Query 041968
Match_columns 87
No_of_seqs 147 out of 832
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 12:34:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041968.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041968hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08100 Dimerisation: Dimeris 99.7 5.8E-17 1.2E-21 93.1 3.4 48 40-87 1-50 (51)
2 KOG3178 Hydroxyindole-O-methyl 99.0 1.9E-09 4E-14 81.9 6.5 63 22-87 3-67 (342)
3 TIGR02716 C20_methyl_CrtF C-20 98.9 2.4E-09 5.3E-14 78.5 4.5 45 38-87 3-47 (306)
4 PF09339 HTH_IclR: IclR helix- 97.1 0.00012 2.7E-09 41.0 -0.1 37 48-87 6-42 (52)
5 PF04967 HTH_10: HTH DNA bindi 96.6 0.0031 6.8E-08 36.2 3.1 41 38-85 5-45 (53)
6 smart00346 HTH_ICLR helix_turn 96.2 0.0048 1E-07 37.3 2.6 37 48-87 8-44 (91)
7 PRK11569 transcriptional repre 95.4 0.012 2.6E-07 42.9 2.5 37 48-87 31-67 (274)
8 TIGR02431 pcaR_pcaU beta-ketoa 95.4 0.013 2.7E-07 41.9 2.4 37 48-87 12-48 (248)
9 PRK10163 DNA-binding transcrip 95.2 0.017 3.7E-07 42.1 2.6 37 48-87 28-64 (271)
10 smart00550 Zalpha Z-DNA-bindin 95.0 0.034 7.3E-07 32.9 3.1 38 46-86 7-45 (68)
11 PRK09834 DNA-binding transcrip 94.3 0.037 8E-07 40.0 2.6 37 48-87 14-50 (263)
12 PF12840 HTH_20: Helix-turn-he 94.0 0.04 8.6E-07 31.5 1.8 39 44-86 9-47 (61)
13 PF02082 Rrf2: Transcriptional 93.7 0.069 1.5E-06 32.3 2.6 42 39-87 8-49 (83)
14 COG1414 IclR Transcriptional r 93.7 0.058 1.3E-06 39.0 2.6 37 48-87 7-43 (246)
15 PF08279 HTH_11: HTH domain; 93.7 0.06 1.3E-06 29.8 2.2 34 49-85 4-37 (55)
16 PF13412 HTH_24: Winged helix- 93.7 0.061 1.3E-06 29.1 2.1 37 46-86 4-40 (48)
17 PRK15090 DNA-binding transcrip 93.7 0.052 1.1E-06 39.0 2.3 36 48-87 17-52 (257)
18 COG3413 Predicted DNA binding 93.5 0.089 1.9E-06 37.1 3.2 43 36-85 158-200 (215)
19 PRK10857 DNA-binding transcrip 93.5 0.086 1.9E-06 36.3 3.1 41 40-87 9-49 (164)
20 PF02796 HTH_7: Helix-turn-hel 93.2 0.12 2.6E-06 28.1 2.8 22 61-85 22-43 (45)
21 PF01022 HTH_5: Bacterial regu 92.9 0.053 1.1E-06 29.6 1.0 36 47-87 4-39 (47)
22 TIGR02010 IscR iron-sulfur clu 92.8 0.13 2.9E-06 33.8 3.0 41 40-87 9-49 (135)
23 PF01978 TrmB: Sugar-specific 92.2 0.047 1E-06 31.7 0.2 36 47-86 10-45 (68)
24 PF08461 HTH_12: Ribonuclease 92.2 0.16 3.4E-06 30.0 2.5 38 50-87 3-42 (66)
25 cd07153 Fur_like Ferric uptake 91.9 0.18 3.9E-06 31.7 2.7 38 47-87 3-45 (116)
26 smart00344 HTH_ASNC helix_turn 91.8 0.19 4E-06 31.3 2.7 37 46-86 4-40 (108)
27 PF04703 FaeA: FaeA-like prote 91.7 0.098 2.1E-06 30.9 1.2 36 49-87 4-39 (62)
28 PF12802 MarR_2: MarR family; 91.6 0.11 2.4E-06 29.1 1.3 37 47-86 7-44 (62)
29 TIGR00738 rrf2_super rrf2 fami 91.5 0.27 5.8E-06 31.6 3.3 41 40-87 9-49 (132)
30 TIGR02944 suf_reg_Xantho FeS a 91.3 0.18 3.9E-06 32.6 2.3 27 58-87 23-49 (130)
31 PF09012 FeoC: FeoC like trans 91.1 0.14 3.1E-06 30.0 1.5 33 50-86 5-37 (69)
32 smart00418 HTH_ARSR helix_turn 90.6 0.35 7.6E-06 26.2 2.8 32 50-86 2-33 (66)
33 PF13404 HTH_AsnC-type: AsnC-t 90.6 0.24 5.2E-06 26.8 2.0 36 46-84 4-39 (42)
34 PRK06266 transcription initiat 90.3 0.53 1.2E-05 32.8 4.1 36 48-87 25-60 (178)
35 PF00165 HTH_AraC: Bacterial r 90.3 0.18 4E-06 26.6 1.4 24 59-85 7-30 (42)
36 smart00420 HTH_DEOR helix_turn 90.0 0.41 9E-06 25.3 2.7 33 50-86 5-37 (53)
37 PRK10141 DNA-binding transcrip 89.4 0.43 9.4E-06 31.3 2.9 44 40-87 11-54 (117)
38 TIGR00122 birA_repr_reg BirA b 89.4 0.36 7.8E-06 28.0 2.3 35 47-86 2-36 (69)
39 COG3355 Predicted transcriptio 89.2 0.38 8.2E-06 32.2 2.5 37 46-85 28-64 (126)
40 PF12324 HTH_15: Helix-turn-he 89.1 0.38 8.1E-06 29.7 2.2 32 50-85 29-60 (77)
41 smart00347 HTH_MARR helix_turn 88.7 0.56 1.2E-05 27.9 2.9 37 46-86 11-47 (101)
42 PRK06474 hypothetical protein; 88.7 0.42 9.1E-06 33.1 2.5 44 41-87 7-51 (178)
43 PRK11014 transcriptional repre 88.5 0.61 1.3E-05 30.7 3.2 41 40-87 9-49 (141)
44 smart00419 HTH_CRP helix_turn_ 88.1 0.39 8.5E-06 25.2 1.7 26 59-87 7-32 (48)
45 PF08220 HTH_DeoR: DeoR-like h 88.0 0.51 1.1E-05 26.8 2.2 33 50-86 5-37 (57)
46 COG1959 Predicted transcriptio 87.9 0.53 1.1E-05 31.8 2.6 26 59-87 24-49 (150)
47 PRK13239 alkylmercury lyase; P 87.4 0.78 1.7E-05 33.0 3.3 36 48-87 25-60 (206)
48 PRK11920 rirA iron-responsive 87.3 0.62 1.3E-05 31.5 2.7 41 39-87 8-48 (153)
49 cd00092 HTH_CRP helix_turn_hel 87.2 0.52 1.1E-05 26.4 1.9 27 58-87 23-49 (67)
50 PRK13558 bacterio-opsin activa 86.7 0.76 1.6E-05 36.7 3.3 43 36-85 610-652 (665)
51 PRK11179 DNA-binding transcrip 86.5 0.8 1.7E-05 30.6 2.8 28 46-74 10-37 (153)
52 PF01047 MarR: MarR family; I 86.4 0.31 6.8E-06 27.1 0.7 35 48-86 6-40 (59)
53 PF00325 Crp: Bacterial regula 86.3 0.35 7.6E-06 25.0 0.8 24 60-86 2-25 (32)
54 PF01418 HTH_6: Helix-turn-hel 86.2 0.64 1.4E-05 27.8 2.1 37 48-87 19-58 (77)
55 TIGR00373 conserved hypothetic 86.1 0.79 1.7E-05 31.3 2.7 36 48-87 17-52 (158)
56 PRK11169 leucine-responsive tr 85.7 0.76 1.7E-05 31.1 2.4 29 45-74 14-42 (164)
57 TIGR02702 SufR_cyano iron-sulf 85.1 0.94 2E-05 31.6 2.7 36 48-87 4-39 (203)
58 COG4190 Predicted transcriptio 84.4 0.96 2.1E-05 30.9 2.4 48 35-86 54-101 (144)
59 cd00090 HTH_ARSR Arsenical Res 84.2 1.3 2.8E-05 24.4 2.6 33 49-86 11-43 (78)
60 TIGR02337 HpaR homoprotocatech 84.0 1.4 3E-05 27.9 3.0 36 46-85 29-64 (118)
61 PF01726 LexA_DNA_bind: LexA D 83.6 0.87 1.9E-05 26.8 1.7 31 54-87 19-50 (65)
62 COG1522 Lrp Transcriptional re 83.5 1.3 2.8E-05 28.9 2.7 28 46-74 9-36 (154)
63 PRK11511 DNA-binding transcrip 83.5 1.7 3.6E-05 28.2 3.2 24 59-85 24-47 (127)
64 PF13936 HTH_38: Helix-turn-he 83.4 1.1 2.4E-05 24.2 2.0 24 59-85 19-42 (44)
65 PF13463 HTH_27: Winged helix 82.9 0.85 1.8E-05 25.7 1.5 31 53-86 11-41 (68)
66 COG2345 Predicted transcriptio 82.8 1.3 2.7E-05 32.2 2.6 33 50-86 16-48 (218)
67 PF10668 Phage_terminase: Phag 82.7 2 4.2E-05 25.2 3.0 28 51-81 13-40 (60)
68 PRK00215 LexA repressor; Valid 82.3 1.8 3.8E-05 30.0 3.2 31 54-87 17-48 (205)
69 PF06163 DUF977: Bacterial pro 82.0 1.9 4E-05 29.0 3.0 42 42-87 9-50 (127)
70 PF03374 ANT: Phage antirepres 81.8 2.4 5.2E-05 26.5 3.4 35 48-85 12-46 (111)
71 TIGR02531 yecD_yerC TrpR-relat 81.5 2.2 4.8E-05 26.6 3.1 33 48-86 41-73 (88)
72 PHA00738 putative HTH transcri 81.4 1.8 3.9E-05 28.3 2.7 38 46-87 13-50 (108)
73 PF07381 DUF1495: Winged helix 81.3 3.4 7.3E-05 26.1 3.9 39 44-85 8-47 (90)
74 PF00356 LacI: Bacterial regul 81.0 1.6 3.4E-05 24.1 2.0 21 62-85 1-21 (46)
75 PRK11302 DNA-binding transcrip 80.6 1.5 3.2E-05 31.5 2.4 39 46-87 17-58 (284)
76 TIGR02844 spore_III_D sporulat 80.2 2.7 5.8E-05 25.9 3.1 32 49-85 10-41 (80)
77 PRK11557 putative DNA-binding 80.1 1.7 3.8E-05 31.2 2.6 39 46-87 13-54 (278)
78 PF01325 Fe_dep_repress: Iron 79.6 1.8 3.9E-05 24.9 2.1 25 57-84 19-43 (60)
79 PRK10219 DNA-binding transcrip 79.2 3.1 6.8E-05 25.7 3.3 24 59-85 20-43 (107)
80 smart00531 TFIIE Transcription 78.9 2.2 4.9E-05 28.5 2.7 35 49-87 5-39 (147)
81 PF13309 HTH_22: HTH domain 78.7 2.3 4.9E-05 24.8 2.3 37 40-85 28-64 (64)
82 PF02002 TFIIE_alpha: TFIIE al 78.4 1.3 2.9E-05 27.7 1.4 33 50-86 18-50 (105)
83 smart00342 HTH_ARAC helix_turn 78.1 9.9 0.00021 21.3 5.2 31 50-85 42-73 (84)
84 PF13601 HTH_34: Winged helix 78.0 0.94 2E-05 27.5 0.6 38 46-87 1-38 (80)
85 PRK03573 transcriptional regul 77.7 3.2 6.9E-05 27.0 3.1 32 51-85 37-68 (144)
86 PRK11512 DNA-binding transcrip 77.6 3.1 6.6E-05 27.2 3.0 33 49-85 44-76 (144)
87 PF06971 Put_DNA-bind_N: Putat 77.3 4.4 9.5E-05 22.8 3.2 34 46-82 13-47 (50)
88 PRK03902 manganese transport t 77.3 2.7 5.9E-05 27.5 2.7 27 57-86 19-45 (142)
89 TIGR01764 excise DNA binding d 76.6 2.9 6.4E-05 21.6 2.3 22 61-85 2-23 (49)
90 PRK10681 DNA-binding transcrip 76.5 3.1 6.7E-05 30.0 3.0 36 48-87 10-45 (252)
91 TIGR01889 Staph_reg_Sar staphy 76.4 2.9 6.3E-05 26.3 2.5 37 47-86 27-66 (109)
92 TIGR01610 phage_O_Nterm phage 76.3 3.5 7.7E-05 25.5 2.9 26 58-86 45-70 (95)
93 PRK11337 DNA-binding transcrip 76.0 2.6 5.6E-05 30.5 2.5 39 46-87 29-70 (292)
94 PRK11050 manganese transport r 75.8 3.4 7.3E-05 27.7 2.9 33 50-86 42-74 (152)
95 TIGR00498 lexA SOS regulatory 75.6 3.9 8.5E-05 28.1 3.2 28 57-87 22-50 (199)
96 TIGR01884 cas_HTH CRISPR locus 75.5 3 6.5E-05 29.0 2.7 36 47-86 145-180 (203)
97 PF00440 TetR_N: Bacterial reg 75.5 2.7 5.9E-05 22.5 1.9 21 59-82 15-35 (47)
98 smart00345 HTH_GNTR helix_turn 75.3 1.8 3.9E-05 23.4 1.2 26 59-87 18-44 (60)
99 PF12728 HTH_17: Helix-turn-he 75.2 3.2 6.9E-05 22.4 2.2 22 61-85 2-23 (51)
100 PF13443 HTH_26: Cro/C1-type H 74.9 3 6.4E-05 23.3 2.1 30 51-85 3-32 (63)
101 PF13022 HTH_Tnp_1_2: Helix-tu 74.6 3.2 6.9E-05 28.4 2.5 30 52-84 26-55 (142)
102 COG1737 RpiR Transcriptional r 74.5 2 4.3E-05 31.5 1.6 39 46-87 19-60 (281)
103 PF13545 HTH_Crp_2: Crp-like h 74.4 1.9 4E-05 24.9 1.2 26 59-87 27-52 (76)
104 cd04762 HTH_MerR-trunc Helix-T 73.8 3.8 8.2E-05 21.0 2.2 22 61-85 1-22 (49)
105 PF13518 HTH_28: Helix-turn-he 73.4 6 0.00013 21.0 3.0 21 62-85 14-34 (52)
106 PF13384 HTH_23: Homeodomain-l 73.2 3.2 7E-05 22.2 1.9 23 60-85 17-39 (50)
107 PF13542 HTH_Tnp_ISL3: Helix-t 72.9 6.3 0.00014 21.1 3.1 31 49-85 19-49 (52)
108 PRK11639 zinc uptake transcrip 72.8 3.7 8.1E-05 28.1 2.5 44 44-87 25-70 (169)
109 PRK13509 transcriptional repre 72.5 3.8 8.3E-05 29.6 2.7 35 49-87 9-43 (251)
110 PF04539 Sigma70_r3: Sigma-70 72.4 2.9 6.3E-05 24.4 1.7 27 57-86 17-43 (78)
111 PRK09775 putative DNA-binding 71.9 4.7 0.0001 31.9 3.2 33 50-87 5-37 (442)
112 TIGR01321 TrpR trp operon repr 71.5 6.8 0.00015 24.9 3.3 39 44-87 41-79 (94)
113 COG2512 Predicted membrane-ass 71.3 3.1 6.8E-05 30.7 2.0 37 47-86 197-233 (258)
114 PF13744 HTH_37: Helix-turn-he 71.3 13 0.00027 22.2 4.4 31 50-85 23-53 (80)
115 PF04182 B-block_TFIIIC: B-blo 71.3 3.5 7.5E-05 24.5 1.9 38 46-86 3-41 (75)
116 PF01475 FUR: Ferric uptake re 71.3 2.4 5.1E-05 26.9 1.2 44 44-87 7-52 (120)
117 PRK10572 DNA-binding transcrip 71.1 5.8 0.00013 28.4 3.4 33 50-85 188-221 (290)
118 PF01381 HTH_3: Helix-turn-hel 70.7 4 8.6E-05 22.0 1.9 24 59-85 8-31 (55)
119 PF04545 Sigma70_r4: Sigma-70, 70.5 4.9 0.00011 21.6 2.3 25 58-85 18-42 (50)
120 PRK04424 fatty acid biosynthes 70.4 4.2 9.2E-05 28.2 2.4 35 49-87 11-45 (185)
121 PRK01381 Trp operon repressor; 70.3 5.1 0.00011 25.8 2.6 39 44-87 41-79 (99)
122 PRK15482 transcriptional regul 70.3 4.2 9.1E-05 29.5 2.5 39 46-87 17-58 (285)
123 PRK14096 pgi glucose-6-phospha 69.8 5.4 0.00012 32.4 3.2 38 49-87 467-504 (528)
124 PRK09462 fur ferric uptake reg 69.5 6.1 0.00013 26.1 3.0 44 44-87 16-62 (148)
125 PRK10411 DNA-binding transcrip 68.9 5.2 0.00011 28.8 2.7 36 48-87 7-42 (240)
126 smart00421 HTH_LUXR helix_turn 68.7 8.3 0.00018 20.1 2.9 22 60-84 18-39 (58)
127 TIGR03826 YvyF flagellar opero 68.3 8.3 0.00018 26.0 3.4 31 52-85 37-68 (137)
128 PF08280 HTH_Mga: M protein tr 68.2 3.3 7.1E-05 23.5 1.3 33 46-82 6-38 (59)
129 COG1675 TFA1 Transcription ini 68.2 5 0.00011 28.2 2.4 35 49-87 22-56 (176)
130 PRK10906 DNA-binding transcrip 67.8 4.5 9.8E-05 29.3 2.2 36 48-87 8-43 (252)
131 PF02186 TFIIE_beta: TFIIE bet 67.4 6.5 0.00014 23.2 2.5 26 49-74 9-34 (65)
132 TIGR03697 NtcA_cyano global ni 66.7 4.3 9.3E-05 27.0 1.8 25 59-86 142-166 (193)
133 PRK13503 transcriptional activ 66.4 8 0.00017 27.3 3.2 33 50-85 176-209 (278)
134 PRK09802 DNA-binding transcrip 66.3 5.2 0.00011 29.3 2.3 37 47-87 19-55 (269)
135 smart00354 HTH_LACI helix_turn 66.2 6 0.00013 23.0 2.2 21 62-85 2-22 (70)
136 PRK11753 DNA-binding transcrip 65.8 4.6 0.0001 27.2 1.8 24 60-86 168-191 (211)
137 COG4189 Predicted transcriptio 64.9 11 0.00024 28.3 3.7 36 38-74 16-51 (308)
138 COG0735 Fur Fe2+/Zn2+ uptake r 64.7 6.3 0.00014 26.3 2.3 43 45-87 21-65 (145)
139 PHA02943 hypothetical protein; 64.6 7.2 0.00016 27.2 2.6 26 49-76 15-40 (165)
140 PF07638 Sigma70_ECF: ECF sigm 64.6 6.3 0.00014 26.9 2.3 25 59-86 150-174 (185)
141 PRK11161 fumarate/nitrate redu 64.6 4.7 0.0001 27.9 1.7 24 60-86 184-207 (235)
142 TIGR03613 RutR pyrimidine util 64.2 8.7 0.00019 25.8 2.9 28 52-82 19-47 (202)
143 PRK10434 srlR DNA-bindng trans 64.2 5.6 0.00012 28.8 2.1 35 48-86 8-42 (256)
144 TIGR03384 betaine_BetI transcr 63.8 10 0.00022 24.9 3.1 27 53-82 20-47 (189)
145 COG1510 Predicted transcriptio 63.6 6.8 0.00015 27.7 2.3 17 58-74 39-55 (177)
146 cd07377 WHTH_GntR Winged helix 63.4 9.2 0.0002 20.8 2.5 22 61-85 26-47 (66)
147 PHA02591 hypothetical protein; 63.4 13 0.00027 23.2 3.2 31 50-85 51-81 (83)
148 PRK09975 DNA-binding transcrip 63.4 11 0.00023 25.5 3.3 26 54-82 24-50 (213)
149 PF01710 HTH_Tnp_IS630: Transp 63.1 9.6 0.00021 24.5 2.9 26 58-86 69-94 (119)
150 PF04218 CENP-B_N: CENP-B N-te 62.9 11 0.00025 20.9 2.8 34 46-85 11-44 (53)
151 COG4977 Transcriptional regula 62.5 8.1 0.00018 29.6 2.8 25 58-85 234-258 (328)
152 PRK15121 right oriC-binding tr 62.2 11 0.00024 27.3 3.3 25 59-86 20-44 (289)
153 PRK11886 bifunctional biotin-- 62.2 7.3 0.00016 28.8 2.4 37 47-87 6-42 (319)
154 PRK13918 CRP/FNR family transc 61.7 6.3 0.00014 26.5 1.9 25 59-86 148-172 (202)
155 PRK09391 fixK transcriptional 61.6 5.9 0.00013 27.7 1.8 26 59-87 178-203 (230)
156 PF08221 HTH_9: RNA polymerase 61.4 5.5 0.00012 23.0 1.3 43 28-83 5-47 (62)
157 PRK15340 transcriptional regul 61.4 21 0.00046 25.7 4.6 36 47-85 111-147 (216)
158 PRK10371 DNA-binding transcrip 61.1 11 0.00023 27.8 3.1 33 50-85 196-229 (302)
159 PRK13502 transcriptional activ 61.1 12 0.00026 26.6 3.3 34 49-85 180-214 (282)
160 PF06413 Neugrin: Neugrin; In 61.1 9.8 0.00021 27.6 2.9 31 53-86 21-52 (225)
161 COG1378 Predicted transcriptio 60.9 7.6 0.00017 28.3 2.3 31 53-87 24-54 (247)
162 PRK10046 dpiA two-component re 59.8 9.7 0.00021 26.2 2.6 34 50-86 167-200 (225)
163 cd06170 LuxR_C_like C-terminal 59.6 16 0.00034 19.2 3.0 22 59-83 14-35 (57)
164 PRK15431 ferrous iron transpor 59.5 12 0.00027 23.0 2.7 30 50-83 7-36 (78)
165 COG2344 AT-rich DNA-binding pr 59.3 7.9 0.00017 28.0 2.1 32 49-83 20-52 (211)
166 PRK00767 transcriptional regul 58.9 14 0.0003 24.5 3.1 26 54-82 22-48 (197)
167 PF13551 HTH_29: Winged helix- 58.8 14 0.00031 22.3 3.0 21 62-85 14-34 (112)
168 PRK09940 transcriptional regul 58.7 12 0.00027 27.5 3.1 33 50-85 139-172 (253)
169 PRK15186 AraC family transcrip 58.5 14 0.0003 27.5 3.3 33 50-85 186-219 (291)
170 PRK09685 DNA-binding transcrip 58.4 10 0.00022 27.2 2.6 33 50-85 202-236 (302)
171 COG1349 GlpR Transcriptional r 58.4 7.6 0.00017 28.1 1.9 34 49-86 9-42 (253)
172 PRK04214 rbn ribonuclease BN/u 58.4 9 0.00019 29.6 2.4 27 57-86 307-333 (412)
173 TIGR02297 HpaA 4-hydroxyphenyl 58.3 13 0.00028 26.4 3.1 25 58-85 200-224 (287)
174 TIGR03070 couple_hipB transcri 58.1 12 0.00025 19.9 2.3 23 59-84 14-36 (58)
175 PRK09393 ftrA transcriptional 58.1 14 0.0003 27.1 3.3 31 52-85 225-256 (322)
176 PRK15044 transcriptional regul 57.9 22 0.00047 27.0 4.3 36 47-85 194-230 (295)
177 PF03444 HrcA_DNA-bdg: Winged 57.7 17 0.00037 22.4 3.1 40 40-87 8-47 (78)
178 COG4367 Uncharacterized protei 57.7 10 0.00023 24.1 2.2 23 59-84 22-44 (97)
179 PRK09978 DNA-binding transcrip 57.4 15 0.00032 27.4 3.3 34 49-85 146-180 (274)
180 TIGR02787 codY_Gpos GTP-sensin 57.2 10 0.00022 28.2 2.4 35 49-86 187-221 (251)
181 COG4565 CitB Response regulato 57.1 11 0.00023 27.7 2.5 34 51-87 164-197 (224)
182 PRK10668 DNA-binding transcrip 57.1 16 0.00036 24.7 3.4 26 54-82 24-50 (215)
183 PRK09480 slmA division inhibit 57.0 16 0.00034 24.2 3.2 22 58-82 28-49 (194)
184 PF04760 IF2_N: Translation in 56.9 4.1 8.9E-05 22.5 0.3 16 59-74 2-17 (54)
185 PRK14165 winged helix-turn-hel 56.9 10 0.00022 27.3 2.4 26 59-87 20-45 (217)
186 COG1309 AcrR Transcriptional r 56.7 19 0.00041 22.2 3.4 22 59-83 31-52 (201)
187 PF04552 Sigma54_DBD: Sigma-54 56.5 3.6 7.9E-05 28.3 0.0 24 59-85 48-71 (160)
188 PF14947 HTH_45: Winged helix- 56.4 7.8 0.00017 23.0 1.5 27 58-87 17-43 (77)
189 PRK15185 transcriptional regul 56.3 16 0.00034 27.9 3.4 34 49-85 210-244 (309)
190 PHA00542 putative Cro-like pro 56.0 13 0.00027 22.5 2.4 24 59-85 30-53 (82)
191 PRK09954 putative kinase; Prov 55.7 12 0.00027 27.8 2.7 35 47-85 5-39 (362)
192 PF12793 SgrR_N: Sugar transpo 55.5 11 0.00025 24.3 2.2 25 59-86 18-42 (115)
193 PRK14996 TetR family transcrip 55.5 15 0.00033 24.5 3.0 26 54-82 21-47 (192)
194 cd07977 TFIIE_beta_winged_heli 55.2 24 0.00053 21.2 3.5 26 49-74 13-40 (75)
195 TIGR03879 near_KaiC_dom probab 55.1 15 0.00033 22.2 2.6 25 59-86 31-55 (73)
196 cd04761 HTH_MerR-SF Helix-Turn 55.0 14 0.0003 19.2 2.2 20 61-83 1-20 (49)
197 PF08784 RPA_C: Replication pr 54.9 7.9 0.00017 23.9 1.3 38 46-86 48-88 (102)
198 PF01371 Trp_repressor: Trp re 54.8 14 0.00031 23.0 2.5 37 44-86 35-72 (87)
199 PF00196 GerE: Bacterial regul 54.5 12 0.00025 20.7 1.9 26 46-74 7-32 (58)
200 PRK04217 hypothetical protein; 54.5 13 0.00029 24.1 2.4 24 59-85 57-80 (110)
201 cd06171 Sigma70_r4 Sigma70, re 54.5 16 0.00036 18.4 2.4 24 59-85 25-48 (55)
202 PRK13501 transcriptional activ 54.5 16 0.00034 26.2 3.0 32 51-85 182-214 (290)
203 PF10975 DUF2802: Protein of u 54.4 10 0.00022 22.6 1.7 25 59-83 43-67 (70)
204 PRK00118 putative DNA-binding 54.3 14 0.0003 23.8 2.4 23 59-84 32-54 (104)
205 COG2169 Ada Adenosine deaminas 53.9 21 0.00045 25.4 3.5 30 53-85 90-119 (187)
206 PF10078 DUF2316: Uncharacteri 53.7 14 0.00031 23.2 2.4 24 59-85 22-45 (89)
207 PRK14101 bifunctional glucokin 53.7 11 0.00025 30.6 2.4 38 47-87 358-398 (638)
208 COG3645 Uncharacterized phage- 53.6 18 0.0004 24.5 3.0 34 49-85 36-69 (135)
209 PF13560 HTH_31: Helix-turn-he 53.4 12 0.00027 20.9 1.9 24 59-85 13-36 (64)
210 PRK13756 tetracycline represso 53.2 20 0.00043 25.1 3.3 27 54-83 17-44 (205)
211 PF08281 Sigma70_r4_2: Sigma-7 53.2 14 0.00031 19.9 2.1 22 59-83 25-46 (54)
212 PRK10870 transcriptional repre 53.1 15 0.00033 25.1 2.6 30 53-85 63-93 (176)
213 TIGR00635 ruvB Holliday juncti 52.7 15 0.00032 26.5 2.6 25 58-85 253-277 (305)
214 PHA02701 ORF020 dsRNA-binding 52.3 21 0.00046 25.3 3.3 40 46-85 5-45 (183)
215 smart00422 HTH_MERR helix_turn 51.9 16 0.00034 20.5 2.2 21 61-84 1-21 (70)
216 TIGR02366 DHAK_reg probable di 51.2 28 0.00061 22.8 3.7 25 50-74 12-37 (176)
217 PRK15008 HTH-type transcriptio 51.1 21 0.00046 24.4 3.1 26 54-82 31-57 (212)
218 PF10771 DUF2582: Protein of u 50.9 18 0.0004 21.4 2.4 24 50-74 13-36 (65)
219 COG4901 Ribosomal protein S25 50.7 12 0.00027 24.3 1.8 38 47-87 43-83 (107)
220 PRK15435 bifunctional DNA-bind 50.7 21 0.00046 27.2 3.4 25 58-85 97-121 (353)
221 PRK12423 LexA repressor; Provi 50.6 22 0.00047 24.7 3.2 30 54-86 19-49 (202)
222 TIGR02698 CopY_TcrY copper tra 50.6 19 0.0004 23.6 2.7 36 46-85 5-44 (130)
223 COG2207 AraC AraC-type DNA-bin 50.5 19 0.00041 21.7 2.6 24 59-85 35-58 (127)
224 PRK13500 transcriptional activ 50.1 22 0.00048 26.0 3.3 33 50-85 211-244 (312)
225 PF09929 DUF2161: Uncharacteri 49.4 25 0.00054 23.3 3.1 24 50-74 64-87 (118)
226 PRK10130 transcriptional regul 48.7 22 0.00047 27.1 3.1 25 58-85 254-278 (350)
227 PRK05472 redox-sensing transcr 48.5 26 0.00056 24.4 3.3 40 43-85 14-54 (213)
228 PRK09392 ftrB transcriptional 47.9 14 0.0003 25.5 1.8 24 60-86 173-196 (236)
229 PHA01976 helix-turn-helix prot 47.7 20 0.00044 20.0 2.2 23 59-84 14-36 (67)
230 TIGR02395 rpoN_sigma RNA polym 47.4 15 0.00033 28.8 2.2 24 59-85 317-340 (429)
231 PF09441 Abp2: ARS binding pro 47.1 19 0.00042 25.3 2.4 18 59-76 69-86 (175)
232 PRK11202 DNA-binding transcrip 46.8 33 0.00071 23.4 3.5 26 54-82 25-51 (203)
233 PF13730 HTH_36: Helix-turn-he 46.6 15 0.00033 19.8 1.5 23 62-87 27-49 (55)
234 PF05344 DUF746: Domain of Unk 46.4 30 0.00065 20.6 2.8 25 58-85 11-35 (65)
235 PF02787 CPSase_L_D3: Carbamoy 45.9 21 0.00045 23.4 2.3 29 50-84 16-44 (123)
236 PRK10402 DNA-binding transcrip 45.6 14 0.00031 25.6 1.6 25 59-86 168-192 (226)
237 COG1321 TroR Mn-dependent tran 45.5 27 0.00059 23.7 2.9 18 57-74 21-38 (154)
238 PRK13413 mpi multiple promoter 45.3 30 0.00065 23.8 3.2 24 59-85 171-194 (200)
239 smart00530 HTH_XRE Helix-turn- 45.1 25 0.00055 17.2 2.2 22 59-83 9-30 (56)
240 PF00392 GntR: Bacterial regul 44.8 13 0.00029 20.9 1.2 27 58-87 21-48 (64)
241 cd01104 HTH_MlrA-CarA Helix-Tu 44.7 19 0.00042 20.1 1.8 19 62-83 2-20 (68)
242 TIGR00180 parB_part ParB-like 44.2 19 0.00041 24.7 2.0 25 59-86 119-143 (187)
243 PRK04172 pheS phenylalanyl-tRN 44.1 24 0.00052 28.0 2.8 35 47-85 8-42 (489)
244 PRK11552 putative DNA-binding 43.9 29 0.00064 24.2 3.0 25 54-82 26-51 (225)
245 TIGR02937 sigma70-ECF RNA poly 43.8 27 0.00059 21.3 2.6 23 59-84 125-147 (158)
246 TIGR02607 antidote_HigA addict 43.7 25 0.00054 20.1 2.2 23 59-84 17-39 (78)
247 cd01392 HTH_LacI Helix-turn-he 43.5 15 0.00033 19.4 1.2 10 65-74 2-11 (52)
248 cd00569 HTH_Hin_like Helix-tur 42.7 27 0.00058 15.6 1.9 21 60-83 21-41 (42)
249 PRK05932 RNA polymerase factor 42.7 20 0.00044 28.4 2.2 24 59-85 342-365 (455)
250 PRK08558 adenine phosphoribosy 42.6 30 0.00065 25.0 2.9 37 44-83 7-43 (238)
251 COG1846 MarR Transcriptional r 42.1 24 0.00051 21.2 2.1 36 46-85 23-58 (126)
252 COG3695 Predicted methylated D 42.0 43 0.00093 21.7 3.3 29 58-87 21-49 (103)
253 PF02042 RWP-RK: RWP-RK domain 41.9 31 0.00066 19.6 2.3 23 61-86 16-38 (52)
254 PRK09334 30S ribosomal protein 41.9 17 0.00038 22.7 1.4 35 50-87 28-65 (86)
255 COG3682 Predicted transcriptio 41.7 40 0.00086 22.4 3.2 28 46-74 7-34 (123)
256 TIGR02985 Sig70_bacteroi1 RNA 41.7 28 0.00062 22.0 2.5 21 59-82 128-148 (161)
257 PRK09726 antitoxin HipB; Provi 41.4 27 0.00058 21.0 2.2 24 59-85 24-47 (88)
258 TIGR00331 hrcA heat shock gene 40.9 33 0.00072 26.0 3.1 31 53-87 15-47 (337)
259 PRK11640 putative transcriptio 40.7 38 0.00081 23.1 3.1 26 54-82 14-40 (191)
260 PRK05638 threonine synthase; V 40.6 27 0.00058 27.2 2.6 33 50-87 376-410 (442)
261 PRK09526 lacI lac repressor; R 40.6 26 0.00057 25.1 2.4 24 59-85 4-27 (342)
262 cd00093 HTH_XRE Helix-turn-hel 40.4 33 0.00072 16.9 2.2 23 59-84 11-33 (58)
263 COG4567 Response regulator con 40.3 47 0.001 23.5 3.5 35 34-71 88-122 (182)
264 cd04764 HTH_MlrA-like_sg1 Heli 40.3 25 0.00055 19.8 1.9 20 61-83 1-20 (67)
265 cd04763 HTH_MlrA-like Helix-Tu 39.3 26 0.00057 19.8 1.8 19 62-83 2-20 (68)
266 COG1405 SUA7 Transcription ini 39.2 53 0.0012 24.6 3.9 25 58-85 155-179 (285)
267 PF04079 DUF387: Putative tran 39.2 25 0.00053 24.1 1.9 25 57-85 10-34 (159)
268 PRK10014 DNA-binding transcrip 39.0 29 0.00063 24.9 2.4 24 59-85 5-28 (342)
269 PF05930 Phage_AlpA: Prophage 38.7 24 0.00051 19.2 1.5 22 61-85 4-25 (51)
270 COG1725 Predicted transcriptio 38.5 24 0.00053 23.4 1.8 25 59-86 34-58 (125)
271 PF06056 Terminase_5: Putative 38.3 37 0.0008 19.4 2.3 16 59-74 12-27 (58)
272 PRK07037 extracytoplasmic-func 38.3 34 0.00074 22.1 2.5 22 59-83 124-145 (163)
273 PF10376 Mei5: Double-strand r 38.1 54 0.0012 23.7 3.7 40 36-80 178-218 (221)
274 TIGR02392 rpoH_proteo alternat 38.1 31 0.00067 24.9 2.4 24 59-85 235-258 (270)
275 PF01035 DNA_binding_1: 6-O-me 37.0 38 0.00082 20.5 2.4 28 58-86 17-44 (85)
276 PRK00135 scpB segregation and 36.8 39 0.00085 23.7 2.7 26 57-85 16-42 (188)
277 PF00376 MerR: MerR family reg 36.5 22 0.00047 18.5 1.1 18 62-82 1-18 (38)
278 PRK14987 gluconate operon tran 36.5 31 0.00066 24.8 2.2 24 59-85 4-27 (331)
279 PRK15201 fimbriae regulatory p 36.3 47 0.001 23.9 3.0 27 45-74 136-162 (198)
280 PF03297 Ribosomal_S25: S25 ri 36.0 28 0.0006 22.5 1.7 26 59-87 58-83 (105)
281 PRK00082 hrcA heat-inducible t 35.8 45 0.00097 25.4 3.1 27 58-87 23-51 (339)
282 PRK09863 putative frv operon r 35.7 37 0.0008 27.2 2.7 31 47-82 6-36 (584)
283 PRK13890 conjugal transfer pro 35.7 45 0.00097 21.5 2.7 23 59-84 17-39 (120)
284 PRK12469 RNA polymerase factor 35.2 35 0.00076 27.5 2.5 24 59-85 368-391 (481)
285 PRK13777 transcriptional regul 35.1 44 0.00095 23.4 2.7 32 50-85 50-81 (185)
286 PRK15411 rcsA colanic acid cap 35.0 53 0.0011 22.7 3.1 39 44-85 139-178 (207)
287 PF05066 HARE-HTH: HB1, ASXL, 34.8 20 0.00044 20.7 0.9 21 51-71 8-28 (72)
288 PRK00080 ruvB Holliday junctio 34.6 37 0.0008 25.1 2.4 25 58-85 274-298 (328)
289 PRK11642 exoribonuclease R; Pr 34.4 46 0.00099 28.5 3.2 38 50-87 24-62 (813)
290 smart00351 PAX Paired Box doma 34.3 58 0.0013 21.0 3.1 24 59-85 32-55 (125)
291 PF09743 DUF2042: Uncharacteri 34.0 49 0.0011 24.6 3.0 34 49-85 59-92 (272)
292 PF11972 HTH_13: HTH DNA bindi 33.8 59 0.0013 18.6 2.7 32 50-85 4-35 (54)
293 PF04297 UPF0122: Putative hel 33.7 37 0.0008 21.8 2.0 22 59-83 32-53 (101)
294 PF13411 MerR_1: MerR HTH fami 33.5 36 0.00078 19.0 1.8 19 62-83 2-20 (69)
295 PF05331 DUF742: Protein of un 33.3 55 0.0012 21.4 2.8 24 26-51 45-68 (114)
296 PF12627 PolyA_pol_RNAbd: Prob 33.2 70 0.0015 17.6 3.0 32 24-55 26-57 (64)
297 PRK07921 RNA polymerase sigma 32.9 43 0.00093 25.3 2.5 23 58-83 280-302 (324)
298 PRK10265 chaperone-modulator p 32.3 38 0.00082 21.2 1.9 24 59-85 6-29 (101)
299 COG5631 Predicted transcriptio 32.1 1.8E+02 0.004 20.7 5.4 43 31-73 62-111 (199)
300 PF00126 HTH_1: Bacterial regu 32.1 36 0.00077 18.9 1.6 33 47-85 3-35 (60)
301 PRK06596 RNA polymerase factor 32.1 45 0.00097 24.4 2.5 24 59-85 247-270 (284)
302 COG3655 Predicted transcriptio 31.9 30 0.00065 21.0 1.3 24 49-74 6-29 (73)
303 TIGR00426 competence protein C 31.8 77 0.0017 18.0 3.0 28 57-87 40-67 (69)
304 PRK07405 RNA polymerase sigma 31.8 49 0.0011 24.7 2.7 23 58-83 274-296 (317)
305 TIGR00637 ModE_repress ModE mo 31.8 46 0.001 20.7 2.2 33 47-85 6-38 (99)
306 PF08765 Mor: Mor transcriptio 31.4 1.4E+02 0.0029 18.7 4.7 57 25-85 36-94 (108)
307 TIGR02885 spore_sigF RNA polym 31.1 48 0.001 23.0 2.4 23 59-84 198-220 (231)
308 PRK11475 DNA-binding transcrip 30.8 59 0.0013 22.7 2.8 27 45-74 137-163 (207)
309 cd00131 PAX Paired Box domain 30.7 17 0.00037 23.7 0.1 34 46-85 22-55 (128)
310 TIGR02997 Sig70-cyanoRpoD RNA 30.3 55 0.0012 24.0 2.7 24 58-84 267-290 (298)
311 TIGR02393 RpoD_Cterm RNA polym 29.9 57 0.0012 23.0 2.6 25 58-85 101-125 (238)
312 PRK11924 RNA polymerase sigma 29.6 60 0.0013 20.9 2.6 22 59-83 140-161 (179)
313 cd06445 ATase The DNA repair p 29.5 64 0.0014 19.1 2.5 28 58-86 15-42 (79)
314 TIGR00721 tfx DNA-binding prot 29.0 73 0.0016 21.4 2.9 23 59-84 20-42 (137)
315 TIGR02850 spore_sigG RNA polym 28.8 56 0.0012 23.3 2.5 23 59-84 221-243 (254)
316 PF02954 HTH_8: Bacterial regu 28.6 53 0.0011 17.1 1.8 29 52-85 12-40 (42)
317 TIGR00589 ogt O-6-methylguanin 28.5 1.3E+02 0.0029 18.0 3.8 27 58-85 17-43 (80)
318 PLN02853 Probable phenylalanyl 28.3 65 0.0014 26.2 2.9 38 45-85 3-40 (492)
