76 Aligned_cols=31 Identities=23% Similarity=0.349 Sum_probs=23.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9999999964999889999828998798899
Q gi|254780444|r 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 11 ~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
..|..+....+.+.++||++++++++++++.
T Consensus 26 ~~L~~l~~~~~~~~~~la~~l~~~~~~vt~~ 56 (126)
T COG1846 26 QVLLALYEAGGITVKELAERLGLDRSTVTRL 56 (126)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999848999999999978788889999
No 424
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=24.22 E-value=50 Score=13.74 Aligned_cols=19 Identities=11% Similarity=0.242 Sum_probs=9.5
Q ss_pred CCCCHHHHHHHHCCCHHHH
Q ss_conf 4999889999828998798
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSF 38 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti 38 (223)
.|+|..++|..+|++.+++
T Consensus 164 eglS~~EIAe~Lgis~~tV 182 (207)
T PRK12544 164 IELETPEICHNEDLTVSNL 182 (207)
T ss_pred CCCCHHHHHHHHCCCHHHH
T ss_conf 1999999999979799999
No 425
>TIGR02225 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011932 Proteins in this entry are part of the wider so-called "phage" integrase fmaily which describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This entry represents the chromosomally-encoded polypeptide XerD, which is closely related to, and interacts with, another chromosomally-encoded polypeptide, XerC (IPR011931 from INTERPRO). These proteins are site-specific tyrosine recombinases, which act by catalyzing the cutting and rejoining of the recombining DNA molecules . They form a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids. XerD is composed of two domains, an N-terminal alpha-helical domain, and a C-terminal domain composed mostly of alpha helices, with a three-stranded antiprallel beta sheet along one edge . The active site is found at the extreme C-terminal end of the polypeptide. Most of the C-terminal domain is structurally homologous to that of other "phage" integrases, but the active site regions of these enzymes are stucturally distinct.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0007049 cell cycle, 0007059 chromosome segregation, 0015074 DNA integration, 0051301 cell division.
Probab=24.18 E-value=50 Score=13.74 Aligned_cols=26 Identities=19% Similarity=0.304 Sum_probs=18.4
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 589999999999996499988999982
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNLTPSGLARKA 31 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gls~~~lA~~~ 31 (223)
+..+|..+|+.|.++ |.+++-.||.+
T Consensus 44 ~~~~i~~fl~~l~~~-g~~~~S~AR~l 69 (305)
T TIGR02225 44 DRGDIEDFLAELKEA-GLSARSIARAL 69 (305)
T ss_pred CHHHHHHHHHHHHHC-CCCCHHHHHHH
T ss_conf 878999999999866-87700288999
No 426
>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=23.97 E-value=51 Score=13.71 Aligned_cols=20 Identities=15% Similarity=0.310 Sum_probs=10.7
Q ss_pred CCCHHHHHHHHCCCHHHHHH
Q ss_conf 99988999982899879889
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~ 40 (223)
+...++||..+||+.++.++
T Consensus 167 ~Y~~~~LA~L~GV~~~nW~~ 186 (230)
T pfam06323 167 DYEYAELASLVGVSKKNWSE 186 (230)
T ss_pred CCCHHHHHHHHCCCHHHHHH
T ss_conf 45499999982998656636
No 427
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=23.79 E-value=51 Score=13.69 Aligned_cols=36 Identities=19% Similarity=0.238 Sum_probs=30.6
Q ss_pred CHHHHHHHHHHHHHHCCCC-------HHHHHHHHCCCHHHHHH
Q ss_conf 5899999999999964999-------88999982899879889
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNLT-------PSGLARKAGLDPTSFNK 40 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gls-------~~~lA~~~Gv~~~ti~~ 40 (223)
.+++|.+.|.++...-.+. -.+||...|||.+++.-
T Consensus 11 l~~~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vRE 53 (241)
T COG2186 11 LADEVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVRE 53 (241)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCHHHHH
T ss_conf 7999999999999839999999998899999997899568999
No 428
>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=23.56 E-value=52 Score=13.66 Aligned_cols=29 Identities=24% Similarity=0.401 Sum_probs=24.2
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999649998899998289987988997
Q gi|254780444|r 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 13 i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
+.+| .++|++...+|.++|++.+++++..
