Query 045477
Match_columns 89
No_of_seqs 123 out of 1001
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 02:27:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045477.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045477hhsearch_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 1.4E-17 3.1E-22 94.6 4.9 51 24-76 1-51 (51)
2 KOG3178 Hydroxyindole-O-methyl 99.4 2.6E-12 5.6E-17 96.5 7.8 77 5-86 2-78 (342)
3 TIGR02716 C20_methyl_CrtF C-20 99.2 1.7E-11 3.8E-16 89.4 6.0 55 22-85 3-57 (306)
4 PF09339 HTH_IclR: IclR helix- 98.2 9.2E-07 2E-11 49.5 2.0 46 32-84 6-51 (52)
5 smart00346 HTH_ICLR helix_turn 97.6 0.00012 2.7E-09 44.2 4.8 47 32-85 8-54 (91)
6 PF12802 MarR_2: MarR family; 97.4 0.00039 8.4E-09 39.2 4.1 53 31-89 7-59 (62)
7 PRK11569 transcriptional repre 97.3 0.00039 8.4E-09 50.4 4.7 48 32-86 31-78 (274)
8 PRK10163 DNA-binding transcrip 97.3 0.0005 1.1E-08 49.8 4.7 48 32-86 28-75 (271)
9 PF13412 HTH_24: Winged helix- 97.2 0.00081 1.8E-08 36.5 4.2 45 30-82 4-48 (48)
10 PF01978 TrmB: Sugar-specific 97.2 0.00047 1E-08 40.1 3.1 48 30-85 9-56 (68)
11 COG1414 IclR Transcriptional r 97.2 0.00076 1.7E-08 48.5 4.7 50 31-87 6-55 (246)
12 PRK09834 DNA-binding transcrip 97.1 0.0011 2.3E-08 47.8 5.1 48 32-86 14-61 (263)
13 PF01047 MarR: MarR family; I 97.1 0.00076 1.6E-08 37.8 3.3 51 31-89 5-55 (59)
14 TIGR02431 pcaR_pcaU beta-ketoa 97.1 0.00081 1.8E-08 47.9 4.2 46 32-84 12-57 (248)
15 smart00550 Zalpha Z-DNA-bindin 97.1 0.0021 4.5E-08 37.8 5.1 51 29-86 6-57 (68)
16 PF02082 Rrf2: Transcriptional 97.0 0.0017 3.7E-08 39.2 4.8 42 38-84 17-58 (83)
17 PF12840 HTH_20: Helix-turn-he 97.0 0.0014 3.1E-08 37.4 4.1 53 26-86 7-59 (61)
18 cd07153 Fur_like Ferric uptake 97.0 0.002 4.4E-08 40.6 5.1 53 31-86 3-56 (116)
19 PRK15090 DNA-binding transcrip 97.0 0.0012 2.7E-08 47.2 4.4 46 32-85 17-62 (257)
20 PF13463 HTH_27: Winged helix 96.9 0.0017 3.7E-08 37.1 4.0 39 45-88 17-55 (68)
21 smart00347 HTH_MARR helix_turn 96.8 0.004 8.7E-08 37.4 5.2 49 30-86 11-59 (101)
22 PF01022 HTH_5: Bacterial regu 96.7 0.0019 4.1E-08 35.2 2.9 43 31-82 4-46 (47)
23 TIGR00738 rrf2_super rrf2 fami 96.7 0.0049 1.1E-07 39.7 4.9 35 45-84 24-58 (132)
24 TIGR02944 suf_reg_Xantho FeS a 96.6 0.0048 1E-07 39.9 4.8 44 35-84 15-58 (130)
25 PF09012 FeoC: FeoC like trans 96.6 0.0046 9.9E-08 36.2 3.9 45 33-85 4-48 (69)
26 TIGR02010 IscR iron-sulfur clu 96.5 0.0069 1.5E-07 39.7 5.0 35 45-84 24-58 (135)
27 PF04703 FaeA: FaeA-like prote 96.5 0.0048 1E-07 36.1 3.6 45 33-84 4-48 (62)
28 PRK10857 DNA-binding transcrip 96.4 0.0068 1.5E-07 41.4 4.7 35 45-84 24-58 (164)
29 TIGR02337 HpaR homoprotocatech 96.4 0.011 2.4E-07 37.4 5.2 50 31-88 30-79 (118)
30 TIGR01889 Staph_reg_Sar staphy 96.3 0.012 2.6E-07 37.2 4.9 53 31-89 27-81 (109)
31 COG1959 Predicted transcriptio 96.3 0.0094 2E-07 40.1 4.5 43 37-84 16-58 (150)
32 smart00420 HTH_DEOR helix_turn 96.2 0.016 3.5E-07 30.9 4.6 44 34-85 5-48 (53)
33 smart00344 HTH_ASNC helix_turn 96.2 0.012 2.6E-07 36.6 4.5 45 30-82 4-48 (108)
34 PRK06474 hypothetical protein; 96.2 0.011 2.5E-07 40.7 4.7 56 25-86 7-62 (178)
35 smart00419 HTH_CRP helix_turn_ 96.1 0.0096 2.1E-07 31.5 3.4 36 45-85 7-42 (48)
36 PRK03573 transcriptional regul 96.1 0.092 2E-06 34.2 8.7 48 35-89 37-84 (144)
37 PRK11512 DNA-binding transcrip 96.0 0.022 4.9E-07 37.3 5.2 48 34-89 45-92 (144)
38 COG3355 Predicted transcriptio 95.9 0.02 4.4E-07 37.9 4.7 49 30-85 28-76 (126)
39 cd00092 HTH_CRP helix_turn_hel 95.9 0.016 3.4E-07 32.8 3.7 36 45-85 24-59 (67)
40 COG4190 Predicted transcriptio 95.8 0.017 3.6E-07 38.9 4.1 57 20-84 55-111 (144)
41 smart00418 HTH_ARSR helix_turn 95.8 0.027 5.8E-07 30.7 4.4 42 34-84 2-43 (66)
42 PF08220 HTH_DeoR: DeoR-like h 95.7 0.025 5.4E-07 32.0 4.1 44 33-84 4-47 (57)
43 cd00090 HTH_ARSR Arsenical Res 95.6 0.039 8.5E-07 30.8 4.7 46 31-85 9-54 (78)
44 PF08279 HTH_11: HTH domain; 95.6 0.028 6.1E-07 31.0 3.9 40 33-79 4-43 (55)
45 TIGR00122 birA_repr_reg BirA b 95.6 0.029 6.3E-07 32.5 4.0 44 31-83 2-45 (69)
46 PF00325 Crp: Bacterial regula 95.5 0.014 3E-07 29.9 2.3 31 46-81 2-32 (32)
47 PRK10141 DNA-binding transcrip 95.5 0.041 8.9E-07 35.8 4.9 55 22-84 9-63 (117)
48 PF01475 FUR: Ferric uptake re 95.5 0.02 4.4E-07 36.4 3.4 57 28-87 7-64 (120)
49 PRK11639 zinc uptake transcrip 95.4 0.036 7.7E-07 37.9 4.7 55 28-85 25-80 (169)
50 COG0735 Fur Fe2+/Zn2+ uptake r 95.4 0.037 8E-07 37.0 4.5 56 30-88 22-78 (145)
51 PF06163 DUF977: Bacterial pro 95.3 0.057 1.2E-06 35.8 5.1 52 27-86 10-61 (127)
52 PRK09462 fur ferric uptake reg 95.2 0.048 1E-06 36.2 4.7 56 28-85 16-72 (148)
53 smart00345 HTH_GNTR helix_turn 95.2 0.048 1E-06 29.8 4.0 36 45-85 18-54 (60)
54 PF01726 LexA_DNA_bind: LexA D 95.2 0.047 1E-06 32.0 4.1 43 37-85 18-60 (65)
55 PF01325 Fe_dep_repress: Iron 95.2 0.05 1.1E-06 31.3 4.1 37 45-86 21-57 (60)
56 PRK06266 transcription initiat 95.2 0.098 2.1E-06 36.2 6.2 46 32-85 25-70 (178)
57 TIGR02702 SufR_cyano iron-sulf 95.2 0.046 9.9E-07 38.0 4.6 45 32-84 4-48 (203)
58 PF08461 HTH_12: Ribonuclease 95.1 0.046 9.9E-07 32.1 3.9 47 34-84 3-51 (66)
59 PRK11014 transcriptional repre 95.1 0.046 9.9E-07 36.0 4.3 37 44-85 23-59 (141)
60 PRK10870 transcriptional repre 94.9 0.072 1.6E-06 36.5 4.9 40 45-89 70-109 (176)
61 TIGR00373 conserved hypothetic 94.8 0.057 1.2E-06 36.7 4.3 46 32-85 17-62 (158)
62 PF13601 HTH_34: Winged helix 94.8 0.058 1.3E-06 32.6 3.8 49 30-86 1-49 (80)
63 PRK11920 rirA iron-responsive 94.7 0.061 1.3E-06 36.2 4.2 35 45-84 23-57 (153)
64 PF02002 TFIIE_alpha: TFIIE al 94.6 0.06 1.3E-06 33.7 3.7 46 33-86 17-62 (105)
65 TIGR01610 phage_O_Nterm phage 94.6 0.11 2.4E-06 32.2 4.8 36 45-85 46-81 (95)
66 COG1510 Predicted transcriptio 94.5 0.045 9.8E-07 38.1 3.2 40 45-89 40-79 (177)
67 COG2512 Predicted membrane-ass 94.5 0.068 1.5E-06 39.2 4.2 49 31-86 197-245 (258)
68 PF04967 HTH_10: HTH DNA bindi 94.3 0.046 9.9E-07 31.0 2.4 41 22-73 5-45 (53)
69 PHA00738 putative HTH transcri 94.2 0.15 3.2E-06 33.0 4.8 48 30-85 13-60 (108)
70 PRK11169 leucine-responsive tr 94.1 0.088 1.9E-06 35.5 3.9 47 29-83 14-60 (164)
71 PF08784 RPA_C: Replication pr 94.0 0.11 2.5E-06 32.2 4.1 51 29-84 47-98 (102)
72 PRK11179 DNA-binding transcrip 93.9 0.14 2.9E-06 34.1 4.6 46 30-83 10-55 (153)
73 COG1522 Lrp Transcriptional re 93.9 0.14 3.1E-06 33.4 4.6 48 29-84 8-55 (154)
74 TIGR01884 cas_HTH CRISPR locus 93.9 0.14 3.1E-06 35.5 4.7 47 31-85 145-191 (203)
75 PF04182 B-block_TFIIIC: B-blo 93.8 0.13 2.9E-06 30.5 4.0 50 30-85 3-52 (75)
76 PRK13777 transcriptional regul 93.8 0.31 6.7E-06 34.0 6.2 48 34-89 50-97 (185)
77 COG1846 MarR Transcriptional r 93.6 0.19 4.1E-06 30.7 4.5 52 30-89 23-74 (126)
78 PF02796 HTH_7: Helix-turn-hel 93.1 0.12 2.6E-06 27.8 2.7 23 46-73 21-43 (45)
79 PRK03902 manganese transport t 93.1 0.27 5.8E-06 32.2 4.8 35 45-84 21-55 (142)
80 PRK15431 ferrous iron transpor 93.1 0.33 7.1E-06 29.7 4.8 45 33-85 6-50 (78)
81 PF00392 GntR: Bacterial regul 93.0 0.14 3.1E-06 29.1 3.0 38 44-86 21-59 (64)
82 PF13545 HTH_Crp_2: Crp-like h 93.0 0.15 3.2E-06 29.5 3.2 35 45-84 27-61 (76)
83 PRK11050 manganese transport r 93.0 0.3 6.5E-06 32.7 5.0 44 33-84 41-84 (152)
84 PRK13509 transcriptional repre 93.0 0.22 4.7E-06 35.9 4.6 45 32-84 8-52 (251)
85 COG2345 Predicted transcriptio 92.8 0.2 4.3E-06 36.0 4.1 43 34-84 16-58 (218)
86 cd07377 WHTH_GntR Winged helix 92.8 0.27 5.8E-06 27.2 3.9 33 47-84 26-58 (66)
87 COG1378 Predicted transcriptio 92.7 0.31 6.7E-06 35.3 5.1 44 33-84 20-63 (247)
88 COG4565 CitB Response regulato 92.7 0.2 4.3E-06 36.1 4.0 46 32-84 161-206 (224)
89 PF03444 HrcA_DNA-bdg: Winged 92.4 0.37 8E-06 29.5 4.4 34 45-83 22-55 (78)
90 TIGR02787 codY_Gpos GTP-sensin 92.1 1.1 2.3E-05 33.0 7.2 71 6-85 162-232 (251)
91 TIGR00498 lexA SOS regulatory 92.0 0.44 9.5E-06 32.7 4.9 51 30-85 7-60 (199)
92 PRK10906 DNA-binding transcrip 91.9 0.3 6.5E-06 35.2 4.2 45 32-84 8-52 (252)
93 PF14947 HTH_45: Winged helix- 91.6 0.53 1.1E-05 28.0 4.4 43 35-83 9-51 (77)
94 COG1675 TFA1 Transcription ini 91.4 0.48 1E-05 33.0 4.6 46 32-85 21-66 (176)
95 PRK09802 DNA-binding transcrip 91.4 0.38 8.1E-06 35.0 4.2 46 31-84 19-64 (269)
96 TIGR02698 CopY_TcrY copper tra 91.3 0.56 1.2E-05 30.7 4.7 51 30-84 5-55 (130)
97 TIGR03697 NtcA_cyano global ni 91.3 0.28 6.1E-06 32.7 3.3 34 46-84 143-176 (193)
98 PF05158 RNA_pol_Rpc34: RNA po 91.2 0.39 8.4E-06 36.2 4.3 49 33-87 88-136 (327)
99 PF03965 Penicillinase_R: Peni 91.1 0.46 9.9E-06 30.1 4.0 52 30-85 4-55 (115)
100 PRK09334 30S ribosomal protein 90.8 0.34 7.4E-06 30.1 3.1 49 31-84 25-74 (86)
101 PRK10046 dpiA two-component re 90.8 0.56 1.2E-05 32.3 4.5 45 33-84 166-210 (225)