319 TIGR02948 SigW_bacill RNA poly 28.0 65 0.0014 21.1 2.6 16 59-74 151-166 (187)
320 PRK12525 RNA polymerase sigma 27.9 63 0.0014 21.2 2.5 16 59-74 133-148 (168)
321 PF00382 TFIIB: Transcription 27.9 1.2E+02 0.0027 17.1 4.2 17 58-74 52-68 (71)
322 TIGR02999 Sig-70_X6 RNA polyme 27.5 66 0.0014 21.1 2.5 16 59-74 149-164 (183)
323 PRK09642 RNA polymerase sigma 27.4 64 0.0014 20.7 2.4 16 59-74 121-136 (160)
324 TIGR02684 dnstrm_HI1420 probab 27.4 54 0.0012 20.2 1.9 18 65-85 48-65 (89)
325 PRK09047 RNA polymerase factor 27.4 62 0.0014 20.7 2.3 16 59-74 121-136 (161)
326 PRK12547 RNA polymerase sigma 27.3 68 0.0015 20.9 2.5 16 59-74 127-142 (164)
327 PF13693 HTH_35: Winged helix- 26.9 74 0.0016 19.4 2.4 23 59-84 14-36 (78)
328 PRK05949 RNA polymerase sigma 26.9 68 0.0015 24.2 2.7 23 58-83 284-306 (327)
329 PTZ00326 phenylalanyl-tRNA syn 26.8 78 0.0017 25.7 3.2 38 45-85 6-43 (494)
330 PF08256 Antimicrobial20: Aure 26.8 40 0.00087 14.0 0.8 8 49-56 1-8 (13)
331 PRK09413 IS2 repressor TnpA; R 26.7 71 0.0015 20.3 2.5 24 59-85 28-51 (121)
332 PRK06759 RNA polymerase factor 26.7 71 0.0015 20.3 2.5 16 59-74 121-136 (154)
333 PF00888 Cullin: Cullin family 26.6 41 0.00089 26.4 1.6 27 58-87 532-558 (588)
334 PRK07500 rpoH2 RNA polymerase 26.4 64 0.0014 23.7 2.5 24 59-85 244-267 (289)
335 COG1386 scpB Chromosome segreg 26.2 81 0.0018 22.2 2.8 18 57-74 20-38 (184)
336 PF05491 RuvB_C: Holliday junc 26.0 77 0.0017 19.4 2.4 27 48-74 11-39 (76)
337 TIGR02846 spore_sigmaK RNA pol 26.0 70 0.0015 22.3 2.5 22 59-83 193-214 (227)
338 PRK08583 RNA polymerase sigma 25.6 71 0.0015 22.6 2.5 23 59-84 220-242 (257)
339 PRK09210 RNA polymerase sigma 25.5 67 0.0014 24.5 2.5 23 58-83 323-345 (367)
340 PRK12427 flagellar biosynthesi 25.5 69 0.0015 22.7 2.4 23 59-84 198-220 (231)
341 cd06459 M3B_Oligoendopeptidase 25.5 2.9E+02 0.0063 20.7 6.6 33 53-86 393-425 (427)
342 PF01498 HTH_Tnp_Tc3_2: Transp 25.5 62 0.0013 18.3 1.9 27 58-85 11-40 (72)
343 PRK10840 transcriptional regul 25.2 97 0.0021 20.8 3.1 26 46-74 154-179 (216)
344 PF03965 Penicillinase_R: Peni 25.1 39 0.00085 21.2 1.0 27 46-73 4-30 (115)
345 PRK05602 RNA polymerase sigma 25.1 74 0.0016 21.1 2.4 16 59-74 143-158 (186)
346 PRK05572 sporulation sigma fac 25.0 71 0.0015 22.6 2.5 23 59-84 217-239 (252)
347 TIGR02479 FliA_WhiG RNA polyme 25.0 76 0.0016 22.0 2.5 22 59-83 190-211 (224)
348 PRK12518 RNA polymerase sigma 24.9 81 0.0017 20.5 2.6 16 59-74 135-150 (175)
349 PRK12534 RNA polymerase sigma 24.8 92 0.002 20.6 2.9 16 59-74 152-167 (187)
350 PRK09645 RNA polymerase sigma 24.8 83 0.0018 20.5 2.6 16 59-74 133-148 (173)
351 PRK09210 RNA polymerase sigma 24.8 71 0.0015 24.4 2.5 25 58-85 230-254 (367)
352 PRK13626 transcriptional regul 24.7 45 0.00097 26.6 1.5 25 59-86 22-46 (552)
353 PRK09483 response regulator; P 24.7 1E+02 0.0022 20.2 3.0 26 46-74 152-177 (217)
354 PF08668 HDOD: HDOD domain; I 24.6 68 0.0015 21.5 2.2 32 50-86 11-42 (196)
355 PRK05803 sporulation sigma fac 24.6 75 0.0016 22.2 2.5 23 59-84 194-216 (233)
356 PHA03103 double-strand RNA-bin 24.5 90 0.002 22.1 2.8 33 52-85 20-53 (183)
357 PRK00441 argR arginine repress 24.4 1.2E+02 0.0026 20.4 3.3 34 50-87 9-47 (149)
358 PRK09641 RNA polymerase sigma 24.3 78 0.0017 20.8 2.4 16 59-74 151-166 (187)
359 PRK09652 RNA polymerase sigma 24.0 82 0.0018 20.3 2.4 16 59-74 143-158 (182)
360 PRK12529 RNA polymerase sigma 24.0 82 0.0018 20.9 2.5 16 59-74 142-157 (178)
361 PF13413 HTH_25: Helix-turn-he 23.8 73 0.0016 18.2 1.9 17 58-74 8-24 (62)
362 PF07789 DUF1627: Protein of u 23.5 56 0.0012 22.7 1.6 17 58-74 4-20 (155)
363 PRK09649 RNA polymerase sigma 23.4 84 0.0018 21.0 2.4 16 59-74 145-160 (185)
364 PRK11922 RNA polymerase sigma 23.4 83 0.0018 22.0 2.5 22 59-83 164-185 (231)
365 PRK11923 algU RNA polymerase s 23.3 82 0.0018 20.9 2.4 16 59-74 153-168 (193)
366 PF11268 DUF3071: Protein of u 23.3 85 0.0018 21.9 2.5 16 59-74 68-83 (170)
367 PRK09943 DNA-binding transcrip 23.3 75 0.0016 21.5 2.2 24 59-85 19-42 (185)
368 PLN03238 probable histone acet 23.2 1.1E+02 0.0025 23.2 3.3 19 58-76 221-239 (290)
369 PRK12837 3-ketosteroid-delta-1 23.2 59 0.0013 25.7 1.9 19 60-81 375-393 (513)
370 TIGR02959 SigZ RNA polymerase 23.2 89 0.0019 20.6 2.5 16 59-74 115-130 (170)
371 PRK03975 tfx putative transcri 23.2 1.1E+02 0.0024 20.6 3.0 23 59-84 20-42 (141)
372 PRK13719 conjugal transfer tra 23.1 1E+02 0.0023 22.3 3.0 28 44-74 145-172 (217)
373 PF12844 HTH_19: Helix-turn-he 23.1 72 0.0016 17.4 1.8 23 59-84 11-33 (64)
374 PRK08215 sporulation sigma fac 23.1 82 0.0018 22.4 2.5 22 59-83 224-245 (258)
375 TIGR02980 SigBFG RNA polymeras 23.1 82 0.0018 21.7 2.4 22 59-83 193-214 (227)
376 TIGR02835 spore_sigmaE RNA pol 23.1 85 0.0018 22.0 2.5 22 59-83 197-218 (234)
377 PRK07598 RNA polymerase sigma 23.1 85 0.0018 24.8 2.7 23 58-83 368-390 (415)
378 PRK08301 sporulation sigma fac 22.9 87 0.0019 21.8 2.5 16 59-74 197-212 (234)
379 COG1164 Oligoendopeptidase F [ 22.8 3E+02 0.0064 22.7 5.9 56 27-83 518-581 (598)
380 PRK13919 putative RNA polymera 22.8 94 0.002 20.5 2.6 16 59-74 150-165 (186)
381 PF01527 HTH_Tnp_1: Transposas 22.7 57 0.0012 18.4 1.3 24 59-85 22-45 (76)
382 TIGR03859 PQQ_PqqD coenzyme PQ 22.5 85 0.0018 18.7 2.1 18 50-70 36-53 (81)
383 COG2378 Predicted transcriptio 22.5 98 0.0021 23.2 2.8 34 48-85 11-44 (311)
384 TIGR02394 rpoS_proteo RNA poly 22.4 84 0.0018 22.8 2.4 22 59-83 241-262 (285)
385 TIGR02950 SigM_subfam RNA poly 22.3 90 0.002 19.7 2.3 16 59-74 120-135 (154)
386 COG3357 Predicted transcriptio 22.2 80 0.0017 20.2 2.0 25 49-73 7-31 (97)
387 PRK06986 fliA flagellar biosyn 22.2 91 0.002 21.8 2.5 21 59-82 199-219 (236)
388 PRK12530 RNA polymerase sigma 22.2 91 0.002 20.9 2.4 16 59-74 149-164 (189)
389 COG2771 CsgD DNA-binding HTH d 22.0 1.4E+02 0.0031 15.8 3.0 25 47-74 9-33 (65)
390 PRK00423 tfb transcription ini 21.9 1.7E+02 0.0037 21.8 4.0 17 58-74 180-196 (310)
391 PRK12845 3-ketosteroid-delta-1 21.9 65 0.0014 26.0 1.9 21 59-82 423-443 (564)
392 TIGR02939 RpoE_Sigma70 RNA pol 21.8 96 0.0021 20.4 2.5 16 59-74 153-168 (190)
393 PRK07406 RNA polymerase sigma 21.8 95 0.0021 24.1 2.7 23 59-84 330-352 (373)
394 PRK09648 RNA polymerase sigma 21.6 98 0.0021 20.5 2.5 16 59-74 154-169 (189)
395 PRK12513 RNA polymerase sigma 21.5 97 0.0021 20.7 2.5 16 59-74 154-169 (194)
396 PF12833 HTH_18: Helix-turn-he 21.5 1.7E+02 0.0037 16.5 4.5 23 59-84 44-67 (81)
397 TIGR02612 mob_myst_A mobile my 21.4 95 0.0021 21.1 2.4 24 59-85 37-60 (150)
398 PRK09647 RNA polymerase sigma 21.4 95 0.0021 21.4 2.4 16 59-74 153-168 (203)
399 TIGR02954 Sig70_famx3 RNA poly 21.4 1.1E+02 0.0023 19.9 2.6 16 59-74 134-149 (169)
400 TIGR02989 Sig-70_gvs1 RNA poly 21.3 1E+02 0.0022 19.6 2.5 16 59-74 126-141 (159)
401 PRK05911 RNA polymerase sigma 21.3 93 0.002 22.3 2.4 22 59-83 220-241 (257)
402 PRK12539 RNA polymerase sigma 21.0 1.1E+02 0.0023 20.4 2.5 16 59-74 146-161 (184)
403 PRK09651 RNA polymerase sigma 20.9 1.1E+02 0.0023 20.2 2.5 16 59-74 134-149 (172)
404 COG2197 CitB Response regulato 20.9 1.3E+02 0.0028 20.9 3.0 38 45-86 151-190 (211)
405 PF04031 Las1: Las1-like ; In 20.7 2.6E+02 0.0057 18.8 4.5 25 49-73 90-114 (154)
406 TIGR02952 Sig70_famx2 RNA poly 20.7 1.1E+02 0.0023 19.7 2.5 16 59-74 137-152 (170)
407 PRK09706 transcriptional repre 20.6 97 0.0021 19.9 2.2 23 59-84 17-39 (135)
408 COG4496 Uncharacterized protei 20.4 95 0.0021 19.9 2.0 38 44-87 43-80 (100)
409 TIGR02941 Sigma_B RNA polymera 20.4 1E+02 0.0022 21.8 2.5 23 59-84 220-242 (255)
410 TIGR00281 segregation and cond 20.2 1.3E+02 0.0028 21.1 2.9 17 58-74 14-31 (186)
411 PRK12527 RNA polymerase sigma 20.1 1.1E+02 0.0024 19.6 2.5 16 59-74 120-135 (159)
412 PRK01905 DNA-binding protein F 20.1 1.1E+02 0.0023 18.1 2.2 31 50-85 42-72 (77)
No 1
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=99.66 E-value=5.8e-17 Score=93.05 Aligned_cols=48 Identities=52% Similarity=0.924 Sum_probs=43.4
Q ss_pred HHHHHHHHhCchHHHHhCC-CCCCHHHHHHhcC-CCCCChhhHHHHHhcC
Q 041968 40 MSLKCAVELGIPDVIHKHG-QPMTLSQIASALD-IQKNKAHCIQRLMRIL 87 (87)
Q Consensus 40 ~aL~aaveLgI~d~L~~~~-gp~S~~ELA~~~~-~~~~~~~~L~RlLR~L 87 (87)
|+||+|+||||||+|+++| +|+|++||+++++ .+|.++..|+|+||+|
T Consensus 1 MaLk~aveLgI~dii~~~g~~~ls~~eia~~l~~~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 1 MALKCAVELGIPDIIHNAGGGPLSLSEIAARLPTSNPSAPPMLDRIMRLL 50 (51)
T ss_dssp HHHHHHHHTTHHHHHHHHTTS-BEHHHHHHTSTCT-TTHHHHHHHHHHHH
T ss_pred CcHHHHHHcCcHHHHHHcCCCCCCHHHHHHHcCCCCcchHHHHHHHHHHh
Confidence 6899999999999999987 9999999999999 7888889999999986
No 2
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=98.95 E-value=1.9e-09 Score=81.95 Aligned_cols=63 Identities=30% Similarity=0.394 Sum_probs=54.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcC--CCCCChhhHHHHHhcC
Q 041968 22 LLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALD--IQKNKAHCIQRLMRIL 87 (87)
Q Consensus 22 ~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~--~~~~~~~~L~RlLR~L 87 (87)
+.+...+++++.+++..++++++|+||||||+|+++++ ..|+|..+. ..|+++.+++|+||.|
T Consensus 3 e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~~---p~~ia~~l~~~~~~~~p~ll~r~lr~L 67 (342)
T KOG3178|consen 3 ENEASLRAMRLANGFALPMVLKAACELGVFDILANAGS---PSEIASLLPTPKNPEAPVLLDRILRLL 67 (342)
T ss_pred hhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCCC---HHHHHHhccCCCCCCChhHHHHHHHHH
Confidence 45667889999999999999999999999999998644 788888877 5667889999999976
No 3
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=98.87 E-value=2.4e-09 Score=78.50 Aligned_cols=45 Identities=20% Similarity=0.285 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 38 NSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 38 ~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
..++|++|++|||||.|++ +|.|++|||+++|+++ ..++|+||+|
T Consensus 3 ~~~~l~aa~~Lglfd~L~~--gp~t~~eLA~~~~~~~---~~~~~lL~~L 47 (306)
T TIGR02716 3 EFSCMKAAIELDLFSHMAE--GPKDLATLAADTGSVP---PRLEMLLETL 47 (306)
T ss_pred hHHHHHHHHHcCcHHHHhc--CCCCHHHHHHHcCCCh---HHHHHHHHHH
Confidence 4689999999999999984 8999999999999999 9999999986
No 4
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=97.07 E-value=0.00012 Score=41.04 Aligned_cols=37 Identities=41% Similarity=0.680 Sum_probs=31.2
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+.|.+.+...++++|+.|||+.+|.+. ..++|+|+.|
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~---stv~r~L~tL 42 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPK---STVHRLLQTL 42 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-H---HHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 457888888778899999999999999 8899998754
No 5
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=96.57 E-value=0.0031 Score=36.21 Aligned_cols=41 Identities=34% Similarity=0.477 Sum_probs=33.0
Q ss_pred HHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 38 NSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 38 ~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.-.+|++|.++|-|| . +...|+.|||+.+|+++ ..+..-||
T Consensus 5 Q~e~L~~A~~~GYfd-~---PR~~tl~elA~~lgis~---st~~~~LR 45 (53)
T PF04967_consen 5 QREILKAAYELGYFD-V---PRRITLEELAEELGISK---STVSEHLR 45 (53)
T ss_pred HHHHHHHHHHcCCCC-C---CCcCCHHHHHHHhCCCH---HHHHHHHH
Confidence 456899999999998 3 36789999999999988 65555554
No 6
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=96.20 E-value=0.0048 Score=37.27 Aligned_cols=37 Identities=24% Similarity=0.421 Sum_probs=31.6
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+.|.+.|.+.+++.|+.|||+.+|++. ..++|+++.|
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~---~tv~r~l~~L 44 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSK---STAHRLLNTL 44 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCH---HHHHHHHHHH
Confidence 567888887657999999999999999 8899988754
No 7
>PRK11569 transcriptional repressor IclR; Provisional
Probab=95.42 E-value=0.012 Score=42.86 Aligned_cols=37 Identities=16% Similarity=0.342 Sum_probs=31.7
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
|.|.+.+++.++++|+.|||+.+|.++ ..++|+|+.|
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpk---sTv~RlL~tL 67 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPN---STTHRLLTTM 67 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 456777887668999999999999999 8999999754
No 8
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member 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.
Probab=95.37 E-value=0.013 Score=41.94 Aligned_cols=37 Identities=19% Similarity=0.366 Sum_probs=32.0
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+.|.+.+.+.++|+|+.|||+.+|.++ ..++|+|.-|
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpk---sT~~RlL~tL 48 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTR---AAARRFLLTL 48 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 567888887668999999999999999 8999999754
No 9
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=95.16 E-value=0.017 Score=42.07 Aligned_cols=37 Identities=27% Similarity=0.463 Sum_probs=31.5
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+.|.+.+.+.++++|+.|||+.+|.++ ..++|+|..|
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpk---Stv~RlL~tL 64 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPL---STTFRLLKVL 64 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 457788877668899999999999999 8899998754
No 10
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=94.97 E-value=0.034 Score=32.88 Aligned_cols=38 Identities=24% Similarity=0.351 Sum_probs=30.1
Q ss_pred HHhCchHHHHhCCC-CCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 46 VELGIPDVIHKHGQ-PMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 46 veLgI~d~L~~~~g-p~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.+-.|.+.|...++ ++|+.|||..+|++. ..+.|+|.-
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~---~~v~r~L~~ 45 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPK---KEVNRVLYS 45 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence 45567888887655 399999999999999 778887753
No 11
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=94.35 E-value=0.037 Score=40.03 Aligned_cols=37 Identities=16% Similarity=0.313 Sum_probs=31.2
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+.|.+.+..+++++|+.|||+.+|+++ ..++|+|+.|
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~k---stv~RlL~tL 50 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHR---TTVRRLLETL 50 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 456777876667899999999999999 8899998754
No 12
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=94.03 E-value=0.04 Score=31.51 Aligned_cols=39 Identities=23% Similarity=0.367 Sum_probs=29.7
Q ss_pred HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
--..+.|.+.|.. ++|.|+.|||+.+|+++ ..+++-|+.
T Consensus 9 ~p~R~~Il~~L~~-~~~~t~~ela~~l~~~~---~t~s~hL~~ 47 (61)
T PF12840_consen 9 DPTRLRILRLLAS-NGPMTVSELAEELGISQ---STVSYHLKK 47 (61)
T ss_dssp SHHHHHHHHHHHH-CSTBEHHHHHHHHTS-H---HHHHHHHHH
T ss_pred CHHHHHHHHHHhc-CCCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence 3456778888843 59999999999999988 777776654
No 13
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=93.74 E-value=0.069 Score=32.32 Aligned_cols=42 Identities=24% Similarity=0.479 Sum_probs=28.0
Q ss_pred HHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 39 SMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 39 ~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
..++++.+.|. ....+++.|..|||+.+++++ ..+.++++-|
T Consensus 8 ~~Al~~l~~la----~~~~~~~~s~~eiA~~~~i~~---~~l~kil~~L 49 (83)
T PF02082_consen 8 DYALRILLYLA----RHPDGKPVSSKEIAERLGISP---SYLRKILQKL 49 (83)
T ss_dssp HHHHHHHHHHH----CTTTSC-BEHHHHHHHHTS-H---HHHHHHHHHH
T ss_pred HHHHHHHHHHH----hCCCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 34555555541 122236799999999999999 9999998753
No 14
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=93.72 E-value=0.058 Score=39.02 Aligned_cols=37 Identities=27% Similarity=0.506 Sum_probs=31.1
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+.|.|.|++.++++++.|||+.+|.++ ..++|+|..|
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpk---sT~~RlL~tL 43 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPK---STVHRLLQTL 43 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence 567888887556678999999999999 8899998643
No 15
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=93.72 E-value=0.06 Score=29.82 Aligned_cols=34 Identities=21% Similarity=0.449 Sum_probs=26.2
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|...|.++++++|..|||+.++++. ..++|-+.
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~---rTi~~~i~ 37 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSR---RTIRRDIK 37 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-H---HHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCH---HHHHHHHH
Confidence 45666755568899999999999988 77777654
No 16
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=93.69 E-value=0.061 Score=29.14 Aligned_cols=37 Identities=16% Similarity=0.346 Sum_probs=28.2
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.+..|.+.|.++ +.+|..|||..+|++. ..+.+.++-
T Consensus 4 ~~~~Il~~l~~~-~~~t~~ela~~~~is~---~tv~~~l~~ 40 (48)
T PF13412_consen 4 TQRKILNYLREN-PRITQKELAEKLGISR---STVNRYLKK 40 (48)
T ss_dssp HHHHHHHHHHHC-TTS-HHHHHHHHTS-H---HHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHhCCCH---HHHHHHHHH
Confidence 356678888874 6799999999999988 778877764
No 17
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=93.66 E-value=0.052 Score=39.01 Aligned_cols=36 Identities=11% Similarity=0.416 Sum_probs=29.8
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+.|.+.+.+. +++|++|||+.+|.++ ..++|+|+.|
T Consensus 17 l~IL~~l~~~-~~l~l~eia~~lgl~k---stv~Rll~tL 52 (257)
T PRK15090 17 FGILQALGEE-REIGITELSQRVMMSK---STVYRFLQTM 52 (257)
T ss_pred HHHHHHhhcC-CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 4566777754 6899999999999999 8899999754
No 18
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=93.53 E-value=0.089 Score=37.07 Aligned_cols=43 Identities=23% Similarity=0.309 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 36 YINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 36 ~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
-.+-.+|+.|.++|-|| .. .-+++.|||+.+|+.+ ..+...||
T Consensus 158 drQ~~vL~~A~~~GYFd-~P---R~~~l~dLA~~lGISk---st~~ehLR 200 (215)
T COG3413 158 DRQLEVLRLAYKMGYFD-YP---RRVSLKDLAKELGISK---STLSEHLR 200 (215)
T ss_pred HHHHHHHHHHHHcCCCC-CC---ccCCHHHHHHHhCCCH---HHHHHHHH
Confidence 34667999999999999 33 6789999999999987 54444444
No 19
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=93.51 E-value=0.086 Score=36.25 Aligned_cols=41 Identities=15% Similarity=0.378 Sum_probs=31.0
Q ss_pred HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.+|++.+.+. ....++|.|+.|||+++++++ ..+.++|+.|
T Consensus 9 yAl~~l~~lA----~~~~~~~vs~~eIA~~~~ip~---~~l~kIl~~L 49 (164)
T PRK10857 9 YAVTAMLDVA----LNSEAGPVPLADISERQGISL---SYLEQLFSRL 49 (164)
T ss_pred HHHHHHHHHH----hCCCCCcCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence 4555666555 223347999999999999999 9999998764
No 20
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=93.20 E-value=0.12 Score=28.05 Aligned_cols=22 Identities=18% Similarity=0.520 Sum_probs=18.0
Q ss_pred CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 61 MTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 61 ~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|..+||..+|+.. ..++|+++
T Consensus 22 ~si~~IA~~~gvsr---~TvyR~l~ 43 (45)
T PF02796_consen 22 MSIAEIAKQFGVSR---STVYRYLN 43 (45)
T ss_dssp --HHHHHHHTTS-H---HHHHHHHC
T ss_pred CCHHHHHHHHCcCH---HHHHHHHh
Confidence 99999999999999 99999986
No 21
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=92.91 E-value=0.053 Score=29.58 Aligned_cols=36 Identities=22% Similarity=0.478 Sum_probs=27.9
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
++.|...|.+ ||.++.||++.++.++ ..+.+-|+.|
T Consensus 4 R~~Il~~L~~--~~~~~~el~~~l~~s~---~~vs~hL~~L 39 (47)
T PF01022_consen 4 RLRILKLLSE--GPLTVSELAEELGLSQ---STVSHHLKKL 39 (47)
T ss_dssp HHHHHHHHTT--SSEEHHHHHHHHTS-H---HHHHHHHHHH
T ss_pred HHHHHHHHHh--CCCchhhHHHhccccc---hHHHHHHHHH
Confidence 4566777774 8999999999999998 7777776643
No 22
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=92.79 E-value=0.13 Score=33.76 Aligned_cols=41 Identities=20% Similarity=0.380 Sum_probs=30.5
Q ss_pred HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.++++.+.|..- ..+++.|+.|||+.+++++ ..+.++|+.|
T Consensus 9 YAl~~l~~La~~----~~~~~~s~~~ia~~~~ip~---~~l~kil~~L 49 (135)
T TIGR02010 9 YAVTAMLDLALN----AETGPVTLADISERQGISL---SYLEQLFAKL 49 (135)
T ss_pred HHHHHHHHHHhC----CCCCcCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence 355565555321 2246899999999999999 9999998754
No 23
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=92.21 E-value=0.047 Score=31.70 Aligned_cols=36 Identities=25% Similarity=0.339 Sum_probs=27.8
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|..|...|.+ .|+.|+.|||..+|++. ..+++.|+-
T Consensus 10 E~~vy~~Ll~-~~~~t~~eIa~~l~i~~---~~v~~~L~~ 45 (68)
T PF01978_consen 10 EAKVYLALLK-NGPATAEEIAEELGISR---STVYRALKS 45 (68)
T ss_dssp HHHHHHHHHH-HCHEEHHHHHHHHTSSH---HHHHHHHHH
T ss_pred HHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence 4455555654 38999999999999998 778887764
No 24
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=92.21 E-value=0.16 Score=30.03 Aligned_cols=38 Identities=18% Similarity=0.444 Sum_probs=29.5
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCCh--hhHHHHHhcC
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKA--HCIQRLMRIL 87 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~--~~L~RlLR~L 87 (87)
|.++|.++++|++..+|+..+.....+. ..++|-||+|
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~m 42 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAM 42 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHH
Confidence 5678888889999999999997543222 7789988864
No 25
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=91.90 E-value=0.18 Score=31.73 Aligned_cols=38 Identities=24% Similarity=0.346 Sum_probs=30.0
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcC-----CCCCChhhHHHHHhcC
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALD-----IQKNKAHCIQRLMRIL 87 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~-----~~~~~~~~L~RlLR~L 87 (87)
+.-|++.|.+.+++.|+.||.+.+. ++. ..++|.|+.|
T Consensus 3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~---~TVYR~L~~L 45 (116)
T cd07153 3 RLAILEVLLESDGHLTAEEIYERLRKKGPSISL---ATVYRTLELL 45 (116)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCH---HHHHHHHHHH
Confidence 3457888887678999999999984 344 7899998764
No 26
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=91.82 E-value=0.19 Score=31.29 Aligned_cols=37 Identities=11% Similarity=0.318 Sum_probs=29.8
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.+..|...|..+ ++.|..|||+.+|+++ ..+.|.++.
T Consensus 4 ~D~~il~~L~~~-~~~~~~~la~~l~~s~---~tv~~~l~~ 40 (108)
T smart00344 4 IDRKILEELQKD-ARISLAELAKKVGLSP---STVHNRVKR 40 (108)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence 467788888874 7899999999999998 777666653
No 27
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=91.66 E-value=0.098 Score=30.86 Aligned_cols=36 Identities=22% Similarity=0.307 Sum_probs=25.9
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.|.+.|.+..+|.|..|||..+|++. ...++.|..|
T Consensus 4 ~Il~~i~~~~~p~~T~eiA~~~gls~---~~aR~yL~~L 39 (62)
T PF04703_consen 4 KILEYIKEQNGPLKTREIADALGLSI---YQARYYLEKL 39 (62)
T ss_dssp CHHHHHHHHTS-EEHHHHHHHHTS-H---HHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCH---HHHHHHHHHH
Confidence 35566665358999999999999988 7777777653
No 28
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=91.62 E-value=0.11 Score=29.09 Aligned_cols=37 Identities=22% Similarity=0.398 Sum_probs=26.6
Q ss_pred HhCchHHHHhCCCC-CCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 47 ELGIPDVIHKHGQP-MTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 47 eLgI~d~L~~~~gp-~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
+..|.-.|...+++ +|..|||+.++.++ ..+.|+++-
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l~~~~---~~vs~~v~~ 44 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERLGISK---STVSRIVKR 44 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHHTS-H---HHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence 34455566665433 89999999999999 888887764
No 29
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=91.49 E-value=0.27 Score=31.61 Aligned_cols=41 Identities=20% Similarity=0.519 Sum_probs=29.8
Q ss_pred HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.+|++.+.+.. ...++|.|..|||+.+++++ ..+.++|+.|
T Consensus 9 ~al~~l~~la~----~~~~~~~s~~eia~~~~i~~---~~v~~il~~L 49 (132)
T TIGR00738 9 YALRALLDLAL----NPDEGPVSVKEIAERQGISR---SYLEKILRTL 49 (132)
T ss_pred HHHHHHHHHHh----CCCCCcCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence 45555555432 22236999999999999999 9999998754
No 30
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=91.32 E-value=0.18 Score=32.64 Aligned_cols=27 Identities=19% Similarity=0.454 Sum_probs=23.9
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+++.|+.|||+.+++++ ..+.++|+.|
T Consensus 23 ~~~~s~~eia~~l~is~---~~v~~~l~~L 49 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNA---PTVSKILKQL 49 (130)
T ss_pred CCCccHHHHHHHHCcCH---HHHHHHHHHH
Confidence 47899999999999999 8899888754
No 31
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=91.13 E-value=0.14 Score=30.00 Aligned_cols=33 Identities=15% Similarity=0.387 Sum_probs=23.4
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|-+.|.+ .+.+|..|||..++++| +.+.-+|..
T Consensus 5 i~~~l~~-~~~~S~~eLa~~~~~s~---~~ve~mL~~ 37 (69)
T PF09012_consen 5 IRDYLRE-RGRVSLAELAREFGISP---EAVEAMLEQ 37 (69)
T ss_dssp HHHHHHH-S-SEEHHHHHHHTT--H---HHHHHHHHH
T ss_pred HHHHHHH-cCCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence 4566776 48999999999999999 777666643
No 32
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=90.61 E-value=0.35 Score=26.19 Aligned_cols=32 Identities=9% Similarity=0.288 Sum_probs=25.0
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|+..|. .++.|..+|++.+++++ ..+.+.++.