T Consensus 14 a~rl-~~~G~~~~~I~~aL~vd~~~is~~~ 42 (185)
T pfam07506 14 AARL-LERGVPRAEIAAALGLDPQTVSKMV 42 (185)
T ss_pred HHHH-HHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999-9869999999999867999999999
No 429
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=23.55 E-value=52 Score=13.66 Aligned_cols=41 Identities=12% Similarity=0.187 Sum_probs=32.1
Q ss_pred CHHHHHHHHHHHHHHCC--------CCHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 58999999999999649--------998899998289987988997515
Q gi|254780444|r 5 SHKKIWEAIDRMAERHN--------LTPSGLARKAGLDPTSFNKSKRFG 45 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~g--------ls~~~lA~~~Gv~~~ti~~~~~~~ 45 (223)
++.+|...|+.|+++.+ +|..++|+.+|++.....+.++..
T Consensus 99 ~~~~i~~~L~~l~~~~~~~f~gF~d~s~~ei~~~TGL~~~~A~~A~~Re 147 (302)
T PRK12702 99 PYPCLRHILQQVRQDSHLDLIGFGDWTASELAAATGIPLEEAERAQKRE 147 (302)
T ss_pred CHHHHHHHHHHHHHHHCCCCCCHHHCCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 7999999999998975767557312999999988596999999997557
No 430
>pfam08784 RPA_C Replication protein A C terminal. This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.
Probab=23.51 E-value=52 Score=13.66 Aligned_cols=35 Identities=14% Similarity=0.273 Sum_probs=26.5
Q ss_pred HHHHHHHHHH-HHHHCCCCHHHHHHHH-CCCHHHHHH
Q ss_conf 8999999999-9996499988999982-899879889
Q gi|254780444|r 6 HKKIWEAIDR-MAERHNLTPSGLARKA-GLDPTSFNK 40 (223)
Q Consensus 6 ~~~i~~~i~~-l~~~~gls~~~lA~~~-Gv~~~ti~~ 40 (223)
..+|...|+. .-.+.|++..+||+++ |++...|..
T Consensus 49 ~~~V~~~i~~~~~~~eG~h~~~l~~~l~~~~~~~i~~ 85 (103)
T pfam08784 49 QDQVLNLIKQSCPGEEGVHVDELAAQLNGLPVNDIRQ 85 (103)
T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf 9999999995488988727999999982999999999
No 431
>pfam02002 TFIIE_alpha TFIIE alpha subunit. The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits.
Probab=22.99 E-value=53 Score=13.59 Aligned_cols=35 Identities=20% Similarity=0.289 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999999999964999889999828998798899
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
++-..-||+|..+..+|-.+||.++|+....+.+.
T Consensus 13 ~e~v~vid~L~~~~~v~dedLa~~l~~~~n~vRki 47 (105)
T pfam02002 13 DEAVLVLDALLRKGEVTEEDLAELLGIDLNELRKL 47 (105)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 23899999997168838999999978988899999
No 432
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=22.94 E-value=53 Score=13.59 Aligned_cols=34 Identities=12% Similarity=0.265 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999999999649998899998289987988997
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
++|+.-+++| ++|+|..++++.+++.+=.+.+.+
T Consensus 429 ~Rl~~i~eAl--rrG~sveeI~elT~ID~wFL~ki~ 462 (1063)
T PRK05294 429 ERIFYIAEAF--RRGASVEEIHELTKIDPWFLEQIE 462 (1063)
T ss_pred HHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 5999999999--859999999998787699999999
No 433
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=22.86 E-value=53 Score=13.57 Aligned_cols=19 Identities=21% Similarity=0.366 Sum_probs=16.7
Q ss_pred CHHHHHHHHCCCHHHHHHH
Q ss_conf 9889999828998798899
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~ 41 (223)
|..+||+..|+|.+|+.+.
T Consensus 22 s~~~la~~~~vSr~tvr~A 40 (60)
T smart00345 22 SERELAAQLGVSRTTVREA 40 (60)
T ss_pred CHHHHHHHHCCCHHHHHHH
T ss_conf 0999999989499999999
No 434
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=22.77 E-value=53 Score=13.56 Aligned_cols=23 Identities=17% Similarity=0.216 Sum_probs=20.2
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 64999889999828998798899
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+.|.|-+..|++++++|+++|+.