102 PRK00215 LexA repressor; Valid 90.7 0.78 1.7E-05 31.6 5.2 37 45-85 22-58 (205)
103 PF13404 HTH_AsnC-type: AsnC-t 90.7 0.6 1.3E-05 24.9 3.6 33 30-70 4-36 (42)
104 PRK10434 srlR DNA-bindng trans 90.5 0.47 1E-05 34.2 4.1 45 32-84 8-52 (256)
105 COG1321 TroR Mn-dependent tran 90.5 0.78 1.7E-05 31.0 4.9 37 45-86 23-59 (154)
106 PF07381 DUF1495: Winged helix 90.5 1.1 2.4E-05 28.0 5.2 48 28-81 8-65 (90)
107 PRK11753 DNA-binding transcrip 90.3 0.42 9E-06 32.3 3.5 35 46-85 168-202 (211)
108 PRK04214 rbn ribonuclease BN/u 90.2 0.48 1E-05 36.4 4.1 37 44-85 308-344 (412)
109 COG1349 GlpR Transcriptional r 90.1 0.5 1.1E-05 34.1 3.9 44 33-84 9-52 (253)
110 PF10007 DUF2250: Uncharacteri 89.9 0.99 2.1E-05 28.3 4.6 49 30-86 8-56 (92)
111 PF08221 HTH_9: RNA polymerase 89.8 0.62 1.4E-05 26.8 3.4 45 33-85 17-61 (62)
112 PF03297 Ribosomal_S25: S25 ri 89.7 0.47 1E-05 30.5 3.1 47 33-84 45-92 (105)
113 smart00529 HTH_DTXR Helix-turn 89.5 0.57 1.2E-05 28.2 3.3 32 49-85 2-33 (96)
114 PRK14096 pgi glucose-6-phospha 89.5 0.56 1.2E-05 37.7 4.0 42 32-78 466-507 (528)
115 PRK13918 CRP/FNR family transc 89.4 0.5 1.1E-05 31.8 3.3 34 45-83 148-181 (202)
116 PRK11161 fumarate/nitrate redu 89.4 0.52 1.1E-05 32.6 3.5 35 46-85 184-218 (235)
117 PRK04424 fatty acid biosynthes 89.1 0.32 7E-06 33.6 2.2 45 32-84 10-54 (185)
118 PRK00135 scpB segregation and 88.8 1 2.2E-05 31.5 4.6 44 32-86 93-136 (188)
119 PHA02943 hypothetical protein; 88.7 1 2.3E-05 31.0 4.4 44 33-85 15-58 (165)
120 PRK14165 winged helix-turn-hel 88.6 1.2 2.7E-05 31.8 5.0 36 45-85 20-55 (217)
121 PRK04172 pheS phenylalanyl-tRN 88.3 1.1 2.3E-05 35.4 4.8 47 31-85 8-54 (489)
122 PRK09391 fixK transcriptional 88.1 0.65 1.4E-05 32.4 3.2 34 46-84 179-212 (230)
123 PRK11534 DNA-binding transcrip 88.0 1 2.2E-05 31.2 4.2 39 43-86 27-65 (224)
124 PF12793 SgrR_N: Sugar transpo 88.0 0.79 1.7E-05 29.6 3.3 38 45-87 18-55 (115)
125 PRK10411 DNA-binding transcrip 87.8 1.2 2.7E-05 31.8 4.6 44 32-83 7-50 (240)
126 PF13730 HTH_36: Helix-turn-he 87.7 0.74 1.6E-05 25.1 2.7 30 47-81 26-55 (55)
127 TIGR00635 ruvB Holliday juncti 87.3 1.2 2.6E-05 32.1 4.3 36 44-84 253-289 (305)
128 PF13936 HTH_38: Helix-turn-he 87.1 0.98 2.1E-05 24.1 2.9 24 45-73 19-42 (44)
129 COG4901 Ribosomal protein S25 86.9 1.3 2.8E-05 28.5 3.8 50 30-84 42-92 (107)
130 PRK09954 putative kinase; Prov 86.5 1.4 2.9E-05 32.8 4.3 44 31-82 5-48 (362)
131 COG4189 Predicted transcriptio 86.1 2.7 5.9E-05 31.2 5.6 55 21-83 15-69 (308)
132 PRK01381 Trp operon repressor; 86.0 1.4 2.9E-05 28.1 3.5 41 29-78 42-82 (99)
133 TIGR00331 hrcA heat shock gene 85.9 1.6 3.5E-05 32.9 4.5 35 45-84 20-56 (337)
134 COG1802 GntR Transcriptional r 85.8 1.6 3.6E-05 30.4 4.3 40 43-87 36-75 (230)
135 smart00531 TFIIE Transcription 85.8 1.6 3.5E-05 29.0 4.0 39 33-79 5-43 (147)
136 PF00165 HTH_AraC: Bacterial r 85.7 1 2.2E-05 23.4 2.4 28 45-77 7-34 (42)
137 TIGR03338 phnR_burk phosphonat 85.7 1.5 3.3E-05 30.0 4.0 39 43-86 31-69 (212)
138 PF10668 Phage_terminase: Phag 84.4 1.6 3.4E-05 25.4 3.0 29 35-70 13-41 (60)
139 PRK09775 putative DNA-binding 84.3 1.7 3.8E-05 34.0 4.2 40 34-84 5-44 (442)
140 COG3413 Predicted DNA binding 84.3 0.71 1.5E-05 32.3 1.9 50 20-76 158-207 (215)
141 PRK11886 bifunctional biotin-- 84.2 1.7 3.8E-05 32.0 4.0 43 31-81 6-48 (319)
142 PRK00082 hrcA heat-inducible t 83.7 2.3 5.1E-05 32.1 4.5 35 45-84 24-60 (339)
143 PRK10402 DNA-binding transcrip 83.4 1.5 3.3E-05 30.4 3.2 36 45-85 168-203 (226)
144 PRK11414 colanic acid/biofilm 83.3 2.4 5.2E-05 29.3 4.2 38 43-85 31-68 (221)
145 PF01638 HxlR: HxlR-like helix 83.3 2.3 5E-05 25.7 3.6 37 45-85 17-53 (90)
146 PRK13239 alkylmercury lyase; P 83.3 1.7 3.8E-05 30.9 3.5 39 31-77 24-62 (206)
147 PF12324 HTH_15: Helix-turn-he 83.2 1.3 2.8E-05 27.0 2.4 34 34-75 29-62 (77)
148 smart00342 HTH_ARAC helix_turn 82.9 1.8 3.8E-05 24.4 2.9 28 46-78 1-28 (84)
149 TIGR01321 TrpR trp operon repr 82.9 2.5 5.4E-05 26.6 3.7 41 28-77 41-81 (94)
150 PF13518 HTH_28: Helix-turn-he 82.2 3.4 7.4E-05 21.8 3.7 28 48-80 14-41 (52)
151 PRK00080 ruvB Holliday junctio 82.2 2.9 6.2E-05 30.8 4.4 37 44-85 274-311 (328)
152 PRK12423 LexA repressor; Provi 82.1 4.2 9.2E-05 28.2 5.1 37 45-85 24-60 (202)
153 PF13443 HTH_26: Cro/C1-type H 82.0 1.5 3.2E-05 24.4 2.3 31 34-73 2-32 (63)
154 PRK11511 DNA-binding transcrip 81.8 3.1 6.8E-05 26.7 4.0 41 33-79 13-53 (127)
155 PF00356 LacI: Bacterial regul 81.6 1.2 2.7E-05 24.2 1.7 20 48-72 1-20 (46)
156 PF01418 HTH_6: Helix-turn-hel 81.4 2.3 5E-05 25.1 3.1 43 31-78 18-61 (77)
157 PRK11642 exoribonuclease R; Pr 81.1 2.9 6.3E-05 35.2 4.5 50 33-85 23-72 (813)
158 PF05584 Sulfolobus_pRN: Sulfo 80.8 5.7 0.00012 23.9 4.6 44 32-84 8-51 (72)
159 PHA02591 hypothetical protein; 80.8 3.2 6.9E-05 25.6 3.5 33 33-74 50-82 (83)
160 PRK10430 DNA-binding transcrip 80.7 2.6 5.6E-05 29.2 3.6 35 45-84 177-211 (239)
161 PF13384 HTH_23: Homeodomain-l 80.2 1.3 2.8E-05 23.6 1.6 30 46-80 17-46 (50)
162 PRK10219 DNA-binding transcrip 79.7 4.5 9.7E-05 24.8 4.1 39 35-79 11-49 (107)
163 PF03428 RP-C: Replication pro 79.6 2.8 6.2E-05 29.1 3.4 59 22-87 45-107 (177)
164 COG1725 Predicted transcriptio 79.2 3.4 7.4E-05 27.3 3.5 34 46-84 35-68 (125)
165 COG3682 Predicted transcriptio 79.1 4.2 9E-05 26.9 3.9 52 30-85 7-58 (123)
166 PF04433 SWIRM: SWIRM domain; 79.1 8 0.00017 23.1 5.0 54 24-82 32-85 (86)
167 PRK10225 DNA-binding transcrip 79.0 3.6 7.9E-05 29.1 3.9 38 43-85 29-67 (257)
168 PF13744 HTH_37: Helix-turn-he 78.7 5.7 0.00012 23.5 4.2 46 26-80 15-73 (80)
169 TIGR02812 fadR_gamma fatty aci 78.4 4.3 9.3E-05 28.3 4.1 38 43-85 26-64 (235)
170 PRK10681 DNA-binding transcrip 78.4 3.7 8E-05 29.5 3.9 40 32-79 10-49 (252)
171 PF07789 DUF1627: Protein of u 78.4 4.1 9E-05 27.9 3.8 37 45-86 5-41 (155)
172 PF03374 ANT: Phage antirepres 78.3 3.7 7.9E-05 25.5 3.4 43 31-83 11-53 (111)
173 PRK04984 fatty acid metabolism 77.5 4.5 9.9E-05 28.2 4.0 38 43-85 27-65 (239)
174 COG3695 Predicted methylated D 77.4 3.8 8.2E-05 26.3 3.2 41 33-76 10-50 (103)
175 PRK05638 threonine synthase; V 77.1 6.4 0.00014 30.5 5.1 47 31-84 373-419 (442)
176 PF04539 Sigma70_r3: Sigma-70 77.0 2.3 4.9E-05 24.7 2.0 33 45-82 19-51 (78)
177 PRK09464 pdhR transcriptional 76.9 4.8 0.0001 28.4 4.0 38 43-85 30-68 (254)
178 PRK09990 DNA-binding transcrip 76.6 5 0.00011 28.2 4.1 39 43-86 27-66 (251)
179 PF08280 HTH_Mga: M protein tr 76.5 4.5 9.7E-05 22.7 3.1 39 30-76 6-44 (59)
180 TIGR03879 near_KaiC_dom probab 76.2 2.3 4.9E-05 25.6 1.9 33 45-82 31-63 (73)
181 TIGR02844 spore_III_D sporulat 76.2 4.4 9.6E-05 24.7 3.2 32 33-73 10-41 (80)
182 PRK03837 transcriptional regul 76.0 5.9 0.00013 27.5 4.3 38 43-85 33-71 (241)
183 PRK10421 DNA-binding transcrip 76.0 5.1 0.00011 28.3 4.0 37 43-84 22-59 (253)
184 TIGR03826 YvyF flagellar opero 75.7 4.8 0.0001 26.9 3.5 35 33-73 34-68 (137)
185 PTZ00326 phenylalanyl-tRNA syn 75.5 7.3 0.00016 31.2 5.1 50 28-84 5-54 (494)
186 PRK11302 DNA-binding transcrip 75.5 2.2 4.8E-05 30.5 2.0 44 30-78 17-61 (284)
187 PRK09392 ftrB transcriptional 75.4 3.5 7.6E-05 28.5 3.0 30 46-80 173-202 (236)
188 PF06971 Put_DNA-bind_N: Putat 75.3 6.6 0.00014 21.8 3.5 38 27-70 10-47 (50)
189 PF13542 HTH_Tnp_ISL3: Helix-t 75.1 7.4 0.00016 20.7 3.7 24 47-75 28-51 (52)
190 PLN02853 Probable phenylalanyl 74.8 7 0.00015 31.3 4.8 49 29-84 3-51 (492)
191 PF14394 DUF4423: Domain of un 74.3 13 0.00029 25.4 5.6 54 18-86 21-76 (171)
192 PF01371 Trp_repressor: Trp re 74.3 8.5 0.00018 23.8 4.2 40 28-77 35-75 (87)
193 PRK11557 putative DNA-binding 74.3 2.7 5.9E-05 30.0 2.2 42 30-76 13-55 (278)
194 TIGR01764 excise DNA binding d 74.2 3.7 8.1E-05 21.0 2.3 22 47-73 2-23 (49)
195 PF08222 HTH_CodY: CodY helix- 73.2 2.7 5.9E-05 24.4 1.6 35 45-84 3-37 (61)
196 PF04492 Phage_rep_O: Bacterio 73.1 5.2 0.00011 25.3 3.0 50 31-85 34-88 (100)
197 PRK11523 DNA-binding transcrip 72.6 7.1 0.00015 27.6 4.0 38 43-85 28-66 (253)
198 PF08535 KorB: KorB domain; I 72.6 3 6.5E-05 25.4 1.9 27 45-76 2-28 (93)
199 PF09286 Pro-kuma_activ: Pro-k 72.6 3.6 7.8E-05 26.8 2.3 33 45-82 46-78 (143)
200 PF12728 HTH_17: Helix-turn-he 72.5 4.1 8.9E-05 21.7 2.2 22 47-73 2-23 (51)
201 PHA02701 ORF020 dsRNA-binding 71.5 11 0.00024 26.5 4.7 47 29-82 4-50 (183)
202 TIGR02531 yecD_yerC TrpR-relat 71.3 20 0.00044 22.0 5.4 35 32-76 41-75 (88)
203 cd04762 HTH_MerR-trunc Helix-T 71.0 4.8 0.0001 20.4 2.2 22 47-73 1-22 (49)
204 COG2390 DeoR Transcriptional r 70.9 5.9 0.00013 29.9 3.4 35 45-84 25-59 (321)
205 smart00421 HTH_LUXR helix_turn 70.4 10 0.00022 19.6 3.5 24 46-74 18-41 (58)