T Consensus 2 il~~l~--~~~~~~~~i~~~l~is~---~~v~~~l~~ 33 (66)
T smart00418 2 ILKLLA--EGELCVCELAEILGLSQ---STVSHHLKK 33 (66)
T ss_pred HHHHhh--cCCccHHHHHHHHCCCH---HHHHHHHHH
Confidence 455565 47899999999999988 777777764
No 33
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=90.56 E-value=0.24 Score=26.79 Aligned_cols=36 Identities=11% Similarity=0.280 Sum_probs=25.3
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
++..|.+.|.++ +..|..+||+.+|+++ .....|+=
T Consensus 4 ~D~~Il~~Lq~d-~r~s~~~la~~lglS~--~~v~~Ri~ 39 (42)
T PF13404_consen 4 LDRKILRLLQED-GRRSYAELAEELGLSE--STVRRRIR 39 (42)
T ss_dssp HHHHHHHHHHH--TTS-HHHHHHHHTS-H--HHHHHHHH
T ss_pred HHHHHHHHHHHc-CCccHHHHHHHHCcCH--HHHHHHHH
Confidence 567788888874 8999999999999977 13445543
No 34
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.33 E-value=0.53 Score=32.82 Aligned_cols=36 Identities=17% Similarity=0.278 Sum_probs=30.1
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
..|.+.|..+ |++|..|||..+|+.. ..++|+|..|
T Consensus 25 ~~Vl~~L~~~-g~~tdeeLA~~Lgi~~---~~VRk~L~~L 60 (178)
T PRK06266 25 FEVLKALIKK-GEVTDEEIAEQTGIKL---NTVRKILYKL 60 (178)
T ss_pred hHHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 3478888865 7999999999999998 8899988654
No 35
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=90.30 E-value=0.18 Score=26.57 Aligned_cols=24 Identities=29% Similarity=0.444 Sum_probs=19.0
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.|+.+||..+|.++ ..+.|+.+
T Consensus 7 ~~~~l~~iA~~~g~S~---~~f~r~Fk 30 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSP---SYFSRLFK 30 (42)
T ss_dssp SS--HHHHHHHHTS-H---HHHHHHHH
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 6799999999999988 88998876
No 36
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.98 E-value=0.41 Score=25.34 Aligned_cols=33 Identities=15% Similarity=0.348 Sum_probs=25.5
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|.+.|.+. ++.|..+|+..+++++ ..++|.|..
T Consensus 5 il~~l~~~-~~~s~~~l~~~l~~s~---~tv~~~l~~ 37 (53)
T smart00420 5 ILELLAQQ-GKVSVEELAELLGVSE---MTIRRDLNK 37 (53)
T ss_pred HHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence 45556553 6799999999999988 778877754
No 37
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=89.38 E-value=0.43 Score=31.26 Aligned_cols=44 Identities=23% Similarity=0.343 Sum_probs=33.5
Q ss_pred HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.+|.--..+.|++.|.+ +++.++.||++.++..+ ..+.+-|+.|
T Consensus 11 kaLadptRl~IL~~L~~-~~~~~v~ela~~l~lsq---stvS~HL~~L 54 (117)
T PRK10141 11 KILSDETRLGIVLLLRE-SGELCVCDLCTALDQSQ---PKISRHLALL 54 (117)
T ss_pred HHhCCHHHHHHHHHHHH-cCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 34444577888888875 37899999999999988 7777766654
No 38
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=89.36 E-value=0.36 Score=27.98 Aligned_cols=35 Identities=11% Similarity=0.372 Sum_probs=26.9
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
++.|...+. +++.|..|||+.+|+.. ..+.|-++.
T Consensus 2 ~~~il~~L~--~~~~~~~eLa~~l~vS~---~tv~~~l~~ 36 (69)
T TIGR00122 2 PLRLLALLA--DNPFSGEKLGEALGMSR---TAVNKHIQT 36 (69)
T ss_pred hHHHHHHHH--cCCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence 456777777 46889999999999988 667666543
No 39
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=89.16 E-value=0.38 Score=32.19 Aligned_cols=37 Identities=14% Similarity=0.396 Sum_probs=27.9
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|..++-+|-+..+|.|+.|||+.++.+. ..++|-++
T Consensus 28 ~Dv~v~~~LL~~~~~~tvdelae~lnr~r---Stv~rsl~ 64 (126)
T COG3355 28 LDVEVYKALLEENGPLTVDELAEILNRSR---STVYRSLQ 64 (126)
T ss_pred HHHHHHHHHHhhcCCcCHHHHHHHHCccH---HHHHHHHH
Confidence 46666777764359999999999999987 66666554
No 40
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=89.09 E-value=0.38 Score=29.70 Aligned_cols=32 Identities=28% Similarity=0.463 Sum_probs=22.1
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
++..|++ |+|+|..+||..+|.+. +.+...|.
T Consensus 29 LLr~LA~-G~PVt~~~LA~a~g~~~---e~v~~~L~ 60 (77)
T PF12324_consen 29 LLRLLAK-GQPVTVEQLAAALGWPV---EEVRAALA 60 (77)
T ss_dssp HHHHHTT-TS-B-HHHHHHHHT--H---HHHHHHHH
T ss_pred HHHHHHc-CCCcCHHHHHHHHCCCH---HHHHHHHH
Confidence 5667886 79999999999999877 66666653
No 41
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=88.71 E-value=0.56 Score=27.87 Aligned_cols=37 Identities=14% Similarity=0.381 Sum_probs=29.1
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.++.|+..|... ++.|..+|+..++.++ ..+.|.++-
T Consensus 11 ~~~~il~~l~~~-~~~~~~~la~~~~~s~---~~i~~~l~~ 47 (101)
T smart00347 11 TQFLVLRILYEE-GPLSVSELAKRLGVSP---STVTRVLDR 47 (101)
T ss_pred HHHHHHHHHHHc-CCcCHHHHHHHHCCCc---hhHHHHHHH
Confidence 356677777754 6799999999999988 778887764
No 42
>PRK06474 hypothetical protein; Provisional
Probab=88.67 E-value=0.42 Score=33.14 Aligned_cols=44 Identities=18% Similarity=0.319 Sum_probs=33.7
Q ss_pred HHHHHHHhCchHHHHhCCCCCCHHHHHHhc-CCCCCChhhHHHHHhcC
Q 041968 41 SLKCAVELGIPDVIHKHGQPMTLSQIASAL-DIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 41 aL~aaveLgI~d~L~~~~gp~S~~ELA~~~-~~~~~~~~~L~RlLR~L 87 (87)
+|.--..+.|++.|...+++.|+.||+..+ +++. ..++|-|+.|
T Consensus 7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~---aTvYrhL~~L 51 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQ---ATLYRHLQTM 51 (178)
T ss_pred hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCH---HHHHHHHHHH
Confidence 344456788889898765569999999999 4666 7799988754
No 43
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=88.50 E-value=0.61 Score=30.75 Aligned_cols=41 Identities=10% Similarity=0.329 Sum_probs=30.9
Q ss_pred HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.++++.+.++.. ..|++.|..|||+..|+++ ..++++|+.|
T Consensus 9 YAl~~~i~la~~----~~g~~~s~~~ia~~~~is~---~~vrk~l~~L 49 (141)
T PRK11014 9 YGLRALIYMASL----PEGRMTSISEVTEVYGVSR---NHMVKIINQL 49 (141)
T ss_pred HHHHHHHHHhcC----CCCCccCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 456666666532 2246889999999999999 8899988754
No 44
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=88.13 E-value=0.39 Score=25.22 Aligned_cols=26 Identities=27% Similarity=0.510 Sum_probs=21.8
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
-|.|..|||+.+++++ ..+.|.|+.|
T Consensus 7 ~~~s~~~la~~l~~s~---~tv~~~l~~L 32 (48)
T smart00419 7 LPLTRQEIAELLGLTR---ETVSRTLKRL 32 (48)
T ss_pred eccCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 4689999999999998 8888887753
No 45
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=88.02 E-value=0.51 Score=26.78 Aligned_cols=33 Identities=12% Similarity=0.344 Sum_probs=27.0
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|.+.|.+. +.+|+.|||+.+++.+ ..++|=|..
T Consensus 5 Il~~l~~~-~~~s~~ela~~~~VS~---~TiRRDl~~ 37 (57)
T PF08220_consen 5 ILELLKEK-GKVSVKELAEEFGVSE---MTIRRDLNK 37 (57)
T ss_pred HHHHHHHc-CCEEHHHHHHHHCcCH---HHHHHHHHH
Confidence 56677664 8999999999999999 888886654
No 46
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=87.91 E-value=0.53 Score=31.82 Aligned_cols=26 Identities=19% Similarity=0.415 Sum_probs=23.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
++.|+.+||+..+++| ..|.|+|.-|
T Consensus 24 ~~~s~~~IA~~~~is~---~~L~kil~~L 49 (150)
T COG1959 24 GPVSSAEIAERQGISP---SYLEKILSKL 49 (150)
T ss_pred CcccHHHHHHHhCcCH---HHHHHHHHHH
Confidence 4899999999999999 9999998654
No 47
>PRK13239 alkylmercury lyase; Provisional
Probab=87.37 E-value=0.78 Score=33.00 Aligned_cols=36 Identities=17% Similarity=0.438 Sum_probs=28.9
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.-|+..|++ |+|.|..+||+.+|.+. +.+.++|+.|
T Consensus 25 ~~llr~la~-G~pvt~~~lA~~~~~~~---~~v~~~L~~l 60 (206)
T PRK13239 25 VPLLRLLAK-GRPVSVTTLAAALGWPV---EEVEAVLEAM 60 (206)
T ss_pred HHHHHHHHc-CCCCCHHHHHHHhCCCH---HHHHHHHHhC
Confidence 345666774 79999999999999988 7788887653
No 48
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=87.32 E-value=0.62 Score=31.49 Aligned_cols=41 Identities=12% Similarity=0.268 Sum_probs=30.9
Q ss_pred HHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 39 SMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 39 ~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
-.++++.+.|-.. .+++.|+.|||+..++++ ..|.++|+.|
T Consensus 8 ~YAlr~L~~LA~~-----~~~~~s~~eIA~~~~is~---~~L~kIl~~L 48 (153)
T PRK11920 8 NYAIRMLMYCAAN-----DGKLSRIPEIARAYGVSE---LFLFKILQPL 48 (153)
T ss_pred hHHHHHHHHHHhC-----CCCcCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence 3466666665421 246789999999999999 9999998754
No 49
>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=87.19 E-value=0.52 Score=26.45 Aligned_cols=27 Identities=26% Similarity=0.466 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
..++|..|||+.+|+++ ..+.|+|+.|
T Consensus 23 ~~~~s~~ela~~~g~s~---~tv~r~l~~L 49 (67)
T cd00092 23 QLPLTRQEIADYLGLTR---ETVSRTLKEL 49 (67)
T ss_pred cCCcCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 37899999999999998 8888888643
No 50
>PRK13558 bacterio-opsin activator; Provisional
Probab=86.70 E-value=0.76 Score=36.69 Aligned_cols=43 Identities=14% Similarity=0.159 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 36 YINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 36 ~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.-+-.+|++|.+.|-|| +. ...|..|||..+|+.+ ..+...||
T Consensus 610 ~~q~e~l~~a~~~gyf~-~p---r~~~~~e~a~~l~is~---~t~~~~lr 652 (665)
T PRK13558 610 DRQLTALQKAYVSGYFE-WP---RRVEGEELAESMGISR---STFHQHLR 652 (665)
T ss_pred HHHHHHHHHHHHcCCCC-CC---ccCCHHHHHHHhCCCH---HHHHHHHH
Confidence 45678999999999998 43 6789999999999988 66666555
No 51
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=86.48 E-value=0.8 Score=30.59 Aligned_cols=28 Identities=11% Similarity=0.339 Sum_probs=24.9
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
.+..|.+.|.++ +..|.+|||+.+|+++
T Consensus 10 ~D~~Il~~Lq~d-~R~s~~eiA~~lglS~ 37 (153)
T PRK11179 10 LDRGILEALMEN-ARTPYAELAKQFGVSP 37 (153)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCH
Confidence 678889999874 8999999999999987
No 52
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=86.42 E-value=0.31 Score=27.06 Aligned_cols=35 Identities=20% Similarity=0.400 Sum_probs=25.2
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
..+...|.+. +++|..|||..+++++ ..+.|+++-
T Consensus 6 ~~iL~~l~~~-~~~~~~~la~~~~~~~---~~~t~~i~~ 40 (59)
T PF01047_consen 6 FRILRILYEN-GGITQSELAEKLGISR---STVTRIIKR 40 (59)
T ss_dssp HHHHHHHHHH-SSEEHHHHHHHHTS-H---HHHHHHHHH
T ss_pred HHHHHHHHHc-CCCCHHHHHHHHCCCh---hHHHHHHHH
Confidence 3444556654 6799999999999999 777777653
No 53
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=86.29 E-value=0.35 Score=24.99 Aligned_cols=24 Identities=29% Similarity=0.580 Sum_probs=18.4
Q ss_pred CCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 60 PMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 60 p~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|+|-.|||..+|+.+ +.+.|+|.-
T Consensus 2 ~mtr~diA~~lG~t~---ETVSR~l~~ 25 (32)
T PF00325_consen 2 PMTRQDIADYLGLTR---ETVSRILKK 25 (32)
T ss_dssp E--HHHHHHHHTS-H---HHHHHHHHH
T ss_pred CcCHHHHHHHhCCcH---HHHHHHHHH
Confidence 578899999999999 989998853
No 54
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=86.21 E-value=0.64 Score=27.76 Aligned_cols=37 Identities=24% Similarity=0.316 Sum_probs=24.4
Q ss_pred hCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
-.|++.|-++. ...|..|||+.+++.+ ..+.|+.|-|
T Consensus 19 ~~Ia~yil~~~~~~~~~si~elA~~~~vS~---sti~Rf~kkL 58 (77)
T PF01418_consen 19 KKIADYILENPDEIAFMSISELAEKAGVSP---STIVRFCKKL 58 (77)
T ss_dssp HHHHHHHHH-HHHHCT--HHHHHHHCTS-H---HHHHHHHHHC
T ss_pred HHHHHHHHhCHHHHHHccHHHHHHHcCCCH---HHHHHHHHHh
Confidence 34555444322 5789999999999999 8899988754
No 55
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=86.11 E-value=0.79 Score=31.28 Aligned_cols=36 Identities=14% Similarity=0.057 Sum_probs=29.0
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
..|+|+|..+ +++|-.|||..+|++. ..++|+|..|
T Consensus 17 v~Vl~aL~~~-~~~tdEeLa~~Lgi~~---~~VRk~L~~L 52 (158)
T TIGR00373 17 GLVLFSLGIK-GEFTDEEISLELGIKL---NEVRKALYAL 52 (158)
T ss_pred HHHHHHHhcc-CCCCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 3477888754 7999999999999988 7788887643
No 56
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=85.69 E-value=0.76 Score=31.08 Aligned_cols=29 Identities=7% Similarity=0.234 Sum_probs=25.4
Q ss_pred HHHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 45 AVELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 45 aveLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
.+|..|.++|.+ ++.+|..|||+++|+++
T Consensus 14 ~~D~~IL~~Lq~-d~R~s~~eiA~~lglS~ 42 (164)
T PRK11169 14 RIDRNILNELQK-DGRISNVELSKRVGLSP 42 (164)
T ss_pred HHHHHHHHHhcc-CCCCCHHHHHHHHCcCH
Confidence 368889999987 48999999999999987
No 57
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=85.06 E-value=0.94 Score=31.56 Aligned_cols=36 Identities=25% Similarity=0.315 Sum_probs=28.5
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
..|...|.+. ++.|..|||+.+|+++ ..+.|.|+.|
T Consensus 4 ~~IL~~L~~~-~~~t~~eLA~~lgis~---~tV~~~L~~L 39 (203)
T TIGR02702 4 EDILSYLLKQ-GQATAAALAEALAISP---QAVRRHLKDL 39 (203)
T ss_pred HHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 3466677654 7799999999999999 8888887653
No 58
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=84.43 E-value=0.96 Score=30.85 Aligned_cols=48 Identities=13% Similarity=0.302 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 35 NYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 35 g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
++-..+.+-+=-.+.+.+.|+. .+|.|..|+|+.+|=++ ..+.|=||.
T Consensus 54 Sye~la~vLsp~nleLl~~Ia~-~~P~Si~ElAe~vgRdv---~nvhr~Ls~ 101 (144)
T COG4190 54 SYEDLARVLSPRNLELLELIAQ-EEPASINELAELVGRDV---KNVHRTLST 101 (144)
T ss_pred cHHHHHHHhChhHHHHHHHHHh-cCcccHHHHHHHhCcch---HHHHHHHHH
Confidence 4444444445556778888986 39999999999999998 778887764
No 59
>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=84.17 E-value=1.3 Score=24.44 Aligned_cols=33 Identities=21% Similarity=0.442 Sum_probs=24.4
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.|.+.+... +.+..||+..++++. ..+.|.++.
T Consensus 11 ~il~~l~~~--~~~~~ei~~~~~i~~---~~i~~~l~~ 43 (78)
T cd00090 11 RILRLLLEG--PLTVSELAERLGLSQ---STVSRHLKK 43 (78)
T ss_pred HHHHHHHHC--CcCHHHHHHHHCcCH---hHHHHHHHH
Confidence 455556642 399999999999988 667777654
No 60
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=84.00 E-value=1.4 Score=27.87 Aligned_cols=36 Identities=14% Similarity=0.255 Sum_probs=27.3
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+..|...|.+ .+++|..|||..+++++ ..+.|+++
T Consensus 29 ~q~~iL~~l~~-~~~~t~~ela~~~~~~~---~tvs~~l~ 64 (118)
T TIGR02337 29 QQWRILRILAE-QGSMEFTQLANQACILR---PSLTGILA 64 (118)
T ss_pred HHHHHHHHHHH-cCCcCHHHHHHHhCCCc---hhHHHHHH
Confidence 33446666765 37899999999999998 66777765
No 61
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=83.56 E-value=0.87 Score=26.79 Aligned_cols=31 Identities=35% Similarity=0.611 Sum_probs=20.7
Q ss_pred HHhCCCCCCHHHHHHhcCCC-CCChhhHHHHHhcC
Q 041968 54 IHKHGQPMTLSQIASALDIQ-KNKAHCIQRLMRIL 87 (87)
Q Consensus 54 L~~~~gp~S~~ELA~~~~~~-~~~~~~L~RlLR~L 87 (87)
+.+.|-|-|+.|||+.+|+. + ..+.+.|+.|
T Consensus 19 ~~~~G~~Pt~rEIa~~~g~~S~---~tv~~~L~~L 50 (65)
T PF01726_consen 19 IEENGYPPTVREIAEALGLKST---STVQRHLKAL 50 (65)
T ss_dssp HHHHSS---HHHHHHHHTSSSH---HHHHHHHHHH
T ss_pred HHHcCCCCCHHHHHHHhCCCCh---HHHHHHHHHH
Confidence 44456777999999999996 5 6677666543
No 62
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=83.52 E-value=1.3 Score=28.90 Aligned_cols=28 Identities=7% Similarity=0.278 Sum_probs=24.1
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
++..|.+.|.++ ++.|..|||+++|+++
T Consensus 9 ~D~~IL~~L~~d-~r~~~~eia~~lglS~ 36 (154)
T COG1522 9 IDRRILRLLQED-ARISNAELAERVGLSP 36 (154)
T ss_pred HHHHHHHHHHHh-CCCCHHHHHHHHCCCH
Confidence 567788888874 7899999999999987
No 63
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=83.49 E-value=1.7 Score=28.19 Aligned_cols=24 Identities=21% Similarity=0.522 Sum_probs=22.0
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.|+.+||+.+|+++ ..+.|+++
T Consensus 24 ~~~sl~~lA~~~g~S~---~~l~r~Fk 47 (127)
T PRK11511 24 SPLSLEKVSERSGYSK---WHLQRMFK 47 (127)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 7899999999999999 88988876
No 64
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=83.40 E-value=1.1 Score=24.16 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=16.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
...|..|||..+|.++ ..+.|.+|
T Consensus 19 ~G~s~~~IA~~lg~s~---sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSR---STVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT--H---HHHHHHHH
T ss_pred cCCCHHHHHHHHCcCc---HHHHHHHh
Confidence 4599999999999999 88988875
No 65
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=82.87 E-value=0.85 Score=25.75 Aligned_cols=31 Identities=29% Similarity=0.506 Sum_probs=20.4
Q ss_pred HHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 53 VIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 53 ~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.|...+++.|..+|+..++.+. ..+.|+++-
T Consensus 11 ~l~~~~~~~t~~~l~~~~~~~~---~~vs~~i~~ 41 (68)
T PF13463_consen 11 ALAHSDGPMTQSDLAERLGISK---STVSRIIKK 41 (68)
T ss_dssp HHT--TS-BEHHHHHHHTT--H---HHHHHHHHH
T ss_pred HHHccCCCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence 3443358999999999999998 777777653
No 66
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=82.78 E-value=1.3 Score=32.19 Aligned_cols=33 Identities=21% Similarity=0.422 Sum_probs=25.9
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|...|.++ +|+|+.|||..+|+++ ...+|-|-.
T Consensus 16 il~lL~~~-g~~sa~elA~~Lgis~---~avR~HL~~ 48 (218)
T COG2345 16 ILELLKKS-GPVSADELAEELGISP---MAVRRHLDD 48 (218)
T ss_pred HHHHHhcc-CCccHHHHHHHhCCCH---HHHHHHHHH
Confidence 34445554 8999999999999999 888877654
No 67
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=82.70 E-value=2 Score=25.25 Aligned_cols=28 Identities=18% Similarity=0.345 Sum_probs=21.7
Q ss_pred hHHHHhCCCCCCHHHHHHhcCCCCCChhhHH
Q 041968 51 PDVIHKHGQPMTLSQIASALDIQKNKAHCIQ 81 (87)
Q Consensus 51 ~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~ 81 (87)
|++--+++|.++..|||+.+|+++ ..+.
T Consensus 13 ~e~y~~~~g~i~lkdIA~~Lgvs~---~tIr 40 (60)
T PF10668_consen 13 FEIYKESNGKIKLKDIAEKLGVSE---STIR 40 (60)
T ss_pred HHHHHHhCCCccHHHHHHHHCCCH---HHHH
Confidence 444455579999999999999988 5554
No 68
>PRK00215 LexA repressor; Validated
Probab=82.29 E-value=1.8 Score=29.98 Aligned_cols=31 Identities=26% Similarity=0.472 Sum_probs=24.5
Q ss_pred HHhCCCCCCHHHHHHhcCC-CCCChhhHHHHHhcC
Q 041968 54 IHKHGQPMTLSQIASALDI-QKNKAHCIQRLMRIL 87 (87)
Q Consensus 54 L~~~~gp~S~~ELA~~~~~-~~~~~~~L~RlLR~L 87 (87)
+.+.+.+.|..|||+.+|. ++ ..+.|+++.|
T Consensus 17 ~~~~~~~~s~~ela~~~~~~~~---~tv~~~l~~L 48 (205)
T PRK00215 17 IEETGYPPSRREIADALGLRSP---SAVHEHLKAL 48 (205)
T ss_pred HHHhCCCCCHHHHHHHhCCCCh---HHHHHHHHHH
Confidence 3444678999999999999 88 7788887643
No 69
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=82.00 E-value=1.9 Score=28.99 Aligned_cols=42 Identities=17% Similarity=0.377 Sum_probs=34.4
Q ss_pred HHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 42 LKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 42 L~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
=+..+...|.+.+.++ |.+|..|++..+|++- ..+.+.+|-|
T Consensus 9 er~eLk~rIvElVRe~-GRiTi~ql~~~TGasR---~Tvk~~lreL 50 (127)
T PF06163_consen 9 EREELKARIVELVREH-GRITIKQLVAKTGASR---NTVKRYLREL 50 (127)
T ss_pred HHHHHHHHHHHHHHHc-CCccHHHHHHHHCCCH---HHHHHHHHHH
Confidence 3556777888888775 8999999999999988 7888888753
No 70
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=81.83 E-value=2.4 Score=26.54 Aligned_cols=35 Identities=17% Similarity=0.198 Sum_probs=29.8
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
...+|.+...++..|+.|.|..+|+.+ .-|.++||
T Consensus 12 a~~~d~~~~~~~~~ti~~~AK~L~i~~---~~l~~~Lr 46 (111)
T PF03374_consen 12 AEFYDAFVDSDGLYTIREAAKLLGIGR---NKLFQWLR 46 (111)
T ss_pred hHHHHHHHcCCCCccHHHHHHHhCCCH---HHHHHHHH
Confidence 345788877679999999999999998 77888887
No 71
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=81.47 E-value=2.2 Score=26.64 Aligned_cols=33 Identities=24% Similarity=0.327 Sum_probs=25.9
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
..|+..+. +..|..|||+.+|++. ..++|+.|.
T Consensus 41 ~~I~~ll~---~G~S~~eIA~~LgISr---sTIyRi~R~ 73 (88)
T TIGR02531 41 LQVAKMLK---QGKTYSDIEAETGAST---ATISRVKRC 73 (88)
T ss_pred HHHHHHHH---CCCCHHHHHHHHCcCH---HHHHHHHHh
Confidence 34555555 3479999999999999 999998873
No 72
>PHA00738 putative HTH transcription regulator
Probab=81.40 E-value=1.8 Score=28.31 Aligned_cols=38 Identities=21% Similarity=0.288 Sum_probs=30.0
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.++.|++.|.. +++.++.||++.+++.. ..+.+-|+.|
T Consensus 13 tRr~IL~lL~~-~e~~~V~eLae~l~lSQ---ptVS~HLKvL 50 (108)
T PHA00738 13 LRRKILELIAE-NYILSASLISHTLLLSY---TTVLRHLKIL 50 (108)
T ss_pred HHHHHHHHHHH-cCCccHHHHHHhhCCCH---HHHHHHHHHH
Confidence 46678888875 35799999999999987 7777777654
No 73
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=81.32 E-value=3.4 Score=26.05 Aligned_cols=39 Identities=15% Similarity=0.171 Sum_probs=30.9
Q ss_pred HHHHhCchHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 44 CAVELGIPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 44 aaveLgI~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.-+...|+.-|.+. +.+.++.|||..+++++ ..+.-.|+
T Consensus 8 S~~R~~vl~~L~~~yp~~~~~~eIar~v~~~~---snV~GaL~ 47 (90)
T PF07381_consen 8 SKVRKKVLEYLCSIYPEPAYPSEIARSVGSDY---SNVLGALR 47 (90)
T ss_pred HHHHHHHHHHHHHcCCCcCCHHHHHHHHCCCH---HHHHHHHh
Confidence 55677888888876 69999999999999999 55554443
No 74
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=80.97 E-value=1.6 Score=24.08 Aligned_cols=21 Identities=24% Similarity=0.479 Sum_probs=17.2
Q ss_pred CHHHHHHhcCCCCCChhhHHHHHh
Q 041968 62 TLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 62 S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|..|||+.+|+++ ..+.|+|+
T Consensus 1 Ti~dIA~~agvS~---~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSK---STVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSH---HHHHHHHT
T ss_pred CHHHHHHHHCcCH---HHHHHHHh
Confidence 6789999999988 77877774
No 75
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=80.56 E-value=1.5 Score=31.48 Aligned_cols=39 Identities=18% Similarity=0.298 Sum_probs=30.3
Q ss_pred HHhCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 46 VELGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 46 veLgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.|-.|++.|.++. .-.|+.|||+++++++ ..+-|+.|-|
T Consensus 17 ~e~~Ia~yil~n~~~v~~~si~~lA~~~~vS~---aTv~Rf~kkl 58 (284)
T PRK11302 17 SERKVAEVILASPQTAIHSSIATLAKMANVSE---PTVNRFCRSL 58 (284)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCH---HHHHHHHHHc
Confidence 4556666666544 4579999999999999 8899998854
No 76
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=80.16 E-value=2.7 Score=25.90 Aligned_cols=32 Identities=16% Similarity=0.241 Sum_probs=25.9
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
-|.+.|.+ +..|+.+||+..|+.. ..+.|.|.
T Consensus 10 ~I~e~l~~--~~~ti~dvA~~~gvS~---~TVsr~L~ 41 (80)
T TIGR02844 10 EIGKYIVE--TKATVRETAKVFGVSK---STVHKDVT 41 (80)
T ss_pred HHHHHHHH--CCCCHHHHHHHhCCCH---HHHHHHhc
Confidence 35677776 7889999999999988 77877764
No 77
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=80.13 E-value=1.7 Score=31.19 Aligned_cols=39 Identities=10% Similarity=0.238 Sum_probs=30.0
Q ss_pred HHhCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 46 VELGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 46 veLgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.|-.|++.|-++. .-.|+.|||+++++++ ..+.|+.|-|
T Consensus 13 ~e~~ia~yil~n~~~v~~~si~elA~~~~vS~---aTv~Rf~kkl 54 (278)
T PRK11557 13 SDRKLADYLLLQPDTARHLSSQQLANEAGVSQ---SSVVKFAQKL 54 (278)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCH---HHHHHHHHHc
Confidence 3455666665543 5689999999999999 8899998854
No 78
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=79.60 E-value=1.8 Score=24.89 Aligned_cols=25 Identities=20% Similarity=0.468 Sum_probs=18.8
Q ss_pred CCCCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 57 HGQPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 57 ~~gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
.+++++..+||+.+++.| ......+
T Consensus 19 ~~~~v~~~~iA~~L~vs~---~tvt~ml 43 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSP---PTVTEML 43 (60)
T ss_dssp CTSSBBHHHHHHHHTS-H---HHHHHHH
T ss_pred CCCCccHHHHHHHHCCCh---HHHHHHH
Confidence 469999999999999988 5444443
No 79
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=79.16 E-value=3.1 Score=25.68 Aligned_cols=24 Identities=29% Similarity=0.547 Sum_probs=21.8
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.|+++||+.+++++ ..|.|+++
T Consensus 20 ~~~~~~~lA~~~~~S~---~~l~r~f~ 43 (107)
T PRK10219 20 QPLNIDVVAKKSGYSK---WYLQRMFR 43 (107)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 7899999999999999 88988875
No 80
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=78.89 E-value=2.2 Score=28.51 Aligned_cols=35 Identities=17% Similarity=0.344 Sum_probs=28.7
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
-|+|.|..+ +.+|-.+||..+|.+. .-++++|..|
T Consensus 5 ~v~d~L~~~-~~~~dedLa~~l~i~~---n~vRkiL~~L 39 (147)
T smart00531 5 LVLDALMRN-GCVTEEDLAELLGIKQ---KQLRKILYLL 39 (147)
T ss_pred eehHHHHhc-CCcCHHHHHHHhCCCH---HHHHHHHHHH
Confidence 478888764 7899999999999998 7788887543
No 81
>PF13309 HTH_22: HTH domain
Probab=78.68 E-value=2.3 Score=24.80 Aligned_cols=37 Identities=24% Similarity=0.360 Sum_probs=28.7
Q ss_pred HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+++..-+-|+|+ +. | ++..+|+.+|++. ..++|-||
T Consensus 28 ~iV~~L~~~G~F~-lK--g---av~~vA~~L~iS~---~TVY~YLr 64 (64)
T PF13309_consen 28 EIVRQLYEKGIFL-LK--G---AVEYVAEKLGISR---ATVYRYLR 64 (64)
T ss_pred HHHHHHHHCCCcc-cC--c---HHHHHHHHHCCCH---HHHHHHcC
Confidence 4566667778886 33 2 6899999999999 88998776
No 82
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 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 entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=78.43 E-value=1.3 Score=27.68 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=22.9
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|++.|... |.++-.|||..++.++ .-++++|..
T Consensus 18 Il~~L~~~-~~l~de~la~~~~l~~---~~vRkiL~~ 50 (105)
T PF02002_consen 18 ILDALLRK-GELTDEDLAKKLGLKP---KEVRKILYK 50 (105)
T ss_dssp HHHHHHHH---B-HHHHHHTT-S-H---HHHHHHHHH
T ss_pred HHHHHHHc-CCcCHHHHHHHhCCCH---HHHHHHHHH
Confidence 57888754 7899999999999998 778888754
No 83
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=78.06 E-value=9.9 Score=21.27 Aligned_cols=31 Identities=10% Similarity=0.312 Sum_probs=24.3
Q ss_pred chHHHHhCCCCCCHHHHHHhcCC-CCCChhhHHHHHh
Q 041968 50 IPDVIHKHGQPMTLSQIASALDI-QKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~-~~~~~~~L~RlLR 85 (87)
+.+.|.+ ++.++.|||..+|. ++ ..+.|..+
T Consensus 42 a~~~l~~--~~~~~~~ia~~~g~~s~---~~f~r~Fk 73 (84)
T smart00342 42 ARRLLRD--TDLSVTEIALRVGFSSQ---SYFSRAFK 73 (84)
T ss_pred HHHHHHc--CCCCHHHHHHHhCCCCh---HHHHHHHH
Confidence 4455553 48999999999999 88 88888765
No 84
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=78.00 E-value=0.94 Score=27.48 Aligned_cols=38 Identities=18% Similarity=0.350 Sum_probs=29.0
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
|+|+|.-.|... +.++..||.+.++++. ..|.+-|+.|
T Consensus 1 vRl~Il~~L~~~-~~~~f~~L~~~l~lt~---g~Ls~hL~~L 38 (80)
T PF13601_consen 1 VRLAILALLYAN-EEATFSELKEELGLTD---GNLSKHLKKL 38 (80)
T ss_dssp HHHHHHHHHHHH-SEEEHHHHHHHTT--H---HHHHHHHHHH
T ss_pred CHHHHHHHHhhc-CCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence 467778888763 7899999999999998 7788877653
No 85
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=77.74 E-value=3.2 Score=26.98 Aligned_cols=32 Identities=22% Similarity=0.283 Sum_probs=23.6
Q ss_pred hHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 51 PDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 51 ~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
...|...+++.|..|||..+++++ ..+.|++.
T Consensus 37 L~~l~~~~~~~t~~eLa~~l~~~~---~tvt~~v~ 68 (144)
T PRK03573 37 LHNIHQLPPEQSQIQLAKAIGIEQ---PSLVRTLD 68 (144)
T ss_pred HHHHHHcCCCCCHHHHHHHhCCCh---hhHHHHHH
Confidence 344554445689999999999999 66766654
No 86
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=77.61 E-value=3.1 Score=27.21 Aligned_cols=33 Identities=12% Similarity=0.192 Sum_probs=25.3
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|.-.|.. .+++|..|||..+++++ ..+.|++.