T Consensus 14 ~~~~s~t~AA~~L~iSQpavS~~ 36 (308)
T PRK12683 14 RQNFNLTEVANALYTSQSGVSKQ 36 (308)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 86899999999978977799999
No 435
>smart00526 H15 Domain in histone families 1 and 5.
Probab=22.76 E-value=48 Score=13.87 Aligned_cols=25 Identities=24% Similarity=0.294 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 9999999999996499988999982
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKA 31 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~ 31 (223)
+=|.+||.+|-+..|-|..++++-+
T Consensus 9 ~MI~~AI~~l~e~~GsS~~aI~kyI 33 (66)
T smart00526 9 EMITEAISALKERKGSSLQAIKKYI 33 (66)
T ss_pred HHHHHHHHHCCCCCCCCHHHHHHHH
T ss_conf 9999999984887896899999999
No 436
>pfam01316 Arg_repressor Arginine repressor, DNA binding domain.
Probab=22.73 E-value=54 Score=13.56 Aligned_cols=36 Identities=11% Similarity=0.178 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHCCC-CHHHHHHHHC-----CCHHHHHHHHH
Q ss_conf 999999999996499-9889999828-----99879889975
Q gi|254780444|r 8 KIWEAIDRMAERHNL-TPSGLARKAG-----LDPTSFNKSKR 43 (223)
Q Consensus 8 ~i~~~i~~l~~~~gl-s~~~lA~~~G-----v~~~ti~~~~~ 43 (223)
.-.++|.++..+..+ ||.+|...+. ++++|+|+.-+
T Consensus 5 ~R~~~I~~li~~~~i~tQ~eL~~~L~~~G~~vTQATlSRDl~ 46 (70)
T pfam01316 5 QRQELIKEIITEEKISTQEELVALLKAEGINVTQATVSRDLK 46 (70)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEEHHHHHHHH
T ss_conf 999999999970897899999999997698564178887799
No 437
>PRK04158 transcriptional repressor CodY; Validated
Probab=22.68 E-value=54 Score=13.55 Aligned_cols=10 Identities=10% Similarity=0.610 Sum_probs=3.9
Q ss_pred CCCCCEEEEE
Q ss_conf 4878689993
Q gi|254780444|r 151 YRKGDILILN 160 (223)
Q Consensus 151 i~~Gd~vlVd 160 (223)
|.+.|+|+..
T Consensus 136 F~ddDLILaE 145 (256)
T PRK04158 136 FTDDDLILAE 145 (256)
T ss_pred CCCCCEEEHH
T ss_conf 8866351112
No 438
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=22.65 E-value=54 Score=13.55 Aligned_cols=26 Identities=12% Similarity=0.080 Sum_probs=17.5
Q ss_pred CCCCCCEEEEECCCCC-CCCCEEEEEE
Q ss_conf 1487868999368974-0588899997
Q gi|254780444|r 150 LYRKGDILILNSAIQV-NCGDRLLIKP 175 (223)
Q Consensus 150 ~i~~Gd~vlVd~~~~~-~~g~~v~~~~ 175 (223)
.|.+||+|+|.++... ..|+++|=..
T Consensus 46 ~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 46 RILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred EECCCCEEEEEECCCCCCCCCEEEEEC
T ss_conf 857999999974566533355899833
No 439
>PRK13501 transcriptional activator RhaR; Provisional
Probab=22.63 E-value=54 Score=13.55 Aligned_cols=25 Identities=20% Similarity=0.246 Sum_probs=15.9
Q ss_pred EEEECCCCCCCCCCCCCEEEEECCCCC
Q ss_conf 999628332421487868999368974
Q gi|254780444|r 139 RHKTQDTSMLPLYRKGDILILNSAIQV 165 (223)
Q Consensus 139 ~l~V~GDSM~P~i~~Gd~vlVd~~~~~ 165 (223)
...|+|... .+.+||+++|.++...
T Consensus 50 ~~~i~~~~~--~l~~Gdl~~i~p~~~H 74 (290)
T PRK13501 50 LHVLNDHPY--RITCGDVFYIQAADHH 74 (290)
T ss_pred EEEECCEEE--EEECCEEEEECCCCCC
T ss_conf 999999999--9648979998999845
No 440
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=22.63 E-value=54 Score=13.55 Aligned_cols=22 Identities=18% Similarity=0.249 Sum_probs=18.6
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 64999889999828998798899
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+.| |-++.|++++++++++|+.