206 PRK11337 DNA-binding transcrip 70.1 4.2 9E-05 29.3 2.4 42 30-76 29-71 (292)
207 PF07638 Sigma70_ECF: ECF sigm 69.5 5.5 0.00012 27.0 2.8 26 45-75 150-175 (185)
208 smart00526 H15 Domain in histo 69.5 14 0.00031 20.9 4.2 50 34-84 11-64 (66)
209 PF01381 HTH_3: Helix-turn-hel 69.4 4.2 9.1E-05 21.8 1.8 24 45-73 8-31 (55)
210 PRK05472 redox-sensing transcr 69.1 14 0.0003 25.6 4.8 47 27-79 14-60 (213)
211 PF04545 Sigma70_r4: Sigma-70, 68.8 5.5 0.00012 21.2 2.2 25 45-74 19-43 (50)
212 PF07106 TBPIP: Tat binding pr 68.6 11 0.00025 25.3 4.2 46 33-84 5-51 (169)
213 PRK15121 right oriC-binding tr 67.8 10 0.00022 27.4 4.0 40 34-79 10-49 (289)
214 COG2378 Predicted transcriptio 67.5 8.7 0.00019 28.6 3.7 42 32-81 11-52 (311)
215 PRK13626 transcriptional regul 67.1 7.1 0.00015 30.9 3.3 37 45-86 22-58 (552)
216 PF10771 DUF2582: Protein of u 66.7 12 0.00026 21.9 3.5 41 33-81 12-52 (65)
217 PF00440 TetR_N: Bacterial reg 66.3 7.2 0.00016 20.6 2.3 22 45-71 15-36 (47)
218 COG5631 Predicted transcriptio 66.1 43 0.00094 23.5 7.2 65 16-86 63-134 (199)
219 PRK15411 rcsA colanic acid cap 65.7 10 0.00022 26.2 3.6 39 28-76 139-181 (207)
220 PRK10572 DNA-binding transcrip 65.5 12 0.00027 26.6 4.1 40 34-79 188-227 (290)
221 KOG3233 RNA polymerase III, su 65.4 3.1 6.8E-05 31.1 1.0 47 35-87 90-136 (297)
222 PF13551 HTH_29: Winged helix- 65.3 12 0.00025 22.6 3.4 27 48-79 14-40 (112)
223 PF06413 Neugrin: Neugrin; In 65.3 8.6 0.00019 27.7 3.2 33 35-73 19-51 (225)
224 PF03979 Sigma70_r1_1: Sigma-7 64.8 5.6 0.00012 23.8 1.9 35 45-81 20-54 (82)
225 TIGR03882 cyclo_dehyd_2 bacter 64.5 13 0.00028 25.8 3.9 38 45-85 41-78 (193)
226 smart00354 HTH_LACI helix_turn 64.4 5.9 0.00013 22.8 1.9 17 64-80 28-44 (70)
227 COG2865 Predicted transcriptio 64.0 9.7 0.00021 30.3 3.5 45 34-86 407-451 (467)
228 COG1386 scpB Chromosome segreg 63.9 22 0.00048 24.8 5.0 46 31-87 94-139 (184)
229 PF05491 RuvB_C: Holliday junc 63.7 20 0.00043 21.7 4.1 52 30-86 9-61 (76)
230 PF01710 HTH_Tnp_IS630: Transp 62.9 15 0.00033 23.3 3.8 25 45-74 70-94 (119)
231 cd06445 ATase The DNA repair p 62.9 23 0.0005 20.9 4.3 39 33-74 4-42 (79)
232 KOG2165 Anaphase-promoting com 62.5 8.6 0.00019 32.3 3.0 36 45-85 615-650 (765)
233 PRK15418 transcriptional regul 62.2 11 0.00024 28.1 3.4 34 45-83 28-61 (318)
234 PF04760 IF2_N: Translation in 62.1 3.5 7.7E-05 22.6 0.6 29 45-81 2-31 (54)
235 COG3432 Predicted transcriptio 62.0 7.1 0.00015 24.7 2.0 43 34-83 20-63 (95)
236 PRK04217 hypothetical protein; 61.8 14 0.0003 23.8 3.4 32 33-73 49-80 (110)
237 PHA00542 putative Cro-like pro 61.6 13 0.00029 22.2 3.1 24 45-73 30-53 (82)
238 PF08721 Tn7_Tnp_TnsA_C: TnsA 61.4 25 0.00054 20.0 4.2 41 34-82 32-76 (79)
239 PF00126 HTH_1: Bacterial regu 61.1 21 0.00046 19.7 3.8 37 31-77 3-39 (60)
240 PF13814 Replic_Relax: Replica 61.1 19 0.00042 24.0 4.2 44 37-85 3-46 (191)
241 PF05402 PqqD: Coenzyme PQQ sy 61.0 6.4 0.00014 22.1 1.6 37 45-82 28-68 (68)
242 COG4977 Transcriptional regula 61.0 13 0.00027 28.3 3.5 38 34-77 225-262 (328)
243 PF00196 GerE: Bacterial regul 60.9 12 0.00026 20.5 2.7 31 30-70 7-37 (58)
244 PRK15482 transcriptional regul 60.8 8 0.00017 27.8 2.4 42 30-76 17-59 (285)
245 TIGR00180 parB_part ParB-like 60.4 14 0.0003 25.3 3.4 27 45-76 119-145 (187)
246 TIGR02063 RNase_R ribonuclease 60.3 17 0.00038 29.9 4.5 50 33-84 6-55 (709)
247 PRK13503 transcriptional activ 60.3 18 0.00038 25.4 4.0 38 34-77 176-213 (278)
248 cd06170 LuxR_C_like C-terminal 59.7 22 0.00047 18.4 3.5 23 46-73 15-37 (57)
249 smart00088 PINT motif in prote 59.3 34 0.00073 20.0 5.2 51 25-83 6-56 (88)
250 smart00753 PAM PCI/PINT associ 59.3 34 0.00073 20.0 5.2 51 25-83 6-56 (88)
251 TIGR03433 padR_acidobact trans 59.2 39 0.00085 20.7 5.1 47 34-84 9-58 (100)
252 TIGR00589 ogt O-6-methylguanin 59.0 31 0.00067 20.7 4.4 40 32-74 5-44 (80)
253 TIGR02297 HpaA 4-hydroxyphenyl 58.8 18 0.0004 25.5 3.9 40 34-79 191-230 (287)
254 PF14357 DUF4404: Domain of un 58.3 7.9 0.00017 23.7 1.7 29 51-80 57-85 (85)
255 COG2524 Predicted transcriptio 58.3 22 0.00048 26.6 4.3 35 45-84 24-58 (294)
256 TIGR03070 couple_hipB transcri 58.3 11 0.00024 19.8 2.2 23 45-72 14-36 (58)
257 PF05331 DUF742: Protein of un 58.2 17 0.00036 23.6 3.3 33 45-82 54-86 (114)
258 COG1737 RpiR Transcriptional r 58.2 6.4 0.00014 28.6 1.5 45 30-79 19-64 (281)
259 PF08281 Sigma70_r4_2: Sigma-7 58.0 12 0.00026 20.0 2.3 23 45-72 25-47 (54)
260 PF00538 Linker_histone: linke 57.8 14 0.0003 21.7 2.7 50 35-85 10-65 (77)
261 PF13591 MerR_2: MerR HTH fami 57.4 15 0.00031 22.1 2.8 31 47-86 1-31 (84)
262 PRK15340 transcriptional regul 57.1 41 0.00088 24.1 5.4 42 33-80 113-154 (216)
263 PF02295 z-alpha: Adenosine de 56.9 25 0.00055 20.4 3.7 49 30-84 5-53 (66)
264 PRK13558 bacterio-opsin activa 56.8 10 0.00022 30.2 2.6 51 19-76 609-659 (665)
265 COG3655 Predicted transcriptio 56.6 11 0.00023 22.8 2.0 25 30-59 3-27 (73)
266 cd04761 HTH_MerR-SF Helix-Turn 56.5 12 0.00027 19.2 2.2 27 47-82 1-27 (49)
267 COG3620 Predicted transcriptio 56.3 12 0.00025 26.3 2.4 31 45-76 17-58 (187)
268 PRK10371 DNA-binding transcrip 56.3 21 0.00045 26.1 3.9 39 33-77 195-233 (302)
269 PF04218 CENP-B_N: CENP-B N-te 55.9 25 0.00054 19.3 3.4 34 30-73 11-44 (53)
270 cd04895 ACT_ACR_1 ACT domain-c 55.7 12 0.00025 22.3 2.1 23 61-83 8-30 (72)
271 PRK15044 transcriptional regul 55.6 33 0.00072 25.8 4.9 44 25-74 188-231 (295)
272 PRK00118 putative DNA-binding 55.2 13 0.00028 23.7 2.4 23 45-72 32-54 (104)
273 PHA01976 helix-turn-helix prot 55.2 12 0.00026 20.8 2.1 23 45-72 14-36 (67)
274 PF09106 SelB-wing_2: Elongati 55.1 20 0.00043 19.9 3.0 40 45-86 16-55 (59)
275 PRK15186 AraC family transcrip 55.1 19 0.00042 26.6 3.6 36 33-74 185-220 (291)
276 PRK13824 replication initiatio 55.0 17 0.00037 28.3 3.5 36 47-87 83-119 (404)
277 COG4465 CodY Pleiotropic trans 54.9 46 0.00099 24.4 5.4 44 33-83 193-236 (261)
278 PRK10736 hypothetical protein; 54.9 18 0.00038 28.0 3.5 35 45-84 320-354 (374)
279 COG4367 Uncharacterized protei 54.8 15 0.00033 23.1 2.6 24 45-73 22-45 (97)
280 PRK13501 transcriptional activ 54.7 22 0.00048 25.4 3.8 40 34-79 181-220 (290)
281 cd04896 ACT_ACR-like_3 ACT dom 54.6 12 0.00025 22.4 2.0 22 61-82 7-28 (75)
282 COG0640 ArsR Predicted transcr 54.4 38 0.00082 19.1 4.9 53 24-84 20-72 (110)
283 PRK13502 transcriptional activ 54.3 22 0.00048 25.1 3.7 39 33-77 180-218 (282)
284 cd06171 Sigma70_r4 Sigma70, re 54.3 17 0.00036 18.3 2.4 25 45-74 25-49 (55)
285 PRK09393 ftrA transcriptional 54.1 24 0.00052 25.7 4.0 40 33-78 222-261 (322)
286 PF04552 Sigma54_DBD: Sigma-54 53.6 4.3 9.4E-05 27.7 0.0 24 45-73 48-71 (160)
287 COG3645 Uncharacterized phage- 53.3 18 0.00039 24.3 2.9 40 33-82 36-75 (135)
288 PRK09940 transcriptional regul 53.2 21 0.00045 26.1 3.5 36 33-74 138-173 (253)
289 PF13560 HTH_31: Helix-turn-he 53.1 11 0.00024 21.0 1.7 24 45-73 13-36 (64)
290 KOG4062 6-O-methylguanine-DNA 53.0 24 0.00052 24.6 3.5 48 27-80 87-134 (178)
291 COG4742 Predicted transcriptio 52.9 36 0.00079 25.1 4.7 50 27-85 11-60 (260)
292 PRK09764 DNA-binding transcrip 52.9 28 0.00061 24.4 4.1 37 44-85 26-63 (240)
293 cd04780 HTH_MerR-like_sg5 Heli 52.7 16 0.00036 22.4 2.5 29 47-84 1-29 (95)
294 COG3177 Fic family protein [Fu 52.6 23 0.00051 26.7 3.8 38 45-87 303-340 (348)
295 PRK10265 chaperone-modulator p 52.5 15 0.00033 22.9 2.4 32 46-86 7-38 (101)
296 PF00888 Cullin: Cullin family 52.4 7.7 0.00017 30.4 1.2 35 45-84 533-567 (588)
297 smart00422 HTH_MERR helix_turn 52.1 15 0.00033 20.4 2.2 28 47-83 1-28 (70)
298 PRK15185 transcriptional regul 52.1 23 0.0005 26.7 3.6 36 33-74 210-245 (309)
299 COG3398 Uncharacterized protei 51.9 35 0.00075 25.0 4.4 47 29-83 101-147 (240)
300 PRK13890 conjugal transfer pro 51.3 20 0.00043 23.0 2.8 23 45-72 17-39 (120)
301 PF01853 MOZ_SAS: MOZ/SAS fami 51.3 22 0.00047 25.1 3.2 43 35-85 139-181 (188)
302 COG2344 AT-rich DNA-binding pr 51.2 23 0.00049 25.4 3.3 38 33-76 20-57 (211)
303 TIGR02147 Fsuc_second hypothet 51.2 65 0.0014 23.7 5.8 53 19-85 120-173 (271)
304 PF02387 IncFII_repA: IncFII R 51.0 27 0.00059 26.0 3.9 40 45-85 94-139 (281)
305 PF05732 RepL: Firmicute plasm 51.0 21 0.00046 24.3 3.1 33 47-84 76-108 (165)
306 PRK09978 DNA-binding transcrip 50.7 25 0.00054 26.0 3.6 36 33-74 146-181 (274)
307 PRK15481 transcriptional regul 50.7 30 0.00064 26.2 4.1 37 44-85 26-63 (431)
308 PRK10840 transcriptional regul 50.7 13 0.00027 25.1 1.9 37 30-76 154-194 (216)
309 PF13022 HTH_Tnp_1_2: Helix-tu 50.2 20 0.00043 24.3 2.7 31 36-73 26-56 (142)
310 PRK14999 histidine utilization 50.1 31 0.00067 24.1 3.9 36 45-85 34-70 (241)