T Consensus 44 ~vL~~l~~-~~~~t~~eLa~~l~i~~---~tvsr~l~ 76 (144)
T PRK11512 44 KVLCSIRC-AACITPVELKKVLSVDL---GALTRMLD 76 (144)
T ss_pred HHHHHHHH-cCCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 34555654 47899999999999999 77777764
No 87
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=77.35 E-value=4.4 Score=22.80 Aligned_cols=34 Identities=18% Similarity=0.345 Sum_probs=23.4
Q ss_pred HHhCchHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 46 VELGIPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 46 veLgI~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
.=+.+.+.+.+.| .-+|..|||+.+|++| ..++|
T Consensus 13 ~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~---~qVRK 47 (50)
T PF06971_consen 13 LYLRYLEQLKEEGVERVSSQELAEALGITP---AQVRK 47 (50)
T ss_dssp HHHHHHHHHHHTT-SEE-HHHHHHHHTS-H---HHHHH
T ss_pred HHHHHHHHHHHcCCeeECHHHHHHHHCCCH---HHhcc
Confidence 3345566666655 6789999999999998 66654
No 88
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=77.26 E-value=2.7 Score=27.53 Aligned_cols=27 Identities=19% Similarity=0.321 Sum_probs=22.2
Q ss_pred CCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 57 HGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 57 ~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.+++.++.+||..+++++ ..+.+.++-
T Consensus 19 ~~~~~~~~ela~~l~vs~---~svs~~l~~ 45 (142)
T PRK03902 19 EKGYARVSDIAEALSVHP---SSVTKMVQK 45 (142)
T ss_pred cCCCcCHHHHHHHhCCCh---hHHHHHHHH
Confidence 358889999999999988 777777654
No 89
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=76.62 E-value=2.9 Score=21.60 Aligned_cols=22 Identities=27% Similarity=0.490 Sum_probs=18.7
Q ss_pred CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 61 MTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 61 ~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+|..|+|+.+|+++ ..++++.+
T Consensus 2 lt~~e~a~~lgis~---~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSK---DTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHH
Confidence 58899999999998 88888765
No 90
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=76.48 E-value=3.1 Score=30.04 Aligned_cols=36 Identities=14% Similarity=0.230 Sum_probs=29.5
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
-.|.+.|.+. |.+++.|||+.+++.+ ..++|=|+.|
T Consensus 10 ~~I~~~l~~~-~~v~v~eLa~~~~VS~---~TIRRDL~~L 45 (252)
T PRK10681 10 GQLLQALKRS-DKLHLKDAAALLGVSE---MTIRRDLNAH 45 (252)
T ss_pred HHHHHHHHHc-CCCcHHHHHHHhCCCH---HHHHHHHHHh
Confidence 3567888764 8999999999999999 8888876643
No 91
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=76.37 E-value=2.9 Score=26.28 Aligned_cols=37 Identities=19% Similarity=0.297 Sum_probs=27.0
Q ss_pred HhCchHHHH--h-CCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 47 ELGIPDVIH--K-HGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 47 eLgI~d~L~--~-~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
+..+...|. . .+++.|..|||..++.++ ..+.|+++-
T Consensus 27 q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~---stvs~~i~~ 66 (109)
T TIGR01889 27 ELLILYYLGKLENNEGKLTLKEIIKEILIKQ---SALVKIIKK 66 (109)
T ss_pred HHHHHHHHHhhhccCCcCcHHHHHHHHCCCH---HHHHHHHHH
Confidence 344455555 2 248999999999999999 778777654
No 92
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=76.26 E-value=3.5 Score=25.54 Aligned_cols=26 Identities=12% Similarity=0.199 Sum_probs=22.4
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
..++|..|||+.+|+++ ..+.|++.-
T Consensus 45 ~~~is~~eLa~~~g~sr---~tVsr~L~~ 70 (95)
T TIGR01610 45 QDRVTATVIAELTGLSR---THVSDAIKS 70 (95)
T ss_pred CCccCHHHHHHHHCcCH---HHHHHHHHH
Confidence 37899999999999999 888887754
No 93
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=76.05 E-value=2.6 Score=30.55 Aligned_cols=39 Identities=26% Similarity=0.400 Sum_probs=30.3
Q ss_pred HHhCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 46 VELGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 46 veLgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.|-.|++.|-++. ...|..|||+.+++++ ..+-|+.|.|
T Consensus 29 ~e~~Ia~yil~~~~~v~~~si~~lA~~~~vS~---aTi~Rf~kkL 70 (292)
T PRK11337 29 LESRVVEWLLKPGDLSEATALKDIAEALAVSE---AMIVKVAKKL 70 (292)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCh---HHHHHHHHHc
Confidence 3566777666543 4579999999999999 8899998764
No 94
>PRK11050 manganese transport regulator MntR; Provisional
Probab=75.83 E-value=3.4 Score=27.72 Aligned_cols=33 Identities=18% Similarity=0.340 Sum_probs=25.9
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|...+.. +++.+..|||+.+++++ ..+.|.++-
T Consensus 42 I~~~l~~-~~~~t~~eLA~~l~is~---stVsr~l~~ 74 (152)
T PRK11050 42 IADLIAE-VGEARQVDIAARLGVSQ---PTVAKMLKR 74 (152)
T ss_pred HHHHHHh-cCCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence 4555654 47899999999999998 778877754
No 95
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=75.64 E-value=3.9 Score=28.10 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=21.9
Q ss_pred CCCCCCHHHHHHhcCCC-CCChhhHHHHHhcC
Q 041968 57 HGQPMTLSQIASALDIQ-KNKAHCIQRLMRIL 87 (87)
Q Consensus 57 ~~gp~S~~ELA~~~~~~-~~~~~~L~RlLR~L 87 (87)
.+-|.|..|||+.+|.+ + ..+.+.|+.|
T Consensus 22 ~~~~~~~~ela~~~~~~s~---~tv~~~l~~L 50 (199)
T TIGR00498 22 TGYPPSIREIARAVGLRSP---SAAEEHLKAL 50 (199)
T ss_pred cCCCCcHHHHHHHhCCCCh---HHHHHHHHHH
Confidence 35678999999999998 7 6677766543
No 96
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=75.55 E-value=3 Score=29.01 Aligned_cols=36 Identities=25% Similarity=0.328 Sum_probs=28.0
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
+..|...|.++ ++.|..|||+.++.++ ..+.|.++.
T Consensus 145 ~~~IL~~l~~~-g~~s~~eia~~l~is~---stv~r~L~~ 180 (203)
T TIGR01884 145 ELKVLEVLKAE-GEKSVKNIAKKLGKSL---STISRHLRE 180 (203)
T ss_pred HHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence 44566667653 6899999999999998 777777754
No 97
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=75.47 E-value=2.7 Score=22.51 Aligned_cols=21 Identities=19% Similarity=0.355 Sum_probs=18.4
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
...|..+||+++|+++ ..+++
T Consensus 15 ~~~s~~~Ia~~~gvs~---~~~y~ 35 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSK---GSFYR 35 (47)
T ss_dssp TTSSHHHHHHHHTSCH---HHHHH
T ss_pred HhCCHHHHHHHHccch---hhHHH
Confidence 7899999999999988 76765
No 98
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=75.29 E-value=1.8 Score=23.35 Aligned_cols=26 Identities=12% Similarity=0.344 Sum_probs=21.1
Q ss_pred CCC-CHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 59 QPM-TLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 59 gp~-S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+.+ |..|||+.++++. ..+.|.++.|
T Consensus 18 ~~l~s~~~la~~~~vs~---~tv~~~l~~L 44 (60)
T smart00345 18 DKLPSERELAAQLGVSR---TTVREALSRL 44 (60)
T ss_pred CcCcCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 455 8999999999988 7788877643
No 99
>PF12728 HTH_17: Helix-turn-helix domain
Probab=75.20 E-value=3.2 Score=22.37 Aligned_cols=22 Identities=27% Similarity=0.492 Sum_probs=19.0
Q ss_pred CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 61 MTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 61 ~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+|+.|+|+.+|+++ ..++++.+
T Consensus 2 lt~~e~a~~l~is~---~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISR---STVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHH
Confidence 58899999999988 88888775
No 100
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=74.88 E-value=3 Score=23.26 Aligned_cols=30 Identities=13% Similarity=0.382 Sum_probs=18.1
Q ss_pred hHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 51 PDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 51 ~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
-+.+.+ ..+|..+||+.+|+++ ..+.|++.
T Consensus 3 ~~~m~~--~~it~~~La~~~gis~---~tl~~~~~ 32 (63)
T PF13443_consen 3 KELMAE--RGITQKDLARKTGISR---STLSRILN 32 (63)
T ss_dssp HHHHHH--TT--HHHHHHHHT--H---HHHHHHHT
T ss_pred HHHHHH--cCCCHHHHHHHHCcCH---HHHHHHHh
Confidence 344554 4568888998888888 77777654
No 101
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=74.57 E-value=3.2 Score=28.36 Aligned_cols=30 Identities=20% Similarity=0.399 Sum_probs=19.2
Q ss_pred HHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 52 DVIHKHGQPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 52 d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
|.+...++-.|-.|||..+|+++ ..|+|-.
T Consensus 26 e~~~~~~~r~T~~eiAee~Gis~---~tLYrWr 55 (142)
T PF13022_consen 26 ELMPENGERRTQAEIAEEVGISR---STLYRWR 55 (142)
T ss_dssp HHS------S-HHHHHHHHTS-H---HHHHHHH
T ss_pred HHhhhccccchHHHHHHHhCCCH---HHHHHHH
Confidence 55554457899999999999999 9999865
No 102
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=74.49 E-value=2 Score=31.48 Aligned_cols=39 Identities=21% Similarity=0.302 Sum_probs=29.0
Q ss_pred HHhCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 46 VELGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 46 veLgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.|-.|+|.|-++. .-.|+.|||+.+|+.+ ..+-|+.|-|
T Consensus 19 ~er~iA~yil~~~~~~~~~si~elA~~a~VS~---aTv~Rf~~kL 60 (281)
T COG1737 19 SERKIADYILANPDEVALLSIAELAERAGVSP---ATVVRFARKL 60 (281)
T ss_pred HHHHHHHHHHhCHHHHHHHHHHHHHHHhCCCH---HHHHHHHHHc
Confidence 3455666665433 4569999999999999 8899988754
No 103
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=74.42 E-value=1.9 Score=24.90 Aligned_cols=26 Identities=27% Similarity=0.586 Sum_probs=22.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
-+.|-.+||..+|++. ..+.|+|+.|
T Consensus 27 ~~lt~~~iA~~~g~sr---~tv~r~l~~l 52 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSR---ETVSRILKRL 52 (76)
T ss_dssp EESSHHHHHHHHTSCH---HHHHHHHHHH
T ss_pred ecCCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 6789999999999999 8899988753
No 104
>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=73.84 E-value=3.8 Score=20.98 Aligned_cols=22 Identities=18% Similarity=0.382 Sum_probs=17.4
Q ss_pred CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 61 MTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 61 ~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+|..|+|+.+|+++ ..+.+..+
T Consensus 1 ~s~~e~a~~lgvs~---~tl~~~~~ 22 (49)
T cd04762 1 LTTKEAAELLGVSP---STLRRWVK 22 (49)
T ss_pred CCHHHHHHHHCcCH---HHHHHHHH
Confidence 47889999999988 77777654
No 105
>PF13518 HTH_28: Helix-turn-helix domain
Probab=73.39 E-value=6 Score=20.98 Aligned_cols=21 Identities=19% Similarity=0.475 Sum_probs=18.6
Q ss_pred CHHHHHHhcCCCCCChhhHHHHHh
Q 041968 62 TLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 62 S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|..++|...|+++ ..++|.++
T Consensus 14 s~~~~a~~~gis~---~tv~~w~~ 34 (52)
T PF13518_consen 14 SVREIAREFGISR---STVYRWIK 34 (52)
T ss_pred CHHHHHHHHCCCH---hHHHHHHH
Confidence 9999999999988 77888765
No 106
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=73.23 E-value=3.2 Score=22.15 Aligned_cols=23 Identities=17% Similarity=0.423 Sum_probs=17.9
Q ss_pred CCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 60 PMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 60 p~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..|..+||+.+|+++ ..++|..+
T Consensus 17 G~s~~~ia~~lgvs~---~Tv~~w~k 39 (50)
T PF13384_consen 17 GWSIREIAKRLGVSR---STVYRWIK 39 (50)
T ss_dssp T--HHHHHHHHTS-H---HHHHHHHT
T ss_pred CCCHHHHHHHHCcCH---HHHHHHHH
Confidence 579999999999999 88988875
No 107
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=72.91 E-value=6.3 Score=21.14 Aligned_cols=31 Identities=13% Similarity=0.326 Sum_probs=24.0
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
-|.+.+. ...|..++|+.+|++. ..+.|++.
T Consensus 19 ~i~~~~~---~~~s~~~vA~~~~vs~---~TV~ri~~ 49 (52)
T PF13542_consen 19 YILKLLR---ESRSFKDVARELGVSW---STVRRIFD 49 (52)
T ss_pred HHHHHHh---hcCCHHHHHHHHCCCH---HHHHHHHH
Confidence 3444444 2369999999999999 88999875
No 108
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=72.77 E-value=3.7 Score=28.06 Aligned_cols=44 Identities=11% Similarity=0.155 Sum_probs=32.9
Q ss_pred HHHHhCchHHHHhCCCCCCHHHHHHhcCCC-C-CChhhHHHHHhcC
Q 041968 44 CAVELGIPDVIHKHGQPMTLSQIASALDIQ-K-NKAHCIQRLMRIL 87 (87)
Q Consensus 44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~-~-~~~~~L~RlLR~L 87 (87)
+-.+.-|++.|.+.+++.|+.||...+.-. | -+...+||.|+.|
T Consensus 25 T~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L 70 (169)
T PRK11639 25 TPQRLEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFL 70 (169)
T ss_pred CHHHHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHH
Confidence 556777889888767899999999998632 1 1237899998764
No 109
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=72.50 E-value=3.8 Score=29.59 Aligned_cols=35 Identities=14% Similarity=0.162 Sum_probs=29.1
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.|.+.|.+ .+.+++.|||+.+++.+ ..++|-|+.|
T Consensus 9 ~Il~~l~~-~~~~~~~ela~~l~vS~---~TirRdL~~L 43 (251)
T PRK13509 9 ILLELLAQ-LGFVTVEKVIERLGISP---ATARRDINKL 43 (251)
T ss_pred HHHHHHHH-cCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 46777876 48999999999999999 8888887743
No 110
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=72.42 E-value=2.9 Score=24.39 Aligned_cols=27 Identities=26% Similarity=0.332 Sum_probs=19.6
Q ss_pred CCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 57 HGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 57 ~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.|.+-|..|||..+|+++ .-+..+|++
T Consensus 17 lgr~Pt~eEiA~~lgis~---~~v~~~l~~ 43 (78)
T PF04539_consen 17 LGREPTDEEIAEELGISV---EEVRELLQA 43 (78)
T ss_dssp HSS--BHHHHHHHHTS-H---HHHHHHHHH
T ss_pred hCCCCCHHHHHHHHcccH---HHHHHHHHh
Confidence 357889999999999999 777777753
No 111
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=71.87 E-value=4.7 Score=31.88 Aligned_cols=33 Identities=18% Similarity=0.481 Sum_probs=26.7
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
|-..|. .||.|+.||++.+|++- ..+.|.|+.|
T Consensus 5 ~~~~L~--~g~~~~~eL~~~l~~sq---~~~s~~L~~L 37 (442)
T PRK09775 5 LTTLLL--QGPLSAAELAARLGVSQ---ATLSRLLAAL 37 (442)
T ss_pred HHHHHh--cCCCCHHHHHHHhCCCH---HHHHHHHHHh
Confidence 334555 48999999999999988 7888888765
No 112
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=71.47 E-value=6.8 Score=24.93 Aligned_cols=39 Identities=23% Similarity=0.198 Sum_probs=30.8
Q ss_pred HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.+.+.||+..|.+ +++|=.|||+.+|+.. ..+.|.=|+|
T Consensus 41 l~~R~~i~~~Ll~--~~~tQrEIa~~lGiS~---atIsR~sn~l 79 (94)
T TIGR01321 41 LGDRIRIVNELLN--GNMSQREIASKLGVSI---ATITRGSNNL 79 (94)
T ss_pred HHHHHHHHHHHHh--CCCCHHHHHHHhCCCh---hhhhHHHhhc
Confidence 4567888987763 7899999999999988 7777765543
No 113
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=71.34 E-value=3.1 Score=30.70 Aligned_cols=37 Identities=30% Similarity=0.505 Sum_probs=31.8
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|..|.+.|.++||-.+=+||.+.+|.+. ..+.|++|=
T Consensus 197 e~~il~~i~~~GGri~Q~eL~r~lglsk---tTvsR~L~~ 233 (258)
T COG2512 197 EKEILDLIRERGGRITQAELRRALGLSK---TTVSRILRR 233 (258)
T ss_pred HHHHHHHHHHhCCEEeHHHHHHhhCCCh---HHHHHHHHH
Confidence 4557788888889999999999999998 788888874
No 114
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=71.31 E-value=13 Score=22.20 Aligned_cols=31 Identities=23% Similarity=0.354 Sum_probs=22.3
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|-+.+. ...+|-.|+|+.+|++. ..+.|+++
T Consensus 23 i~~~~~--~~~ltQ~e~A~~lgisq---~~vS~l~~ 53 (80)
T PF13744_consen 23 IRELRE--ERGLTQAELAERLGISQ---PRVSRLEN 53 (80)
T ss_dssp HHHHHH--CCT--HHHHHHHHTS-H---HHHHHHHT
T ss_pred HHHHHH--HcCCCHHHHHHHHCCCh---hHHHHHHc
Confidence 666666 36799999999999988 77888774
No 115
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit 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 []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=71.29 E-value=3.5 Score=24.52 Aligned_cols=38 Identities=16% Similarity=0.239 Sum_probs=28.5
Q ss_pred HHhCchHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 46 VELGIPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 46 veLgI~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.+..+.+.|+++. ...+..||+..++.|| ..+...++.
T Consensus 3 ~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~---r~i~~~~k~ 41 (75)
T PF04182_consen 3 IQYCLLERIARSRYNGITQSDLSKLLGIDP---RSIFYRLKK 41 (75)
T ss_pred hHHHHHHHHHhcCCCCEehhHHHHHhCCCc---hHHHHHHHH
Confidence 3456778888754 7788999999999999 666655543
No 116
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=71.29 E-value=2.4 Score=26.89 Aligned_cols=44 Identities=16% Similarity=0.245 Sum_probs=31.3
Q ss_pred HHHHhCchHHHHhCCCCCCHHHHHHhcCCC-C-CChhhHHHHHhcC
Q 041968 44 CAVELGIPDVIHKHGQPMTLSQIASALDIQ-K-NKAHCIQRLMRIL 87 (87)
Q Consensus 44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~-~-~~~~~L~RlLR~L 87 (87)
+..+.-|.+.|.+.+++.|+.||-..+... + -+...++|.|..|
T Consensus 7 T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L 52 (120)
T PF01475_consen 7 TPQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLL 52 (120)
T ss_dssp HHHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHH
Confidence 345667888888777899999999998631 1 1226789988754
No 117
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=71.11 E-value=5.8 Score=28.40 Aligned_cols=33 Identities=15% Similarity=0.286 Sum_probs=26.3
Q ss_pred chHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.+.|.++ .+++|+++||+.++.++ ..+.|+.|
T Consensus 188 ~~~~i~~~~~~~isl~~lA~~~~lS~---~~l~r~Fk 221 (290)
T PRK10572 188 ACQYISDHLASEFDIESVAQHVCLSP---SRLAHLFR 221 (290)
T ss_pred HHHHHHhcccCCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 34455443 38999999999999999 88999876
No 118
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=70.75 E-value=4 Score=22.02 Aligned_cols=24 Identities=21% Similarity=0.414 Sum_probs=18.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..+|..|+|+.+|+++ ..+.|+.+
T Consensus 8 ~gls~~~la~~~gis~---~~i~~~~~ 31 (55)
T PF01381_consen 8 KGLSQKELAEKLGISR---STISRIEN 31 (55)
T ss_dssp TTS-HHHHHHHHTS-H---HHHHHHHT
T ss_pred cCCCHHHHHHHhCCCc---chhHHHhc
Confidence 5689999999999988 77877764
No 119
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=70.49 E-value=4.9 Score=21.60 Aligned_cols=25 Identities=28% Similarity=0.534 Sum_probs=19.2
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
....|..|||..+|++. ..+.++.+
T Consensus 18 ~~~~t~~eIa~~lg~s~---~~V~~~~~ 42 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISR---STVRRILK 42 (50)
T ss_dssp TST-SHHHHHHHHTSCH---HHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcH---HHHHHHHH
Confidence 36889999999999988 66666543
No 120
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=70.37 E-value=4.2 Score=28.19 Aligned_cols=35 Identities=14% Similarity=0.188 Sum_probs=28.9
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.|.+.|.+. +.+++.|||+.+++++ ..++|=|+.|
T Consensus 11 ~Il~~l~~~-~~~~~~~La~~~~vS~---~TiRRDl~~L 45 (185)
T PRK04424 11 ALQELIEEN-PFITDEELAEKFGVSI---QTIRLDRMEL 45 (185)
T ss_pred HHHHHHHHC-CCEEHHHHHHHHCcCH---HHHHHHHHHH
Confidence 456777764 8999999999999999 8888877654
No 121
>PRK01381 Trp operon repressor; Provisional
Probab=70.34 E-value=5.1 Score=25.76 Aligned_cols=39 Identities=15% Similarity=0.154 Sum_probs=30.4
Q ss_pred HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.+..++|+..|. .|.+|=.|||+.+|+.. ..+.|.=|+|
T Consensus 41 l~~R~~I~~~L~--~g~~sQREIa~~lGvSi---aTITRgsn~L 79 (99)
T PRK01381 41 LGTRVRIVEELL--RGELSQREIKQELGVGI---ATITRGSNSL 79 (99)
T ss_pred HHHHHHHHHHHH--cCCcCHHHHHHHhCCce---eeehhhHHHh
Confidence 456789999888 47899999999999987 5566655443
No 122
>PRK15482 transcriptional regulator MurR; Provisional
Probab=70.29 E-value=4.2 Score=29.46 Aligned_cols=39 Identities=21% Similarity=0.320 Sum_probs=29.9
Q ss_pred HHhCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 46 VELGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 46 veLgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.|-.|++.|-++. .-.|..|||+++++++ ..+-|+.|-|
T Consensus 17 ~e~~Ia~yIl~n~~~v~~~si~elA~~~~vS~---aTv~Rf~kkL 58 (285)
T PRK15482 17 NEQKIADFLRANVSELKSVSSRKMAKQLGISQ---SSIVKFAQKL 58 (285)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCH---HHHHHHHHHh
Confidence 3556677665543 5689999999999999 8888887754
No 123
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=69.80 E-value=5.4 Score=32.43 Aligned_cols=38 Identities=21% Similarity=0.509 Sum_probs=29.3
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.|-..+.+.+++.|++||++++|.+. ..+.++.|||+|
T Consensus 467 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~ 504 (528)
T PRK14096 467 KVEELLKEDGGELSIEEIAAALGAPE-QVETIYKILRHL 504 (528)
T ss_pred HHHHHHhccCCCCCHHHHHHHcCCCc-cHHHHHHHHHHH
Confidence 44556655569999999999999843 338899999975
No 124
>PRK09462 fur ferric uptake regulator; Provisional
Probab=69.49 E-value=6.1 Score=26.12 Aligned_cols=44 Identities=11% Similarity=0.128 Sum_probs=31.7
Q ss_pred HHHHhCchHHHHhC-CCCCCHHHHHHhcCC-CC-CChhhHHHHHhcC
Q 041968 44 CAVELGIPDVIHKH-GQPMTLSQIASALDI-QK-NKAHCIQRLMRIL 87 (87)
Q Consensus 44 aaveLgI~d~L~~~-~gp~S~~ELA~~~~~-~~-~~~~~L~RlLR~L 87 (87)
+-.+.-|++.|.+. +++.|+.||-..+.- .| -+...+||.|..|
T Consensus 16 T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L 62 (148)
T PRK09462 16 TLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQF 62 (148)
T ss_pred CHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHH
Confidence 44566788888864 479999999998853 12 2337899998764
No 125
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=68.94 E-value=5.2 Score=28.77 Aligned_cols=36 Identities=28% Similarity=0.446 Sum_probs=29.3
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
..|.+.|.++ +..+..|||+.+++.+ ..++|-|..|
T Consensus 7 ~~Il~~l~~~-~~~~~~eLa~~l~VS~---~TiRRdL~~L 42 (240)
T PRK10411 7 QAIVDLLLNH-TSLTTEALAEQLNVSK---ETIRRDLNEL 42 (240)
T ss_pred HHHHHHHHHc-CCCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence 3467778764 7999999999999999 8888887643
No 126
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=68.68 E-value=8.3 Score=20.12 Aligned_cols=22 Identities=23% Similarity=0.356 Sum_probs=17.0
Q ss_pred CCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 60 PMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 60 p~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
..|..|||..+++++ ..+++.+
T Consensus 18 g~s~~eia~~l~is~---~tv~~~~ 39 (58)
T smart00421 18 GLTNKEIAERLGISE---KTVKTHL 39 (58)
T ss_pred CCCHHHHHHHHCCCH---HHHHHHH
Confidence 479999999999987 6555543
No 127
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=68.34 E-value=8.3 Score=26.01 Aligned_cols=31 Identities=23% Similarity=0.455 Sum_probs=23.8
Q ss_pred HHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 52 DVIHKHG-QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 52 d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+-|-+++ ...|+.|+++.||+++ ..+.+++|
T Consensus 37 ~yLr~~p~~~ati~eV~e~tgVs~---~~I~~~Ir 68 (137)
T TIGR03826 37 KFLRKHENRQATVSEIVEETGVSE---KLILKFIR 68 (137)
T ss_pred HHHHHCCCCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 3344433 4589999999999999 88888776
No 128
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 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 [].; PDB: 2WTE_A 3SQN_A.
Probab=68.22 E-value=3.3 Score=23.48 Aligned_cols=33 Identities=24% Similarity=0.423 Sum_probs=25.4
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHH
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
-++.|.+.|-+ .+..|..|||..+++.. ..+.+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~ela~~l~~S~---rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLKELAKKLNISE---RTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHHHHHHHCTS-H---HHHHH
T ss_pred HHHHHHHHHHc-CCCCcHHHHHHHHCCCH---HHHHH
Confidence 45677888877 58999999999999987 55544
No 129
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=68.20 E-value=5 Score=28.22 Aligned_cols=35 Identities=23% Similarity=0.359 Sum_probs=29.1
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
-|+|.+-+. |..|-.|||..+|+.. .-++|+|+.|
T Consensus 22 ~v~~~l~~k-ge~tDeela~~l~i~~---~~vrriL~~L 56 (176)
T COG1675 22 LVVDALLEK-GELTDEELAELLGIKK---NEVRRILYAL 56 (176)
T ss_pred HHHHHHHhc-CCcChHHHHHHhCccH---HHHHHHHHHH
Confidence 467888763 5899999999999988 7799998764
No 130
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=67.78 E-value=4.5 Score=29.31 Aligned_cols=36 Identities=11% Similarity=0.223 Sum_probs=29.1
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
-.|.+.|.+ .+.+++.|||+.+++++ ..++|=|..|
T Consensus 8 ~~Il~~l~~-~~~~~~~ela~~l~vS~---~TiRRdL~~L 43 (252)
T PRK10906 8 DAIIELVKQ-QGYVSTEELVEHFSVSP---QTIRRDLNDL 43 (252)
T ss_pred HHHHHHHHH-cCCEeHHHHHHHhCCCH---HHHHHHHHHH
Confidence 356777866 47899999999999999 8899976643
No 131
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=67.45 E-value=6.5 Score=23.16 Aligned_cols=26 Identities=23% Similarity=0.413 Sum_probs=18.7
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
.+.|.|.+.+.|+|++||.+.+..+.
T Consensus 9 ~~VeymK~r~~Plt~~eI~d~l~~d~ 34 (65)
T PF02186_consen 9 KAVEYMKKRDHPLTLEEILDYLSLDI 34 (65)
T ss_dssp HHHHHHHHH-S-B-HHHHHHHHTSSS
T ss_pred HHHHHHHhcCCCcCHHHHHHHHcCCC
Confidence 34567777689999999999999876
No 132
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=66.71 E-value=4.3 Score=26.96 Aligned_cols=25 Identities=24% Similarity=0.280 Sum_probs=22.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
-|+|-.|||..+|+.+ +.+.|+|+-
T Consensus 142 ~~~t~~~iA~~lG~tr---etvsR~l~~ 166 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTR---VTITRLLGD 166 (193)
T ss_pred CCCCHHHHHHHhCCcH---HHHHHHHHH
Confidence 3689999999999999 999999864
No 133
>PRK13503 transcriptional activator RhaS; Provisional
Probab=66.39 E-value=8 Score=27.28 Aligned_cols=33 Identities=9% Similarity=0.267 Sum_probs=25.7
Q ss_pred chHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.+.|.++- .++|++++|+.+++++ ..+.|+.+
T Consensus 176 ~~~~I~~~~~~~~tl~~lA~~~~lS~---~~l~r~Fk 209 (278)
T PRK13503 176 LLAWLEDHFAEEVNWEALADQFSLSL---RTLHRQLK 209 (278)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 444454432 7999999999999999 88888875
No 134
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=66.27 E-value=5.2 Score=29.28 Aligned_cols=37 Identities=8% Similarity=0.195 Sum_probs=29.5
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
...|.+.|.+. +.+|+.|||+.+++++ ..++|=|+.|
T Consensus 19 ~~~Il~~L~~~-~~vtv~eLa~~l~VS~---~TIRRDL~~L 55 (269)
T PRK09802 19 REQIIQRLRQQ-GSVQVNDLSALYGVST---VTIRNDLAFL 55 (269)
T ss_pred HHHHHHHHHHc-CCEeHHHHHHHHCCCH---HHHHHHHHHH
Confidence 34577878764 6799999999999999 8888876543
No 135
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=66.23 E-value=6 Score=22.97 Aligned_cols=21 Identities=19% Similarity=0.436 Sum_probs=14.8
Q ss_pred CHHHHHHhcCCCCCChhhHHHHHh
Q 041968 62 TLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 62 S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|..|||+.+|+.. ..+.|+++
T Consensus 2 t~~~iA~~~gvS~---~TVSr~ln 22 (70)
T smart00354 2 TIKDVARLAGVSK---ATVSRVLN 22 (70)
T ss_pred CHHHHHHHHCCCH---HHHHHHHC
Confidence 5678888888776 66666654
No 136
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=65.79 E-value=4.6 Score=27.25 Aligned_cols=24 Identities=13% Similarity=0.382 Sum_probs=21.9
Q ss_pred CCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 60 PMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 60 p~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
++|-.|||+.+|+.+ ..+.|+|+-
T Consensus 168 ~~t~~~lA~~lG~tr---~tvsR~l~~ 191 (211)
T PRK11753 168 KITRQEIGRIVGCSR---EMVGRVLKM 191 (211)
T ss_pred CCCHHHHHHHhCCCH---HHHHHHHHH
Confidence 788999999999999 999999864
No 137
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=64.91 E-value=11 Score=28.32 Aligned_cols=36 Identities=25% Similarity=0.474 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 38 NSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 38 ~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
+-.+|...+++.|.+.|+. .+|+.+.|||+++|.+.
T Consensus 16 v~kalaS~vRv~Il~lL~~-k~plNvneiAe~lgLpq 51 (308)
T COG4189 16 VLKALASKVRVAILQLLHR-KGPLNVNEIAEALGLPQ 51 (308)
T ss_pred HHHHHHHHHHHHHHHHHHH-hCCCCHHHHHHHhCCch
Confidence 4567778889999999987 48999999999999854
No 138
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=64.71 E-value=6.3 Score=26.34 Aligned_cols=43 Identities=9% Similarity=0.199 Sum_probs=32.7
Q ss_pred HHHhCchHHHHhCCCCCCHHHHHHhcCC-CC-CChhhHHHHHhcC
Q 041968 45 AVELGIPDVIHKHGQPMTLSQIASALDI-QK-NKAHCIQRLMRIL 87 (87)
Q Consensus 45 aveLgI~d~L~~~~gp~S~~ELA~~~~~-~~-~~~~~L~RlLR~L 87 (87)
--++.|.+.|.+++++.|+.||=..+.- .| -.+..+||.|..|
T Consensus 21 ~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l 65 (145)
T COG0735 21 PQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLL 65 (145)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHH
Confidence 3567789999987788999999988863 22 2347899998764
No 139
>PHA02943 hypothetical protein; Provisional
Probab=64.64 E-value=7.2 Score=27.23 Aligned_cols=26 Identities=19% Similarity=0.174 Sum_probs=20.2
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNK 76 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~ 76 (87)
.|.+.|. .|..|.+|||+.+|++.+.
T Consensus 15 eILE~Lk--~G~~TtseIAkaLGlS~~q 40 (165)
T PHA02943 15 KTLRLLA--DGCKTTSRIANKLGVSHSM 40 (165)
T ss_pred HHHHHHh--cCCccHHHHHHHHCCCHHH
Confidence 3556663 5899999999999998733
No 140
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=64.57 E-value=6.3 Score=26.87 Aligned_cols=25 Identities=24% Similarity=0.480 Sum_probs=21.4
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
+..|..|||+.+|+++ ..++|-++.
T Consensus 150 ~Gls~~EIA~~lgiS~---~tV~r~l~~ 174 (185)
T PF07638_consen 150 EGLSVEEIAERLGISE---RTVRRRLRR 174 (185)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence 4589999999999999 888887764
No 141
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=64.55 E-value=4.7 Score=27.86 Aligned_cols=24 Identities=29% Similarity=0.371 Sum_probs=21.6
Q ss_pred CCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 60 PMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 60 p~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|+|-.+||+.+|+.+ ..+.|+|+-
T Consensus 184 ~lt~~~iA~~lG~sr---~tvsR~l~~ 207 (235)
T PRK11161 184 TMTRGDIGNYLGLTV---ETISRLLGR 207 (235)
T ss_pred cccHHHHHHHhCCcH---HHHHHHHHH
Confidence 689999999999999 999998864
No 142
>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=64.16 E-value=8.7 Score=25.76 Aligned_cols=28 Identities=25% Similarity=0.361 Sum_probs=21.5
Q ss_pred HHHHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 52 DVIHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 52 d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+.+.+.| ...|+.+||++.|+++ ..+++
T Consensus 19 ~lf~e~G~~~~s~~~IA~~agvs~---~~lY~ 47 (202)
T TIGR03613 19 DTFSRFGFHGTSLEQIAELAGVSK---TNLLY 47 (202)
T ss_pred HHHHHhCcccCCHHHHHHHhCCCH---HHHHH
Confidence 3455555 7889999999999988 66654
No 143
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=64.16 E-value=5.6 Score=28.80 Aligned_cols=35 Identities=17% Similarity=0.291 Sum_probs=28.3
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
..|.+.|.+. +.+++.|||+.+++++ ..++|=|+.
T Consensus 8 ~~Il~~L~~~-~~v~v~eLa~~l~VS~---~TIRRDL~~ 42 (256)
T PRK10434 8 AAILEYLQKQ-GKTSVEELAQYFDTTG---TTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHc-CCEEHHHHHHHHCCCH---HHHHHHHHH
Confidence 3567788874 7899999999999998 888776554
No 144
>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=63.82 E-value=10 Score=24.94 Aligned_cols=27 Identities=26% Similarity=0.354 Sum_probs=20.9
Q ss_pred HHHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 53 VIHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 53 ~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
.+.+.| ...|+.+||++.|++. ..+++
T Consensus 20 lf~~~G~~~~s~~~IA~~agvsk---~~ly~ 47 (189)
T TIGR03384 20 SIGERGSLDVTIAQIARRAGVSS---GIISH 47 (189)
T ss_pred HHHhcCcccCCHHHHHHHhCCCH---HHHHH
Confidence 355556 7899999999999988 55554
No 145
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=63.55 E-value=6.8 Score=27.70 Aligned_cols=17 Identities=47% Similarity=0.757 Sum_probs=15.8
Q ss_pred CCCCCHHHHHHhcCCCC
Q 041968 58 GQPMTLSQIASALDIQK 74 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~ 74 (87)
.+|+|++||++.+|.+.
T Consensus 39 ~~Pmtl~Ei~E~lg~Sk 55 (177)
T COG1510 39 RKPLTLDEIAEALGMSK 55 (177)
T ss_pred CCCccHHHHHHHHCCCc
Confidence 59999999999999977
No 146
>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=63.44 E-value=9.2 Score=20.83 Aligned_cols=22 Identities=14% Similarity=0.362 Sum_probs=17.6
Q ss_pred CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 61 MTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 61 ~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|..+||..++++. ..+.+.+.
T Consensus 26 ~~~~~la~~~~is~---~~v~~~l~ 47 (66)
T cd07377 26 PSERELAEELGVSR---TTVREALR 47 (66)
T ss_pred CCHHHHHHHHCCCH---HHHHHHHH
Confidence 35999999999988 76776654
No 147
>PHA02591 hypothetical protein; Provisional
Probab=63.43 E-value=13 Score=23.23 Aligned_cols=31 Identities=19% Similarity=0.402 Sum_probs=24.3
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
++..|.+ ...|..+||+.+|++- ..+.+.++
T Consensus 51 vA~eL~e--qGlSqeqIA~~LGVsq---etVrKYL~ 81 (83)
T PHA02591 51 VTHELAR--KGFTVEKIASLLGVSV---RKVRRYLE 81 (83)
T ss_pred HHHHHHH--cCCCHHHHHHHhCCCH---HHHHHHHh
Confidence 4445664 6689999999999988 77887775
No 148
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=63.37 E-value=11 Score=25.53 Aligned_cols=26 Identities=27% Similarity=0.363 Sum_probs=20.4
Q ss_pred HHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 54 IHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 54 L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+.+.| ..+|+.+||++.|+++ ..+++
T Consensus 24 f~~~G~~~~ti~~Ia~~agvsk---~t~Y~ 50 (213)
T PRK09975 24 FALRGVSNTTLNDIADAANVTR---GAIYW 50 (213)
T ss_pred HHHcCcccCCHHHHHHHcCCCH---HHHHH
Confidence 44445 6799999999999988 66665
No 149
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=63.11 E-value=9.6 Score=24.45 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
...+|..|||+.+|+++ ..+.|.|.-
T Consensus 69 ~pd~tl~Ela~~l~Vs~---~ti~~~Lkr 94 (119)
T PF01710_consen 69 NPDATLRELAERLGVSP---STIWRALKR 94 (119)
T ss_pred CCCcCHHHHHHHcCCCH---HHHHHHHHH
Confidence 47889999999999988 888887753
No 150
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=62.92 E-value=11 Score=20.94 Aligned_cols=34 Identities=12% Similarity=0.280 Sum_probs=22.4
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
-++.|.+.+. .|+ +..+||...|+.. ..+..+++
T Consensus 11 eK~~iI~~~e--~g~-s~~~ia~~fgv~~---sTv~~I~K 44 (53)
T PF04218_consen 11 EKLEIIKRLE--EGE-SKRDIAREFGVSR---STVSTILK 44 (53)
T ss_dssp HHHHHHHHHH--CTT--HHHHHHHHT--C---CHHHHHHH
T ss_pred HHHHHHHHHH--cCC-CHHHHHHHhCCCH---HHHHHHHH
Confidence 3455556555 355 9999999999998 77877764
No 151
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=62.52 E-value=8.1 Score=29.58 Aligned_cols=25 Identities=24% Similarity=0.615 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.|.|+.|||..++..+ ..+.|+.|
T Consensus 234 e~plsl~~LA~~~~~S~---R~leRlF~ 258 (328)
T COG4977 234 EEPLSLEELADRAGLSR---RQLERLFR 258 (328)
T ss_pred cCCcCHHHHHHHhCCCH---HHHHHHHH
Confidence 38999999999999999 88999876
No 152
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=62.19 E-value=11 Score=27.34 Aligned_cols=25 Identities=28% Similarity=0.521 Sum_probs=22.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.+.|+++||+.+|.++ ..+.|+.+.