T Consensus 14 ~~g-S~t~AA~~L~~sqsavS~~ 35 (291)
T TIGR03418 14 RLA-SFTAAARELGSTQPAVSQQ 35 (291)
T ss_pred HHC-CHHHHHHHHCCCHHHHHHH
T ss_conf 819-9999999988788899999
No 441
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=22.61 E-value=52 Score=13.63 Aligned_cols=22 Identities=18% Similarity=0.157 Sum_probs=18.8
Q ss_pred CHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 9889999828998798899751
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRF 44 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~ 44 (223)
|..++|+.+|++.++|++..+.
T Consensus 19 Si~~aak~l~~~~~~I~~~l~~ 40 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred HHHHHHHHHCCCCCCHHHHHCC
T ss_conf 7999999858883238887067
No 442
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=22.46 E-value=54 Score=13.52 Aligned_cols=19 Identities=0% Similarity=0.006 Sum_probs=8.2
Q ss_pred CCCCHHHHHHHHCCCHHHH
Q ss_conf 4999889999828998798
Q gi|254780444|r 20 HNLTPSGLARKAGLDPTSF 38 (223)
Q Consensus 20 ~gls~~~lA~~~Gv~~~ti 38 (223)
.|+|..++|..+|++.+|+
T Consensus 134 ~~~s~~EIA~~l~is~~tV 152 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTV 152 (173)
T ss_pred CCCCHHHHHHHHCCCHHHH
T ss_conf 3999999999989399999
No 443
>pfam10723 RepB-RCR_reg Replication regulatory protein RepB. This is a family of proteins which regulate replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of replication of RCR plasmids occurs mainly at initiation of leading strand synthesis at the dso, such that Rep protein concentration controls plasmid replication.
Probab=22.34 E-value=55 Score=13.51 Aligned_cols=23 Identities=13% Similarity=0.323 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 99999999996499988999982
Q gi|254780444|r 9 IWEAIDRMAERHNLTPSGLARKA 31 (223)
Q Consensus 9 i~~~i~~l~~~~gls~~~lA~~~ 31 (223)
+.+.+..|.++.|+||+++=..+
T Consensus 52 lK~~L~elc~~~GlTQAe~IE~L 74 (85)
T pfam10723 52 LKDDLQELCEEEGLTQAEVIEQL 74 (85)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 99999999987297199999999
No 444
>pfam09012 FeoC FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependant transcriptional repressor.
Probab=22.23 E-value=55 Score=13.50 Aligned_cols=31 Identities=19% Similarity=0.317 Sum_probs=22.7
Q ss_pred HHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999999-9964999889999828998798899
Q gi|254780444|r 11 EAIDRM-AERHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 11 ~~i~~l-~~~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
..|+.. ..+...|.++||+..+++++.+..+
T Consensus 3 ~~lr~~l~~~g~~s~~~Ls~~f~~~~~~v~~M 34 (68)
T pfam09012 3 TELKQYLQERGRASLAELARHFKMSPDAVEAM 34 (68)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 89999999919847999998979399999999
No 445
>TIGR00589 ogt methylated-DNA-[protein]-cysteine S-methyltransferase; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme . This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources .; GO: 0003824 catalytic activity, 0006281 DNA repair.
Probab=21.79 E-value=56 Score=13.44 Aligned_cols=26 Identities=23% Similarity=0.506 Sum_probs=19.3
Q ss_pred CHHHHHHHHHHHHHHCCC--CHHHHHHHHC
Q ss_conf 589999999999996499--9889999828
Q gi|254780444|r 5 SHKKIWEAIDRMAERHNL--TPSGLARKAG 32 (223)
Q Consensus 5 ~~~~i~~~i~~l~~~~gl--s~~~lA~~~G 32 (223)
.+.+||.+|..- .+|- |.++||.++|
T Consensus 3 FQq~VW~aL~~I--p~G~t~sY~~lA~~iG 30 (80)
T TIGR00589 3 FQQKVWQALRTI--PYGETKSYGELAKRIG 30 (80)
T ss_pred HHHHHHHHHCCC--CCCCCCCHHHHHHHHC
T ss_conf 688999984337--8876326899999718
No 446
>pfam10771 DUF2582 Protein of unknown function (DUF2582). This family is conserved in bacteria and archaea. The function is not known.