311 TIGR03613 RutR pyrimidine util 50.0 22 0.00049 23.6 3.1 30 35-70 18-47 (202)
312 PF05066 HARE-HTH: HB1, ASXL, 50.0 10 0.00022 21.9 1.2 48 35-84 8-62 (72)
313 PRK13719 conjugal transfer tra 49.9 13 0.00028 26.8 1.9 38 28-75 145-186 (217)
314 TIGR02404 trehalos_R_Bsub treh 49.7 26 0.00056 24.3 3.5 36 45-85 22-58 (233)
315 TIGR02018 his_ut_repres histid 49.6 32 0.00069 23.9 3.9 37 44-85 22-59 (230)
316 PRK11303 DNA-binding transcrip 49.3 14 0.00029 26.4 2.0 21 47-72 1-21 (328)
317 PF14502 HTH_41: Helix-turn-he 49.0 35 0.00075 18.9 3.2 34 45-83 5-38 (48)
318 TIGR03337 phnR transcriptional 48.8 73 0.0016 21.8 5.6 49 32-85 8-59 (231)
319 cd00073 H15 linker histone 1 a 48.7 41 0.0009 20.2 3.9 50 35-85 12-65 (88)
320 PLN00104 MYST -like histone ac 48.6 40 0.00086 26.9 4.6 46 19-83 358-403 (450)
321 TIGR00637 ModE_repress ModE mo 48.5 36 0.00077 21.1 3.6 37 31-77 6-42 (99)
322 COG1733 Predicted transcriptio 48.4 54 0.0012 21.1 4.5 36 45-84 35-70 (120)
323 COG2207 AraC AraC-type DNA-bin 48.2 40 0.00087 20.1 3.8 41 33-79 24-64 (127)
324 PLN03238 probable histone acet 48.1 51 0.0011 24.8 4.9 31 45-83 222-252 (290)
325 TIGR02395 rpoN_sigma RNA polym 48.0 14 0.00031 28.8 2.1 24 45-73 317-340 (429)
326 TIGR00475 selB selenocysteine- 47.9 30 0.00066 27.9 4.0 36 45-85 487-522 (581)
327 PF02319 E2F_TDP: E2F/DP famil 47.5 12 0.00027 21.8 1.3 37 45-84 23-62 (71)
328 TIGR02607 antidote_HigA addict 47.5 30 0.00065 19.6 3.0 23 45-72 17-39 (78)
329 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 47.4 19 0.00042 20.0 2.0 40 31-79 9-48 (50)
330 PRK13500 transcriptional activ 47.3 37 0.0008 24.8 4.1 40 33-78 210-249 (312)
331 PF04157 EAP30: EAP30/Vps36 fa 46.8 19 0.00041 25.3 2.4 32 45-81 189-220 (223)
332 PF10078 DUF2316: Uncharacteri 46.8 21 0.00045 22.2 2.3 24 45-73 22-45 (89)
333 PRK09685 DNA-binding transcrip 46.5 33 0.00072 24.4 3.7 36 33-74 201-237 (302)
334 PRK11475 DNA-binding transcrip 46.4 29 0.00064 24.1 3.3 38 29-76 137-178 (207)
335 TIGR03384 betaine_BetI transcr 46.3 29 0.00063 22.6 3.2 27 37-69 20-46 (189)
336 cd04766 HTH_HspR Helix-Turn-He 46.2 25 0.00055 21.1 2.6 29 47-84 2-30 (91)
337 PF02186 TFIIE_beta: TFIIE bet 46.2 39 0.00085 19.6 3.3 24 33-59 9-32 (65)
338 PF09681 Phage_rep_org_N: N-te 46.1 39 0.00084 22.0 3.6 35 45-84 52-86 (121)
339 PRK09526 lacI lac repressor; R 45.7 18 0.00039 25.9 2.2 24 45-73 4-27 (342)
340 COG0664 Crp cAMP-binding prote 45.7 37 0.00081 22.1 3.6 36 45-85 170-205 (214)
341 TIGR02325 C_P_lyase_phnF phosp 45.4 33 0.00071 23.7 3.4 36 45-85 30-66 (238)
342 COG2188 PhnF Transcriptional r 45.2 27 0.00059 24.6 3.0 32 48-84 33-64 (236)
343 PRK09492 treR trehalose repres 45.1 19 0.00042 25.4 2.2 24 45-73 3-26 (315)
344 PF10376 Mei5: Double-strand r 45.0 40 0.00086 24.2 3.8 41 20-69 178-219 (221)
345 PRK09975 DNA-binding transcrip 45.0 33 0.00072 23.0 3.3 28 37-70 23-50 (213)
346 PRK10014 DNA-binding transcrip 44.6 20 0.00043 25.7 2.3 24 45-73 5-28 (342)
347 TIGR02392 rpoH_proteo alternat 44.3 23 0.00051 25.4 2.6 24 45-73 235-258 (270)
348 KOG1767 40S ribosomal protein 44.2 14 0.0003 23.9 1.2 35 45-84 59-93 (110)
349 PRK10130 transcriptional regul 44.2 40 0.00087 25.5 3.9 38 34-77 245-282 (350)
350 PRK15201 fimbriae regulatory p 43.8 39 0.00085 24.0 3.5 37 29-75 136-176 (198)
351 cd00131 PAX Paired Box domain 43.6 12 0.00025 24.4 0.8 53 20-82 12-64 (128)
352 TIGR01481 ccpA catabolite cont 43.5 20 0.00043 25.6 2.1 22 47-73 2-23 (329)
353 smart00530 HTH_XRE Helix-turn- 43.3 41 0.00089 16.3 3.3 14 45-59 9-22 (56)
354 PF02787 CPSase_L_D3: Carbamoy 43.3 32 0.00069 22.3 2.9 26 45-75 22-47 (123)
355 cd04900 ACT_UUR-like_1 ACT dom 43.1 24 0.00053 20.1 2.1 19 62-80 9-27 (73)
356 COG5647 Cullin, a subunit of E 43.0 34 0.00073 29.0 3.5 50 27-84 606-655 (773)
357 TIGR03859 PQQ_PqqD coenzyme PQ 42.9 31 0.00068 20.5 2.6 36 45-81 42-80 (81)
358 smart00351 PAX Paired Box doma 42.7 36 0.00078 21.8 3.1 44 30-83 22-65 (125)
359 PRK10512 selenocysteinyl-tRNA- 42.4 62 0.0013 26.5 5.0 36 45-85 505-540 (614)
360 PF13309 HTH_22: HTH domain 42.1 23 0.0005 20.2 1.9 43 26-73 21-64 (64)
361 PF03551 PadR: Transcriptional 42.0 25 0.00054 20.2 2.1 41 45-86 8-52 (75)
362 cd04781 HTH_MerR-like_sg6 Heli 42.0 30 0.00064 21.9 2.5 31 47-86 1-31 (120)
363 PRK05932 RNA polymerase factor 41.9 20 0.00044 28.2 2.1 23 45-72 342-364 (455)
364 PRK11063 metQ DL-methionine tr 41.6 22 0.00048 25.8 2.2 40 45-85 120-159 (271)
365 cd04769 HTH_MerR2 Helix-Turn-H 41.3 31 0.00067 21.7 2.6 31 47-86 1-31 (116)
366 PRK14101 bifunctional glucokin 41.3 25 0.00054 28.5 2.6 44 31-79 358-402 (638)
367 PF08765 Mor: Mor transcriptio 41.3 87 0.0019 19.5 4.9 49 20-76 49-97 (108)
368 PRK10703 DNA-binding transcrip 41.3 21 0.00046 25.6 2.0 22 47-73 2-23 (341)
369 PF01035 DNA_binding_1: 6-O-me 41.1 52 0.0011 19.7 3.4 39 32-73 5-43 (85)
370 PF13411 MerR_1: MerR HTH fami 40.8 23 0.0005 19.7 1.7 30 47-85 1-30 (69)
371 PRK09480 slmA division inhibit 40.8 40 0.00086 22.1 3.1 14 45-59 29-42 (194)
372 TIGR02044 CueR Cu(I)-responsiv 40.8 31 0.00067 22.1 2.5 30 47-85 1-30 (127)
373 cd04897 ACT_ACR_3 ACT domain-c 40.5 27 0.00058 20.9 2.0 24 61-84 8-31 (75)
374 COG1693 Repressor of nif and g 40.4 36 0.00078 25.9 3.1 49 31-85 8-60 (325)
375 PF02042 RWP-RK: RWP-RK domain 40.4 35 0.00076 19.1 2.4 25 46-75 15-39 (52)
376 cd00592 HTH_MerR-like Helix-Tu 40.1 35 0.00075 20.5 2.6 27 47-82 1-27 (100)
377 PRK14987 gluconate operon tran 40.0 23 0.0005 25.3 2.0 24 45-73 4-27 (331)
378 COG2197 CitB Response regulato 40.0 28 0.00061 24.2 2.4 41 30-76 152-192 (211)
379 TIGR00281 segregation and cond 39.6 90 0.002 21.8 4.8 44 33-87 91-134 (186)
380 PRK15435 bifunctional DNA-bind 39.6 56 0.0012 24.8 4.1 28 45-77 98-125 (353)
381 PF06224 HTH_42: Winged helix 39.3 99 0.0021 22.5 5.3 50 33-86 89-142 (327)
382 TIGR02937 sigma70-ECF RNA poly 39.1 35 0.00076 20.8 2.5 24 45-73 125-148 (158)
383 cd04783 HTH_MerR1 Helix-Turn-H 38.9 32 0.0007 21.9 2.4 28 47-83 1-28 (126)
384 PRK11083 DNA-binding response 38.9 57 0.0012 21.3 3.7 49 28-78 156-209 (228)
385 PRK07037 extracytoplasmic-func 38.8 34 0.00073 22.0 2.5 22 45-71 124-145 (163)
386 PRK00135 scpB segregation and 38.7 40 0.00087 23.5 3.0 27 45-76 18-45 (188)
387 PRK08558 adenine phosphoribosy 38.7 50 0.0011 23.7 3.5 39 27-72 6-44 (238)
388 COG2186 FadR Transcriptional r 38.6 39 0.00084 24.0 3.0 35 45-84 32-67 (241)
389 PF00376 MerR: MerR family reg 38.4 31 0.00067 17.7 1.8 26 48-82 1-26 (38)
390 COG4496 Uncharacterized protei 38.3 55 0.0012 20.7 3.2 39 28-76 43-81 (100)
391 cd04770 HTH_HMRTR Helix-Turn-H 38.3 37 0.00079 21.4 2.6 29 47-84 1-29 (123)
392 PRK09863 putative frv operon r 38.2 49 0.0011 26.4 3.7 36 31-75 6-41 (584)
393 PRK09726 antitoxin HipB; Provi 37.8 31 0.00067 20.6 2.1 14 45-59 24-37 (88)
394 PF12298 Bot1p: Eukaryotic mit 37.6 65 0.0014 22.2 3.8 36 30-74 21-56 (172)
395 PRK11402 DNA-binding transcrip 37.5 53 0.0011 22.9 3.5 34 47-85 34-67 (241)
396 PF09743 DUF2042: Uncharacteri 37.3 66 0.0014 23.7 4.1 41 32-79 58-98 (272)
397 TIGR02985 Sig70_bacteroi1 RNA 37.0 44 0.00095 21.0 2.8 23 45-72 128-150 (161)
398 COG2169 Ada Adenosine deaminas 36.8 56 0.0012 23.1 3.4 35 36-77 89-123 (187)
399 PF05930 Phage_AlpA: Prophage 36.8 26 0.00057 18.8 1.5 23 46-73 3-25 (51)
400 PRK10401 DNA-binding transcrip 36.8 27 0.00059 25.2 2.0 22 47-73 2-23 (346)
401 PRK10668 DNA-binding transcrip 36.7 53 0.0011 22.1 3.3 21 37-59 23-43 (215)
402 PF05344 DUF746: Domain of Unk 36.4 46 0.00099 19.6 2.5 26 45-75 12-37 (65)
403 cd01109 HTH_YyaN Helix-Turn-He 36.4 42 0.0009 20.9 2.6 29 47-84 1-29 (113)
404 cd01108 HTH_CueR Helix-Turn-He 36.3 41 0.00089 21.5 2.6 29 47-84 1-29 (127)
405 PRK10727 DNA-binding transcrip 35.9 28 0.0006 25.1 1.9 21 47-72 2-22 (343)
406 COG3703 ChaC Uncharacterized p 35.8 51 0.0011 23.4 3.1 36 45-82 130-169 (190)
407 PRK12469 RNA polymerase factor 35.8 32 0.0007 27.5 2.4 23 45-72 368-390 (481)
408 COG4567 Response regulator con 35.7 66 0.0014 22.5 3.6 56 18-78 88-154 (182)
409 PF06056 Terminase_5: Putative 35.6 38 0.00081 19.1 2.0 14 45-59 12-25 (58)
410 cd00569 HTH_Hin_like Helix-tur 35.6 34 0.00074 15.1 1.7 21 46-71 21-41 (42)
411 cd04886 ACT_ThrD-II-like C-ter 35.6 38 0.00082 18.1 2.1 19 62-80 6-24 (73)
412 COG1813 Predicted transcriptio 35.5 29 0.00062 24.0 1.8 34 34-72 80-113 (165)
413 PF01842 ACT: ACT domain; Int 35.4 29 0.00064 18.5 1.6 19 62-80 8-26 (66)
414 PF09079 Cdc6_C: CDC6, C termi 35.3 57 0.0012 19.1 2.9 34 49-84 25-58 (85)
415 PF07037 DUF1323: Putative tra 35.3 37 0.00081 22.4 2.2 22 47-73 1-22 (122)
416 PRK15320 transcriptional activ 35.2 46 0.00099 24.3 2.8 43 29-77 167-209 (251)