T Consensus 20 ~~~~l~~lA~~~~~S~---~~l~r~F~~ 44 (289)
T PRK15121 20 QPLSLDNVAAKAGYSK---WHLQRMFKD 44 (289)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence 7899999999999999 889998763
No 153
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=62.16 E-value=7.3 Score=28.83 Aligned_cols=37 Identities=19% Similarity=0.293 Sum_probs=28.7
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+..|.+.|.+ +.+.+..|||+.++++. ..+.|.++.|
T Consensus 6 ~~~il~~L~~-~~~~s~~~LA~~lgvsr---~tV~~~l~~L 42 (319)
T PRK11886 6 MLQLLSLLAD-GDFHSGEQLGEELGISR---AAIWKHIQTL 42 (319)
T ss_pred HHHHHHHHHc-CCCcCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 4456777775 47899999999999988 7777776643
No 154
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=61.70 E-value=6.3 Score=26.46 Aligned_cols=25 Identities=12% Similarity=0.181 Sum_probs=22.0
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
-|+|-.|||..+|+.+ +.+.|+|+-
T Consensus 148 ~~~t~~~iA~~lG~tr---etvsR~l~~ 172 (202)
T PRK13918 148 IYATHDELAAAVGSVR---ETVTKVIGE 172 (202)
T ss_pred ecCCHHHHHHHhCccH---HHHHHHHHH
Confidence 3679999999999999 889998864
No 155
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=61.60 E-value=5.9 Score=27.73 Aligned_cols=26 Identities=27% Similarity=0.401 Sum_probs=22.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
-++|-.|||+.+|+.+ +.+.|+++-|
T Consensus 178 i~lt~~~IA~~lGisr---etlsR~L~~L 203 (230)
T PRK09391 178 LPMSRRDIADYLGLTI---ETVSRALSQL 203 (230)
T ss_pred ecCCHHHHHHHHCCCH---HHHHHHHHHH
Confidence 3678899999999999 9999998743
No 156
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=61.37 E-value=5.5 Score=22.99 Aligned_cols=43 Identities=14% Similarity=0.236 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 28 QVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 28 ~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
.+.+-.||-... .|++.|.+. |..|+.+|++.++.++ ..+..-
T Consensus 5 ~ii~~~fG~~~~---------~V~~~Ll~~-G~ltl~~i~~~t~l~~---~~Vk~~ 47 (62)
T PF08221_consen 5 LIIEEHFGEIVA---------KVGEVLLSR-GRLTLREIVRRTGLSP---KQVKKA 47 (62)
T ss_dssp HHHHHHHHHHHH---------HHHHHHHHC--SEEHHHHHHHHT--H---HHHHHH
T ss_pred HHHHHHcChHHH---------HHHHHHHHc-CCcCHHHHHHHhCCCH---HHHHHH
Confidence 344445555544 356677664 7999999999999887 545443
No 157
>PRK15340 transcriptional regulator InvF; Provisional
Probab=61.36 E-value=21 Score=25.74 Aligned_cols=36 Identities=8% Similarity=0.098 Sum_probs=28.0
Q ss_pred HhCchHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 47 ELGIPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 47 eLgI~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
--|+...|-.+ ..+.|+++||+.+|+++ ..+.|+.|
T Consensus 111 ~y~l~~~Ll~~~~~~~sleeLA~~~gvS~---r~f~RlFk 147 (216)
T PRK15340 111 SYWLVGYLLAQSTSGNTMRMLGEDYGVSY---THFRRLCS 147 (216)
T ss_pred HHHHHHHHHhCccCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 34555555443 38889999999999999 99999876
No 158
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=61.13 E-value=11 Score=27.77 Aligned_cols=33 Identities=12% Similarity=0.336 Sum_probs=25.6
Q ss_pred chHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.+.|.++ ..+.|+++||+.+|+++ ..+.|+++
T Consensus 196 ~~~~i~~~~~~~~tl~~lA~~~~~S~---~~l~r~Fk 229 (302)
T PRK10371 196 MLGFIAENYDQALTINDVAEHVKLNA---NYAMGIFQ 229 (302)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 33444443 37899999999999999 88988876
No 159
>PRK13502 transcriptional activator RhaR; Provisional
Probab=61.13 E-value=12 Score=26.62 Aligned_cols=34 Identities=9% Similarity=0.234 Sum_probs=26.7
Q ss_pred CchHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 49 GIPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 49 gI~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.+.|.++ ..+++++++|+.++++| ..|.|+.|
T Consensus 180 ~~~~~I~~~~~~~~~~~~lA~~~~iS~---~~L~r~fk 214 (282)
T PRK13502 180 KLITALANSLECPFALDAFCQQEQCSE---RVLRQQFR 214 (282)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 444555442 37899999999999999 99999876
No 160
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=61.13 E-value=9.8 Score=27.64 Aligned_cols=31 Identities=19% Similarity=0.487 Sum_probs=25.1
Q ss_pred HHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 53 VIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 53 ~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.|++. +...|+..||+..++.| +.++|||+.
T Consensus 21 ~L~~~~p~~~t~~~Lae~F~vsp---e~irrILks 52 (225)
T PF06413_consen 21 YLHKEDPEEWTVERLAESFKVSP---EAIRRILKS 52 (225)
T ss_pred HHHHhCccccCHHHHHhhCCCCH---HHHHHHHhc
Confidence 35543 25579999999999999 999999973
No 161
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=60.85 E-value=7.6 Score=28.32 Aligned_cols=31 Identities=16% Similarity=0.187 Sum_probs=24.9
Q ss_pred HHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 53 VIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 53 ~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.|-.. |+.|+.||++.+|++- .-++-+||-|
T Consensus 24 aLl~~-g~~tA~eis~~sgvP~---~kvY~vl~sL 54 (247)
T COG1378 24 ALLCL-GEATAKEISEASGVPR---PKVYDVLRSL 54 (247)
T ss_pred HHHHh-CCccHHHHHHHcCCCc---hhHHHHHHHH
Confidence 44433 8999999999999988 6688888754
No 162
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=59.78 E-value=9.7 Score=26.21 Aligned_cols=34 Identities=21% Similarity=0.368 Sum_probs=24.4
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|.+.+++..+..|..|||+.+++.+ ..+++-+++
T Consensus 167 Vl~~~~~g~~g~s~~eIa~~l~iS~---~Tv~~~~~~ 200 (225)
T PRK10046 167 VRKLFKEPGVQHTAETVAQALTISR---TTARRYLEY 200 (225)
T ss_pred HHHHHHcCCCCcCHHHHHHHhCccH---HHHHHHHHH
Confidence 4555664224689999999999988 767665554
No 163
>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=59.57 E-value=16 Score=19.15 Aligned_cols=22 Identities=23% Similarity=0.277 Sum_probs=16.6
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
+..|..|||+.+++++ ..+++.
T Consensus 14 ~~~s~~eia~~l~~s~---~tv~~~ 35 (57)
T cd06170 14 EGKTNKEIADILGISE---KTVKTH 35 (57)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHH
Confidence 3579999999999977 555443
No 164
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=59.49 E-value=12 Score=23.03 Aligned_cols=30 Identities=20% Similarity=0.355 Sum_probs=23.0
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
|=|.|+.+ |-.++.||+..+++++ +.++=+
T Consensus 7 lRd~l~~~-gr~s~~~Ls~~~~~p~---~~VeaM 36 (78)
T PRK15431 7 VRDLLALR-GRMEAAQISQTLNTPQ---PMINAM 36 (78)
T ss_pred HHHHHHHc-CcccHHHHHHHHCcCH---HHHHHH
Confidence 44677764 8999999999999988 655433
No 165
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=59.32 E-value=7.9 Score=28.02 Aligned_cols=32 Identities=19% Similarity=0.402 Sum_probs=24.9
Q ss_pred CchHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 49 GIPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 49 gI~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
.+++.|...+ .-+|..|||+++|+++ ..++|=
T Consensus 20 R~le~l~a~~v~rvsS~els~~~~vds---atIRrD 52 (211)
T COG2344 20 RVLERLHASGVERVSSKELSEALGVDS---ATIRRD 52 (211)
T ss_pred HHHHHHHHcCCceecHHHHHHHhCCCH---HHHhhh
Confidence 4566676655 6679999999999999 777663
No 166
>PRK00767 transcriptional regulator BetI; Validated
Probab=58.87 E-value=14 Score=24.51 Aligned_cols=26 Identities=27% Similarity=0.318 Sum_probs=20.3
Q ss_pred HHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 54 IHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 54 L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+.+.| ...|..+||+++|+.. ..+++
T Consensus 22 f~~~G~~~~s~~~Ia~~aGvs~---gslY~ 48 (197)
T PRK00767 22 IGEVGLLDATIAQIARRAGVST---GIISH 48 (197)
T ss_pred HHHcCcccCCHHHHHHHhCCCH---HHHHH
Confidence 55555 7789999999999987 55554
No 167
>PF13551 HTH_29: Winged helix-turn helix
Probab=58.84 E-value=14 Score=22.26 Aligned_cols=21 Identities=29% Similarity=0.567 Sum_probs=19.0
Q ss_pred CHHHHHHhcCCCCCChhhHHHHHh
Q 041968 62 TLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 62 S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|..++|..+|+++ ..++|.++
T Consensus 14 ~~~~ia~~lg~s~---~Tv~r~~~ 34 (112)
T PF13551_consen 14 TIAEIARRLGISR---RTVYRWLK 34 (112)
T ss_pred cHHHHHHHHCcCH---HHHHHHHH
Confidence 7999999999999 88988875
No 168
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=58.70 E-value=12 Score=27.47 Aligned_cols=33 Identities=15% Similarity=0.457 Sum_probs=26.0
Q ss_pred chHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.+.+..+ .++.|+++||+.++.++ ..+.|.++
T Consensus 139 v~~~I~~~~~~~~tl~~LA~~~gmS~---s~l~R~FK 172 (253)
T PRK09940 139 VRNIVNMKLAHPWKLKDICDCLYISE---SLLKKKLK 172 (253)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 34455432 38999999999999999 88999876
No 169
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=58.51 E-value=14 Score=27.53 Aligned_cols=33 Identities=18% Similarity=0.344 Sum_probs=26.1
Q ss_pred chHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|.+.|..+ ..+.|+++||+.+|.++ ..+.|.++
T Consensus 186 i~~~I~~~~~~~~sl~~lA~~~gmS~---stl~R~Fk 219 (291)
T PRK15186 186 IYNIIISDISRKWALKDISDSLYMSC---STLKRKLK 219 (291)
T ss_pred HHHHHHhCccCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 34445443 38999999999999999 88999876
No 170
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=58.44 E-value=10 Score=27.18 Aligned_cols=33 Identities=21% Similarity=0.319 Sum_probs=25.1
Q ss_pred chHHHHhC-CCC-CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKH-GQP-MTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~-~gp-~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.+.|.++ ..| +|+++||+.+|+++ ..|.|+.+
T Consensus 202 ~~~~I~~~l~~~~ls~~~lA~~~giS~---r~L~r~Fk 236 (302)
T PRK09685 202 VVALIDQSIQEEILRPEWIAGELGISV---RSLYRLFA 236 (302)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 34445442 255 89999999999999 88998875
No 171
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=58.44 E-value=7.6 Score=28.13 Aligned_cols=34 Identities=12% Similarity=0.306 Sum_probs=28.2
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.|.+.|.+. |.+++.|||+.+++.+ ..++|=|+.
T Consensus 9 ~Il~~l~~~-g~v~v~eLa~~~~VS~---~TIRRDL~~ 42 (253)
T COG1349 9 KILELLKEK-GKVSVEELAELFGVSE---MTIRRDLNE 42 (253)
T ss_pred HHHHHHHHc-CcEEHHHHHHHhCCCH---HHHHHhHHH
Confidence 467778764 8999999999999999 888885543
No 172
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=58.37 E-value=9 Score=29.64 Aligned_cols=27 Identities=15% Similarity=0.256 Sum_probs=23.0
Q ss_pred CCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 57 HGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 57 ~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.++|.|..||++++++++ +.+++++..
T Consensus 307 ~g~~~t~~~La~~l~~~~---~~v~~iL~~ 333 (412)
T PRK04214 307 HGKALDVDEIRRLEPMGY---DELGELLCE 333 (412)
T ss_pred cCCCCCHHHHHHHhCCCH---HHHHHHHHH
Confidence 468999999999999999 878887754
No 173
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=58.34 E-value=13 Score=26.37 Aligned_cols=25 Identities=24% Similarity=0.371 Sum_probs=22.6
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..++|++++|+.+++++ ..|.|+.|
T Consensus 200 ~~~~sl~~lA~~~~~S~---~~l~r~Fk 224 (287)
T TIGR02297 200 KQHLRLPEYADRLGISE---SRLNDICR 224 (287)
T ss_pred ccCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 37899999999999999 88988876
No 174
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=58.14 E-value=12 Score=19.86 Aligned_cols=23 Identities=13% Similarity=0.157 Sum_probs=17.4
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
..+|..|+|..+|+++ ..+.++.
T Consensus 14 ~gltq~~lA~~~gvs~---~~vs~~e 36 (58)
T TIGR03070 14 LGLTQADLADLAGVGL---RFIRDVE 36 (58)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHH
Confidence 5678889999998877 6666654
No 175
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=58.13 E-value=14 Score=27.10 Aligned_cols=31 Identities=19% Similarity=0.380 Sum_probs=24.7
Q ss_pred HHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 52 DVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 52 d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.|.++ ..+.|+++||+.+|.++ ..+.|+++
T Consensus 225 ~~i~~~~~~~~sl~~lA~~~~~S~---~~l~r~fk 256 (322)
T PRK09393 225 DWMRAHLAEPHTVASLAARAAMSP---RTFLRRFE 256 (322)
T ss_pred HHHHhccCCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 334433 37899999999999999 88998876
No 176
>PRK15044 transcriptional regulator SirC; Provisional
Probab=57.94 E-value=22 Score=26.98 Aligned_cols=36 Identities=11% Similarity=0.200 Sum_probs=29.0
Q ss_pred HhCchHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 47 ELGIPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 47 eLgI~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.-++.+.|..+ +.+.|+.|||+.+|.++ ..|.|.++
T Consensus 194 ~~kV~~~I~~nl~~~~SLeeLA~~lgmS~---~tL~R~Fk 230 (295)
T PRK15044 194 KEKVYNIIISDLTRKWSQAEVAGKLFMSV---SSLKRKLA 230 (295)
T ss_pred HHHHHHHHHhCcccCCCHHHHHHHhCCCH---HHHHHHHH
Confidence 34566766653 38999999999999999 88999876
No 177
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=57.75 E-value=17 Score=22.37 Aligned_cols=40 Identities=35% Similarity=0.349 Sum_probs=28.2
Q ss_pred HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.+|++.|++= +. .+.|+...+||+.++.+| ..++..|..|
T Consensus 8 ~IL~alV~~Y----~~-~~~PVgSk~ia~~l~~s~---aTIRN~M~~L 47 (78)
T PF03444_consen 8 EILKALVELY----IE-TGEPVGSKTIAEELGRSP---ATIRNEMADL 47 (78)
T ss_pred HHHHHHHHHH----Hh-cCCCcCHHHHHHHHCCCh---HHHHHHHHHH
Confidence 3455555532 33 369999999999999988 7777776543
No 178
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.70 E-value=10 Score=24.14 Aligned_cols=23 Identities=22% Similarity=0.455 Sum_probs=20.8
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
.++|.++||..++..+ .-++++|
T Consensus 22 ~~LS~~~iA~~Ln~t~---~~lekil 44 (97)
T COG4367 22 CPLSDEEIATALNWTE---VKLEKIL 44 (97)
T ss_pred ccccHHHHHHHhCCCH---HHHHHHH
Confidence 7899999999999999 7788887
No 179
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=57.38 E-value=15 Score=27.40 Aligned_cols=34 Identities=26% Similarity=0.396 Sum_probs=27.1
Q ss_pred CchHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 49 GIPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 49 gI~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.+.|.++ ..+.|++++|..+|+++ ..+.|+++
T Consensus 146 ~v~~yI~~~~~~~lsl~~lA~~~g~S~---~~L~R~Fk 180 (274)
T PRK09978 146 RVCTVINNNIAHEWTLARIASELLMSP---SLLKKKLR 180 (274)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 345555543 37999999999999999 89999876
No 180
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=57.17 E-value=10 Score=28.16 Aligned_cols=35 Identities=20% Similarity=0.247 Sum_probs=26.8
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.|++.|...+|-++..+||+++|+.+ ..+.+-+|.
T Consensus 187 ~IL~~L~~~egrlse~eLAerlGVSR---s~ireAlrk 221 (251)
T TIGR02787 187 HIFEELDGNEGLLVASKIADRVGITR---SVIVNALRK 221 (251)
T ss_pred HHHHHhccccccccHHHHHHHHCCCH---HHHHHHHHH
Confidence 57788875448999999999999988 655555543
No 181
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=57.12 E-value=11 Score=27.65 Aligned_cols=34 Identities=24% Similarity=0.412 Sum_probs=25.5
Q ss_pred hHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 51 PDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 51 ~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
-+.+...+.+.|+.|+|+.+|++. ...+|-|-+|
T Consensus 164 ~~~~~~~~~~~Taeela~~~giSR---vTaRRYLeyl 197 (224)
T COG4565 164 REALKEPDQELTAEELAQALGISR---VTARRYLEYL 197 (224)
T ss_pred HHHHhCcCCccCHHHHHHHhCccH---HHHHHHHHHH
Confidence 344553358999999999999988 7777766553
No 182
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=57.07 E-value=16 Score=24.69 Aligned_cols=26 Identities=23% Similarity=0.397 Sum_probs=20.2
Q ss_pred HHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 54 IHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 54 L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+.+.| ...|+.+||+..|+.+ ..+++
T Consensus 24 f~e~G~~~~t~~~Ia~~agvs~---~tlY~ 50 (215)
T PRK10668 24 FSQQGVSATSLADIAKAAGVTR---GAIYW 50 (215)
T ss_pred HHHcCcccCCHHHHHHHhCCCh---HHHHH
Confidence 45555 6789999999999988 55554
No 183
>PRK09480 slmA division inhibitor protein; Provisional
Probab=56.99 E-value=16 Score=24.16 Aligned_cols=22 Identities=18% Similarity=0.475 Sum_probs=18.2
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHH
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
|...|+.+||++.|+.+ ..+++
T Consensus 28 G~~~ti~~Ia~~agvs~---gt~Y~ 49 (194)
T PRK09480 28 GERITTAKLAARVGVSE---AALYR 49 (194)
T ss_pred CCccCHHHHHHHhCCCH---hHHHH
Confidence 47889999999999988 55554
No 184
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=56.93 E-value=4.1 Score=22.52 Aligned_cols=16 Identities=19% Similarity=0.449 Sum_probs=12.4
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
.++++.|||..+|+++
T Consensus 2 ~~i~V~elAk~l~v~~ 17 (54)
T PF04760_consen 2 EKIRVSELAKELGVPS 17 (54)
T ss_dssp -EE-TTHHHHHHSSSH
T ss_pred CceEHHHHHHHHCcCH
Confidence 3678899999999977
No 185
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=56.90 E-value=10 Score=27.33 Aligned_cols=26 Identities=15% Similarity=0.257 Sum_probs=22.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
..+|..|||+.+++++ ..+.|.++-|
T Consensus 20 ~~IS~~eLA~~L~iS~---~Tvsr~Lk~L 45 (217)
T PRK14165 20 VKISSSEFANHTGTSS---KTAARILKQL 45 (217)
T ss_pred CCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence 5689999999999999 8888887643
No 186
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=56.67 E-value=19 Score=22.21 Aligned_cols=22 Identities=27% Similarity=0.339 Sum_probs=18.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
..+|..+||++.|+++ ..++|-
T Consensus 31 ~~~t~~~Ia~~agvs~---~~~Y~~ 52 (201)
T COG1309 31 AATTVDEIAKAAGVSK---GTLYRH 52 (201)
T ss_pred CCCCHHHHHHHhCCCc---chhHHH
Confidence 6789999999999988 666653
No 187
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=56.53 E-value=3.6 Score=28.28 Aligned_cols=24 Identities=25% Similarity=0.623 Sum_probs=0.0
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|+|..|+|..+|+++ ..+.|..+
T Consensus 48 ~PLt~~~iA~~lgl~~---STVSRav~ 71 (160)
T PF04552_consen 48 KPLTMKDIADELGLHE---STVSRAVK 71 (160)
T ss_dssp ---------------------------
T ss_pred cCCCHHHHHHHhCCCH---hHHHHHHc
Confidence 7999999999999999 88888764
No 188
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=56.43 E-value=7.8 Score=23.04 Aligned_cols=27 Identities=7% Similarity=0.166 Sum_probs=18.8
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.++.+..+|+..++++. ..+.+.+..|
T Consensus 17 ~~~~~~t~i~~~~~L~~---~~~~~yL~~L 43 (77)
T PF14947_consen 17 KGGAKKTEIMYKANLNY---STLKKYLKEL 43 (77)
T ss_dssp TT-B-HHHHHTTST--H---HHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence 48999999999999998 7787777643
No 189
>PRK15185 transcriptional regulator HilD; Provisional
Probab=56.30 E-value=16 Score=27.85 Aligned_cols=34 Identities=12% Similarity=0.275 Sum_probs=27.5
Q ss_pred CchHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 49 GIPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 49 gI~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.+.|..+. .+.|++++|+.++.++ ..|.|.++
T Consensus 210 rV~~~I~~n~~~~~SledLA~~lgmS~---~tL~R~FK 244 (309)
T PRK15185 210 RVYNIISSSPSRQWKLTDVADHIFMST---STLKRKLA 244 (309)
T ss_pred HHHHHHHhCccCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 3556665543 8899999999999999 88998875
No 190
>PHA00542 putative Cro-like protein
Probab=56.04 E-value=13 Score=22.46 Aligned_cols=24 Identities=29% Similarity=0.343 Sum_probs=19.4
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..+|..|+|+.+|+++ ..+.|+.+
T Consensus 30 ~glTq~elA~~lgIs~---~tIsr~e~ 53 (82)
T PHA00542 30 AGWSQEQIADATDVSQ---PTICRIYS 53 (82)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHc
Confidence 5689999999999988 77777654
No 191
>PRK09954 putative kinase; Provisional
Probab=55.68 E-value=12 Score=27.79 Aligned_cols=35 Identities=17% Similarity=0.289 Sum_probs=27.2
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+..|.+.|.++ +++|..|||+.+++.. ..+.+.++
T Consensus 5 ~~~il~~l~~~-~~~s~~~la~~l~~s~---~~v~~~i~ 39 (362)
T PRK09954 5 EKEILAILRRN-PLIQQNEIADILQISR---SRVAAHIM 39 (362)
T ss_pred HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 44577788875 6999999999999987 66666554
No 192
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=55.51 E-value=11 Score=24.33 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=21.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.++|++|||..+.+.+ ....++|+-
T Consensus 18 ~~vtl~elA~~l~cS~---Rn~r~lLkk 42 (115)
T PF12793_consen 18 VEVTLDELAELLFCSR---RNARTLLKK 42 (115)
T ss_pred cceeHHHHHHHhCCCH---HHHHHHHHH
Confidence 6789999999999999 888888763
No 193
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=55.46 E-value=15 Score=24.50 Aligned_cols=26 Identities=23% Similarity=0.332 Sum_probs=19.8
Q ss_pred HHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 54 IHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 54 L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+.+.| ...|+.+||++.|+++ ..+++
T Consensus 21 f~e~G~~~tSi~~Ia~~aGvsk---~~lY~ 47 (192)
T PRK14996 21 ALAEGFAAMTVRRIASEAQVAA---GQVHH 47 (192)
T ss_pred HHhcChhhccHHHHHHHhCCCc---HHHHH
Confidence 44445 6789999999999988 65654
No 194
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=55.23 E-value=24 Score=21.18 Aligned_cols=26 Identities=31% Similarity=0.484 Sum_probs=21.9
Q ss_pred CchHHHHhCC-CCCCHHHHHHhcC-CCC
Q 041968 49 GIPDVIHKHG-QPMTLSQIASALD-IQK 74 (87)
Q Consensus 49 gI~d~L~~~~-gp~S~~ELA~~~~-~~~ 74 (87)
.+.+.|.+.+ .|+|.+||...++ .+.
T Consensus 13 ~aV~ymK~r~~~Plt~~EIl~~ls~~d~ 40 (75)
T cd07977 13 KIVDYMKKRHQHPLTLDEILDYLSLLDI 40 (75)
T ss_pred HHHHHHHhcCCCCccHHHHHHHHhccCc
Confidence 3567788878 9999999999999 766
No 195
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=55.14 E-value=15 Score=22.21 Aligned_cols=25 Identities=20% Similarity=0.218 Sum_probs=20.4
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
...|..|||+.+|+++ ..+...++.
T Consensus 31 eGlS~kEIAe~LGIS~---~TVk~~l~~ 55 (73)
T TIGR03879 31 AGKTASEIAEELGRTE---QTVRNHLKG 55 (73)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHhc
Confidence 5689999999999998 777766653
No 196
>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=54.99 E-value=14 Score=19.22 Aligned_cols=20 Identities=10% Similarity=0.245 Sum_probs=15.8
Q ss_pred CCHHHHHHhcCCCCCChhhHHHH
Q 041968 61 MTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 61 ~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
.|+.|+|+.+|+++ ..+.+.
T Consensus 1 ~~~~e~a~~~gv~~---~tlr~~ 20 (49)
T cd04761 1 YTIGELAKLTGVSP---STLRYY 20 (49)
T ss_pred CcHHHHHHHHCcCH---HHHHHH
Confidence 37889999999988 766654
No 197
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein 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. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=54.88 E-value=7.9 Score=23.92 Aligned_cols=38 Identities=11% Similarity=0.301 Sum_probs=24.7
Q ss_pred HHhCchHHHHh---CCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 46 VELGIPDVIHK---HGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 46 veLgI~d~L~~---~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
+.-.|++.|.. ....+++.+|++.++.+. .-++-.++.
T Consensus 48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~---~~v~~al~~ 88 (102)
T PF08784_consen 48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSE---NEVRKALDF 88 (102)
T ss_dssp HHHHHHHHHHC----TTTEEHHHHHHHSTS-H---HHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCCcccHHHHHHHhCcCH---HHHHHHHHH
Confidence 34456666654 236799999999998877 556555544
No 198
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=54.76 E-value=14 Score=23.01 Aligned_cols=37 Identities=16% Similarity=0.242 Sum_probs=28.6
Q ss_pred HHHHhCchH-HHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 44 CAVELGIPD-VIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 44 aaveLgI~d-~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.+-.+.|+. .|. +..|=.||++.+|+.. -.+.|+=|.
T Consensus 35 l~~R~~va~~lL~---~g~syreIa~~tgvS~---aTItRvsr~ 72 (87)
T PF01371_consen 35 LAQRWQVAKELLD---EGKSYREIAEETGVSI---ATITRVSRC 72 (87)
T ss_dssp HHHHHHHHHHHHH---TTSSHHHHHHHHTSTH---HHHHHHHHH
T ss_pred HHHHHHHHHHHHH---CCCCHHHHHHHhCCCH---HHHHHHHHH
Confidence 456778888 666 5689999999999988 666666554
No 199
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=54.50 E-value=12 Score=20.72 Aligned_cols=26 Identities=31% Similarity=0.397 Sum_probs=19.9
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
-|..|...+. ...|..|||..+++.+
T Consensus 7 ~E~~vl~~l~---~G~~~~eIA~~l~is~ 32 (58)
T PF00196_consen 7 RELEVLRLLA---QGMSNKEIAEELGISE 32 (58)
T ss_dssp HHHHHHHHHH---TTS-HHHHHHHHTSHH
T ss_pred HHHHHHHHHH---hcCCcchhHHhcCcch
Confidence 4566777777 4579999999999987
No 200
>PRK04217 hypothetical protein; Provisional
Probab=54.48 E-value=13 Score=24.07 Aligned_cols=24 Identities=8% Similarity=0.257 Sum_probs=19.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
...|..|||+.+|++. ..+++.++
T Consensus 57 eGlS~~EIAk~LGIS~---sTV~r~L~ 80 (110)
T PRK04217 57 EGLTQEEAGKRMGVSR---GTVWRALT 80 (110)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 4569999999999998 77777664
No 201
>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=54.47 E-value=16 Score=18.42 Aligned_cols=24 Identities=17% Similarity=0.414 Sum_probs=19.0
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
...|..+||..+|++. ..++|.++
T Consensus 25 ~~~~~~~ia~~~~~s~---~~i~~~~~ 48 (55)
T cd06171 25 EGLSYEEIAEILGISR---STVRQRLH 48 (55)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 4579999999999988 76766543
No 202
>PRK13501 transcriptional activator RhaR; Provisional
Probab=54.47 E-value=16 Score=26.25 Aligned_cols=32 Identities=9% Similarity=0.327 Sum_probs=25.5
Q ss_pred hHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 51 PDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 51 ~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.|.++ ..++|++|+|+.++.++ ..|.|+.+
T Consensus 182 ~~~I~~~~~e~~sl~~lA~~~~lS~---~~l~r~Fk 214 (290)
T PRK13501 182 MSALQQSLGAYFDMADFCHKNQLVE---RSLKQLFR 214 (290)
T ss_pred HHHHHHhhccCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 4444432 37899999999999999 98999876
No 203
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=54.40 E-value=10 Score=22.60 Aligned_cols=25 Identities=12% Similarity=0.260 Sum_probs=19.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...+++||++.||++..-++++.+|
T Consensus 43 ~Ga~~~el~~~CgL~~aEAeLl~~L 67 (70)
T PF10975_consen 43 QGASVEELMEECGLSRAEAELLLSL 67 (70)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHH
Confidence 3489999999999977555777665
No 204
>PRK00118 putative DNA-binding protein; Validated
Probab=54.26 E-value=14 Score=23.78 Aligned_cols=23 Identities=13% Similarity=0.388 Sum_probs=19.2
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
+..|..|||+.+|+++ ..+++.+
T Consensus 32 eg~S~~EIAe~lGIS~---~TV~r~L 54 (104)
T PRK00118 32 DDYSLGEIAEEFNVSR---QAVYDNI 54 (104)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHH
Confidence 5789999999999998 7666654
No 205
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=53.92 E-value=21 Score=25.42 Aligned_cols=30 Identities=20% Similarity=0.422 Sum_probs=24.9
Q ss_pred HHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 53 VIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 53 ~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|.++..+.+.++||.++|.+| ..+.|+.+
T Consensus 90 ~ie~~~~~~~le~la~~lg~sp---~~~~R~FK 119 (187)
T COG2169 90 LIEQNPEKRWLEELADELGVSP---STLHRLFK 119 (187)
T ss_pred HHHcCCCcccHHHHHHHhCCCh---HHHHHHHH
Confidence 3544458889999999999999 99999875
No 206
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=53.66 E-value=14 Score=23.23 Aligned_cols=24 Identities=21% Similarity=0.419 Sum_probs=20.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..+|.+++|..+++++ .-+.++|-
T Consensus 22 ~~ls~~~ia~dL~~s~---~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSP---EHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHHc
Confidence 4689999999999999 77888874
No 207
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=53.66 E-value=11 Score=30.59 Aligned_cols=38 Identities=24% Similarity=0.319 Sum_probs=29.7
Q ss_pred HhCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 47 ELGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 47 eLgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
|-.|++.|-++. .-.|+.|||+++++++ ..+.|+.|-|
T Consensus 358 E~~IA~yIl~n~~~v~~~si~eLA~~~~vS~---aTV~Rf~kkL 398 (638)
T PRK14101 358 ERRVADLALNHPRSIINDPIVDIARKADVSQ---PTVIRFCRSL 398 (638)
T ss_pred HHHHHHHHHhCHHHHHhccHHHHHHHhCCCH---HHHHHHHHHh
Confidence 556666665543 5679999999999999 8899998854
No 208
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=53.56 E-value=18 Score=24.49 Aligned_cols=34 Identities=15% Similarity=0.264 Sum_probs=28.7
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
--+|.+.+..|.++..|+|..+++-+ ..|.+.||
T Consensus 36 ~f~D~v~~~~gli~~re~AK~lkige---~~l~~~L~ 69 (135)
T COG3645 36 EFADAVVEASGLILFRELAKLLKIGE---NRLFAWLR 69 (135)
T ss_pred HHHHHHhcCccceeHHHHHHHHccCH---HHHHHHHH
Confidence 34788888779999999999999887 66877776
No 209
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=53.39 E-value=12 Score=20.94 Aligned_cols=24 Identities=21% Similarity=0.439 Sum_probs=17.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..+|..++|..+|+++ ..+.|+.+
T Consensus 13 ~gls~~~lA~~~g~s~---s~v~~iE~ 36 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQ---STVSRIER 36 (64)
T ss_dssp HTS-HHHHHHHHTS-H---HHHHHHHT
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHC
Confidence 4589999999999988 77777653
No 210
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=53.22 E-value=20 Score=25.07 Aligned_cols=27 Identities=15% Similarity=0.330 Sum_probs=20.4
Q ss_pred HHhCC-CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 54 IHKHG-QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 54 L~~~~-gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
+.+.| ..+|..+||+++|+.+ ..+|+-
T Consensus 17 ~~e~G~~~lsmr~lA~~lgv~~---~slY~h 44 (205)
T PRK13756 17 LNEVGIEGLTTRKLAQKLGVEQ---PTLYWH 44 (205)
T ss_pred HHHcCcccCCHHHHHHHhCCCc---hHHHHH
Confidence 44434 6789999999999988 666653
No 211
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=53.21 E-value=14 Score=19.85 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=13.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...|..|||+.+|+++ ..+.+.
T Consensus 25 ~g~s~~eIa~~l~~s~---~~v~~~ 46 (54)
T PF08281_consen 25 QGMSYAEIAEILGISE---STVKRR 46 (54)
T ss_dssp S---HHHHHHHCTS-H---HHHHHH
T ss_pred HCcCHHHHHHHHCcCH---HHHHHH
Confidence 5689999999999988 544433
No 212
>PRK10870 transcriptional repressor MprA; Provisional
Probab=53.07 E-value=15 Score=25.09 Aligned_cols=30 Identities=13% Similarity=0.288 Sum_probs=22.7
Q ss_pred HHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 53 VIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 53 ~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|... ++++|..|||..+++++ ..+.|++.
T Consensus 63 ~L~~~~~~~it~~eLa~~l~l~~---~tvsr~v~ 93 (176)
T PRK10870 63 TLESQENHSIQPSELSCALGSSR---TNATRIAD 93 (176)
T ss_pred HHhcCCCCCcCHHHHHHHHCCCH---HHHHHHHH
Confidence 34432 47899999999999998 77777654
No 213
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=52.71 E-value=15 Score=26.51 Aligned_cols=25 Identities=28% Similarity=0.477 Sum_probs=19.9
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+++.++.++|+.+|.++ ..+.++++
T Consensus 253 ~~~~~~~~ia~~lg~~~---~~~~~~~e 277 (305)
T TIGR00635 253 GGPVGLKTLAAALGEDA---DTIEDVYE 277 (305)
T ss_pred CCcccHHHHHHHhCCCc---chHHHhhh
Confidence 57899999999999998 55555444
No 214
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=52.35 E-value=21 Score=25.30 Aligned_cols=40 Identities=28% Similarity=0.481 Sum_probs=29.9
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCCh-hhHHHHHh
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKA-HCIQRLMR 85 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~-~~L~RlLR 85 (87)
.+-.|.|.|.+.|...|+-+||.++|++.... ..||+|.|
T Consensus 5 ~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~ 45 (183)
T PHA02701 5 CASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLE 45 (183)
T ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhh
Confidence 45678899988764699999999999966221 35777765
No 215
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=51.88 E-value=16 Score=20.50 Aligned_cols=21 Identities=10% Similarity=0.203 Sum_probs=16.4
Q ss_pred CCHHHHHHhcCCCCCChhhHHHHH
Q 041968 61 MTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 61 ~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
.|+.|+|+.+|+++ ..|.+..