Probab=21.78 E-value=56 Score=13.44 Aligned_cols=28 Identities=21% Similarity=0.281 Sum_probs=20.9
Q ss_pred HHHHHHH-CCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999996-499988999982899879889
Q gi|254780444|r 13 IDRMAER-HNLTPSGLARKAGLDPTSFNK 40 (223)
Q Consensus 13 i~~l~~~-~gls~~~lA~~~Gv~~~ti~~ 40 (223)
|..++.+ .++|.++|.+++|++...+..
T Consensus 13 IW~~L~e~~~~s~~~lk~~~~l~~~~~~~ 41 (65)
T pfam10771 13 VWHLLNENGEWSLSELKRKTGLSDKDLAL 41 (65)
T ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 99996568859499999885989899999
No 447
>COG3905 Predicted transcriptional regulator [Transcription]
Probab=21.74 E-value=56 Score=13.43 Aligned_cols=31 Identities=29% Similarity=0.449 Sum_probs=24.8
Q ss_pred CCCCC---HHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 97755---89999999999996499988999982
Q gi|254780444|r 1 MTSFS---HKKIWEAIDRMAERHNLTPSGLARKA 31 (223)
Q Consensus 1 ~~~~~---~~~i~~~i~~l~~~~gls~~~lA~~~ 31 (223)
|+++| -+++..+||.|++...-|.+.+++.+
T Consensus 2 ~ta~tirl~del~~rLd~lAe~~~rsrs~i~~~A 35 (83)
T COG3905 2 MTAFTIRLDDELKRRLDELAEATDRSRSYIAEQA 35 (83)
T ss_pred CCCEEEECCHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 8415776498999999999997526716668999
No 448
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=21.50 E-value=57 Score=13.40 Aligned_cols=22 Identities=14% Similarity=0.215 Sum_probs=18.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9998899998289987988997
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNKSK 42 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~~~ 42 (223)
-+|.+++|+-+|++.-|+++..
T Consensus 2 pmsrqdIadylGlt~ETVsR~l 23 (32)
T pfam00325 2 PMSRQEIADYLGLTRETVSRLL 23 (32)
T ss_pred CCCHHHHHHHHCCHHHHHHHHH
T ss_conf 8658899998472599999999
No 449
>TIGR01149 mtrG tetrahydromethanopterin S-methyltransferase, subunit G; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane.
Probab=21.49 E-value=57 Score=13.40 Aligned_cols=26 Identities=15% Similarity=0.420 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 99999999999964999889999828
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLARKAG 32 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA~~~G 32 (223)
+.+.++||.+=++-..+-+|++.++|
T Consensus 17 ~~~~~rLDeie~kveFv~~E~~Qr~G 42 (72)
T TIGR01149 17 NEVKKRLDEIEEKVEFVNGEVAQRIG 42 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99998741786788789999888607
No 450
>pfam00816 Histone_HNS H-NS histone family.
Probab=21.42 E-value=57 Score=13.39 Aligned_cols=18 Identities=28% Similarity=0.276 Sum_probs=9.2
Q ss_pred HHHHHHHHHHCCCCHHHH
Q ss_conf 999999999649998899
Q gi|254780444|r 10 WEAIDRMAERHNLTPSGL 27 (223)
Q Consensus 10 ~~~i~~l~~~~gls~~~l 27 (223)
...|..++++.|+|..+|
T Consensus 26 ~~~i~~~~~~~glt~~el 43 (91)
T pfam00816 26 LAEIRELAAEYGLTLEEL 43 (91)
T ss_pred HHHHHHHHHHHCCCHHHH
T ss_conf 999999999909999998
No 451
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=21.34 E-value=57 Score=13.38 Aligned_cols=17 Identities=0% Similarity=0.216 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHCCC
Q ss_conf 89999999999996499
Q gi|254780444|r 6 HKKIWEAIDRMAERHNL 22 (223)
Q Consensus 6 ~~~i~~~i~~l~~~~gl 22 (223)
|.-+.+.|..+++..|.