417 cd04786 HTH_MerR-like_sg7 Heli 35.2 43 0.00094 21.8 2.6 29 47-84 1-29 (131)
418 PRK00901 methylated-DNA--prote 35.1 88 0.0019 21.1 4.1 30 28-57 72-101 (155)
419 PRK06596 RNA polymerase factor 34.8 41 0.00088 24.5 2.6 24 45-73 247-270 (284)
420 TIGR02366 DHAK_reg probable di 34.7 86 0.0019 20.3 4.0 25 33-59 11-35 (176)
421 cd04789 HTH_Cfa Helix-Turn-Hel 34.6 50 0.0011 20.3 2.7 28 47-83 2-29 (102)
422 PRK10339 DNA-binding transcrip 34.5 27 0.00058 25.0 1.6 22 47-73 2-23 (327)
423 cd04764 HTH_MlrA-like_sg1 Heli 34.5 33 0.00071 19.1 1.7 19 47-70 1-19 (67)
424 PRK15008 HTH-type transcriptio 34.4 56 0.0012 22.2 3.2 27 37-69 30-56 (212)
425 PRK13413 mpi multiple promoter 34.3 57 0.0012 22.2 3.2 24 45-73 171-194 (200)
426 TIGR02948 SigW_bacill RNA poly 34.1 27 0.00059 22.9 1.5 14 45-59 151-164 (187)
427 PRK13698 plasmid-partitioning 34.1 77 0.0017 24.2 4.0 41 28-76 159-201 (323)
428 PF01399 PCI: PCI domain; Int 34.0 91 0.002 18.2 3.7 50 25-82 42-91 (105)
429 PRK13756 tetracycline represso 34.0 59 0.0013 22.5 3.3 27 38-70 17-43 (205)
430 PRK12528 RNA polymerase sigma 34.0 25 0.00053 22.7 1.3 14 45-59 128-141 (161)
431 PRK13749 transcriptional regul 34.0 47 0.001 21.6 2.5 32 46-86 3-34 (121)
432 PF09824 ArsR: ArsR transcript 34.0 88 0.0019 21.6 3.9 48 25-84 13-60 (160)
433 TIGR02417 fruct_sucro_rep D-fr 34.0 31 0.00067 24.6 1.9 10 49-59 2-11 (327)
434 PF09269 DUF1967: Domain of un 33.9 24 0.00052 20.5 1.1 32 49-84 18-49 (69)
435 cd04763 HTH_MlrA-like Helix-Tu 33.8 44 0.00095 18.7 2.2 27 47-82 1-28 (68)
436 cd04768 HTH_BmrR-like Helix-Tu 33.7 50 0.0011 20.1 2.6 30 47-85 1-30 (96)
437 cd01111 HTH_MerD Helix-Turn-He 33.7 48 0.001 20.7 2.5 29 47-84 1-29 (107)
438 PF10975 DUF2802: Protein of u 33.7 24 0.00053 20.7 1.1 25 45-71 43-67 (70)
439 cd04775 HTH_Cfa-like Helix-Tur 33.6 47 0.001 20.4 2.4 27 47-82 2-28 (102)
440 PRK00767 transcriptional regul 33.3 62 0.0013 21.2 3.1 21 37-59 21-41 (197)
441 PF12627 PolyA_pol_RNAbd: Prob 33.3 87 0.0019 17.1 3.6 29 11-39 29-57 (64)
442 cd04782 HTH_BltR Helix-Turn-He 33.2 51 0.0011 20.1 2.6 29 47-84 1-29 (97)
443 cd01104 HTH_MlrA-CarA Helix-Tu 33.1 35 0.00076 18.8 1.7 21 47-72 1-21 (68)
444 PRK04158 transcriptional repre 33.1 80 0.0017 23.4 3.9 44 33-83 190-233 (256)
445 PF08256 Antimicrobial20: Aure 33.0 33 0.0007 14.0 1.1 8 33-40 1-8 (13)
446 PRK12547 RNA polymerase sigma 32.9 27 0.00058 22.7 1.3 14 45-59 127-140 (164)
447 PF15467 SGIII: Secretogranin- 32.9 42 0.00091 26.3 2.5 50 35-85 120-170 (453)
448 PRK09483 response regulator; P 32.9 76 0.0017 20.7 3.6 36 30-75 152-191 (217)
449 TIGR02054 MerD mercuric resist 32.7 50 0.0011 21.3 2.5 30 46-84 3-32 (120)
450 cd04788 HTH_NolA-AlbR Helix-Tu 32.7 52 0.0011 20.0 2.5 29 47-84 1-29 (96)
451 TIGR02719 repress_PhaQ poly-be 32.7 1.5E+02 0.0033 19.7 6.6 61 20-84 15-76 (138)
452 PHA03103 double-strand RNA-bin 32.6 1.3E+02 0.0028 21.1 4.7 34 45-83 26-59 (183)
453 cd04927 ACT_ACR-like_2 Second 32.5 45 0.00098 19.4 2.1 20 62-81 8-27 (76)
454 PRK12531 RNA polymerase sigma 32.5 31 0.00066 23.2 1.6 14 45-59 156-169 (194)
455 PF13413 HTH_25: Helix-turn-he 32.5 48 0.001 18.8 2.2 14 45-59 9-22 (62)
456 cd02758 MopB_Tetrathionate-Ra 32.4 63 0.0014 27.0 3.6 39 34-79 328-366 (735)
457 PRK12534 RNA polymerase sigma 32.4 43 0.00094 22.1 2.3 14 45-59 152-165 (187)
458 PF08668 HDOD: HDOD domain; I 32.4 43 0.00093 22.3 2.3 36 33-77 10-45 (196)
459 PRK12427 flagellar biosynthesi 32.3 51 0.0011 23.2 2.7 26 45-75 198-223 (231)
460 PRK14996 TetR family transcrip 32.3 54 0.0012 21.7 2.7 21 37-59 20-40 (192)
461 TIGR02405 trehalos_R_Ecol treh 32.2 41 0.00089 23.9 2.3 22 47-73 2-23 (311)
462 cd04784 HTH_CadR-PbrR Helix-Tu 31.8 53 0.0011 20.9 2.5 29 47-84 1-29 (127)
463 COG1405 SUA7 Transcription ini 31.7 1.4E+02 0.0031 22.1 5.1 30 45-79 156-185 (285)
464 cd01392 HTH_LacI Helix-turn-he 31.5 28 0.0006 18.2 1.0 35 46-81 8-42 (52)
465 COG0350 Ada Methylated DNA-pro 31.4 95 0.0021 21.1 3.9 30 28-57 87-116 (168)
466 PF11268 DUF3071: Protein of u 31.2 36 0.00078 23.5 1.7 14 45-59 68-81 (170)
467 cd01106 HTH_TipAL-Mta Helix-Tu 31.2 58 0.0013 19.9 2.6 28 47-83 1-28 (103)
468 TIGR01714 phage_rep_org_N phag 30.8 1.1E+02 0.0024 19.9 3.9 37 44-85 49-85 (119)
469 COG1654 BirA Biotin operon rep 30.7 83 0.0018 19.0 3.1 33 45-82 18-50 (79)
470 PF01498 HTH_Tnp_Tc3_2: Transp 30.7 50 0.0011 18.6 2.1 31 45-82 12-46 (72)
471 cd01279 HTH_HspR-like Helix-Tu 30.6 66 0.0014 19.7 2.7 28 47-83 2-29 (98)
472 cd02762 MopB_1 The MopB_1 CD i 30.5 1.7E+02 0.0037 23.0 5.6 37 35-78 248-284 (539)
473 cd04773 HTH_TioE_rpt2 Second H 30.5 60 0.0013 20.2 2.6 29 47-84 1-29 (108)
474 PF00486 Trans_reg_C: Transcri 30.5 1E+02 0.0022 17.1 3.6 48 29-78 8-60 (77)
475 PRK00441 argR arginine repress 30.4 87 0.0019 20.9 3.5 39 33-79 8-51 (149)
476 PRK10079 phosphonate metabolis 30.4 76 0.0017 22.1 3.4 33 48-85 37-69 (241)
477 cd00093 HTH_XRE Helix-turn-hel 30.2 75 0.0016 15.4 3.3 21 46-71 12-32 (58)
478 PF11972 HTH_13: HTH DNA bindi 30.2 1.1E+02 0.0024 17.3 3.4 36 34-77 4-39 (54)
479 TIGR02999 Sig-70_X6 RNA polyme 30.2 57 0.0012 21.4 2.5 20 45-69 149-168 (183)
480 COG1309 AcrR Transcriptional r 30.1 96 0.0021 18.9 3.5 22 45-71 31-52 (201)
481 PRK09642 RNA polymerase sigma 30.1 56 0.0012 20.9 2.5 19 45-68 121-139 (160)
482 PF09645 F-112: F-112 protein; 30.0 59 0.0013 20.8 2.4 40 34-78 12-51 (110)
483 TIGR02989 Sig-70_gvs1 RNA poly 29.9 34 0.00074 21.8 1.4 14 45-59 126-139 (159)
484 TIGR02047 CadR-PbrR Cd(II)/Pb( 29.7 60 0.0013 20.8 2.5 29 47-84 1-29 (127)
485 COG4533 ABC-type uncharacteriz 29.6 76 0.0017 26.1 3.6 37 45-86 22-58 (564)
486 PF02746 MR_MLE_N: Mandelate r 29.5 1.2E+02 0.0026 18.6 3.9 19 23-41 89-107 (117)
487 PF04297 UPF0122: Putative hel 29.2 56 0.0012 20.7 2.2 24 45-73 32-55 (101)
488 PRK07921 RNA polymerase sigma 29.2 50 0.0011 24.8 2.3 22 45-71 281-302 (324)
489 COG0789 SoxR Predicted transcr 29.1 67 0.0015 19.8 2.6 32 47-87 1-32 (124)
490 TIGR02939 RpoE_Sigma70 RNA pol 28.9 32 0.0007 22.6 1.2 14 45-59 153-166 (190)
491 PLN03239 histone acetyltransfe 28.9 1.5E+02 0.0032 23.0 4.8 50 19-84 265-314 (351)
492 PRK12537 RNA polymerase sigma 28.8 51 0.0011 21.8 2.2 14 45-59 148-161 (182)
493 PRK09751 putative ATP-dependen 28.7 73 0.0016 29.1 3.5 34 45-83 988-1021(1490)
494 COG1695 Predicted transcriptio 28.7 1.1E+02 0.0024 19.4 3.7 51 30-84 10-63 (138)
495 cd04777 HTH_MerR-like_sg1 Heli 28.7 68 0.0015 19.7 2.6 29 47-84 1-29 (107)
496 PF00395 SLH: S-layer homology 28.7 49 0.0011 17.0 1.7 30 24-53 14-45 (45)
497 PRK10227 DNA-binding transcrip 28.5 65 0.0014 21.0 2.6 30 47-85 1-30 (135)
498 PF09382 RQC: RQC domain; Int 28.4 60 0.0013 19.6 2.3 23 64-86 55-77 (106)
499 cd04913 ACT_AKii-LysC-BS-like_ 28.3 61 0.0013 17.5 2.1 19 62-80 10-28 (75)
500 PF09940 DUF2172: Domain of un 28.3 42 0.00092 26.2 1.8 46 30-82 341-386 (386)
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=99.71 E-value=1.4e-17 Score=94.56 Aligned_cols=51 Identities=57% Similarity=0.862 Sum_probs=45.8
Q ss_pred HHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 24 MTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 24 ~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
++||+|+||||||+|+++| ++|+|++||+++++ ..||.++..|+|+||+|+
T Consensus 1 MaLk~aveLgI~dii~~~g-~~~ls~~eia~~l~-~~~p~~~~~L~RimR~L~ 51 (51)
T PF08100_consen 1 MALKCAVELGIPDIIHNAG-GGPLSLSEIAARLP-TSNPSAPPMLDRIMRLLV 51 (51)
T ss_dssp HHHHHHHHTTHHHHHHHHT-TS-BEHHHHHHTST-CT-TTHHHHHHHHHHHHH
T ss_pred CcHHHHHHcCcHHHHHHcC-CCCCCHHHHHHHcC-CCCcchHHHHHHHHHHhC
Confidence 6899999999999999987 58999999999999 788889999999999996
No 2
>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]
Probab=99.36 E-value=2.6e-12 Score=96.50 Aligned_cols=77 Identities=45% Similarity=0.730 Sum_probs=67.3
Q ss_pred HhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 5 ARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 5 ~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
++.+....++++++++..++++++|+||||||+|++++ + .+|||..+...++|.+|.++.|+||.|++++++++.
T Consensus 2 ~e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~--~---p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~k~~ 76 (342)
T KOG3178|consen 2 EENEASLRAMRLANGFALPMVLKAACELGVFDILANAG--S---PSEIASLLPTPKNPEAPVLLDRILRLLVSYSILKCR 76 (342)
T ss_pred chhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCC--C---HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhceee
Confidence 56677889999999999999999999999999999975 2 888888877225788999999999999999999976
Q ss_pred cc
Q 045477 85 VD 86 (89)
Q Consensus 85 ~~ 86 (89)
..