T Consensus 1 ~s~~eva~~~gvs~---~tlr~~~ 21 (70)
T smart00422 1 YTIGEVAKLAGVSV---RTLRYYE 21 (70)
T ss_pred CCHHHHHHHHCcCH---HHHHHHH
Confidence 37889999999988 7776654
No 216
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=51.16 E-value=28 Score=22.80 Aligned_cols=25 Identities=20% Similarity=0.432 Sum_probs=19.9
Q ss_pred chHHHHhCC-CCCCHHHHHHhcCCCC
Q 041968 50 IPDVIHKHG-QPMTLSQIASALDIQK 74 (87)
Q Consensus 50 I~d~L~~~~-gp~S~~ELA~~~~~~~ 74 (87)
.++.+.+.+ ..+|+.||+++.|++.
T Consensus 12 ~~~Ll~~k~~~~ITV~~I~~~AgvsR 37 (176)
T TIGR02366 12 FKDLMEVQAFSKISVSDIMSTAQIRR 37 (176)
T ss_pred HHHHHHHCCCccCCHHHHHHHhCCCH
Confidence 345566656 8899999999999976
No 217
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=51.05 E-value=21 Score=24.42 Aligned_cols=26 Identities=23% Similarity=0.291 Sum_probs=20.0
Q ss_pred HHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 54 IHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 54 L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+.+.| ...|+.+||+++|+++ ..+++
T Consensus 31 f~e~Gy~~~s~~dIA~~aGvs~---gtiY~ 57 (212)
T PRK15008 31 FSQFGFHGTRLEQIAELAGVSK---TNLLY 57 (212)
T ss_pred HHHhCcccCCHHHHHHHhCcCH---HHHHH
Confidence 45555 6789999999999988 65554
No 218
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=50.94 E-value=18 Score=21.36 Aligned_cols=24 Identities=8% Similarity=0.256 Sum_probs=19.1
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
|.+.|.. .++.|+.||++.++.+.
T Consensus 13 Vw~~L~~-~~~~s~~el~k~~~l~~ 36 (65)
T PF10771_consen 13 VWQLLNE-NGEWSVSELKKATGLSD 36 (65)
T ss_dssp HHHHHCC-SSSEEHHHHHHHCT-SC
T ss_pred HHHHHhh-CCCcCHHHHHHHhCcCH
Confidence 5667775 48999999999999866
No 219
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=50.72 E-value=12 Score=24.33 Aligned_cols=38 Identities=24% Similarity=0.246 Sum_probs=29.0
Q ss_pred HhCchHHHHhC---CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 47 ELGIPDVIHKH---GQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 47 eLgI~d~L~~~---~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
+=.++|.+.+. ..-+|...||++.|++- ..-+++||.|
T Consensus 43 dee~~~ki~KEV~~~r~VTpy~la~r~gI~~---SvAr~vLR~L 83 (107)
T COG4901 43 DEELLDKIRKEVPRERVVTPYVLASRYGING---SVARIVLRHL 83 (107)
T ss_pred cHHHHHHHHHhcccceeecHHHHHHHhccch---HHHHHHHHHH
Confidence 33456655442 27789999999999998 8888899876
No 220
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=50.66 E-value=21 Score=27.23 Aligned_cols=25 Identities=24% Similarity=0.529 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.+.|+.+||+.+|.++ ..+.|+.+
T Consensus 97 ~~~lsl~eLA~~lG~S~---~~L~R~Fk 121 (353)
T PRK15435 97 ETPVTLEALADQVAMSP---FHLHRLFK 121 (353)
T ss_pred CCCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 47899999999999998 88988875
No 221
>PRK12423 LexA repressor; Provisional
Probab=50.64 E-value=22 Score=24.74 Aligned_cols=30 Identities=27% Similarity=0.504 Sum_probs=19.8
Q ss_pred HHhCCCCCCHHHHHHhcCC-CCCChhhHHHHHhc
Q 041968 54 IHKHGQPMTLSQIASALDI-QKNKAHCIQRLMRI 86 (87)
Q Consensus 54 L~~~~gp~S~~ELA~~~~~-~~~~~~~L~RlLR~ 86 (87)
+.+.+-+-|..|||+.+|+ .+ ..+++-|+.
T Consensus 19 i~~~g~~Ps~~eia~~~g~~s~---~~v~~~l~~ 49 (202)
T PRK12423 19 IAQAGQPPSLAEIAQAFGFASR---SVARKHVQA 49 (202)
T ss_pred HHHcCCCCCHHHHHHHhCCCCh---HHHHHHHHH
Confidence 3333445699999999995 66 555555543
No 222
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=50.59 E-value=19 Score=23.60 Aligned_cols=36 Identities=19% Similarity=0.194 Sum_probs=24.3
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcC----CCCCChhhHHHHHh
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALD----IQKNKAHCIQRLMR 85 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~----~~~~~~~~L~RlLR 85 (87)
.|+-|.++|.+. ++.|+.||.+.++ .+. ..+.++|+
T Consensus 5 ~E~~VM~vlW~~-~~~t~~eI~~~l~~~~~~~~---tTv~T~L~ 44 (130)
T TIGR02698 5 AEWEVMRVVWTL-GETTSRDIIRILAEKKDWSD---STIKTLLG 44 (130)
T ss_pred HHHHHHHHHHcC-CCCCHHHHHHHHhhccCCcH---HHHHHHHH
Confidence 466677888764 7899999777763 344 55555554
No 223
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=50.45 E-value=19 Score=21.73 Aligned_cols=24 Identities=29% Similarity=0.690 Sum_probs=21.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.++.++|..+|.++ ..|.|.++
T Consensus 35 ~~~~l~~la~~~g~S~---~~l~r~f~ 58 (127)
T COG2207 35 EPLTLEDLARRLGMSR---RTLSRLFK 58 (127)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 5689999999999999 88888876
No 224
>PRK13500 transcriptional activator RhaR; Provisional
Probab=50.07 E-value=22 Score=26.04 Aligned_cols=33 Identities=9% Similarity=0.276 Sum_probs=26.5
Q ss_pred chHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.+.|.++ ..++|+++||+.+++++ ..|.|+.|
T Consensus 211 i~~yI~~~~~e~isl~~lA~~~~iS~---~~L~r~FK 244 (312)
T PRK13500 211 LITRLAASLKSPFALDKFCDEASCSE---RVLRQQFR 244 (312)
T ss_pred HHHHHHHcccCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 44555543 37899999999999999 88998876
No 225
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=49.39 E-value=25 Score=23.32 Aligned_cols=24 Identities=17% Similarity=0.314 Sum_probs=18.6
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
++..|..+ ||.+..+|++.++++.
T Consensus 64 ~A~~L~~~-Gp~~~~~l~~~~~~~~ 87 (118)
T PF09929_consen 64 CAAALAEH-GPSRPADLRKATGVPK 87 (118)
T ss_pred HHHHHHHc-CCCCHHHHHHhcCCCh
Confidence 34456653 8999999999998765
No 226
>PRK10130 transcriptional regulator EutR; Provisional
Probab=48.70 E-value=22 Score=27.10 Aligned_cols=25 Identities=16% Similarity=0.477 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..|+|+.|||+.+++++ ..|.|..+
T Consensus 254 ~~~ltv~~lA~~~gvS~---r~L~r~Fk 278 (350)
T PRK10130 254 SEPVTVLDLCNQLHVSR---RTLQNAFH 278 (350)
T ss_pred cCCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 37899999999999999 88888775
No 227
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=48.45 E-value=26 Score=24.41 Aligned_cols=40 Identities=13% Similarity=0.252 Sum_probs=30.3
Q ss_pred HHHHHhCchHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 43 KCAVELGIPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 43 ~aaveLgI~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|.-....|.+.|.+.+ ..+|+.|||+..|++| ..++|=|+
T Consensus 14 r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~---~tirrDl~ 54 (213)
T PRK05472 14 RLPLYYRYLKELKEEGVERVSSKELAEALGVDS---AQIRKDLS 54 (213)
T ss_pred HhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCH---HHHHHHHH
Confidence 4555667778887643 3889999999999999 77777443
No 228
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=47.87 E-value=14 Score=25.54 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=20.8
Q ss_pred CCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 60 PMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 60 p~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|.|-.|||..+|+.+ +.+.|+++-
T Consensus 173 ~~t~~~iA~~lG~tr---etvsR~l~~ 196 (236)
T PRK09392 173 PYEKRVLASYLGMTP---ENLSRAFAA 196 (236)
T ss_pred eCCHHHHHHHhCCCh---hHHHHHHHH
Confidence 566789999999999 889998864
No 229
>PHA01976 helix-turn-helix protein
Probab=47.73 E-value=20 Score=19.96 Aligned_cols=23 Identities=4% Similarity=0.157 Sum_probs=17.5
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
..+|..|+|..+|+++ ..+.++.
T Consensus 14 ~glt~~~lA~~~gvs~---~~v~~~e 36 (67)
T PHA01976 14 RAWSAPELSRRAGVRH---SLIYDFE 36 (67)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHH
Confidence 5689999999999877 5565543
No 230
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=47.35 E-value=15 Score=28.84 Aligned_cols=24 Identities=29% Similarity=0.621 Sum_probs=21.8
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|+|..++|..+|+|+ ..+.|+.+
T Consensus 317 kPLtlkdiA~~lglhe---STVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGLHE---STISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCCCc---cchhhhhc
Confidence 8999999999999999 88888754
No 231
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=47.07 E-value=19 Score=25.28 Aligned_cols=18 Identities=22% Similarity=0.267 Sum_probs=14.1
Q ss_pred CCCCHHHHHHhcCCCCCC
Q 041968 59 QPMTLSQIASALDIQKNK 76 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~ 76 (87)
.-.|-.|||-.+|++|.+
T Consensus 69 eikTW~~La~~LGVepp~ 86 (175)
T PF09441_consen 69 EIKTWAQLALELGVEPPD 86 (175)
T ss_pred hHhHHHHHHHHhCCCCCC
Confidence 566888999999987744
No 232
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=46.76 E-value=33 Score=23.39 Aligned_cols=26 Identities=15% Similarity=0.273 Sum_probs=20.1
Q ss_pred HHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 54 IHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 54 L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+.+.| ..+|+.+||++.|+++ ..+++
T Consensus 25 ~~~~G~~~~si~~IA~~Agvs~---~t~Y~ 51 (203)
T PRK11202 25 SAERSFSSLSLREVAREAGIAP---TSFYR 51 (203)
T ss_pred HhcCCcccCCHHHHHHHhCCCc---chHHH
Confidence 34445 6789999999999988 66665
No 233
>PF13730 HTH_36: Helix-turn-helix domain
Probab=46.60 E-value=15 Score=19.80 Aligned_cols=23 Identities=22% Similarity=0.452 Sum_probs=19.2
Q ss_pred CHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 62 TLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 62 S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
|.+.||..+|+.. ..+.|.++-|
T Consensus 27 S~~~la~~~g~s~---~Tv~~~i~~L 49 (55)
T PF13730_consen 27 SQETLAKDLGVSR---RTVQRAIKEL 49 (55)
T ss_pred CHHHHHHHHCcCH---HHHHHHHHHH
Confidence 8999999999988 7788877643
No 234
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=46.36 E-value=30 Score=20.63 Aligned_cols=25 Identities=24% Similarity=0.412 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.++|+.|.|..+|+++ ..+.+-.|
T Consensus 11 s~~~s~~~Aa~~lG~~~---~~v~~wv~ 35 (65)
T PF05344_consen 11 SQQISVAQAADRLGTDP---GTVRRWVR 35 (65)
T ss_pred cccccHHHHHHHHCcCH---HHHHHHHH
Confidence 48999999999999999 66655443
No 235
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 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 the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=45.92 E-value=21 Score=23.41 Aligned_cols=29 Identities=10% Similarity=0.311 Sum_probs=17.7
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
|++.+. ...|++||.+.+++|| =.|.++-
T Consensus 16 i~eAlr---rG~sveeI~e~T~ID~---wFL~~i~ 44 (123)
T PF02787_consen 16 IAEALR---RGYSVEEIHELTKIDP---WFLEQIK 44 (123)
T ss_dssp HHHHHH---TTB-HHHHHHHH---H---HHHHHHH
T ss_pred HHHHHH---cCCCHHHHHHHHCccH---HHHHHHH
Confidence 345555 3479999999999999 6666654
No 236
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=45.64 E-value=14 Score=25.59 Aligned_cols=25 Identities=12% Similarity=0.046 Sum_probs=21.6
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
-+.|-.|||+.+|+.+ +.+.|+|+-
T Consensus 168 ~~~t~~~lA~~lG~sr---etvsR~L~~ 192 (226)
T PRK10402 168 YHEKHTQAAEYLGVSY---RHLLYVLAQ 192 (226)
T ss_pred ccchHHHHHHHHCCcH---HHHHHHHHH
Confidence 3568899999999999 999998864
No 237
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=45.46 E-value=27 Score=23.68 Aligned_cols=18 Identities=17% Similarity=0.123 Sum_probs=16.2
Q ss_pred CCCCCCHHHHHHhcCCCC
Q 041968 57 HGQPMTLSQIASALDIQK 74 (87)
Q Consensus 57 ~~gp~S~~ELA~~~~~~~ 74 (87)
.++++...+||+.+++.|
T Consensus 21 ~~~~~~~~diA~~L~Vsp 38 (154)
T COG1321 21 EKGFARTKDIAERLKVSP 38 (154)
T ss_pred ccCcccHHHHHHHhCCCc
Confidence 358999999999999988
No 238
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=45.30 E-value=30 Score=23.77 Aligned_cols=24 Identities=21% Similarity=0.452 Sum_probs=20.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+..|..+||..+|+.. ..++|++.
T Consensus 171 ~g~s~~~iak~lgis~---~Tv~r~~k 194 (200)
T PRK13413 171 KGTSKSEIARKLGVSR---TTLARFLK 194 (200)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 3479999999999988 88998875
No 239
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=45.11 E-value=25 Score=17.21 Aligned_cols=22 Identities=18% Similarity=0.462 Sum_probs=14.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
..+|..++|+.+|+++ ..+.++
T Consensus 9 ~~~s~~~la~~~~i~~---~~i~~~ 30 (56)
T smart00530 9 KGLTQEELAEKLGVSR---STLSRI 30 (56)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHH
Confidence 4568888888888766 444443
No 240
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=44.83 E-value=13 Score=20.89 Aligned_cols=27 Identities=15% Similarity=0.404 Sum_probs=19.8
Q ss_pred CCCC-CHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 58 GQPM-TLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 58 ~gp~-S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
|..+ |..+||+..+++. ..+.+.|+.|
T Consensus 21 g~~lps~~~la~~~~vsr---~tvr~al~~L 48 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSR---TTVREALRRL 48 (64)
T ss_dssp TSBE--HHHHHHHHTS-H---HHHHHHHHHH
T ss_pred CCEeCCHHHHHHHhccCC---cHHHHHHHHH
Confidence 4677 9999999999988 7777776643
No 241
>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=44.66 E-value=19 Score=20.08 Aligned_cols=19 Identities=11% Similarity=0.247 Sum_probs=15.0
Q ss_pred CHHHHHHhcCCCCCChhhHHHH
Q 041968 62 TLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 62 S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
|..|+|+.+|+++ ..|++-
T Consensus 2 s~~eva~~~gvs~---~tlr~w 20 (68)
T cd01104 2 TIGAVARLTGVSP---DTLRAW 20 (68)
T ss_pred CHHHHHHHHCcCH---HHHHHH
Confidence 6789999999888 666654
No 242
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=44.19 E-value=19 Score=24.74 Aligned_cols=25 Identities=24% Similarity=0.391 Sum_probs=21.5
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
...|..|||+.+|.++ ..+.|.|++
T Consensus 119 ~g~s~~~iA~~lg~s~---~~V~r~l~l 143 (187)
T TIGR00180 119 FSMTQEDLAKKIGKSR---AHITNLLRL 143 (187)
T ss_pred hCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence 4578999999999998 888888875
No 243
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=44.05 E-value=24 Score=27.99 Aligned_cols=35 Identities=17% Similarity=0.268 Sum_probs=26.2
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+..|...|.. .++.|..+||+.+++++ ..+.|++.
T Consensus 8 e~~vL~~L~~-~~~~s~~eLA~~l~l~~---~tVt~~i~ 42 (489)
T PRK04172 8 EKKVLKALKE-LKEATLEELAEKLGLPP---EAVMRAAE 42 (489)
T ss_pred HHHHHHHHHh-CCCCCHHHHHHHhCcCH---HHHHHHHH
Confidence 3445556665 36899999999999999 77777664
No 244
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=43.86 E-value=29 Score=24.20 Aligned_cols=25 Identities=20% Similarity=0.167 Sum_probs=18.4
Q ss_pred HHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 54 IHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 54 L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+++.| . .|+.+||++.|++. ..+++
T Consensus 26 F~~~Gy~-~s~~~IA~~AGvsk---~tiy~ 51 (225)
T PRK11552 26 FGEYGLH-ATTRDIAAQAGQNI---AAITY 51 (225)
T ss_pred HHHhCcc-CCHHHHHHHhCCCH---HHHHH
Confidence 34445 6 89999999999987 55544
No 245
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=43.81 E-value=27 Score=21.35 Aligned_cols=23 Identities=22% Similarity=0.387 Sum_probs=18.2
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
...|..|||+.+|+++ ..+++.+
T Consensus 125 ~g~s~~eIA~~l~~s~---~~v~~~~ 147 (158)
T TIGR02937 125 EGLSYKEIAEILGISV---GTVKRRL 147 (158)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHHH
Confidence 5689999999999988 6555543
No 246
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=43.73 E-value=25 Score=20.12 Aligned_cols=23 Identities=17% Similarity=0.475 Sum_probs=17.5
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
..+|..++|+.+|++. ..+.+++
T Consensus 17 ~~~t~~~lA~~~gis~---~tis~~~ 39 (78)
T TIGR02607 17 LGLSIRALAKALGVSR---STLSRIV 39 (78)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHH
Confidence 5678889999999877 6666654
No 247
>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=43.50 E-value=15 Score=19.38 Aligned_cols=10 Identities=30% Similarity=0.335 Sum_probs=4.9
Q ss_pred HHHHhcCCCC
Q 041968 65 QIASALDIQK 74 (87)
Q Consensus 65 ELA~~~~~~~ 74 (87)
|||+.+|+.+
T Consensus 2 ~lA~~~gvs~ 11 (52)
T cd01392 2 DIARAAGVSV 11 (52)
T ss_pred cHHHHHCcCH
Confidence 3455555544
No 248
>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=42.69 E-value=27 Score=15.57 Aligned_cols=21 Identities=19% Similarity=0.371 Sum_probs=16.0
Q ss_pred CCCHHHHHHhcCCCCCChhhHHHH
Q 041968 60 PMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 60 p~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
..|..++|..+++.. ..+++.
T Consensus 21 ~~s~~~ia~~~~is~---~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSR---STLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCH---HHHHHh
Confidence 358999999999877 666654
No 249
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=42.65 E-value=20 Score=28.43 Aligned_cols=24 Identities=29% Similarity=0.538 Sum_probs=21.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|+|..|+|..+|+|+ ..+.|..+
T Consensus 342 kPLtlkdvAe~lglhe---STVSRav~ 365 (455)
T PRK05932 342 KPLVLKDIAEELGMHE---STISRATT 365 (455)
T ss_pred cCccHHHHHHHhCCCc---cchhhhhc
Confidence 8999999999999999 88888754
No 250
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=42.62 E-value=30 Score=25.01 Aligned_cols=37 Identities=14% Similarity=0.259 Sum_probs=26.8
Q ss_pred HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
+..++.+.+.|..-..-.|-.||++.+|+++ ..|.|=
T Consensus 7 ~~~~~~~v~~lr~lk~~~ty~el~~~~g~p~---~~l~RY 43 (238)
T PRK08558 7 VRLQLRAVRVLRSLKKTYTYEELSSITGLPE---SVLNRY 43 (238)
T ss_pred HHHHHHHHHHHHHHhcccCHHHHHHHHCCCH---HHHHHH
Confidence 4455666776654346689999999999988 777664
No 251
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=42.12 E-value=24 Score=21.17 Aligned_cols=36 Identities=14% Similarity=0.323 Sum_probs=24.5
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+..+...|... ++.+..+||..+++++ ..+.|+++
T Consensus 23 ~q~~~L~~l~~~-~~~~~~~la~~l~i~~---~~vt~~l~ 58 (126)
T COG1846 23 PQYQVLLALYEA-GGITVKELAERLGLDR---STVTRLLK 58 (126)
T ss_pred HHHHHHHHHHHh-CCCcHHHHHHHHCCCH---HHHHHHHH
Confidence 444555566654 3444389999999999 76777665
No 252
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=41.97 E-value=43 Score=21.72 Aligned_cols=29 Identities=24% Similarity=0.407 Sum_probs=23.6
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
|+-.|-.+||...|... .+..+.|+|+.|
T Consensus 21 GkV~TYGdIA~laG~p~-~ARqVG~il~~l 49 (103)
T COG3695 21 GKVSTYGDIAKLAGLPR-AARQVGRILKHL 49 (103)
T ss_pred CceeeHHHHHHHhCCCh-hHHHHHHHHhhC
Confidence 57889999999999863 338899999864
No 253
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=41.89 E-value=31 Score=19.57 Aligned_cols=23 Identities=17% Similarity=0.325 Sum_probs=16.5
Q ss_pred CCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 61 MTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 61 ~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
++..|-|..+|+.+ ..|.|+.|-
T Consensus 16 lp~~eAA~~Lgv~~---T~LKr~CR~ 38 (52)
T PF02042_consen 16 LPIKEAAKELGVSV---TTLKRRCRR 38 (52)
T ss_pred CCHHHHHHHhCCCH---HHHHHHHHH
Confidence 56677777777777 777777764
No 254
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=41.86 E-value=17 Score=22.71 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=26.6
Q ss_pred chHHHHhC---CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 50 IPDVIHKH---GQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 50 I~d~L~~~---~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.+|.|.+. -.-+|.+.|++++++.- .+-+|+||.|
T Consensus 28 t~dkl~kEV~~~K~ITps~lserlkI~~---SlAr~~Lr~L 65 (86)
T PRK09334 28 LLKRVAKEVKKEKIVTPYTLASKYGIKI---SVAKKVLREL 65 (86)
T ss_pred HHHHHHHHhccCcEEcHHHHHHHhcchH---HHHHHHHHHH
Confidence 45555432 27789999999999988 8888888864
No 255
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=41.74 E-value=40 Score=22.45 Aligned_cols=28 Identities=18% Similarity=0.389 Sum_probs=22.6
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
.|--|-++|... ||.|+.||-+.++.+.
T Consensus 7 aE~eVM~ilW~~-~~~t~~eI~~~l~~~~ 34 (123)
T COG3682 7 AEWEVMEILWSR-GPATVREIIEELPADR 34 (123)
T ss_pred HHHHHHHHHHHc-CCccHHHHHHHHhhcc
Confidence 456677888865 7999999999998764
No 256
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=41.68 E-value=28 Score=21.96 Aligned_cols=21 Identities=19% Similarity=0.292 Sum_probs=16.8
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
...|..|||+.+|+++ ..++.
T Consensus 128 ~~~~~~eIA~~lgis~---~tv~~ 148 (161)
T TIGR02985 128 EGKSYKEIAEELGISV---KTVEY 148 (161)
T ss_pred cCCCHHHHHHHHCCCH---HHHHH
Confidence 5689999999999988 55443
No 257
>PRK09726 antitoxin HipB; Provisional
Probab=41.42 E-value=27 Score=21.02 Aligned_cols=24 Identities=21% Similarity=0.296 Sum_probs=18.1
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..+|..|+|+.+|+.+ ..+.++.+
T Consensus 24 ~gltq~elA~~~gvs~---~tis~~e~ 47 (88)
T PRK09726 24 NGWTQSELAKKIGIKQ---ATISNFEN 47 (88)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHC
Confidence 5688999999999877 66665543
No 258
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=40.89 E-value=33 Score=26.02 Aligned_cols=31 Identities=26% Similarity=0.345 Sum_probs=24.8
Q ss_pred HHHhCCCCCCHHHHHHh--cCCCCCChhhHHHHHhcC
Q 041968 53 VIHKHGQPMTLSQIASA--LDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 53 ~L~~~~gp~S~~ELA~~--~~~~~~~~~~L~RlLR~L 87 (87)
.+.+ ++|.+..+|++. +++.+ ..++|-|..|
T Consensus 15 ~l~~-~~pv~s~~l~~~~~~~vS~---aTiR~d~~~L 47 (337)
T TIGR00331 15 YIKT-GQPVGSKTLLEKYNLGLSS---ATIRNDMADL 47 (337)
T ss_pred HHhc-CCCcCHHHHHhhcCCCCCh---HHHHHHHHHH
Confidence 3443 699999999999 88888 8888887643
No 259
>PRK11640 putative transcriptional regulator; Provisional
Probab=40.73 E-value=38 Score=23.08 Aligned_cols=26 Identities=27% Similarity=0.416 Sum_probs=20.4
Q ss_pred HHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 54 IHKHG-QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 54 L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+.+.| ...|+++|++.+|+.+ ..+|+
T Consensus 14 f~~~Gy~~tsi~~I~~~aGv~k---~slY~ 40 (191)
T PRK11640 14 LEQQGLANTTLEMLAERVDYPL---DELQR 40 (191)
T ss_pred HHHhCcccCCHHHHHHHhCcCH---HHHHH
Confidence 45556 7899999999999987 65654
No 260
>PRK05638 threonine synthase; Validated
Probab=40.63 E-value=27 Score=27.20 Aligned_cols=33 Identities=18% Similarity=0.267 Sum_probs=24.0
Q ss_pred chHHHHhCCCCCCHHHHHHhcC--CCCCChhhHHHHHhcC
Q 041968 50 IPDVIHKHGQPMTLSQIASALD--IQKNKAHCIQRLMRIL 87 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~--~~~~~~~~L~RlLR~L 87 (87)
|...|.+ ++.+..||++.++ +.+ ..+++.|+.|
T Consensus 376 IL~~L~~--~~~~~~el~~~l~~~~s~---~~v~~hL~~L 410 (442)
T PRK05638 376 ILKILSE--REMYGYEIWKALGKPLKY---QAVYQHIKEL 410 (442)
T ss_pred HHHHHhh--CCccHHHHHHHHcccCCc---chHHHHHHHH
Confidence 4455552 6889999999998 555 6788877754
No 261
>PRK09526 lacI lac repressor; Reviewed
Probab=40.59 E-value=26 Score=25.12 Aligned_cols=24 Identities=21% Similarity=0.459 Sum_probs=20.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+..|..|||+..|++. ..+.|+|.
T Consensus 4 ~~~ti~dIA~~aGVS~---~TVSrvLn 27 (342)
T PRK09526 4 KPVTLYDVARYAGVSY---QTVSRVLN 27 (342)
T ss_pred CCCcHHHHHHHhCCCH---HHHHHHhc
Confidence 4579999999999988 88888875
No 262
>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=40.38 E-value=33 Score=16.88 Aligned_cols=23 Identities=22% Similarity=0.430 Sum_probs=15.8
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
...|..++|..++.++ ..+.+++
T Consensus 11 ~~~s~~~~a~~~~~~~---~~v~~~~ 33 (58)
T cd00093 11 KGLTQEELAEKLGVSR---STISRIE 33 (58)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHHH
Confidence 3467788888888776 5555554
No 263
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=40.29 E-value=47 Score=23.47 Aligned_cols=35 Identities=29% Similarity=0.319 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcC
Q 041968 34 FNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALD 71 (87)
Q Consensus 34 ~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~ 71 (87)
.||..-..--.||++|.-|.|+ +|..+++|...+.
T Consensus 88 TGy~sIATAV~AvKlGA~~YLa---KPAdaDdi~aAl~ 122 (182)
T COG4567 88 TGYASIATAVEAVKLGACDYLA---KPADADDILAALL 122 (182)
T ss_pred ecchHHHHHHHHHHhhhhhhcC---CCCChHHHHHHHh
Confidence 4777777777899999999998 7899999887765
No 264
>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=40.29 E-value=25 Score=19.76 Aligned_cols=20 Identities=10% Similarity=0.424 Sum_probs=15.2
Q ss_pred CCHHHHHHhcCCCCCChhhHHHH
Q 041968 61 MTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 61 ~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
.|..|+|+.+|+++ ..|+.-
T Consensus 1 ~~i~evA~~~gvs~---~tlR~~ 20 (67)
T cd04764 1 YTIKEVSEIIGVKP---HTLRYY 20 (67)
T ss_pred CCHHHHHHHHCcCH---HHHHHH
Confidence 36789999999988 666543
No 265
>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=39.34 E-value=26 Score=19.79 Aligned_cols=19 Identities=21% Similarity=0.392 Sum_probs=15.0
Q ss_pred CHHHHHHhcCCCCCChhhHHHH
Q 041968 62 TLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 62 S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
|..|+|+.+|+++ ..|++-
T Consensus 2 ~i~e~A~~~gVs~---~tlr~y 20 (68)
T cd04763 2 TIGEVALLTGIKP---HVLRAW 20 (68)
T ss_pred CHHHHHHHHCcCH---HHHHHH
Confidence 6789999999988 666543
No 266
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=39.21 E-value=53 Score=24.62 Aligned_cols=25 Identities=48% Similarity=0.636 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.|.|..|||..+++++ .-+.|..|
T Consensus 155 ~~prtl~eIa~a~~V~~---kei~rtyr 179 (285)
T COG1405 155 GVPRTLDEIAKALGVSK---KEIGRTYR 179 (285)
T ss_pred CCCccHHHHHHHHCCCH---HHHHHHHH
Confidence 68999999999999988 55555544
No 267
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=39.20 E-value=25 Score=24.09 Aligned_cols=25 Identities=16% Similarity=0.510 Sum_probs=17.1
Q ss_pred CCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 57 HGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 57 ~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
++.|+|..+|++.++ ++ ..+..+|.
T Consensus 10 s~~pvs~~~La~~l~-~~---~~v~~~l~ 34 (159)
T PF04079_consen 10 SGEPVSIEELAEILG-SE---DEVEEALE 34 (159)
T ss_dssp -SS-B-HHHHHHHCT--H---HHHHHHHH
T ss_pred cCCCCCHHHHHHHhC-CH---HHHHHHHH
Confidence 368999999999999 77 66666654
No 268
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=39.01 E-value=29 Score=24.92 Aligned_cols=24 Identities=13% Similarity=0.286 Sum_probs=20.5
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+..|..|||+..|++. ..+.|+|.
T Consensus 5 ~~~Ti~dIA~~agVS~---~TVSr~Ln 28 (342)
T PRK10014 5 KKITIHDVALAAGVSV---STVSLVLS 28 (342)
T ss_pred CCCcHHHHHHHhCCCH---HHHHHHHC
Confidence 4579999999999998 88888875
No 269
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=38.70 E-value=24 Score=19.22 Aligned_cols=22 Identities=23% Similarity=0.566 Sum_probs=17.0
Q ss_pred CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 61 MTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 61 ~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
++..|+++.+|++. ..++|+++
T Consensus 4 l~~~ev~~~~g~s~---~ti~~~~k 25 (51)
T PF05930_consen 4 LRIKEVAELLGVSR---STIYRLIK 25 (51)
T ss_dssp E-HHHHHHHHSS-H---HHHHHHHH
T ss_pred ccHHHHHHHHCCCH---HHHHHHHh
Confidence 56789999999988 88888875
No 270
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=38.47 E-value=24 Score=23.43 Aligned_cols=25 Identities=16% Similarity=0.301 Sum_probs=20.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
.--|+-|||..++++| ..+.|..+-
T Consensus 34 kLPSvRelA~~~~VNp---nTv~raY~e 58 (125)
T COG1725 34 KLPSVRELAKDLGVNP---NTVQRAYQE 58 (125)
T ss_pred CCCcHHHHHHHhCCCH---HHHHHHHHH
Confidence 4459999999999999 777776653
No 271
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=38.35 E-value=37 Score=19.35 Aligned_cols=16 Identities=25% Similarity=0.470 Sum_probs=13.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...+..|||+.+|+++
T Consensus 12 ~G~~~~eIA~~Lg~~~ 27 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPR 27 (58)
T ss_pred cCCCHHHHHHHHCCCh
Confidence 4578999999999876
No 272
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=38.32 E-value=34 Score=22.07 Aligned_cols=22 Identities=18% Similarity=0.215 Sum_probs=17.5
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...|..|||+.+|+++ ..+.+.
T Consensus 124 ~~~s~~EIA~~lgis~---~tV~~~ 145 (163)
T PRK07037 124 HGETQKDIARELGVSP---TLVNFM 145 (163)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHH
Confidence 5689999999999988 555444
No 273
>PF10376 Mei5: Double-strand recombination repair protein ; InterPro: IPR018468 Mei5 is one of a pair of meiosis-specific proteins which facilitate the loading of Dmc1 on to Rad51 on DNA at double-strand breaks during recombination. Recombination is carried out by a large protein complex based around the two RecA homologues, Rad51 and Dmc1 []. This complex may play both a catalytic and a structural role in the interaction between homologous chromosomes during meiosis. Mei5 is seen to contain a coiled-coli region.
Probab=38.10 E-value=54 Score=23.72 Aligned_cols=40 Identities=23% Similarity=0.293 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHhCchHHHHh-CCCCCCHHHHHHhcCCCCCChhhH
Q 041968 36 YINSMSLKCAVELGIPDVIHK-HGQPMTLSQIASALDIQKNKAHCI 80 (87)
Q Consensus 36 ~~~~~aL~aaveLgI~d~L~~-~~gp~S~~ELA~~~~~~~~~~~~L 80 (87)
=|...+-.++.+|. ..+.. .+...|..||...+|+|+ .++
T Consensus 178 Kwr~~~q~~l~eL~--~~~~~~e~~~~TM~eL~~~l~ID~---~LI 218 (221)
T PF10376_consen 178 KWRSASQEALYELQ--SEMSEEEGEKFTMGELIKRLGIDY---DLI 218 (221)
T ss_pred HHHHHHHHHHHHHH--HHHhhccccCccHHHHHHHhCCCc---ccc
Confidence 44566666666654 55665 568889999999999998 654
No 274
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=38.07 E-value=31 Score=24.91 Aligned_cols=24 Identities=17% Similarity=0.411 Sum_probs=19.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.|..|||..+|+++ ..+.++.+
T Consensus 235 ~~~t~~eIA~~lgvS~---~~V~q~~~ 258 (270)
T TIGR02392 235 DKLTLQELAAEYGVSA---ERIRQIEK 258 (270)
T ss_pred CCcCHHHHHHHHCCCH---HHHHHHHH
Confidence 5899999999999998 66665543
No 275
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; 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; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=36.98 E-value=38 Score=20.52 Aligned_cols=28 Identities=21% Similarity=0.296 Sum_probs=20.8
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|...|-.|||+.+| +|..+..+.+.|+.
T Consensus 17 G~v~TYg~iA~~~g-~p~~ar~Vg~al~~ 44 (85)
T PF01035_consen 17 GKVTTYGEIARLLG-RPKAARAVGSALAR 44 (85)
T ss_dssp T-BEEHHHHHHHTT--TTCHHHHHHHHHT
T ss_pred CceEeHHHHHHHHh-hcccHHHHHHHhcc
Confidence 68889999999999 45555778777764
No 276
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=36.78 E-value=39 Score=23.74 Aligned_cols=26 Identities=27% Similarity=0.580 Sum_probs=19.8
Q ss_pred CCCC-CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 57 HGQP-MTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 57 ~~gp-~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.| +|+.+|++.++.++ .-+..++.
T Consensus 16 sg~pgls~~~La~~l~~~~---~~v~~~l~ 42 (188)
T PRK00135 16 SGEEGLSLEQLAEILELEP---TEVQQLLE 42 (188)
T ss_pred cCCCCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 3676 99999999999887 55555544
No 277
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=36.55 E-value=22 Score=18.54 Aligned_cols=18 Identities=17% Similarity=0.394 Sum_probs=12.9
Q ss_pred CHHHHHHhcCCCCCChhhHHH
Q 041968 62 TLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 62 S~~ELA~~~~~~~~~~~~L~R 82 (87)
|..|+|+.+|+++ ..|+.