T Consensus 12 h~~vr~gl~~lL~~~~~ 28 (202)
T PRK09390 12 DEAMRDSLAFLLDSAGF 28 (202)
T ss_pred CHHHHHHHHHHHHHCCC
T ss_conf 99999999999998899
No 452
>PRK04841 transcriptional regulator MalT; Provisional
Probab=21.30 E-value=57 Score=13.37 Aligned_cols=12 Identities=25% Similarity=0.249 Sum_probs=4.4
Q ss_pred HCCCHHH-HHHHH
Q ss_conf 2899879-88997
Q gi|254780444|r 31 AGLDPTS-FNKSK 42 (223)
Q Consensus 31 ~Gv~~~t-i~~~~ 42 (223)
+|-.+|| ++.|-
T Consensus 41 aG~GKTtl~a~w~ 53 (903)
T PRK04841 41 AGYGKTTLASQWA 53 (903)
T ss_pred CCCCHHHHHHHHH
T ss_conf 9988999999998
No 453
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=21.18 E-value=53 Score=13.56 Aligned_cols=26 Identities=19% Similarity=0.256 Sum_probs=12.3
Q ss_pred CCCCCEEEEECC-CCCCCCCEEEEEEE
Q ss_conf 487868999368-97405888999971
Q gi|254780444|r 151 YRKGDILILNSA-IQVNCGDRLLIKPR 176 (223)
Q Consensus 151 i~~Gd~vlVd~~-~~~~~g~~v~~~~~ 176 (223)
+..||+|+|.+- -+...+|+++....
T Consensus 39 i~~gdiVLV~~rd~q~~K~DIi~kY~~ 65 (77)
T cd05793 39 INEGDIVLVAPWDFQDDKADIIYKYTP 65 (77)
T ss_pred ECCCCEEEEECCCCCCCCEEEEEECCH
T ss_conf 648999999756776884889998298
No 454
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=21.08 E-value=58 Score=13.34 Aligned_cols=59 Identities=17% Similarity=0.260 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf 558999999999999649998899998289987988997515788755779899999873
Q gi|254780444|r 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILA 63 (223)
Q Consensus 4 ~~~~~i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~ 63 (223)
+...+...++..++++++|+..+.|..+.+-|.+.--.+--+..-..| ..-+.|..+++
T Consensus 51 ~k~~e~i~~v~~~l~~~~L~kfE~a~l~Nl~P~~~~Ea~~lIpsl~~r-~~de~lq~lL~ 109 (118)
T smart00657 51 FKNREIVRAVRTLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEER-IDEEELEELLD 109 (118)
T ss_pred CCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHC-CCHHHHHHHHH
T ss_conf 699999999999987668969999998368989899999985666612-79999999999
No 455
>TIGR00004 TIGR00004 endoribonuclease L-PSP, putative; InterPro: IPR006056 This family includes proteins encoded by the yabJ gene from Bacillus subtilis that is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The structure of this protein has been solved and the protein is found to form a homotrimer. The trimer has a deep cleft that is a probably ligand binding site and possibly forms an enzymatic active site. However the ligand and reaction are unknown..
Probab=21.01 E-value=58 Score=13.34 Aligned_cols=17 Identities=24% Similarity=0.255 Sum_probs=8.2
Q ss_pred HHHHHHHHHHCCCCCCC
Q ss_conf 89999987321875210
Q gi|254780444|r 55 TESIFKILAATNETICQ 71 (223)
Q Consensus 55 ~~~l~kia~~~~v~~~~ 71 (223)
+++|..++++.|.+++.
T Consensus 55 l~NlkAiL~aAG~~~~~ 71 (129)
T TIGR00004 55 LENLKAILEAAGLSLDD 71 (129)
T ss_pred HHHHHHHHHHHCCCCCC
T ss_conf 99899999982798466
No 456
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=21.01 E-value=58 Score=13.33 Aligned_cols=22 Identities=9% Similarity=0.148 Sum_probs=18.6
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 64999889999828998798899
Q gi|254780444|r 19 RHNLTPSGLARKAGLDPTSFNKS 41 (223)
Q Consensus 19 ~~gls~~~lA~~~Gv~~~ti~~~ 41 (223)
+.| |-+.-|+++|++++++|+.