T Consensus 77 ~~ 78 (342)
T KOG3178|consen 77 LV 78 (342)
T ss_pred ee
Confidence 43
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=99.23 E-value=1.7e-11 Score=89.43 Aligned_cols=55 Identities=25% Similarity=0.338 Sum_probs=51.0
Q ss_pred HHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 22 LHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 22 ~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
...+|++|++|||||+|++ +|.|++|||++++ + ++..++|+||+|++.|+|++..
T Consensus 3 ~~~~l~aa~~Lglfd~L~~----gp~t~~eLA~~~~-~----~~~~~~~lL~~L~~lgll~~~~ 57 (306)
T TIGR02716 3 EFSCMKAAIELDLFSHMAE----GPKDLATLAADTG-S----VPPRLEMLLETLRQMRVINLED 57 (306)
T ss_pred hHHHHHHHHHcCcHHHHhc----CCCCHHHHHHHcC-C----ChHHHHHHHHHHHhCCCeEecC
Confidence 4679999999999999986 6999999999999 9 9999999999999999998753
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=98.20 E-value=9.2e-07 Score=49.47 Aligned_cols=46 Identities=35% Similarity=0.481 Sum_probs=40.7
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+.|.+.+++++ +++|+.|||+.++ . +...++|+|+.|+..|++.++
T Consensus 6 l~iL~~l~~~~--~~~t~~eia~~~g-l----~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESG--GPLTLSEIARALG-L----PKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTB--SCEEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHHcCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCcCeecC
Confidence 46788898876 7899999999999 9 899999999999999999875
No 5
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=97.65 E-value=0.00012 Score=44.17 Aligned_cols=47 Identities=26% Similarity=0.369 Sum_probs=41.5
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+.|.+.|.+.+ +++|+.|||+.++ . +...++|+++.|...|++....
T Consensus 8 ~~Il~~l~~~~--~~~t~~~ia~~l~-i----~~~tv~r~l~~L~~~g~l~~~~ 54 (91)
T smart00346 8 LAVLRALAEEP--GGLTLAELAERLG-L----SKSTAHRLLNTLQELGYVEQDG 54 (91)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCeeecC
Confidence 56788888754 6899999999999 9 8999999999999999998753
No 6
>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=97.36 E-value=0.00039 Score=39.22 Aligned_cols=53 Identities=26% Similarity=0.367 Sum_probs=41.5
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD 89 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~ 89 (89)
+..|.-.|...++ .++|..|||+.++ . ++..+.|+++.|...|++....+.+|
T Consensus 7 q~~vL~~l~~~~~-~~~t~~~la~~l~-~----~~~~vs~~v~~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 7 QFRVLMALARHPG-EELTQSELAERLG-I----SKSTVSRIVKRLEKKGLVERERDPGD 59 (62)
T ss_dssp HHHHHHHHHHSTT-SGEEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred HHHHHHHHHHCCC-CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEeCCCCC
Confidence 3455666776641 3399999999999 9 99999999999999999998866554
No 7
>PRK11569 transcriptional repressor IclR; Provisional
Probab=97.33 E-value=0.00039 Score=50.41 Aligned_cols=48 Identities=25% Similarity=0.333 Sum_probs=42.0
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+.|.+.+++.. +|+|++|||+.+| . +...++|+|+.|+..|++..+.+
T Consensus 31 l~IL~~l~~~~--~~~~lseia~~lg-l----pksTv~RlL~tL~~~G~l~~~~~ 78 (274)
T PRK11569 31 LKLLEWIAESN--GSVALTELAQQAG-L----PNSTTHRLLTTMQQQGFVRQVGE 78 (274)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEcCC
Confidence 56788888754 7899999999999 9 89999999999999999986543
No 8
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=97.27 E-value=0.0005 Score=49.82 Aligned_cols=48 Identities=21% Similarity=0.299 Sum_probs=42.0
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+.|.+.+++.+ .++|++|||+.++ . ....++|+|..|+..|++..+.+
T Consensus 28 l~IL~~~~~~~--~~~tl~eIa~~lg-l----pkStv~RlL~tL~~~G~l~~~~~ 75 (271)
T PRK10163 28 IAILQYLEKSG--GSSSVSDISLNLD-L----PLSTTFRLLKVLQAADFVYQDSQ 75 (271)
T ss_pred HHHHHHHHhCC--CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEcCC
Confidence 56788888765 6899999999999 9 89999999999999999987543
No 9
>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=97.22 E-value=0.00081 Score=36.53 Aligned_cols=45 Identities=18% Similarity=0.389 Sum_probs=38.1
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
.+..|+..|.+. +++|..|||+.++ . ....+.+.++-|...|+++
T Consensus 4 ~~~~Il~~l~~~---~~~t~~ela~~~~-i----s~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLREN---PRITQKELAEKLG-I----SRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHC---TTS-HHHHHHHHT-S-----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCcCcC
Confidence 466788999985 4799999999999 9 8999999999999999874
No 10
>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=97.18 E-value=0.00047 Score=40.08 Aligned_cols=48 Identities=25% Similarity=0.275 Sum_probs=41.1
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.+..|+..|.+. +++|+.|||..++ . +...+++.|+.|...|++....
T Consensus 9 ~E~~vy~~Ll~~---~~~t~~eIa~~l~-i----~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 9 NEAKVYLALLKN---GPATAEEIAEELG-I----SRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHH---CHEEHHHHHHHHT-S----SHHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEc
Confidence 355667677654 6999999999999 9 9999999999999999998765
No 11
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=97.17 E-value=0.00076 Score=48.50 Aligned_cols=50 Identities=28% Similarity=0.465 Sum_probs=43.6
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
-+.|.+.|++.+ .+++++|||+++| . ++..++|+|..|+..|+++++.+.
T Consensus 6 al~iL~~l~~~~--~~l~l~ela~~~g-l----pksT~~RlL~tL~~~G~v~~d~~~ 55 (246)
T COG1414 6 ALAILDLLAEGP--GGLSLAELAERLG-L----PKSTVHRLLQTLVELGYVEQDPED 55 (246)
T ss_pred HHHHHHHHHhCC--CCCCHHHHHHHhC-c----CHHHHHHHHHHHHHCCCEEEcCCC
Confidence 357889998854 5688999999999 9 899999999999999999988754
No 12
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=97.11 E-value=0.0011 Score=47.78 Aligned_cols=48 Identities=19% Similarity=0.193 Sum_probs=41.8
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+.|.+.|.+++ +++|++||++.++ . +...++|+|+.|+..|++....+
T Consensus 14 l~iL~~l~~~~--~~ls~~eia~~lg-l----~kstv~RlL~tL~~~g~v~~~~~ 61 (263)
T PRK09834 14 LMVLRALNRLD--GGATVGLLAELTG-L----HRTTVRRLLETLQEEGYVRRSAS 61 (263)
T ss_pred HHHHHHHHhcC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEecC
Confidence 46778887764 6799999999999 9 99999999999999999987654
No 13
>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=97.09 E-value=0.00076 Score=37.83 Aligned_cols=51 Identities=24% Similarity=0.401 Sum_probs=41.3
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD 89 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~ 89 (89)
+..+...|.+. +++|..|||..++ . ++..+.|+++-|...|++....+.+|
T Consensus 5 q~~iL~~l~~~---~~~~~~~la~~~~-~----~~~~~t~~i~~L~~~g~I~r~~~~~D 55 (59)
T PF01047_consen 5 QFRILRILYEN---GGITQSELAEKLG-I----SRSTVTRIIKRLEKKGLIERERDPDD 55 (59)
T ss_dssp HHHHHHHHHHH---SSEEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred HHHHHHHHHHc---CCCCHHHHHHHHC-C----ChhHHHHHHHHHHHCCCEEeccCCCC
Confidence 34455566666 4799999999999 9 99999999999999999997765543
No 14
>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=97.08 E-value=0.00081 Score=47.85 Aligned_cols=46 Identities=20% Similarity=0.284 Sum_probs=40.7
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+.|.+.++++. .|+|++|||+.+| . ....++|+|..|+..|++..+
T Consensus 12 l~IL~~l~~~~--~~~~l~eia~~lg-l----pksT~~RlL~tL~~~G~l~~~ 57 (248)
T TIGR02431 12 LAVIEAFGAER--PRLTLTDVAEATG-L----TRAAARRFLLTLVELGYVTSD 57 (248)
T ss_pred HHHHHHHhcCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEeC
Confidence 56788887654 7999999999999 9 889999999999999999864
No 15
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.06 E-value=0.0021 Score=37.84 Aligned_cols=51 Identities=20% Similarity=0.236 Sum_probs=43.6
Q ss_pred HHHhChHHHHHhcCCCC-CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 29 VINLGLFEIIAKAGPGA-KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~-~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
..+-.|...|.+.| + ++|+.|||..+| . +...++|+|-.|...|++....+
T Consensus 6 ~~~~~IL~~L~~~g--~~~~ta~eLa~~lg-l----~~~~v~r~L~~L~~~G~V~~~~~ 57 (68)
T smart00550 6 SLEEKILEFLENSG--DETSTALQLAKNLG-L----PKKEVNRVLYSLEKKGKVCKQGG 57 (68)
T ss_pred HHHHHHHHHHHHCC--CCCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecCC
Confidence 35567888998875 4 499999999999 9 99999999999999999986543
No 16
>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=97.05 E-value=0.0017 Score=39.24 Aligned_cols=42 Identities=36% Similarity=0.557 Sum_probs=34.4
Q ss_pred HHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 38 IAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 38 l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|+.++.++++|..|||+.++ + ++..++++|+.|...|+++..
T Consensus 17 la~~~~~~~~s~~eiA~~~~-i----~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 17 LARHPDGKPVSSKEIAERLG-I----SPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHCTTTSC-BEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHhCCCCCCCCHHHHHHHHC-c----CHHHHHHHHHHHhhCCeeEec
Confidence 45444346799999999999 9 999999999999999998755
No 17
>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=97.03 E-value=0.0014 Score=37.37 Aligned_cols=53 Identities=19% Similarity=0.349 Sum_probs=43.2
Q ss_pred HHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 26 MKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 26 L~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
|---..+.|.+.|... +|+|+.|||+.++ . .+..+++=|+.|...|+++...+
T Consensus 7 L~~p~R~~Il~~L~~~---~~~t~~ela~~l~-~----~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 7 LSDPTRLRILRLLASN---GPMTVSELAEELG-I----SQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HTSHHHHHHHHHHHHC---STBEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEEEE
T ss_pred hCCHHHHHHHHHHhcC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeEEecc
Confidence 3334567888888543 7999999999999 9 89999999999999999986643
No 18
>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=97.01 E-value=0.002 Score=40.61 Aligned_cols=53 Identities=26% Similarity=0.335 Sum_probs=42.4
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCC-CCCcchHHHHHHHHhccCceeeecc
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKN-KDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~-~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+..|++.|.+.+ +++|++||.+.+. ... .-+...++|.|+.|+..|++.+...
T Consensus 3 R~~Il~~l~~~~--~~~sa~ei~~~l~-~~~~~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 3 RLAILEVLLESD--GHLTAEEIYERLR-KKGPSISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred HHHHHHHHHhCC--CCCCHHHHHHHHH-hcCCCCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 356888898764 8999999999985 321 1277889999999999999998754
No 19
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=96.99 E-value=0.0012 Score=47.21 Aligned_cols=46 Identities=13% Similarity=0.338 Sum_probs=39.5
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+.|.+.+++. +++|++|||+.++ . +...++|+|+.|+..|++.+..
T Consensus 17 l~IL~~l~~~---~~l~l~eia~~lg-l----~kstv~Rll~tL~~~G~l~~~~ 62 (257)
T PRK15090 17 FGILQALGEE---REIGITELSQRVM-M----SKSTVYRFLQTMKTLGYVAQEG 62 (257)
T ss_pred HHHHHHhhcC---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEcC
Confidence 4567777653 5899999999999 9 8999999999999999998764
No 20
>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=96.94 E-value=0.0017 Score=37.08 Aligned_cols=39 Identities=26% Similarity=0.388 Sum_probs=32.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV 88 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~ 88 (89)
++++..+|+..++ . +...+.|+++.|...|++....+..
T Consensus 17 ~~~t~~~l~~~~~-~----~~~~vs~~i~~L~~~glv~~~~~~~ 55 (68)
T PF13463_consen 17 GPMTQSDLAERLG-I----SKSTVSRIIKKLEEKGLVEKERDPH 55 (68)
T ss_dssp S-BEHHHHHHHTT-------HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEecCCCC
Confidence 7999999999999 9 9999999999999999998776554
No 21
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=96.84 E-value=0.004 Score=37.35 Aligned_cols=49 Identities=24% Similarity=0.401 Sum_probs=41.6
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
.++.|+..|... +++|..+|++.++ . ++..+.|.++.|...|++.....
T Consensus 11 ~~~~il~~l~~~---~~~~~~~la~~~~-~----s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 11 TQFLVLRILYEE---GPLSVSELAKRLG-V----SPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHHC-C----CchhHHHHHHHHHHCCCeEecCC
Confidence 356778888764 5799999999999 9 88899999999999999986543
No 22
>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=96.74 E-value=0.0019 Score=35.20 Aligned_cols=43 Identities=26% Similarity=0.448 Sum_probs=37.4
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
++.|...|.+ +|.++.||++.++ . ++..+.+-|+.|...|+++
T Consensus 4 R~~Il~~L~~----~~~~~~el~~~l~-~----s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 4 RLRILKLLSE----GPLTVSELAEELG-L----SQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHTT----SSEEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHh----CCCchhhHHHhcc-c----cchHHHHHHHHHHHCcCee
Confidence 4567777776 7999999999999 9 9999999999999999986
No 23
>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=96.66 E-value=0.0049 Score=39.69 Aligned_cols=35 Identities=31% Similarity=0.429 Sum_probs=32.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|+|.+|||+.++ + .+..++++|+.|+..|++...