T Consensus 1 ti~e~A~~~gvs~---~tlR~ 18 (38)
T PF00376_consen 1 TIGEVAKLLGVSP---RTLRY 18 (38)
T ss_dssp EHHHHHHHHTS-H---HHHHH
T ss_pred CHHHHHHHHCCCH---HHHHH
Confidence 4679999999988 65554
No 278
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=36.54 E-value=31 Score=24.78 Aligned_cols=24 Identities=21% Similarity=0.454 Sum_probs=19.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+..|..|||+..|++. ..+.|+|+
T Consensus 4 ~~~ti~dIA~~agVS~---~TVSrvLn 27 (331)
T PRK14987 4 KRPVLQDVADRVGVTK---MTVSRFLR 27 (331)
T ss_pred CCCcHHHHHHHhCCCH---HHhhhhhC
Confidence 4569999999999988 77888774
No 279
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=36.25 E-value=47 Score=23.90 Aligned_cols=27 Identities=22% Similarity=0.279 Sum_probs=22.4
Q ss_pred HHHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 45 AVELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 45 aveLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
--|..|+..++ ...|..|||+.+++++
T Consensus 136 pRErEVLrLLA---qGkTnKEIAe~L~IS~ 162 (198)
T PRK15201 136 VTERHLLKLIA---SGYHLSETAALLSLSE 162 (198)
T ss_pred HHHHHHHHHHH---CCCCHHHHHHHhCCCH
Confidence 45777888887 5689999999999987
No 280
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=36.05 E-value=28 Score=22.49 Aligned_cols=26 Identities=23% Similarity=0.303 Sum_probs=23.0
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.-+|+..||+++++.- .+-+++||.|
T Consensus 58 K~ITp~~lserlkI~~---SlAr~~Lr~L 83 (105)
T PF03297_consen 58 KLITPSVLSERLKING---SLARKALREL 83 (105)
T ss_dssp SCECHHHHHHHHCCSC---HHHHHHHHHH
T ss_pred cEeeHHHHHHhHhhHH---HHHHHHHHHH
Confidence 6789999999999998 8888888864
No 281
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=35.85 E-value=45 Score=25.36 Aligned_cols=27 Identities=22% Similarity=0.368 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHh--cCCCCCChhhHHHHHhcC
Q 041968 58 GQPMTLSQIASA--LDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 58 ~gp~S~~ELA~~--~~~~~~~~~~L~RlLR~L 87 (87)
++|.+..+||+. +++.+ ..++|-|..|
T Consensus 23 ~~pv~s~~l~~~~~l~~S~---aTIR~dm~~L 51 (339)
T PRK00082 23 GEPVGSKTLSKRYGLGVSS---ATIRNDMADL 51 (339)
T ss_pred CCCcCHHHHHHHhCCCCCh---HHHHHHHHHH
Confidence 699999999977 88888 8899988754
No 282
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=35.71 E-value=37 Score=27.24 Aligned_cols=31 Identities=29% Similarity=0.426 Sum_probs=23.9
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHH
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+..|.+.|. .++.|..+||+.+|++. ..++|
T Consensus 6 ~~~iL~~L~--~~~~t~~~LA~~l~VS~---RTIr~ 36 (584)
T PRK09863 6 ELKIVDLLE--QQDRSGGELAQQLGVSR---RTIVR 36 (584)
T ss_pred HHHHHHHHH--cCCCCHHHHHHHhCCCH---HHHHH
Confidence 345666674 37999999999999988 66655
No 283
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=35.65 E-value=45 Score=21.52 Aligned_cols=23 Identities=13% Similarity=0.215 Sum_probs=14.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
..+|-.|+|..+|+++ ..+.|+.
T Consensus 17 ~Glsq~eLA~~~Gis~---~~is~iE 39 (120)
T PRK13890 17 RHMTKKELSERSGVSI---SFLSDLT 39 (120)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHH
Confidence 4567777777777766 5555544
No 284
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=35.18 E-value=35 Score=27.45 Aligned_cols=24 Identities=25% Similarity=0.515 Sum_probs=21.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|+|..++|..+|+|+ ..+.|+..
T Consensus 368 kPLtlkdVAe~lglHe---STVSRa~~ 391 (481)
T PRK12469 368 KPLVLRDVAEELGLHE---STISRATG 391 (481)
T ss_pred cCCcHHHHHHHhCCCc---chhhHHhc
Confidence 8999999999999999 88888753
No 285
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=35.05 E-value=44 Score=23.37 Aligned_cols=32 Identities=13% Similarity=0.014 Sum_probs=23.2
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|.-.|... +++|..|||..++.++ ..+.|++.
T Consensus 50 iL~~L~~~-~~itq~eLa~~l~l~~---sTvtr~l~ 81 (185)
T PRK13777 50 ILWIAYHL-KGASISEIAKFGVMHV---STAFNFSK 81 (185)
T ss_pred HHHHHHhC-CCcCHHHHHHHHCCCH---hhHHHHHH
Confidence 44445543 6899999999999987 55666554
No 286
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=35.02 E-value=53 Score=22.72 Aligned_cols=39 Identities=13% Similarity=0.120 Sum_probs=26.0
Q ss_pred HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCCh-hhHHHHHh
Q 041968 44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKA-HCIQRLMR 85 (87)
Q Consensus 44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~-~~L~RlLR 85 (87)
+--|..|+..++ ...|-.|||+++++.+.-- ..+.|+++
T Consensus 139 T~RE~eVL~lla---~G~snkeIA~~L~iS~~TVk~h~~~I~~ 178 (207)
T PRK15411 139 SRTESSMLRMWM---AGQGTIQISDQMNIKAKTVSSHKGNIKR 178 (207)
T ss_pred CHHHHHHHHHHH---cCCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 345666777777 5689999999999987100 13455554
No 287
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=34.77 E-value=20 Score=20.70 Aligned_cols=21 Identities=29% Similarity=0.591 Sum_probs=14.4
Q ss_pred hHHHHhCCCCCCHHHHHHhcC
Q 041968 51 PDVIHKHGQPMTLSQIASALD 71 (87)
Q Consensus 51 ~d~L~~~~gp~S~~ELA~~~~ 71 (87)
.++|.+.++|+|..||....-
T Consensus 8 ~~vL~~~~~pm~~~eI~~~i~ 28 (72)
T PF05066_consen 8 YEVLEEAGRPMTFKEIWEEIQ 28 (72)
T ss_dssp HHHHHHH-S-EEHHHHHHHHH
T ss_pred HHHHHhcCCCcCHHHHHHHHH
Confidence 356666679999999988753
No 288
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=34.63 E-value=37 Score=25.07 Aligned_cols=25 Identities=28% Similarity=0.534 Sum_probs=19.3
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
++|.+++.+|..+|.++ ..+.++++
T Consensus 274 ~~~~~~~~~a~~lg~~~---~~~~~~~e 298 (328)
T PRK00080 274 GGPVGLDTLAAALGEER---DTIEDVYE 298 (328)
T ss_pred CCceeHHHHHHHHCCCc---chHHHHhh
Confidence 58999999999999998 44443333
No 289
>PRK11642 exoribonuclease R; Provisional
Probab=34.44 E-value=46 Score=28.45 Aligned_cols=38 Identities=21% Similarity=0.448 Sum_probs=27.1
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCC-CChhhHHHHHhcC
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQK-NKAHCIQRLMRIL 87 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~-~~~~~L~RlLR~L 87 (87)
|.+.|.+.++|++..||++.++++. ..-..|.+.|+.|
T Consensus 24 Il~~l~~~~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L 62 (813)
T PRK11642 24 ILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAM 62 (813)
T ss_pred HHHHHHhcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHH
Confidence 4555655469999999999999865 2224577777653
No 290
>smart00351 PAX Paired Box domain.
Probab=34.33 E-value=58 Score=20.99 Aligned_cols=24 Identities=13% Similarity=0.408 Sum_probs=19.4
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+..|..+||+.+|+++ ..++|+++
T Consensus 32 ~G~s~~~iA~~~gvs~---~tV~kwi~ 55 (125)
T smart00351 32 NGVRPCDISRQLCVSH---GCVSKILG 55 (125)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 3468899999999998 87887764
No 291
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=33.97 E-value=49 Score=24.56 Aligned_cols=34 Identities=29% Similarity=0.442 Sum_probs=25.7
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.|-|-|..+||.+++.||+..+++|. ..+.|..+
T Consensus 59 EI~~el~~~gGRv~~~dL~~~LnVd~---~~ie~~~~ 92 (272)
T PF09743_consen 59 EIKDELYVHGGRVNLVDLAQALNVDL---DHIERRAQ 92 (272)
T ss_pred HHHHHHHHcCCceEHHHHHHhcCcCH---HHHHHHHH
Confidence 34555656689999999999999988 66666543
No 292
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=33.77 E-value=59 Score=18.62 Aligned_cols=32 Identities=19% Similarity=0.350 Sum_probs=22.9
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.|.+-.. --.|+..+++.+++.+ ....|+++
T Consensus 4 Lidll~~~-P~Vsa~mva~~L~vT~---~~A~~li~ 35 (54)
T PF11972_consen 4 LIDLLLSR-PLVSAPMVAKELGVTP---QAAQRLIA 35 (54)
T ss_pred HHHHHHhC-ccccHHHHHHHhCCCH---HHHHHHHH
Confidence 45666532 2458999999999988 77777765
No 293
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=33.73 E-value=37 Score=21.78 Aligned_cols=22 Identities=27% Similarity=0.478 Sum_probs=13.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...|++|||+.+|++. ..++-.
T Consensus 32 eDlSlsEIAe~~~iSR---qaV~d~ 53 (101)
T PF04297_consen 32 EDLSLSEIAEELGISR---QAVYDS 53 (101)
T ss_dssp S---HHHHHHHCTS-H---HHHHHH
T ss_pred cCCCHHHHHHHHCCCH---HHHHHH
Confidence 5689999999999977 555443
No 294
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=33.53 E-value=36 Score=18.98 Aligned_cols=19 Identities=16% Similarity=0.354 Sum_probs=15.3
Q ss_pred CHHHHHHhcCCCCCChhhHHHH
Q 041968 62 TLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 62 S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
|..|+|+.+|+++ ..|+.-
T Consensus 2 ti~eva~~~gvs~---~tlr~y 20 (69)
T PF13411_consen 2 TIKEVAKLLGVSP---STLRYY 20 (69)
T ss_dssp EHHHHHHHTTTTH---HHHHHH
T ss_pred cHHHHHHHHCcCH---HHHHHH
Confidence 6789999999988 666554
No 295
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=33.27 E-value=55 Score=21.37 Aligned_cols=24 Identities=17% Similarity=0.210 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhCch
Q 041968 26 QAQVWNCAFNYINSMSLKCAVELGIP 51 (87)
Q Consensus 26 ~~~l~~l~~g~~~~~aL~aaveLgI~ 51 (87)
+..+++++-.+ ..+--+|..|+++
T Consensus 45 ~~~Il~lC~~~--~SVAEiAA~L~lP 68 (114)
T PF05331_consen 45 HRAILELCRRP--LSVAEIAARLGLP 68 (114)
T ss_pred HHHHHHHHCCC--ccHHHHHHhhCCC
Confidence 34555555441 2233344444444
No 296
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=33.18 E-value=70 Score=17.61 Aligned_cols=32 Identities=19% Similarity=0.146 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCchHHHH
Q 041968 24 KAQAQVWNCAFNYINSMSLKCAVELGIPDVIH 55 (87)
Q Consensus 24 ~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~ 55 (87)
.-..++.+++.+.-...+++...++|+++.|-
T Consensus 26 Ri~~El~kil~~~~~~~~~~~l~~~gll~~if 57 (64)
T PF12627_consen 26 RIREELEKILSSPNPSRAFKLLDELGLLEYIF 57 (64)
T ss_dssp HHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHS
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHC
Confidence 34466777887788888999999999999874
No 297
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=32.90 E-value=43 Score=25.29 Aligned_cols=23 Identities=30% Similarity=0.626 Sum_probs=19.0
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
+.+.|..|||..+|+.. ..+.+|
T Consensus 280 ~~~~Tl~eIa~~lgvS~---eRVrQI 302 (324)
T PRK07921 280 GQPRTLDQIGKLFGLSR---ERVRQI 302 (324)
T ss_pred CCCcCHHHHHHHHCCCH---HHHHHH
Confidence 36899999999999998 655554
No 298
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=32.33 E-value=38 Score=21.25 Aligned_cols=24 Identities=4% Similarity=0.214 Sum_probs=19.2
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
-..|..|++..+|+++ ..+.++..
T Consensus 6 ~~lt~~Elc~~~gi~~---~~l~eLve 29 (101)
T PRK10265 6 VTFTITEFCLHTGVSE---EELNEIVG 29 (101)
T ss_pred EEeeHHHHHHHHCcCH---HHHHHHHH
Confidence 3578999999999998 77777654
No 299
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=32.14 E-value=1.8e+02 Score=20.67 Aligned_cols=43 Identities=21% Similarity=0.331 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHHhCc-------hHHHHhCCCCCCHHHHHHhcCCC
Q 041968 31 NCAFNYINSMSLKCAVELGI-------PDVIHKHGQPMTLSQIASALDIQ 73 (87)
Q Consensus 31 ~l~~g~~~~~aL~aaveLgI-------~d~L~~~~gp~S~~ELA~~~~~~ 73 (87)
...|+.|..-|+-++.+-++ ..+|...+.|+++.+|+..++.+
T Consensus 62 y~Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrdR~K~laDic~~ln~e 111 (199)
T COG5631 62 YEAFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRDRPKSLADICQMLNRE 111 (199)
T ss_pred HHHHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcCchhhHHHHHHHhccc
Confidence 44678888778777765543 23444457999999999999873
No 300
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=32.09 E-value=36 Score=18.88 Aligned_cols=33 Identities=21% Similarity=0.364 Sum_probs=22.3
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
++.+|..+.+.+ |...-|+.+++++ ..+.|-++
T Consensus 3 ~l~~f~~v~~~g---s~~~AA~~l~is~---~~vs~~i~ 35 (60)
T PF00126_consen 3 QLRYFLAVAETG---SISAAAEELGISQ---SAVSRQIK 35 (60)
T ss_dssp HHHHHHHHHHHS---SHHHHHHHCTSSH---HHHHHHHH
T ss_pred HHHHHHHHHHhC---CHHHHHHHhhccc---hHHHHHHH
Confidence 345666676543 7777888888877 66666554
No 301
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=32.06 E-value=45 Score=24.43 Aligned_cols=24 Identities=13% Similarity=0.340 Sum_probs=19.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.|..|||..+|+++ ..+.++.+
T Consensus 247 ~~~Tl~EIA~~lgvS~---~rVrqi~~ 270 (284)
T PRK06596 247 DKSTLQELAAEYGVSA---ERVRQIEK 270 (284)
T ss_pred CCcCHHHHHHHHCCCH---HHHHHHHH
Confidence 5899999999999998 66666643
No 302
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=31.93 E-value=30 Score=21.03 Aligned_cols=24 Identities=17% Similarity=0.405 Sum_probs=14.1
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
.+...+++ ..++..|||+.+|+..
T Consensus 6 ~l~~~l~~--r~~~~~eLa~~igis~ 29 (73)
T COG3655 6 RLDVMLAD--RKISLKELAEAIGISE 29 (73)
T ss_pred hHHHHHHH--HhhhHHHHHHHHcccH
Confidence 34444553 4566777777777655
No 303
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=31.84 E-value=77 Score=17.99 Aligned_cols=28 Identities=11% Similarity=0.235 Sum_probs=21.9
Q ss_pred CCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 57 HGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 57 ~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.++-.+..||....|++. ....||..++
T Consensus 40 ~g~~~s~~dL~~v~gi~~---~~~~~i~~~~ 67 (69)
T TIGR00426 40 YGPFKTVEDLKQVPGIGN---SLVEKNLAVI 67 (69)
T ss_pred cCCcCCHHHHHcCCCCCH---HHHHHHHhhc
Confidence 345668999999889988 7888887653
No 304
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=31.79 E-value=49 Score=24.73 Aligned_cols=23 Identities=35% Similarity=0.769 Sum_probs=19.1
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
+.+.|..|||..+|+.. ..+.++
T Consensus 274 ~~~~Tl~EIa~~lgiS~---erVRqi 296 (317)
T PRK07405 274 GQPLTLAKIGERLNISR---ERVRQI 296 (317)
T ss_pred CCCcCHHHHHHHHCcCH---HHHHHH
Confidence 37899999999999998 655554
No 305
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=31.77 E-value=46 Score=20.75 Aligned_cols=33 Identities=21% Similarity=0.312 Sum_probs=21.9
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
++.+|..+.+.+ |...=|+.+++++ ..+.|-++
T Consensus 6 ~l~~~~av~~~g---Sis~AA~~L~iS~---stvs~~I~ 38 (99)
T TIGR00637 6 RVALLKAIARMG---SISQAAKDAGISY---KSAWDYIR 38 (99)
T ss_pred HHHHHHHHHHhC---CHHHHHHHHCCCH---HHHHHHHH
Confidence 455677777544 6777788888877 55655554
No 306
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=31.39 E-value=1.4e+02 Score=18.73 Aligned_cols=57 Identities=9% Similarity=0.097 Sum_probs=27.7
Q ss_pred HHHHHHHHHH--HHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 25 AQAQVWNCAF--NYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 25 ~~~~l~~l~~--g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
....+.+.+. .+..|.+.+.-..+.=-.+..... ..++.|||.+.|... ..+++|++
T Consensus 36 ~~~~L~~~~gG~~iyiP~~~~~~~~~R~~~I~~~f~-G~n~~eLA~kyglS~---r~I~~Ii~ 94 (108)
T PF08765_consen 36 VALKLCRYFGGQQIYIPKCDRLLRALRNREIRREFN-GMNVRELARKYGLSE---RQIYRIIK 94 (108)
T ss_dssp HHHHHHHHH-SS------SHHHHHHHHHHHHHHH---SS-HHHHHHHHT--H---HHHHHHHH
T ss_pred HHHHHHHHHCCEeEEeeCccHHHHHHHHHHHHHHhC-CCCHHHHHHHHCcCH---HHHHHHHH
Confidence 3344444444 344566544333333233334332 568999999999998 88888876
No 307
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=31.10 E-value=48 Score=23.04 Aligned_cols=23 Identities=26% Similarity=0.358 Sum_probs=19.0
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
...|..|||+.+|+++ ..++++.
T Consensus 198 ~~~t~~eIA~~lgis~---~~V~~~~ 220 (231)
T TIGR02885 198 KDKTQTEVANMLGISQ---VQVSRLE 220 (231)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHH
Confidence 5789999999999998 6666554
No 308
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=30.85 E-value=59 Score=22.71 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=22.0
Q ss_pred HHHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 45 AVELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 45 aveLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
--|..|.+.+. +..|-.|||+++++.+
T Consensus 137 ~RE~eVL~ll~---~G~snkeIA~~L~iS~ 163 (207)
T PRK11475 137 PTEREILRFMS---RGYSMPQIAEQLERNI 163 (207)
T ss_pred HHHHHHHHHHH---CCCCHHHHHHHHCCCH
Confidence 35677777777 4589999999999987
No 309
>cd00131 PAX Paired Box domain
Probab=30.70 E-value=17 Score=23.73 Aligned_cols=34 Identities=12% Similarity=0.412 Sum_probs=24.5
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
....|.+... +..|..+||..+++.+ ..+.|+++
T Consensus 22 ~R~rIv~~~~---~G~s~~~iA~~~~Vs~---~tV~r~i~ 55 (128)
T cd00131 22 IRQRIVELAQ---SGIRPCDISRQLRVSH---GCVSKILN 55 (128)
T ss_pred HHHHHHHHHH---cCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 3345555444 4579999999999988 87887764
No 310
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=30.28 E-value=55 Score=23.99 Aligned_cols=24 Identities=25% Similarity=0.677 Sum_probs=19.5
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
..+.|..|||..+|+++ ..+.+++
T Consensus 267 ~~~~Tl~EIa~~lgiS~---erVrq~~ 290 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSR---ERVRQIE 290 (298)
T ss_pred CCCcCHHHHHHHHCcCH---HHHHHHH
Confidence 37899999999999998 6565543
No 311
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=29.87 E-value=57 Score=22.96 Aligned_cols=25 Identities=12% Similarity=0.294 Sum_probs=19.9
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|.+-|..|||+.+|+++ .-+.++++
T Consensus 101 g~~pt~~eia~~l~~~~---~~v~~~~~ 125 (238)
T TIGR02393 101 GREPTDEELAERMGMPA---EKVREIKK 125 (238)
T ss_pred CCCCCHHHHHHHhCCCH---HHHHHHHH
Confidence 56778999999999988 66666554
No 312
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=29.61 E-value=60 Score=20.86 Aligned_cols=22 Identities=14% Similarity=0.264 Sum_probs=17.5
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...|..|||+.+|+++ ..+++.
T Consensus 140 ~~~~~~eIA~~lgis~---~tv~~~ 161 (179)
T PRK11924 140 EGLSYREIAEILGVPV---GTVKSR 161 (179)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHH
Confidence 5689999999999988 555444
No 313
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=29.54 E-value=64 Score=19.09 Aligned_cols=28 Identities=25% Similarity=0.260 Sum_probs=21.3
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|...|-.+||+.+|.+. .+..+.+.|+.
T Consensus 15 G~v~TYg~iA~~~g~p~-~~R~Vg~al~~ 42 (79)
T cd06445 15 GEVTTYGQIAKLAGTPK-AARAVGSALAR 42 (79)
T ss_pred CCcCcHHHHHHHHCCCC-cHHHHHHHHHh
Confidence 68899999999999842 22677777764
No 314
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=29.05 E-value=73 Score=21.39 Aligned_cols=23 Identities=13% Similarity=0.268 Sum_probs=18.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
+..|-.|||+.+|+++ ..+.++.
T Consensus 20 ~GlTq~EIAe~LgiS~---stV~~~e 42 (137)
T TIGR00721 20 KGLSQKEIAKELKTTR---ANVSAIE 42 (137)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHH
Confidence 6789999999999988 6555443
No 315
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=28.79 E-value=56 Score=23.25 Aligned_cols=23 Identities=22% Similarity=0.306 Sum_probs=19.0
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
.+.|..|||..+|+.+ ..+.++.
T Consensus 221 ~~~t~~eIA~~lgis~---~~V~~~~ 243 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQ---AQVSRLE 243 (254)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHH
Confidence 6789999999999988 6666654
No 316
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=28.63 E-value=53 Score=17.08 Aligned_cols=29 Identities=21% Similarity=0.434 Sum_probs=19.3
Q ss_pred HHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 52 DVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 52 d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.|.+.+| ...+-|+.+|+++ ..|+|-|+
T Consensus 12 ~aL~~~~g--n~~~aA~~Lgisr---~tL~~klk 40 (42)
T PF02954_consen 12 QALERCGG--NVSKAARLLGISR---RTLYRKLK 40 (42)
T ss_dssp HHHHHTTT---HHHHHHHHTS-H---HHHHHHHH
T ss_pred HHHHHhCC--CHHHHHHHHCCCH---HHHHHHHH
Confidence 34554333 5678899999998 88888775
No 317
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.50 E-value=1.3e+02 Score=18.04 Aligned_cols=27 Identities=15% Similarity=0.223 Sum_probs=20.0
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|...|-.|||+.+|.+. .+..+.+.|+
T Consensus 17 G~v~TYg~iA~~~g~p~-~~RaVg~al~ 43 (80)
T TIGR00589 17 GETKSYGQLAARIGNPK-AVRAVGGANG 43 (80)
T ss_pred CCcCCHHHHHHHhCCCC-hHHHHHHHHH
Confidence 68899999999999532 3466766665
No 318
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=28.26 E-value=65 Score=26.19 Aligned_cols=38 Identities=8% Similarity=0.158 Sum_probs=27.4
Q ss_pred HHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 45 AVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 45 aveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.+..|...|.+.+...+..+||+.+|+++ +.+.+.+.
T Consensus 3 ~~e~~iL~~l~~~~~~~~~~~la~~~g~~~---~~v~~~~~ 40 (492)
T PLN02853 3 MAEEALLGALSNNEEISDSGQFAASHGLDH---NEVVGVIK 40 (492)
T ss_pred hHHHHHHHHHHhcCCCCCHHHHHHHcCCCH---HHHHHHHH
Confidence 456677788876422389999999999988 65655543
No 319
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=28.01 E-value=65 Score=21.14 Aligned_cols=16 Identities=25% Similarity=0.526 Sum_probs=14.3
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 151 ~g~s~~eIA~~lgis~ 166 (187)
T TIGR02948 151 EDLSLKEISEILDLPV 166 (187)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 4689999999999987
No 320
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=27.89 E-value=63 Score=21.16 Aligned_cols=16 Identities=19% Similarity=0.324 Sum_probs=14.4
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 133 eg~s~~EIA~~l~is~ 148 (168)
T PRK12525 133 EGLTYVEIGERLGVSL 148 (168)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5689999999999987
No 321
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=27.88 E-value=1.2e+02 Score=17.13 Aligned_cols=17 Identities=41% Similarity=0.622 Sum_probs=15.1
Q ss_pred CCCCCHHHHHHhcCCCC
Q 041968 58 GQPMTLSQIASALDIQK 74 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~ 74 (87)
+.|.|..||++.++++.
T Consensus 52 ~~~~t~~eIa~~~~Vs~ 68 (71)
T PF00382_consen 52 GVPRTLKEIAEAAGVSE 68 (71)
T ss_dssp TSSSSHHHHHHHCTSSH
T ss_pred CCCcCHHHHHHHhCCCC
Confidence 68999999999999865
No 322
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=27.50 E-value=66 Score=21.13 Aligned_cols=16 Identities=25% Similarity=0.383 Sum_probs=14.7
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 149 ~g~s~~EIA~~lgis~ 164 (183)
T TIGR02999 149 AGLTVEEIAELLGVSV 164 (183)
T ss_pred cCCCHHHHHHHhCCCH
Confidence 6789999999999988
No 323
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=27.39 E-value=64 Score=20.74 Aligned_cols=16 Identities=19% Similarity=0.189 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 121 ~g~s~~EIA~~lgis~ 136 (160)
T PRK09642 121 EEKSYQEIALQEKIEV 136 (160)
T ss_pred hCCCHHHHHHHHCCCH
Confidence 5689999999999988
No 324
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. 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=27.38 E-value=54 Score=20.23 Aligned_cols=18 Identities=11% Similarity=0.325 Sum_probs=14.0
Q ss_pred HHHHhcCCCCCChhhHHHHHh
Q 041968 65 QIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 65 ELA~~~~~~~~~~~~L~RlLR 85 (87)
+||+.+|+++ ..+.|+.+
T Consensus 48 qLAe~~GIs~---stLs~iE~ 65 (89)
T TIGR02684 48 QLARKTGLSR---ESLYKALS 65 (89)
T ss_pred HHHHHHCCCH---HHHHHHHc
Confidence 7999999887 77777654
No 325
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=27.37 E-value=62 Score=20.66 Aligned_cols=16 Identities=19% Similarity=0.385 Sum_probs=14.4
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 121 ~g~s~~EIA~~lgis~ 136 (161)
T PRK09047 121 EDMDVAETAAAMGCSE 136 (161)
T ss_pred hcCCHHHHHHHHCCCH
Confidence 5688999999999987
No 326
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=27.32 E-value=68 Score=20.91 Aligned_cols=16 Identities=6% Similarity=0.009 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 127 ~g~s~~eIA~~lgis~ 142 (164)
T PRK12547 127 SGFSYEDAAAICGCAV 142 (164)
T ss_pred cCCCHHHHHHHhCCCH
Confidence 5689999999999988
No 327
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=26.93 E-value=74 Score=19.44 Aligned_cols=23 Identities=4% Similarity=0.247 Sum_probs=13.1
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
...|+.+||...|..+ ..+.-.|
T Consensus 14 rG~sL~~lsr~~Gl~~---~tl~nal 36 (78)
T PF13693_consen 14 RGTSLAALSREAGLSS---STLRNAL 36 (78)
T ss_dssp TS--HHHHHHHHSS-H---HHHHHTT
T ss_pred cCCCHHHHHHHcCCCH---HHHHHHH
Confidence 4578888888888776 5554433
No 328
>PRK05949 RNA polymerase sigma factor; Validated
Probab=26.86 E-value=68 Score=24.19 Aligned_cols=23 Identities=17% Similarity=0.608 Sum_probs=18.7
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
+++.|..|||..+|+.. ..+.++
T Consensus 284 ~e~~Tl~EIa~~lgiS~---erVrq~ 306 (327)
T PRK05949 284 GKELSLAKVGERLNLSR---ERVRQL 306 (327)
T ss_pred CCCCCHHHHHHHHCcCH---HHHHHH
Confidence 37899999999999988 555444
No 329
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=26.82 E-value=78 Score=25.70 Aligned_cols=38 Identities=13% Similarity=0.169 Sum_probs=27.6
Q ss_pred HHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 45 AVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 45 aveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..+..|...|.+.++..+..+||+.+|+++ +.+.+.+.
T Consensus 6 ~~e~~iL~~l~~~~~~~~~~~la~~~~~~~---~~v~~~~~ 43 (494)
T PTZ00326 6 LEENTILSKLESENEIVNSLALAESLNIDH---QKVVGAIK 43 (494)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHcCCCH---HHHHHHHH
Confidence 345566777775346799999999999988 65655543
No 330
>PF08256 Antimicrobial20: Aurein-like antibiotic peptide; InterPro: IPR013157 This family of antibacterial peptides are secreted from the granular dorsal glands of Litoria aurea (Green and golden bell frog), Litoria raniformis (Southern bell frog), Litoria citropa (Australian blue mountains tree frog) and frogs from genus Uperoleia. They are a part of the FSAP peptide family. Amongst the more active of these are aurein 1.2, aurein 2.2 and aurein 3.1; caerin 1.1, maculatin 1.1, uperin 3.6 []; citropin 1.1, citropin 1.2, citropin 1.3 and a minor peptide are wide-spectrum antibacterial peptides [].; GO: 0006952 defense response
Probab=26.80 E-value=40 Score=13.99 Aligned_cols=8 Identities=38% Similarity=0.684 Sum_probs=5.3
Q ss_pred CchHHHHh
Q 041968 49 GIPDVIHK 56 (87)
Q Consensus 49 gI~d~L~~ 56 (87)
|+||++.+
T Consensus 1 Gl~Di~Kk 8 (13)
T PF08256_consen 1 GLFDIAKK 8 (13)
T ss_pred CHHHHHHH
Confidence 67777654
No 331
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=26.71 E-value=71 Score=20.34 Aligned_cols=24 Identities=17% Similarity=0.126 Sum_probs=18.3
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+..|+.++|...|+++ ..+++=.|
T Consensus 28 ~g~sv~evA~e~gIs~---~tl~~W~r 51 (121)
T PRK09413 28 PGMTVSLVARQHGVAA---SQLFLWRK 51 (121)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHHH
Confidence 5678999999999887 77766443
No 332
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=26.70 E-value=71 Score=20.28 Aligned_cols=16 Identities=19% Similarity=0.189 Sum_probs=14.4
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 121 ~~~s~~EIA~~l~is~ 136 (154)
T PRK06759 121 VGKTMGEIALETEMTY 136 (154)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5689999999999987
No 333
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=26.63 E-value=41 Score=26.41 Aligned_cols=27 Identities=19% Similarity=0.405 Sum_probs=20.4
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
...+|..||++.+|.++ ..+.|.|..|
T Consensus 532 ~~~~t~~ei~~~~~~~~---~~l~~~L~~l 558 (588)
T PF00888_consen 532 NDSLTVEEISEKTGISE---EELKRALKSL 558 (588)
T ss_dssp SSEEEHHHHHHHC---H---HHHHHHHHCC
T ss_pred CCCccHHHHHHHHCcCH---HHHHHHHHHH
Confidence 47899999999999999 8898888654
No 334
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=26.40 E-value=64 Score=23.68 Aligned_cols=24 Identities=21% Similarity=0.343 Sum_probs=19.6
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
.+.|..|||+.+|+++ ..+.++++
T Consensus 244 ~~~t~~EIa~~lgvs~---~~V~q~~~ 267 (289)
T PRK07500 244 DGATLEALGEELGISK---ERVRQIEA 267 (289)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence 6899999999999998 66665543
No 335
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=26.21 E-value=81 Score=22.15 Aligned_cols=18 Identities=33% Similarity=0.687 Sum_probs=15.4
Q ss_pred CCCCCCHHHHHHhcCC-CC
Q 041968 57 HGQPMTLSQIASALDI-QK 74 (87)
Q Consensus 57 ~~gp~S~~ELA~~~~~-~~ 74 (87)
.+.|+|..+|++.++. ++
T Consensus 20 ~~~pls~~~L~~il~~~~~ 38 (184)
T COG1386 20 GGEPLSLKELAEILGIVSA 38 (184)
T ss_pred cCCCCCHHHHHHHhCCCch
Confidence 3589999999999998 44
No 336
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=25.98 E-value=77 Score=19.36 Aligned_cols=27 Identities=26% Similarity=0.361 Sum_probs=17.9
Q ss_pred hCchHHHHh--CCCCCCHHHHHHhcCCCC
Q 041968 48 LGIPDVIHK--HGQPMTLSQIASALDIQK 74 (87)
Q Consensus 48 LgI~d~L~~--~~gp~S~~ELA~~~~~~~ 74 (87)
..+.+.|.+ .+||..++-||..++-++
T Consensus 11 ~~yL~~l~~~f~ggPvGl~tlA~~l~ed~ 39 (76)
T PF05491_consen 11 RRYLKTLIENFKGGPVGLDTLAAALGEDK 39 (76)
T ss_dssp HHHHHHHHHCSTTS-B-HHHHHHHTTS-H
T ss_pred HHHHHHHHHHcCCCCeeHHHHHHHHCCCH
Confidence 344555655 379999999999999877
No 337
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=25.96 E-value=70 Score=22.31 Aligned_cols=22 Identities=27% Similarity=0.431 Sum_probs=17.6
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...|..|||+.+|+++ ..+.+.
T Consensus 193 e~~S~~EIAe~lgis~---~tV~~~ 214 (227)
T TIGR02846 193 RRKTQREIAKILGISR---SYVSRI 214 (227)
T ss_pred CCcCHHHHHHHHCCCH---HHHHHH
Confidence 5689999999999998 555444
No 338
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=25.57 E-value=71 Score=22.64 Aligned_cols=23 Identities=17% Similarity=0.335 Sum_probs=18.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
...|..|||+.+|+++ ..+.+.+
T Consensus 220 ~g~s~~eIA~~l~is~---~tV~~~~ 242 (257)
T PRK08583 220 ENLSQKETGERLGISQ---MHVSRLQ 242 (257)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHHH
Confidence 6789999999999998 6555544
No 339
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=25.53 E-value=67 Score=24.53 Aligned_cols=23 Identities=17% Similarity=0.502 Sum_probs=18.9
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
+.+.|..|||..+|+.. ..+.++
T Consensus 323 ~~~~tl~EIa~~lgvs~---erVrQi 345 (367)
T PRK09210 323 GRTRTLEEVGKVFGVTR---ERIRQI 345 (367)
T ss_pred CCCccHHHHHHHHCCCH---HHHHHH
Confidence 37899999999999988 555554
No 340
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=25.53 E-value=69 Score=22.66 Aligned_cols=23 Identities=35% Similarity=0.455 Sum_probs=19.2
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
+..|..|||+.+|+++ ..+.|+.
T Consensus 198 ~~~t~~EIA~~lgis~---~~V~q~~ 220 (231)
T PRK12427 198 HEMSLKEIALVLDLTE---ARICQLN 220 (231)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHH
Confidence 6899999999999998 6666554
No 341
>cd06459 M3B_Oligoendopeptidase_F Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the PepF Bacillus amyloliquefaciens oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over expressed from a multicopy plasmid.
Probab=25.52 E-value=2.9e+02 Score=20.68 Aligned_cols=33 Identities=3% Similarity=0.152 Sum_probs=26.3
Q ss_pred HHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 53 VIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 53 ~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
+|. .||..+..|+.+.+|+++.++..+.+.+..