T Consensus 15 ~~G-Sfs~AA~~L~~tqsaVS~~ 36 (295)
T PRK03635 15 REG-SFERAAQALHITQSAVSQR 36 (295)
T ss_pred HHC-CHHHHHHHHCCCHHHHHHH
T ss_conf 809-9999999978886699999
No 457
>PRK08931 5'-methylthioadenosine phosphorylase; Provisional
Probab=20.89 E-value=47 Score=13.94 Aligned_cols=49 Identities=14% Similarity=0.089 Sum_probs=26.8
Q ss_pred CEEEEEECCCCCCCCCCCCCEEEEECCC-------CCCCCCEEEEEEECCCEEEEEE
Q ss_conf 5599996283324214878689993689-------7405888999971796899999
Q gi|254780444|r 136 QDTRHKTQDTSMLPLYRKGDILILNSAI-------QVNCGDRLLIKPRTGDIVAKVL 185 (223)
Q Consensus 136 ~~~~l~V~GDSM~P~i~~Gd~vlVd~~~-------~~~~g~~v~~~~~~~~~~iKrl 185 (223)
..++....| ||.+.|++||+|++|.-. ..+-++.+++...-...++.+|
T Consensus 82 ~Iia~nAvG-sL~~~~~PGdlVi~dq~ID~T~~R~~tFf~~~~v~Hv~~~~P~~~~L 137 (289)
T PRK08931 82 DLVSLSACG-SFKEELPPGTFVIVDQFIDRTFAREKSFFGTGCVAHVSMAHPVCPRL 137 (289)
T ss_pred EEEEECCEE-ECCCCCCCCCEEECHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf 899822366-60567899978711111445578888778998634577778533789
No 458
>KOG2251 consensus
Probab=20.68 E-value=59 Score=13.29 Aligned_cols=44 Identities=18% Similarity=0.230 Sum_probs=31.7
Q ss_pred CCCCHHHHHHHHHHHHHHCCC----CHHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 775589999999999996499----988999982899879889975157
Q gi|254780444|r 2 TSFSHKKIWEAIDRMAERHNL----TPSGLARKAGLDPTSFNKSKRFGI 46 (223)
Q Consensus 2 ~~~~~~~i~~~i~~l~~~~gl----s~~~lA~~~Gv~~~ti~~~~~~~~ 46 (223)
|++|++++ +.|++|-++.-. ...+||.++.+..+.|..|.++..
T Consensus 42 TtFtr~Ql-evLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRR 89 (228)
T KOG2251 42 TTFTRKQL-EVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRR 89 (228)
T ss_pred CEECHHHH-HHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHCCCC
T ss_conf 41329999-9999998764175278899999980785313111000342
No 459
>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=20.64 E-value=59 Score=13.29 Aligned_cols=47 Identities=15% Similarity=0.051 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHCCCHHHHHH-H-HHCCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf 99988999982899879889-9-75157887557798999998732187
Q gi|254780444|r 21 NLTPSGLARKAGLDPTSFNK-S-KRFGIEGRNRWPSTESIFKILAATNE 67 (223)
Q Consensus 21 gls~~~lA~~~Gv~~~ti~~-~-~~~~~~g~~r~p~~~~l~kia~~~~v 67 (223)
+++.++||+.+|+++.-+=+ . ..|....-......+....+++.++.
T Consensus 3 ~itV~elA~~l~~~~~~vi~~L~~~Gi~~~~n~~ld~e~a~~i~~~~~~ 51 (52)
T pfam04760 3 KIRVYELAKELGVSSKELIKKLFKLGIMKTHNSTLDEETAELLAEEFGV 51 (52)
T ss_pred CEEHHHHHHHHCCCHHHHHHHHHHCCCEECCCCCCCHHHHHHHHHHHCC
T ss_conf 1739999999888899999999987985567774599999999998198
No 460
>pfam02196 RBD Raf-like Ras-binding domain.
Probab=20.58 E-value=59 Score=13.28 Aligned_cols=22 Identities=23% Similarity=0.431 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHCCCCHHHHH
Q ss_conf 9999999999996499988999
Q gi|254780444|r 7 KKIWEAIDRMAERHNLTPSGLA 28 (223)
Q Consensus 7 ~~i~~~i~~l~~~~gls~~~lA 28 (223)
..|.++|..+++++|+++++..