T Consensus 24 ~~~s~~eia~~~~-i----~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 24 GPVSVKEIAERQG-I----SRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CcCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEec
Confidence 5999999999999 9 899999999999999999764
No 24
>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=96.64 E-value=0.0048 Score=39.95 Aligned_cols=44 Identities=30% Similarity=0.352 Sum_probs=36.5
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
...|+.++ ++++|+.|||++++ + .+..+.++|+.|...|++...
T Consensus 15 l~~la~~~-~~~~s~~eia~~l~-i----s~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 15 LTTLAQND-SQPYSAAEIAEQTG-L----NAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHhCC-CCCccHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEec
Confidence 33444443 37899999999999 9 899999999999999999754
No 25
>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=96.56 E-value=0.0046 Score=36.23 Aligned_cols=45 Identities=16% Similarity=0.297 Sum_probs=37.4
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|-+.|.+. +.+|..|||..++ + ++..+.-+|..|...|.+++..
T Consensus 4 ~i~~~l~~~---~~~S~~eLa~~~~-~----s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 4 EIRDYLRER---GRVSLAELAREFG-I----SPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHHS----SEEHHHHHHHTT-------HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHHc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEEec
Confidence 466778874 6899999999999 9 9999999999999999998764
No 26
>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=96.53 E-value=0.0069 Score=39.69 Aligned_cols=35 Identities=14% Similarity=0.330 Sum_probs=32.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+++|++|||+.++ + .+..+.++|+.|+..|++...
T Consensus 24 ~~~s~~~ia~~~~-i----p~~~l~kil~~L~~~glv~s~ 58 (135)
T TIGR02010 24 GPVTLADISERQG-I----SLSYLEQLFAKLRKAGLVKSV 58 (135)
T ss_pred CcCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCceEEE
Confidence 6899999999999 9 899999999999999999754
No 27
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=96.50 E-value=0.0048 Score=36.12 Aligned_cols=45 Identities=29% Similarity=0.240 Sum_probs=37.9
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.|.+.|.... +|+|..|||+.++ . +....+++|..|...|.+..+
T Consensus 4 ~Il~~i~~~~--~p~~T~eiA~~~g-l----s~~~aR~yL~~Le~eG~V~~~ 48 (62)
T PF04703_consen 4 KILEYIKEQN--GPLKTREIADALG-L----SIYQARYYLEKLEKEGKVERS 48 (62)
T ss_dssp CHHHHHHHHT--S-EEHHHHHHHHT-S-----HHHHHHHHHHHHHCTSEEEE
T ss_pred HHHHHHHHcC--CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence 5677787744 7999999999999 9 999999999999999998865
No 28
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=96.44 E-value=0.0068 Score=41.43 Aligned_cols=35 Identities=14% Similarity=0.316 Sum_probs=33.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|+|++|||+.++ + .+..|.+||+.|...|++...
T Consensus 24 ~~vs~~eIA~~~~-i----p~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 24 GPVPLADISERQG-I----SLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CcCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEeC
Confidence 6999999999999 9 899999999999999999864
No 29
>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=96.37 E-value=0.011 Score=37.45 Aligned_cols=50 Identities=20% Similarity=0.223 Sum_probs=40.9
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV 88 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~ 88 (89)
+..|...|... +++|..|||..++ . ++..+.|+++-|...|++.......
T Consensus 30 q~~iL~~l~~~---~~~t~~ela~~~~-~----~~~tvs~~l~~Le~~GlI~r~~~~~ 79 (118)
T TIGR02337 30 QWRILRILAEQ---GSMEFTQLANQAC-I----LRPSLTGILARLERDGLVTRLKASN 79 (118)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHhC-C----CchhHHHHHHHHHHCCCEEeccCCC
Confidence 33466667654 5899999999999 9 8889999999999999999765443
No 30
>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=96.28 E-value=0.012 Score=37.16 Aligned_cols=53 Identities=19% Similarity=0.258 Sum_probs=41.8
Q ss_pred HhChHHHHH--hcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477 31 NLGLFEIIA--KAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD 89 (89)
Q Consensus 31 ~LgIfd~l~--~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~ 89 (89)
+..|...|. ... ++++|..|||..++ . ++..+.|+++.|...|++....+..|
T Consensus 27 q~~vL~~l~~~~~~-~~~~t~~eL~~~l~-~----~~stvs~~i~~Le~kg~I~r~~~~~D 81 (109)
T TIGR01889 27 ELLILYYLGKLENN-EGKLTLKEIIKEIL-I----KQSALVKIIKKLSKKGYLSKERSEDD 81 (109)
T ss_pred HHHHHHHHHhhhcc-CCcCcHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEeccCCccc
Confidence 344555555 221 27899999999999 9 99999999999999999997766554
No 31
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=96.25 E-value=0.0094 Score=40.10 Aligned_cols=43 Identities=30% Similarity=0.454 Sum_probs=36.6
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 37 IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 37 ~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.|+.++.+++.|+++||+..+ + ++..|.|+|..|...|+++-.
T Consensus 16 ~LA~~~~~~~~s~~~IA~~~~-i----s~~~L~kil~~L~kaGlV~S~ 58 (150)
T COG1959 16 YLALLPGGGPVSSAEIAERQG-I----SPSYLEKILSKLRKAGLVKSV 58 (150)
T ss_pred HHHhCCCCCcccHHHHHHHhC-c----CHHHHHHHHHHHHHcCCEEee
Confidence 456554335899999999999 9 999999999999999999854
No 32
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=96.22 E-value=0.016 Score=30.91 Aligned_cols=44 Identities=25% Similarity=0.371 Sum_probs=37.5
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
|.+.+.+. +++|..+|++.++ . .+..++|.|..|...|++....
T Consensus 5 il~~l~~~---~~~s~~~l~~~l~-~----s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 5 ILELLAQQ---GKVSVEELAELLG-V----SEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHc---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEee
Confidence 56666653 5799999999999 9 8999999999999999988653
No 33
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=96.18 E-value=0.012 Score=36.57 Aligned_cols=45 Identities=22% Similarity=0.420 Sum_probs=40.9
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
.|..|...|... +++|..|||+.++ . ++..+.|.++.|...|++.
T Consensus 4 ~D~~il~~L~~~---~~~~~~~la~~l~-~----s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 4 IDRKILEELQKD---ARISLAELAKKVG-L----SPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHh---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCee
Confidence 577889999874 5899999999999 9 9999999999999999987
No 34
>PRK06474 hypothetical protein; Provisional
Probab=96.17 E-value=0.011 Score=40.71 Aligned_cols=56 Identities=14% Similarity=0.259 Sum_probs=45.2
Q ss_pred HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+|---..+.|++.|...+ +++|+.||++.++.+ ....++|-|+.|+..|++.....
T Consensus 7 ~La~p~R~~Il~~L~~~~--~~~ta~el~~~l~~i----s~aTvYrhL~~L~e~GLI~~~~~ 62 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNK--EGLTPLELVKILKDV----PQATLYRHLQTMVDSGILHVVKE 62 (178)
T ss_pred hhCCHHHHHHHHHHHhCC--CCCCHHHHHHHhcCC----CHHHHHHHHHHHHHCCCEEEeec
Confidence 344456788999998764 569999999999426 67789999999999999997653
No 35
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=96.15 E-value=0.0096 Score=31.53 Aligned_cols=36 Identities=25% Similarity=0.258 Sum_probs=32.3
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
-|+|..|||+.++ . .+..+.|.|+.|...|++....
T Consensus 7 ~~~s~~~la~~l~-~----s~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 7 LPLTRQEIAELLG-L----TRETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred eccCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeC
Confidence 3689999999999 9 8899999999999999997543
No 36
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=96.14 E-value=0.092 Score=34.19 Aligned_cols=48 Identities=19% Similarity=0.194 Sum_probs=39.2
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD 89 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~ 89 (89)
...|...+ ++.|.+|||..++ . ++..+.|++.-|...|++....+..|
T Consensus 37 L~~l~~~~--~~~t~~eLa~~l~-~----~~~tvt~~v~~Le~~GlV~r~~~~~D 84 (144)
T PRK03573 37 LHNIHQLP--PEQSQIQLAKAIG-I----EQPSLVRTLDQLEEKGLISRQTCASD 84 (144)
T ss_pred HHHHHHcC--CCCCHHHHHHHhC-C----ChhhHHHHHHHHHHCCCEeeecCCCC
Confidence 34454443 5689999999999 9 99999999999999999998766544
No 37
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=95.98 E-value=0.022 Score=37.31 Aligned_cols=48 Identities=27% Similarity=0.239 Sum_probs=39.7
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD 89 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~ 89 (89)
|.-.|... +++|..|||..++ . ++..+.|++.-|...|++....+.+|
T Consensus 45 vL~~l~~~---~~~t~~eLa~~l~-i----~~~tvsr~l~~Le~~GlI~R~~~~~D 92 (144)
T PRK11512 45 VLCSIRCA---ACITPVELKKVLS-V----DLGALTRMLDRLVCKGWVERLPNPND 92 (144)
T ss_pred HHHHHHHc---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEeccCccc
Confidence 34445543 6899999999999 9 99999999999999999997765544
No 38
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=95.89 E-value=0.02 Score=37.92 Aligned_cols=49 Identities=20% Similarity=0.333 Sum_probs=40.8
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|..++-+|-+. ++|+|++|||+.++ . +...++|-++-|...|++...+
T Consensus 28 ~Dv~v~~~LL~~--~~~~tvdelae~ln-r----~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 28 LDVEVYKALLEE--NGPLTVDELAEILN-R----SRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HHHHHHHHHHhh--cCCcCHHHHHHHHC-c----cHHHHHHHHHHHHHcCCeeeee
Confidence 355666666642 27999999999999 9 9999999999999999998654
No 39
>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=95.88 E-value=0.016 Score=32.77 Aligned_cols=36 Identities=25% Similarity=0.246 Sum_probs=33.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.++|..|||+.++ . ++..+.|+|+.|...|++....
T Consensus 24 ~~~s~~ela~~~g-~----s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLG-L----TRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecC
Confidence 6899999999999 9 8999999999999999998654
No 40
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=95.83 E-value=0.017 Score=38.86 Aligned_cols=57 Identities=25% Similarity=0.241 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 20 SVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 20 ~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|-..+.+-.=-.+.+...|++. +|.|..|+|+.+| - |+..+.|=||.|..+|++.-.
T Consensus 55 ye~la~vLsp~nleLl~~Ia~~---~P~Si~ElAe~vg-R----dv~nvhr~Ls~l~~~GlI~fe 111 (144)
T COG4190 55 YEDLARVLSPRNLELLELIAQE---EPASINELAELVG-R----DVKNVHRTLSTLADLGLIFFE 111 (144)
T ss_pred HHHHHHHhChhHHHHHHHHHhc---CcccHHHHHHHhC-c----chHHHHHHHHHHHhcCeEEEe
Confidence 4444445555567888999875 6999999999999 8 999999999999999998744
No 41
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=95.81 E-value=0.027 Score=30.73 Aligned_cols=42 Identities=24% Similarity=0.390 Sum_probs=35.7
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|+..|. . ++.|..+|++.++ . .+..+.+.++.|...|++...
T Consensus 2 il~~l~-~---~~~~~~~i~~~l~-i----s~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 2 ILKLLA-E---GELCVCELAEILG-L----SQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred HHHHhh-c---CCccHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeeee
Confidence 455565 2 6899999999999 9 888999999999999999854
No 42
>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=95.74 E-value=0.025 Score=32.04 Aligned_cols=44 Identities=20% Similarity=0.400 Sum_probs=38.7
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.|.+.|.+. +.+|++|||+.++ + .+..++|=+..|...|++..+
T Consensus 4 ~Il~~l~~~---~~~s~~ela~~~~-V----S~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 4 QILELLKEK---GKVSVKELAEEFG-V----SEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHc---CCEEHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEE
Confidence 467778764 6999999999999 9 999999999999999998765
No 43
>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=95.64 E-value=0.039 Score=30.82 Aligned_cols=46 Identities=26% Similarity=0.413 Sum_probs=37.7
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
...|...+.. ++.+..||++.++ + +...+.|.++.|...|++....
T Consensus 9 ~~~il~~l~~----~~~~~~ei~~~~~-i----~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 9 RLRILRLLLE----GPLTVSELAERLG-L----SQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHHHHHHHHH----CCcCHHHHHHHHC-c----CHhHHHHHHHHHHHCCCeEEEE
Confidence 3445666665 3499999999999 9 8889999999999999998653
No 44
>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=95.58 E-value=0.028 Score=30.98 Aligned_cols=40 Identities=18% Similarity=0.382 Sum_probs=34.1
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
.|...|.+++ +++|++|||+.++ + ....++|-+..|...|
T Consensus 4 ~il~~L~~~~--~~it~~eLa~~l~-v----S~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESK--EPITAKELAEELG-V----SRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTT--TSBEHHHHHHHCT-S-----HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcC--CCcCHHHHHHHhC-C----CHHHHHHHHHHHHHCC
Confidence 4667786654 6899999999999 9 9999999999999988
No 45
>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=95.56 E-value=0.029 Score=32.50 Aligned_cols=44 Identities=18% Similarity=0.341 Sum_probs=38.0
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
++.|...+.+ ++.|..|||+.++ + ....+.|-++.|...|+.-+
T Consensus 2 ~~~il~~L~~----~~~~~~eLa~~l~-v----S~~tv~~~l~~L~~~g~~i~ 45 (69)
T TIGR00122 2 PLRLLALLAD----NPFSGEKLGEALG-M----SRTAVNKHIQTLREWGVDVL 45 (69)
T ss_pred hHHHHHHHHc----CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeEE
Confidence 5678888875 5789999999999 9 88999999999999998543
No 46
>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=95.54 E-value=0.014 Score=29.93 Aligned_cols=31 Identities=26% Similarity=0.398 Sum_probs=25.8
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV 81 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~ 81 (89)
|+|-+|||..+| . -+..+.|+|..|...|++
T Consensus 2 ~mtr~diA~~lG-~----t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 2 PMTRQDIADYLG-L----TRETVSRILKKLERQGLI 32 (32)
T ss_dssp E--HHHHHHHHT-S-----HHHHHHHHHHHHHTTSE
T ss_pred CcCHHHHHHHhC-C----cHHHHHHHHHHHHHcCCC
Confidence 688999999999 9 899999999999988874
No 47
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=95.47 E-value=0.041 Score=35.81 Aligned_cols=55 Identities=18% Similarity=0.344 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 22 LHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 22 ~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
...+|.--..+.|+..|.+. +++++.||++.++ . .+..+.+=|+.|...|+++..