T Consensus 393 ~L~-~Ggs~~~~ell~~~g~d~~~~~~~~~~~~~ 425 (427)
T cd06459 393 LLK-AGGSKSPLELLKKAGVDLTSPDFWEEAIDV 425 (427)
T ss_pred HHH-ccCCCCHHHHHHHcCcCCCChHHHHHHHHh
Confidence 444 478899999999999988777888877654
No 342
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=25.47 E-value=62 Score=18.35 Aligned_cols=27 Identities=30% Similarity=0.442 Sum_probs=15.2
Q ss_pred CCCCCHHHHHHhc---CCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASAL---DIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~---~~~~~~~~~L~RlLR 85 (87)
+...|..||+..+ |.+.+. ..+.|.|+
T Consensus 11 ~p~~s~~~i~~~l~~~~~~vS~-~TI~r~L~ 40 (72)
T PF01498_consen 11 NPRISAREIAQELQEAGISVSK-STIRRRLR 40 (72)
T ss_dssp -----HHHHHHHT---T--S-H-HHHHHHHH
T ss_pred CCCCCHHHHHHHHHHccCCcCH-HHHHHHHH
Confidence 3568999999998 543322 78888876
No 343
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=25.16 E-value=97 Score=20.78 Aligned_cols=26 Identities=15% Similarity=0.193 Sum_probs=20.2
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
-|.-|...+. +..|..|||+++++.+
T Consensus 154 rE~evl~~~~---~G~s~~eIA~~l~iS~ 179 (216)
T PRK10840 154 KESEVLRLFA---EGFLVTEIAKKLNRSI 179 (216)
T ss_pred HHHHHHHHHH---CCCCHHHHHHHHCCCH
Confidence 4555666666 4589999999999977
No 344
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=25.15 E-value=39 Score=21.21 Aligned_cols=27 Identities=26% Similarity=0.380 Sum_probs=21.7
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCC
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQ 73 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~ 73 (87)
.|+-|.++|.+. ++.|+.||.+.++-+
T Consensus 4 ~E~~IM~~lW~~-~~~t~~eI~~~l~~~ 30 (115)
T PF03965_consen 4 LELEIMEILWES-GEATVREIHEALPEE 30 (115)
T ss_dssp HHHHHHHHHHHH-SSEEHHHHHHHHCTT
T ss_pred HHHHHHHHHHhC-CCCCHHHHHHHHHhc
Confidence 466778888876 569999999999865
No 345
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=25.12 E-value=74 Score=21.08 Aligned_cols=16 Identities=25% Similarity=0.316 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 143 ~g~s~~EIA~~lgis~ 158 (186)
T PRK05602 143 QGLSNIEAAAVMDISV 158 (186)
T ss_pred cCCCHHHHHHHhCcCH
Confidence 5789999999999988
No 346
>PRK05572 sporulation sigma factor SigF; Validated
Probab=25.05 E-value=71 Score=22.65 Aligned_cols=23 Identities=30% Similarity=0.358 Sum_probs=18.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
+..|..|||..+|+.+ ..++++.
T Consensus 217 ~~~s~~eIA~~lgis~---~~V~~~~ 239 (252)
T PRK05572 217 KDKTQSEVAKRLGISQ---VQVSRLE 239 (252)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHH
Confidence 6799999999999998 6565543
No 347
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=25.01 E-value=76 Score=21.95 Aligned_cols=22 Identities=14% Similarity=0.431 Sum_probs=17.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...|..|||..+|+++ ..+.+.
T Consensus 190 ~~~s~~eIA~~lgis~---~tV~~~ 211 (224)
T TIGR02479 190 EELNLKEIGEVLGLTE---SRVSQI 211 (224)
T ss_pred CCCCHHHHHHHhCCCH---HHHHHH
Confidence 6789999999999988 555543
No 348
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=24.89 E-value=81 Score=20.53 Aligned_cols=16 Identities=25% Similarity=0.380 Sum_probs=14.7
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 135 ~g~s~~eIA~~lg~s~ 150 (175)
T PRK12518 135 EDLPQKEIAEILNIPV 150 (175)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 6789999999999988
No 349
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=24.84 E-value=92 Score=20.59 Aligned_cols=16 Identities=19% Similarity=0.277 Sum_probs=14.7
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||..+|+++
T Consensus 152 ~g~s~~eIA~~lgis~ 167 (187)
T PRK12534 152 EGITYEELAARTDTPI 167 (187)
T ss_pred cCCCHHHHHHHhCCCh
Confidence 5689999999999988
No 350
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=24.84 E-value=83 Score=20.49 Aligned_cols=16 Identities=31% Similarity=0.401 Sum_probs=14.5
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 133 ~g~s~~EIA~~lgis~ 148 (173)
T PRK09645 133 RGWSTAQIAADLGIPE 148 (173)
T ss_pred cCCCHHHHHHHHCcCH
Confidence 5689999999999988
No 351
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=24.82 E-value=71 Score=24.36 Aligned_cols=25 Identities=20% Similarity=0.454 Sum_probs=20.4
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|..-|..|||..+|+++ +-+..+++
T Consensus 230 gr~pt~~EiA~~l~~~~---~~v~~~~~ 254 (367)
T PRK09210 230 GREPTPEEIAEEMDMPP---EKVREILK 254 (367)
T ss_pred CCCCCHHHHHHHhCcCH---HHHHHHHH
Confidence 46669999999999998 76777665
No 352
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=24.71 E-value=45 Score=26.58 Aligned_cols=25 Identities=24% Similarity=0.434 Sum_probs=21.9
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
..+|+.|||..+.|.+ ...+++|+-
T Consensus 22 ~~~~l~~la~~l~cs~---R~~~~~l~~ 46 (552)
T PRK13626 22 QETTLNELAELLNCSR---RHMRTLLNT 46 (552)
T ss_pred ceeeHHHHHHHhcCCh---hHHHHHHHH
Confidence 6789999999999999 888888874
No 353
>PRK09483 response regulator; Provisional
Probab=24.69 E-value=1e+02 Score=20.16 Aligned_cols=26 Identities=23% Similarity=0.317 Sum_probs=18.7
Q ss_pred HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 46 VELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
-|..|...+. ...|..|||+.+++.+
T Consensus 152 rE~~vl~~~~---~G~~~~~Ia~~l~is~ 177 (217)
T PRK09483 152 RELQIMLMIT---KGQKVNEISEQLNLSP 177 (217)
T ss_pred HHHHHHHHHH---CCCCHHHHHHHhCCCH
Confidence 3445555555 4578999999999876
No 354
>PF08668 HDOD: HDOD domain; InterPro: IPR013976 This domain is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These members appear to be involved in the nucleic acid metabolism and signal transduction or possibly other functions and are restricted to bacteria, primarily the proteobacteria. The fact that all the highly conserved residues in the HD superfamily are histidines or aspartates suggests that coordination of divalent cations is essential for the activity of these proteins [].; PDB: 1VQR_D 3LJX_A 3P3Q_B 3MEM_A 3M1T_A 3HC1_A 3I7A_A.
Probab=24.62 E-value=68 Score=21.47 Aligned_cols=32 Identities=13% Similarity=0.375 Sum_probs=24.1
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI 86 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~ 86 (87)
|...+. +...+..+|++.+.-|| .+..+|||.
T Consensus 11 l~~~l~--~~~~~~~~l~~~i~~Dp---~L~~~lL~~ 42 (196)
T PF08668_consen 11 LLSLLN--DPEASIDELAELIESDP---ALAARLLRL 42 (196)
T ss_dssp HHHHHH--STTS-HHHHHHHHHTSH---HHHHHHHHH
T ss_pred HHHHHc--CCCCCHHHHHHHHHHCH---HHHHHHHHH
Confidence 344454 35679999999999999 989998874
No 355
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=24.62 E-value=75 Score=22.21 Aligned_cols=23 Identities=30% Similarity=0.436 Sum_probs=18.8
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
...|..|||+.+|+++ ..+.+.+
T Consensus 194 e~~S~~EIA~~lgis~---~tV~~~~ 216 (233)
T PRK05803 194 KEKTQREIAKALGISR---SYVSRIE 216 (233)
T ss_pred CCcCHHHHHHHHCcCH---HHHHHHH
Confidence 6789999999999998 6565553
No 356
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=24.48 E-value=90 Score=22.09 Aligned_cols=33 Identities=24% Similarity=0.400 Sum_probs=22.3
Q ss_pred HHHHhCCCCCCHHHHHHhcCCCCCCh-hhHHHHHh
Q 041968 52 DVIHKHGQPMTLSQIASALDIQKNKA-HCIQRLMR 85 (87)
Q Consensus 52 d~L~~~~gp~S~~ELA~~~~~~~~~~-~~L~RlLR 85 (87)
+-|.. ++..|+.+||.++|++.... ..|++|.|
T Consensus 20 ~~l~~-~~~~~a~~i~~~l~~~k~~vNr~LY~l~~ 53 (183)
T PHA03103 20 KNLGL-GEGITAIEISRKLNIEKSEVNKQLYKLQR 53 (183)
T ss_pred HHhcc-CCCccHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 33443 58999999999999976211 34666655
No 357
>PRK00441 argR arginine repressor; Provisional
Probab=24.38 E-value=1.2e+02 Score=20.42 Aligned_cols=34 Identities=24% Similarity=0.389 Sum_probs=25.4
Q ss_pred chHHHHhCCCCCCHHHHHHhc-----CCCCCChhhHHHHHhcC
Q 041968 50 IPDVIHKHGQPMTLSQIASAL-----DIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~-----~~~~~~~~~L~RlLR~L 87 (87)
|.+.|.+ .+..|..||++.+ ++.. ..+.|-|+.|
T Consensus 9 I~~ll~~-~~~~~q~eL~~~L~~~G~~vSq---aTisRDl~~L 47 (149)
T PRK00441 9 ILEIINS-KEIETQEELAEELKKMGFDVTQ---ATVSRDIKEL 47 (149)
T ss_pred HHHHHHH-cCCCcHHHHHHHHHhcCCCcCH---HHHHHHHHHc
Confidence 4566766 3788999999997 5655 7788887754
No 358
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=24.32 E-value=78 Score=20.75 Aligned_cols=16 Identities=25% Similarity=0.526 Sum_probs=14.5
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 151 ~~~s~~eIA~~lgis~ 166 (187)
T PRK09641 151 EDLSLKEISEILDLPV 166 (187)
T ss_pred hCCCHHHHHHHHCCCH
Confidence 5689999999999987
No 359
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=24.03 E-value=82 Score=20.28 Aligned_cols=16 Identities=13% Similarity=0.243 Sum_probs=14.4
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 143 ~~~s~~eIA~~lgis~ 158 (182)
T PRK09652 143 EGLSYEEIAEIMGCPI 158 (182)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5679999999999988
No 360
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.01 E-value=82 Score=20.91 Aligned_cols=16 Identities=44% Similarity=0.470 Sum_probs=14.4
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 142 ~g~s~~EIA~~lgis~ 157 (178)
T PRK12529 142 DGMKQKDIAQALDIAL 157 (178)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5689999999999987
No 361
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=23.79 E-value=73 Score=18.20 Aligned_cols=17 Identities=18% Similarity=0.339 Sum_probs=11.2
Q ss_pred CCCCCHHHHHHhcCCCC
Q 041968 58 GQPMTLSQIASALDIQK 74 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~ 74 (87)
...+|..|+|..+++.+
T Consensus 8 ~~glsl~~va~~t~I~~ 24 (62)
T PF13413_consen 8 AKGLSLEDVAEETKISV 24 (62)
T ss_dssp CTT--HHHHHHHCS--H
T ss_pred HcCCCHHHHHHHhCCCH
Confidence 36789999999999877
No 362
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=23.52 E-value=56 Score=22.65 Aligned_cols=17 Identities=12% Similarity=0.214 Sum_probs=15.4
Q ss_pred CCCCCHHHHHHhcCCCC
Q 041968 58 GQPMTLSQIASALDIQK 74 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~ 74 (87)
.|++|++|||...|+.+
T Consensus 4 ~Ga~T~eELA~~FGvtt 20 (155)
T PF07789_consen 4 EGAKTAEELAGKFGVTT 20 (155)
T ss_pred cCcccHHHHHHHhCcch
Confidence 48999999999999876
No 363
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=23.37 E-value=84 Score=21.04 Aligned_cols=16 Identities=6% Similarity=0.034 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||..+|+++
T Consensus 145 ~g~s~~EIA~~lgis~ 160 (185)
T PRK09649 145 LGLSYADAAAVCGCPV 160 (185)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 6789999999999988
No 364
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.36 E-value=83 Score=21.96 Aligned_cols=22 Identities=14% Similarity=0.359 Sum_probs=17.6
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
+..|..|||+.+|+++ ..+++.
T Consensus 164 ~g~s~~EIAe~lgis~---~tVk~~ 185 (231)
T PRK11922 164 EELSVEETAQALGLPE---ETVKTR 185 (231)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHH
Confidence 6789999999999988 544443
No 365
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=23.35 E-value=82 Score=20.94 Aligned_cols=16 Identities=19% Similarity=0.295 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 153 ~g~s~~eIA~~lgis~ 168 (193)
T PRK11923 153 DGLSYEDIASVMQCPV 168 (193)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5789999999999987
No 366
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=23.34 E-value=85 Score=21.86 Aligned_cols=16 Identities=6% Similarity=0.117 Sum_probs=13.4
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|+.|+|+..|++.
T Consensus 68 aGas~eeVA~~~G~~~ 83 (170)
T PF11268_consen 68 AGASAEEVAEEAGVPV 83 (170)
T ss_pred CCCCHHHHHHHhCCCH
Confidence 4579999999999876
No 367
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=23.33 E-value=75 Score=21.46 Aligned_cols=24 Identities=13% Similarity=0.192 Sum_probs=18.4
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..+|..|||+.+|+++ ..+.++.+
T Consensus 19 ~glt~~elA~~~gis~---~~is~~E~ 42 (185)
T PRK09943 19 QGLSQRRAAELSGLTH---SAISTIEQ 42 (185)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHHHc
Confidence 6689999999999877 66666543
No 368
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=23.21 E-value=1.1e+02 Score=23.18 Aligned_cols=19 Identities=11% Similarity=0.228 Sum_probs=16.1
Q ss_pred CCCCCHHHHHHhcCCCCCC
Q 041968 58 GQPMTLSQIASALDIQKNK 76 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~ 76 (87)
++.+|+.+|+..+++.+++
T Consensus 221 ~~~isi~~is~~T~i~~~D 239 (290)
T PLN03238 221 KGDVSIKDLSLATGIRGED 239 (290)
T ss_pred CCCccHHHHHHHhCCCHHH
Confidence 4789999999999997733
No 369
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=23.20 E-value=59 Score=25.67 Aligned_cols=19 Identities=16% Similarity=0.364 Sum_probs=15.6
Q ss_pred CCCHHHHHHhcCCCCCChhhHH
Q 041968 60 PMTLSQIASALDIQKNKAHCIQ 81 (87)
Q Consensus 60 p~S~~ELA~~~~~~~~~~~~L~ 81 (87)
.-|++|||+++|+|+ +.|.
T Consensus 375 aDTleELA~k~gid~---~~L~ 393 (513)
T PRK12837 375 ADTLEELAAKIGVPA---DALT 393 (513)
T ss_pred cCCHHHHHHHcCCCH---HHHH
Confidence 349999999999998 6554
No 370
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=23.19 E-value=89 Score=20.57 Aligned_cols=16 Identities=19% Similarity=0.333 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||..+|+++
T Consensus 115 ~g~s~~eIA~~lgis~ 130 (170)
T TIGR02959 115 EGLSQQEIAEKLGLSL 130 (170)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5689999999999988
No 371
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=23.15 E-value=1.1e+02 Score=20.62 Aligned_cols=23 Identities=17% Similarity=0.281 Sum_probs=17.6
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
...|-.|||+.+|++. ..+.++.
T Consensus 20 ~GlTq~EIAe~LGiS~---~tVs~ie 42 (141)
T PRK03975 20 RGLTQQEIADILGTSR---ANVSSIE 42 (141)
T ss_pred cCCCHHHHHHHHCCCH---HHHHHHH
Confidence 5689999999999987 5554443
No 372
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=23.14 E-value=1e+02 Score=22.34 Aligned_cols=28 Identities=14% Similarity=0.033 Sum_probs=22.2
Q ss_pred HHHHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 44 CAVELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
+.-|..|+..++ ...|..|||+++++.+
T Consensus 145 S~RE~eVL~Lia---~G~SnkEIA~~L~IS~ 172 (217)
T PRK13719 145 TKYQNDVFILYS---FGFSHEYIAQLLNITV 172 (217)
T ss_pred CHHHHHHHHHHH---CCCCHHHHHHHhCCCH
Confidence 446777788787 4589999999999877
No 373
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=23.10 E-value=72 Score=17.42 Aligned_cols=23 Identities=22% Similarity=0.401 Sum_probs=15.2
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
..+|..++|..+|+++ ..+.++.
T Consensus 11 ~~lt~~~~a~~~~i~~---~~i~~~e 33 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISR---STISKIE 33 (64)
T ss_dssp CT--HHHHHHHHTS-H---HHHHHHH
T ss_pred cCCCHHHHHHHHCcCH---HHHHHHH
Confidence 5678999999999877 6666554
No 374
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=23.10 E-value=82 Score=22.40 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=18.1
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...|..|||..+|+++ ..+.++
T Consensus 224 ~~~t~~eIA~~lgis~---~~V~~~ 245 (258)
T PRK08215 224 QGKTQMEVAEEIGISQ---AQVSRL 245 (258)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHH
Confidence 5689999999999988 656554
No 375
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=23.09 E-value=82 Score=21.74 Aligned_cols=22 Identities=36% Similarity=0.449 Sum_probs=17.5
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...|..|||+.+|+++ ..+++.
T Consensus 193 ~~~s~~eIA~~lgis~---~~v~~~ 214 (227)
T TIGR02980 193 EDKTQSEIAERLGISQ---MHVSRL 214 (227)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHH
Confidence 5689999999999988 555444
No 376
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=23.07 E-value=85 Score=21.98 Aligned_cols=22 Identities=32% Similarity=0.427 Sum_probs=17.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
+..|..|||+.+|+++ ..+.+.
T Consensus 197 eg~s~~EIA~~Lgis~---~tV~~~ 218 (234)
T TIGR02835 197 TEKTQKEVADMLGISQ---SYISRL 218 (234)
T ss_pred CCCCHHHHHHHHCCCH---HHHHHH
Confidence 6799999999999988 544443
No 377
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=23.06 E-value=85 Score=24.82 Aligned_cols=23 Identities=26% Similarity=0.641 Sum_probs=18.8
Q ss_pred CCCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 58 GQPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
+++.|..|||..+|++. ..+.++
T Consensus 368 ~~~~Tl~EIA~~LGvS~---erVRqi 390 (415)
T PRK07598 368 GHTYSLAEIGRALDLSR---ERVRQI 390 (415)
T ss_pred CCCCCHHHHHHHHCcCH---HHHHHH
Confidence 47999999999999988 555444
No 378
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=22.93 E-value=87 Score=21.75 Aligned_cols=16 Identities=25% Similarity=0.368 Sum_probs=14.8
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 197 eg~s~~EIA~~lgis~ 212 (234)
T PRK08301 197 EEKTQKEVADMLGISQ 212 (234)
T ss_pred CCCCHHHHHHHHCCCH
Confidence 5789999999999988
No 379
>COG1164 Oligoendopeptidase F [Amino acid transport and metabolism]
Probab=22.84 E-value=3e+02 Score=22.70 Aligned_cols=56 Identities=9% Similarity=0.089 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhC--------chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 27 AQVWNCAFNYINSMSLKCAVELG--------IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 27 ~~l~~l~~g~~~~~aL~aaveLg--------I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
..++...+|++...++..-+.-+ +.+.|. .||..++.||....|+|...++.++-.
T Consensus 518 FYvy~Ya~G~~~a~~l~~~~~~~~~~~~~~~y~~~Lk-~GgS~~p~ell~~~GiD~~~~~~~~~a 581 (598)
T COG1164 518 FYVYQYATGQLAALALYAKILTNDAEAFEKYYIAFLK-SGGSKSPLELLKIAGIDLTTPDPWEEA 581 (598)
T ss_pred ceehHhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHh-CCCCCCHHHHHHHcCCCCCCchHHHHH
Confidence 34566777777777776666655 335555 479999999999999987655555433
No 380
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=22.78 E-value=94 Score=20.47 Aligned_cols=16 Identities=25% Similarity=0.173 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 150 ~~~s~~eIA~~lgis~ 165 (186)
T PRK13919 150 QGYTHREAAQLLGLPL 165 (186)
T ss_pred cCCCHHHHHHHHCcCH
Confidence 5789999999999987
No 381
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=22.74 E-value=57 Score=18.44 Aligned_cols=24 Identities=13% Similarity=0.194 Sum_probs=17.6
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+..|+.++|...|+++ ..|++=.+
T Consensus 22 ~g~sv~~va~~~gi~~---~~l~~W~~ 45 (76)
T PF01527_consen 22 SGESVSEVAREYGISP---STLYNWRK 45 (76)
T ss_dssp HHCHHHHHHHHHTS-H---HHHHHHHH
T ss_pred CCCceEeeeccccccc---ccccHHHH
Confidence 3478999999999988 77776443
No 382
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=22.46 E-value=85 Score=18.71 Aligned_cols=18 Identities=22% Similarity=0.333 Sum_probs=12.8
Q ss_pred chHHHHhCCCCCCHHHHHHhc
Q 041968 50 IPDVIHKHGQPMTLSQIASAL 70 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~ 70 (87)
|++.+. |+.|+.||+..+
T Consensus 36 Iw~lld---g~~tv~eI~~~L 53 (81)
T TIGR03859 36 ILELCD---GKRSLAEIIQEL 53 (81)
T ss_pred HHHHcc---CCCcHHHHHHHH
Confidence 444443 788999988877
No 383
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=22.46 E-value=98 Score=23.15 Aligned_cols=34 Identities=18% Similarity=0.334 Sum_probs=25.4
Q ss_pred hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
+.|..+|..... +|+.+||+.++++. ..++|=++
T Consensus 11 ~~ii~~L~~~~~-vta~~lA~~~~VS~---RTi~RDi~ 44 (311)
T COG2378 11 LQIIQILRAKET-VTAAELADEFEVSV---RTIYRDIA 44 (311)
T ss_pred HHHHHHHHhCcc-chHHHHHHhcCCCH---HHHHHHHH
Confidence 345555665435 99999999999998 88888554
No 384
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=22.38 E-value=84 Score=22.79 Aligned_cols=22 Identities=18% Similarity=0.578 Sum_probs=17.7
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...|..|||..+|+++ ..+.+.
T Consensus 241 e~~s~~EIA~~Lgis~---~tVk~~ 262 (285)
T TIGR02394 241 EPATLEEVAAEVGLTR---ERVRQI 262 (285)
T ss_pred CCccHHHHHHHHCCCH---HHHHHH
Confidence 6789999999999988 545443
No 385
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=22.33 E-value=90 Score=19.73 Aligned_cols=16 Identities=19% Similarity=0.385 Sum_probs=14.7
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
+..|..|||+.+|+++
T Consensus 120 ~g~s~~eIA~~lgis~ 135 (154)
T TIGR02950 120 KEFSYKEIAELLNLSL 135 (154)
T ss_pred ccCcHHHHHHHHCCCH
Confidence 6789999999999988
No 386
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=22.21 E-value=80 Score=20.19 Aligned_cols=25 Identities=20% Similarity=0.373 Sum_probs=21.0
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQ 73 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~ 73 (87)
+|+..|-..+.|.|+.||...++..
T Consensus 7 kii~lL~e~~eplt~~ei~~~~~~~ 31 (97)
T COG3357 7 KIISLLLESDEPLTVAEIFELLNGE 31 (97)
T ss_pred HHHHHHHcCCCcchHHHHHHHHcCC
Confidence 5677777767899999999999875
No 387
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=22.20 E-value=91 Score=21.77 Aligned_cols=21 Identities=14% Similarity=0.430 Sum_probs=17.2
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
...|..|||..+|+++ ..+.+
T Consensus 199 ~g~s~~EIA~~lgis~---~tV~~ 219 (236)
T PRK06986 199 EELNLKEIGAVLGVSE---SRVSQ 219 (236)
T ss_pred cCCCHHHHHHHHCCCH---HHHHH
Confidence 6789999999999988 55543
No 388
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=22.18 E-value=91 Score=20.94 Aligned_cols=16 Identities=25% Similarity=0.318 Sum_probs=14.5
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 149 ~g~s~~EIA~~lgis~ 164 (189)
T PRK12530 149 LELSSEQICQECDIST 164 (189)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5689999999999988
No 389
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=21.95 E-value=1.4e+02 Score=15.82 Aligned_cols=25 Identities=24% Similarity=0.274 Sum_probs=18.4
Q ss_pred HhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968 47 ELGIPDVIHKHGQPMTLSQIASALDIQK 74 (87)
Q Consensus 47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~ 74 (87)
|.-+...+.. | .|..|||..++.++
T Consensus 9 E~~v~~l~~~--G-~s~~eia~~l~is~ 33 (65)
T COG2771 9 EREILRLVAQ--G-KSNKEIARILGISE 33 (65)
T ss_pred HHHHHHHHHC--C-CCHHHHHHHHCCCH
Confidence 4445555662 3 89999999999887
No 390
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=21.92 E-value=1.7e+02 Score=21.79 Aligned_cols=17 Identities=29% Similarity=0.438 Sum_probs=15.4
Q ss_pred CCCCCHHHHHHhcCCCC
Q 041968 58 GQPMTLSQIASALDIQK 74 (87)
Q Consensus 58 ~gp~S~~ELA~~~~~~~ 74 (87)
+-|.|+.||+..++++.
T Consensus 180 ~~prtl~eI~~~~~v~~ 196 (310)
T PRK00423 180 KVPRTLDEIAEVSRVSR 196 (310)
T ss_pred CCCcCHHHHHHHhCCCH
Confidence 68999999999999877
No 391
>PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=21.92 E-value=65 Score=26.01 Aligned_cols=21 Identities=10% Similarity=0.221 Sum_probs=16.6
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQR 82 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~R 82 (87)
+.-|++|||+++|+|+ +.|..
T Consensus 423 kadTleELA~k~gid~---~~L~~ 443 (564)
T PRK12845 423 RADSLADLARKIGVPV---DTFVA 443 (564)
T ss_pred ecCCHHHHHHHcCCCH---HHHHH
Confidence 3459999999999998 65543
No 392
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=21.81 E-value=96 Score=20.36 Aligned_cols=16 Identities=19% Similarity=0.322 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 153 ~~~s~~EIA~~lgis~ 168 (190)
T TIGR02939 153 EGLSYEDIARIMDCPV 168 (190)
T ss_pred cCCCHHHHHHHHCcCH
Confidence 6789999999999987
No 393
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=21.80 E-value=95 Score=24.05 Aligned_cols=23 Identities=17% Similarity=0.378 Sum_probs=18.8
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
.+.|..|||..+|++. ..++++.
T Consensus 330 ~~~Tl~EIA~~lgiS~---eRVRQie 352 (373)
T PRK07406 330 RMKTLEEIGQIFNVTR---ERIRQIE 352 (373)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHH
Confidence 5899999999999998 6565543
No 394
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=21.60 E-value=98 Score=20.54 Aligned_cols=16 Identities=13% Similarity=0.123 Sum_probs=14.3
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
+..|..|||+.+|+++
T Consensus 154 ~g~s~~EIA~~lgis~ 169 (189)
T PRK09648 154 VGLSAEETAEAVGSTP 169 (189)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 4689999999999987
No 395
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=21.46 E-value=97 Score=20.67 Aligned_cols=16 Identities=19% Similarity=0.318 Sum_probs=14.7
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 154 ~g~s~~EIA~~lgis~ 169 (194)
T PRK12513 154 GDLELEEIAELTGVPE 169 (194)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 6789999999999988
No 396
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=21.45 E-value=1.7e+02 Score=16.52 Aligned_cols=23 Identities=13% Similarity=0.319 Sum_probs=14.8
Q ss_pred CCCCHHHHHHhcCC-CCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDI-QKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~-~~~~~~~L~RlL 84 (87)
+..++.|||..+|. ++ ..+.|..
T Consensus 44 ~~~~i~~ia~~~Gf~~~---~~f~~~f 67 (81)
T PF12833_consen 44 TDLSIAEIAEECGFSSQ---SHFSRAF 67 (81)
T ss_dssp TT--HHHHHHHTT-SSH---HHHHHHH
T ss_pred hcccHHHHHHHcCCCCH---HHHHHHH
Confidence 67999999999997 44 5555544
No 397
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=21.44 E-value=95 Score=21.06 Aligned_cols=24 Identities=21% Similarity=0.300 Sum_probs=18.5
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
..+|-.|||..+|+.+ ..+.++.+
T Consensus 37 lGmTq~eLAerlGVS~---~tIs~iE~ 60 (150)
T TIGR02612 37 LGMSGAQLAGRLGVTP---QRVEALEK 60 (150)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHHc
Confidence 6789999999999877 65655543
No 398
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.42 E-value=95 Score=21.36 Aligned_cols=16 Identities=19% Similarity=0.439 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...+..|||+.+|+++
T Consensus 153 ~g~s~~EIA~~Lgis~ 168 (203)
T PRK09647 153 EGLSYEEIAATLGVKL 168 (203)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5689999999999988
No 399
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=21.35 E-value=1.1e+02 Score=19.90 Aligned_cols=16 Identities=19% Similarity=0.439 Sum_probs=14.5
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
+..|..|||+.+|+++
T Consensus 134 ~g~s~~eiA~~lgis~ 149 (169)
T TIGR02954 134 HDLTIKEIAEVMNKPE 149 (169)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5689999999999987
No 400
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=21.31 E-value=1e+02 Score=19.55 Aligned_cols=16 Identities=19% Similarity=0.283 Sum_probs=14.5
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 126 ~g~~~~eIA~~l~is~ 141 (159)
T TIGR02989 126 RGVSLTALAEQLGRTV 141 (159)
T ss_pred cCCCHHHHHHHhCCCH
Confidence 5789999999999987
No 401
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=21.26 E-value=93 Score=22.32 Aligned_cols=22 Identities=14% Similarity=0.416 Sum_probs=18.1
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRL 83 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~Rl 83 (87)
...|..|||+.+|++. ..+.++
T Consensus 220 e~~t~~EIA~~lgis~---~~V~~~ 241 (257)
T PRK05911 220 EELVLKEIGKILGVSE---SRVSQI 241 (257)
T ss_pred cCCCHHHHHHHHCcCH---HHHHHH
Confidence 6789999999999988 555554
No 402
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.99 E-value=1.1e+02 Score=20.39 Aligned_cols=16 Identities=6% Similarity=0.281 Sum_probs=14.4
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
+..|..|||+.+|++.
T Consensus 146 ~g~s~~eIA~~lgis~ 161 (184)
T PRK12539 146 EGLSVAEAATRSGMSE 161 (184)
T ss_pred cCCcHHHHHHHHCcCH
Confidence 5689999999999977
No 403
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.89 E-value=1.1e+02 Score=20.18 Aligned_cols=16 Identities=31% Similarity=0.418 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
+..|..|||+.+|+++
T Consensus 134 ~g~s~~EIA~~lgis~ 149 (172)
T PRK09651 134 DGLTYSEIAHKLGVSV 149 (172)
T ss_pred cCCCHHHHHHHhCCCH
Confidence 6789999999999987
No 404
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=20.87 E-value=1.3e+02 Score=20.95 Aligned_cols=38 Identities=18% Similarity=0.385 Sum_probs=25.1
Q ss_pred HHHhCchHHHHhCCCCCCHHHHHHhcCCCCC--ChhhHHHHHhc
Q 041968 45 AVELGIPDVIHKHGQPMTLSQIASALDIQKN--KAHCIQRLMRI 86 (87)
Q Consensus 45 aveLgI~d~L~~~~gp~S~~ELA~~~~~~~~--~~~~L~RlLR~ 86 (87)
--|.-|...|+ ...|-.|||.+++..+. + ..+.++||-
T Consensus 151 ~RE~eVL~lla---~G~snkeIA~~L~iS~~TVk-~h~~~i~~K 190 (211)
T COG2197 151 PRELEVLRLLA---EGLSNKEIAEELNLSEKTVK-THVSNILRK 190 (211)
T ss_pred HHHHHHHHHHH---CCCCHHHHHHHHCCCHhHHH-HHHHHHHHH
Confidence 34455566666 56899999999998761 1 235566653
No 405
>PF04031 Las1: Las1-like ; InterPro: IPR007174 Las1 is an essential nuclear protein involved in cell morphogenesis and cell surface growth [].
Probab=20.68 E-value=2.6e+02 Score=18.80 Aligned_cols=25 Identities=12% Similarity=0.298 Sum_probs=13.7
Q ss_pred CchHHHHhCCCCCCHHHHHHhcCCC
Q 041968 49 GIPDVIHKHGQPMTLSQIASALDIQ 73 (87)
Q Consensus 49 gI~d~L~~~~gp~S~~ELA~~~~~~ 73 (87)
|+.|...+.....|+..+|+++|++
T Consensus 90 gl~D~~Q~~~~a~si~~~A~~iglP 114 (154)
T PF04031_consen 90 GLVDPSQQGKYARSIASLAKEIGLP 114 (154)
T ss_pred HhhhHhhccchhhhHHHHHHHcCCC
Confidence 4455444333455666666666654
No 406
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=20.65 E-value=1.1e+02 Score=19.68 Aligned_cols=16 Identities=19% Similarity=0.376 Sum_probs=14.4
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 137 ~g~s~~eIA~~l~is~ 152 (170)
T TIGR02952 137 QNLPIAEVARILGKTE 152 (170)
T ss_pred cCCCHHHHHHHHCCCH
Confidence 5689999999999987
No 407
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=20.60 E-value=97 Score=19.89 Aligned_cols=23 Identities=13% Similarity=0.226 Sum_probs=17.4
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
..+|-.++|..+|+++ ..+.++.
T Consensus 17 ~gltq~~lA~~~gvs~---~~is~~E 39 (135)
T PRK09706 17 LKLSQRSLAKAVKVSH---VSISQWE 39 (135)
T ss_pred cCCCHHHHHHHhCCCH---HHHHHHH
Confidence 5678899999999887 6665543
No 408
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.44 E-value=95 Score=19.88 Aligned_cols=38 Identities=21% Similarity=0.275 Sum_probs=29.2
Q ss_pred HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968 44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87 (87)
Q Consensus 44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L 87 (87)
.+-.+.|+..|.+ ..|-..|-..+|++. ..+.|+=|.|
T Consensus 43 laqRlqVa~mL~e---g~tY~~I~~eTGaSt---aTIsRVkRcl 80 (100)
T COG4496 43 LAQRLQVAKMLKE---GRTYRDIEDETGAST---ATISRVKRCL 80 (100)
T ss_pred HHHHHHHHHHHHc---CCCcchhhhccCcch---hhHHHHHHHH
Confidence 5677888888884 457778999999988 7777776653
No 409
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=20.41 E-value=1e+02 Score=21.80 Aligned_cols=23 Identities=17% Similarity=0.335 Sum_probs=18.5
Q ss_pred CCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968 59 QPMTLSQIASALDIQKNKAHCIQRLM 84 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~~~~~~L~RlL 84 (87)
...|..|||..+|+++ ..+.+.+
T Consensus 220 ~g~s~~eIA~~lgis~---~~V~~~~ 242 (255)
T TIGR02941 220 ENLSQKETGERLGISQ---MHVSRLQ 242 (255)
T ss_pred CCCCHHHHHHHHCcCH---HHHHHHH
Confidence 6789999999999988 6555544
No 410
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=20.19 E-value=1.3e+02 Score=21.10 Aligned_cols=17 Identities=35% Similarity=0.698 Sum_probs=15.0
Q ss_pred CCC-CCHHHHHHhcCCCC
Q 041968 58 GQP-MTLSQIASALDIQK 74 (87)
Q Consensus 58 ~gp-~S~~ELA~~~~~~~ 74 (87)
+.| +|..+||+.++.++
T Consensus 14 g~pgls~~~La~il~~~~ 31 (186)
T TIGR00281 14 GEPGVTLAELVRILGKEK 31 (186)
T ss_pred CCCCCCHHHHHHHhCCCc
Confidence 677 99999999999874
No 411
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=20.13 E-value=1.1e+02 Score=19.61 Aligned_cols=16 Identities=31% Similarity=0.463 Sum_probs=14.6
Q ss_pred CCCCHHHHHHhcCCCC
Q 041968 59 QPMTLSQIASALDIQK 74 (87)
Q Consensus 59 gp~S~~ELA~~~~~~~ 74 (87)
...|..|||+.+|+++
T Consensus 120 ~~~s~~eIA~~lgis~ 135 (159)
T PRK12527 120 EGLSHQQIAEHLGISR 135 (159)
T ss_pred cCCCHHHHHHHhCCCH
Confidence 6789999999999987
No 412
>PRK01905 DNA-binding protein Fis; Provisional
Probab=20.12 E-value=1.1e+02 Score=18.11 Aligned_cols=31 Identities=19% Similarity=0.324 Sum_probs=22.6
Q ss_pred chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968 50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR 85 (87)
Q Consensus 50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR 85 (87)
|-..+...+ -+..+-|+.+|+++ ..++|.||
T Consensus 42 i~~aL~~~~--gn~s~aAr~LGIsr---stL~rklk 72 (77)
T PRK01905 42 LEVVMEQAG--GNQSLAAEYLGINR---NTLRKKLQ 72 (77)
T ss_pred HHHHHHHcC--CCHHHHHHHHCCCH---HHHHHHHH
Confidence 445555433 24778899999999 88888886
Done!