T Consensus 21 ~tird~L~~~l~~rgL~~~~~~ 42 (71)
T pfam02196 21 MSVRDALSKALKRRGLNPSECV 42 (71)
T ss_pred CCHHHHHHHHHHHCCCCHHHEE
T ss_conf 7899999999998499989989
No 461
>PRK13503 transcriptional activator RhaS; Provisional
Probab=20.24 E-value=60 Score=13.23 Aligned_cols=26 Identities=8% Similarity=0.041 Sum_probs=18.9
Q ss_pred EEEEECCCCCCCCCCCCCEEEEECCCCC
Q ss_conf 9999628332421487868999368974
Q gi|254780444|r 138 TRHKTQDTSMLPLYRKGDILILNSAIQV 165 (223)
Q Consensus 138 ~~l~V~GDSM~P~i~~Gd~vlVd~~~~~ 165 (223)
..+.|+|.+.. +..||+++|.|+...
T Consensus 46 ~~~~i~g~~~~--l~~Gdl~li~p~~~H 71 (278)
T PRK13503 46 GIHVFNGQPYT--ISGGTVCFVRDHDRH 71 (278)
T ss_pred EEEEECCEEEE--ECCCEEEEECCCCEE
T ss_conf 99999999999--749999999999838
No 462
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=20.18 E-value=36 Score=14.64 Aligned_cols=28 Identities=18% Similarity=0.317 Sum_probs=17.9
Q ss_pred CCCCCEEEEECCCC--CCCCCEEEEEEECC
Q ss_conf 48786899936897--40588899997179
Q gi|254780444|r 151 YRKGDILILNSAIQ--VNCGDRLLIKPRTG 178 (223)
Q Consensus 151 i~~Gd~vlVd~~~~--~~~g~~v~~~~~~~ 178 (223)
|..||+|+|++-.. ...+|+++....++
T Consensus 39 I~~gD~VlV~~~e~~~d~K~dIi~ky~~de 68 (78)
T cd04456 39 IKRGDFLIVDPIEEGEDVKADIIFVYCKDH 68 (78)
T ss_pred EECCCEEEEEEHHHCCCCEEEEEEECCHHH
T ss_conf 836999999881237984699999679899
No 463
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=20.16 E-value=60 Score=13.22 Aligned_cols=41 Identities=15% Similarity=0.358 Sum_probs=26.2
Q ss_pred CCCCC--HHHHHHHH-HHHHHH-CCCCHHHHHHH--HCCCHHHHHHH
Q ss_conf 97755--89999999-999996-49998899998--28998798899
Q gi|254780444|r 1 MTSFS--HKKIWEAI-DRMAER-HNLTPSGLARK--AGLDPTSFNKS 41 (223)
Q Consensus 1 ~~~~~--~~~i~~~i-~~l~~~-~gls~~~lA~~--~Gv~~~ti~~~ 41 (223)
|+||| .++|+.+| +.-.+. .=+.-..|+++ .++|+.||.+-
T Consensus 1 m~mLt~R~~~IL~aiVe~Yi~tg~PVGSk~L~~~~~l~~SsATIRNe 47 (339)
T PRK00082 1 MSMLDERQREILRAIVEDYIATGEPVGSKTLSERYGLGVSSATIRND 47 (339)
T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCHHHHHH
T ss_conf 98657999999999999985149855679999764999781789999
No 464
>pfam04936 DUF658 Protein of unknown function (DUF658). Protein of unknown function found in Lactococcus lactis bacteriophages.
Probab=20.06 E-value=61 Score=13.21 Aligned_cols=28 Identities=21% Similarity=0.205 Sum_probs=22.2
Q ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCC
Q ss_conf 9889999828998798899751578875
Q gi|254780444|r 23 TPSGLARKAGLDPTSFNKSKRFGIEGRN 50 (223)
Q Consensus 23 s~~~lA~~~Gv~~~ti~~~~~~~~~g~~ 50 (223)
|.-+||+..-||+.+|+.|.+.+...++
T Consensus 16 TidElad~f~vs~~svs~WIknGk~~~~ 43 (134)
T pfam04936 16 TIDEIADMFDLSPHSIAGWIKNGKANKK 43 (134)
T ss_pred CHHHHHHHHCCCCHHHHHHHHCCCCCCC
T ss_conf 3999999974570144788864888623
Done!