T Consensus 9 ~fkaLadptRl~IL~~L~~~---~~~~v~ela~~l~-l----sqstvS~HL~~L~~AGLV~~~ 63 (117)
T PRK10141 9 LFKILSDETRLGIVLLLRES---GELCVCDLCTALD-Q----SQPKISRHLALLRESGLLLDR 63 (117)
T ss_pred HHHHhCCHHHHHHHHHHHHc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCceEEE
Confidence 34455556788899999763 5899999999999 9 888999999999999999754
No 48
>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=95.45 E-value=0.02 Score=36.42 Aligned_cols=57 Identities=23% Similarity=0.292 Sum_probs=44.1
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCC-CCCCcchHHHHHHHHhccCceeeeccc
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATK-NKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~-~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
+..+.-|++.|.+.+ +++|+.||-..+. .. +.-+...++|.|..|+..|++......
T Consensus 7 T~~R~~Il~~l~~~~--~~~ta~ei~~~l~-~~~~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 7 TPQRLAILELLKESP--EHLTAEEIYDKLR-KKGPRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHHHHHHS--SSEEHHHHHHHHH-HTTTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred CHHHHHHHHHHHcCC--CCCCHHHHHHHhh-hccCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 345667899999876 7999999999886 32 222667799999999999999987543
No 49
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=95.45 E-value=0.036 Score=37.86 Aligned_cols=55 Identities=18% Similarity=0.248 Sum_probs=44.4
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCC-CCCCcchHHHHHHHHhccCceeeec
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATK-NKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~-~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+-...-|++.|.+.+ +++|++||.+.+. .. +.-+...++|.|+.|+..|++.+..
T Consensus 25 T~qR~~IL~~l~~~~--~hlSa~eI~~~L~-~~~~~is~aTVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 25 TPQRLEVLRLMSLQP--GAISAYDLLDLLR-EAEPQAKPPTVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred CHHHHHHHHHHHhcC--CCCCHHHHHHHHH-hhCCCCCcchHHHHHHHHHHCCCEEEEe
Confidence 456677899998764 7999999999987 43 2226778999999999999999764
No 50
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=95.35 E-value=0.037 Score=36.97 Aligned_cols=56 Identities=25% Similarity=0.271 Sum_probs=45.0
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCC-CCCCcchHHHHHHHHhccCceeeecccC
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATK-NKDAPTMLDRILGLLASYGIVECSVDDV 88 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~-~~~d~~~l~RlLR~L~s~gi~~e~~~~~ 88 (89)
-.+.|.++|.+++ ++.|+.||=..+. .. ++-.+..++|.|..|+..|++.+....+
T Consensus 22 qR~~vl~~L~~~~--~~~sAeei~~~l~-~~~p~islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 22 QRLAVLELLLEAD--GHLSAEELYEELR-EEGPGISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred HHHHHHHHHHhcC--CCCCHHHHHHHHH-HhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 4667899999876 7899999998877 42 3336778999999999999999876543
No 51
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=95.28 E-value=0.057 Score=35.84 Aligned_cols=52 Identities=12% Similarity=0.215 Sum_probs=44.5
Q ss_pred HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+..+...|.+.+.++ |.+|..|+...+| + .-..+.+.+|-|++.|-+-..+.
T Consensus 10 r~eLk~rIvElVRe~---GRiTi~ql~~~TG-a----sR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 10 REELKARIVELVREH---GRITIKQLVAKTG-A----SRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHHHHHHHc---CCccHHHHHHHHC-C----CHHHHHHHHHHHHHcCCeEeCCC
Confidence 456778889999886 6999999999999 9 89999999999999887765543
No 52
>PRK09462 fur ferric uptake regulator; Provisional
Probab=95.20 E-value=0.048 Score=36.15 Aligned_cols=56 Identities=18% Similarity=0.268 Sum_probs=43.3
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCC-CCcchHHHHHHHHhccCceeeec
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNK-DAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~-~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+-...-|++.|.+.. ++++|+.||-+.+. -..| -+...++|.|..|+..|++.+..
T Consensus 16 T~qR~~Il~~l~~~~-~~h~sa~eI~~~l~-~~~~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 16 TLPRLKILEVLQEPD-NHHVSAEDLYKRLI-DMGEEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred CHHHHHHHHHHHhCC-CCCCCHHHHHHHHH-hhCCCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 345667888898642 26999999999886 4322 26788999999999999998764
No 53
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=95.18 E-value=0.048 Score=29.75 Aligned_cols=36 Identities=36% Similarity=0.402 Sum_probs=32.2
Q ss_pred CCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
..+ |..|||+.++ + ....+.|.++.|...|++....
T Consensus 18 ~~l~s~~~la~~~~-v----s~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 18 DKLPSERELAAQLG-V----SRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CcCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 456 9999999999 9 8999999999999999987553
No 54
>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=95.18 E-value=0.047 Score=31.97 Aligned_cols=43 Identities=26% Similarity=0.295 Sum_probs=32.9
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 37 IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 37 ~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.+.+.| -|-|+.|||+.+| .+ .+..+.+.|+.|...|+++...
T Consensus 18 ~~~~~G--~~Pt~rEIa~~~g-~~---S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 18 YIEENG--YPPTVREIAEALG-LK---STSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHHHS--S---HHHHHHHHT-SS---SHHHHHHHHHHHHHTTSEEEGC
T ss_pred HHHHcC--CCCCHHHHHHHhC-CC---ChHHHHHHHHHHHHCcCccCCC
Confidence 344555 6789999999999 82 3789999999999999998664
No 55
>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=95.18 E-value=0.05 Score=31.28 Aligned_cols=37 Identities=27% Similarity=0.405 Sum_probs=33.2
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
++++..+||+.++ + .+..+..+++-|...|++.....
T Consensus 21 ~~v~~~~iA~~L~-v----s~~tvt~ml~~L~~~GlV~~~~y 57 (60)
T PF01325_consen 21 GPVRTKDIAERLG-V----SPPTVTEMLKRLAEKGLVEYEPY 57 (60)
T ss_dssp SSBBHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEETT
T ss_pred CCccHHHHHHHHC-C----ChHHHHHHHHHHHHCCCEEecCC
Confidence 8999999999999 9 89999999999999999986643
No 56
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=95.16 E-value=0.098 Score=36.24 Aligned_cols=46 Identities=17% Similarity=0.218 Sum_probs=40.5
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
..|+++|-.+ |++|.+|||..+| . ....++|+|..|...|++....
T Consensus 25 ~~Vl~~L~~~---g~~tdeeLA~~Lg-i----~~~~VRk~L~~L~e~gLv~~~r 70 (178)
T PRK06266 25 FEVLKALIKK---GEVTDEEIAEQTG-I----KLNTVRKILYKLYDARLADYKR 70 (178)
T ss_pred hHHHHHHHHc---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeEEee
Confidence 4588888875 5899999999999 9 9999999999999999998543
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=95.15 E-value=0.046 Score=38.00 Aligned_cols=45 Identities=22% Similarity=0.373 Sum_probs=39.5
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
..|...|... +++|..|||+.++ + ++..++|.|+.|...|++...
T Consensus 4 ~~IL~~L~~~---~~~t~~eLA~~lg-i----s~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQ---GQATAAALAEALA-I----SPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEe
Confidence 4577777764 5799999999999 9 999999999999999999865
No 58
>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=95.13 E-value=0.046 Score=32.06 Aligned_cols=47 Identities=17% Similarity=0.319 Sum_probs=37.5
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCC--cchHHHHHHHHhccCceeee
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDA--PTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d--~~~l~RlLR~L~s~gi~~e~ 84 (89)
|.++|.+++ +|++..+|++.+. .. +.+ +..++|.||.|-..|+....
T Consensus 3 IL~~L~~~~--~P~g~~~l~~~L~-~~-g~~~se~avRrrLr~me~~Glt~~~ 51 (66)
T PF08461_consen 3 ILRILAESD--KPLGRKQLAEELK-LR-GEELSEEAVRRRLRAMERDGLTRKV 51 (66)
T ss_pred HHHHHHHcC--CCCCHHHHHHHHH-hc-ChhhhHHHHHHHHHHHHHCCCcccc
Confidence 678888876 8999999999987 42 224 47899999999999966543
No 59
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=95.10 E-value=0.046 Score=35.96 Aligned_cols=37 Identities=22% Similarity=0.255 Sum_probs=33.5
Q ss_pred CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 44 GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+.+.|..|||+..+ + ++..++++|+.|...|++.-..
T Consensus 23 g~~~s~~~ia~~~~-i----s~~~vrk~l~~L~~~Glv~s~~ 59 (141)
T PRK11014 23 GRMTSISEVTEVYG-V----SRNHMVKIINQLSRAGYVTAVR 59 (141)
T ss_pred CCccCHHHHHHHHC-c----CHHHHHHHHHHHHhCCEEEEec
Confidence 36889999999999 9 9999999999999999998654
No 60
>PRK10870 transcriptional repressor MprA; Provisional
Probab=94.88 E-value=0.072 Score=36.45 Aligned_cols=40 Identities=28% Similarity=0.317 Sum_probs=36.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD 89 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~ 89 (89)
+++|..|||..++ . ++..+.|++.-|...|++....+.+|
T Consensus 70 ~~it~~eLa~~l~-l----~~~tvsr~v~rLe~kGlV~R~~~~~D 109 (176)
T PRK10870 70 HSIQPSELSCALG-S----SRTNATRIADELEKRGWIERRESDND 109 (176)
T ss_pred CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecCCCCC
Confidence 6899999999999 9 99999999999999999998766544
No 61
>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=94.84 E-value=0.057 Score=36.66 Aligned_cols=46 Identities=13% Similarity=0.104 Sum_probs=39.7
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
..|+++|-.+ +.+|-+|||..+| . ...-++|++..|...|++....
T Consensus 17 v~Vl~aL~~~---~~~tdEeLa~~Lg-i----~~~~VRk~L~~L~e~~Lv~~~r 62 (158)
T TIGR00373 17 GLVLFSLGIK---GEFTDEEISLELG-I----KLNEVRKALYALYDAGLADYKR 62 (158)
T ss_pred HHHHHHHhcc---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCceeee
Confidence 4578888764 5899999999999 9 9999999999999999996443
No 62
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=94.77 E-value=0.058 Score=32.61 Aligned_cols=49 Identities=20% Similarity=0.302 Sum_probs=41.3
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
++++|...|... +.++..+|.+.++ + +...|.+-|+.|...|+++..++
T Consensus 1 vRl~Il~~L~~~---~~~~f~~L~~~l~-l----t~g~Ls~hL~~Le~~GyV~~~k~ 49 (80)
T PF13601_consen 1 VRLAILALLYAN---EEATFSELKEELG-L----TDGNLSKHLKKLEEAGYVEVEKE 49 (80)
T ss_dssp HHHHHHHHHHHH---SEEEHHHHHHHTT-------HHHHHHHHHHHHHTTSEEEEEE
T ss_pred CHHHHHHHHhhc---CCCCHHHHHHHhC-c----CHHHHHHHHHHHHHCCCEEEEEe
Confidence 467888888875 5899999999999 9 99999999999999999986644
No 63
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=94.74 E-value=0.061 Score=36.18 Aligned_cols=35 Identities=29% Similarity=0.261 Sum_probs=32.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+++|+.|||+..+ + ++..|.++|+.|+..|++.-.
T Consensus 23 ~~~s~~eIA~~~~-i----s~~~L~kIl~~L~~aGlv~S~ 57 (153)
T PRK11920 23 KLSRIPEIARAYG-V----SELFLFKILQPLVEAGLVETV 57 (153)
T ss_pred CcCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEee
Confidence 6899999999999 9 999999999999999998854
No 64
>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=94.62 E-value=0.06 Score=33.70 Aligned_cols=46 Identities=20% Similarity=0.345 Sum_probs=34.9
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
.|+++|..+ +.++-++||..++ . ++.-++++|..|-..|++.....
T Consensus 17 ~Il~~L~~~---~~l~de~la~~~~-l----~~~~vRkiL~~L~~~~lv~~~~~ 62 (105)
T PF02002_consen 17 RILDALLRK---GELTDEDLAKKLG-L----KPKEVRKILYKLYEDGLVSYRRR 62 (105)
T ss_dssp HHHHHHHHH-----B-HHHHHHTT--S-----HHHHHHHHHHHHHHSS-EEEEE
T ss_pred HHHHHHHHc---CCcCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCeEEEEE
Confidence 468888865 5799999999999 9 99999999999999999975543
No 65
>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=94.59 E-value=0.11 Score=32.23 Aligned_cols=36 Identities=19% Similarity=0.111 Sum_probs=33.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.++|.+|||+.++ + ++..+.|++..|...|++....
T Consensus 46 ~~is~~eLa~~~g-~----sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 46 DRVTATVIAELTG-L----SRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred CccCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeeeec
Confidence 6899999999999 9 8999999999999999998654
No 66
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=94.51 E-value=0.045 Score=38.14 Aligned_cols=40 Identities=23% Similarity=0.245 Sum_probs=35.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD 89 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~ 89 (89)
+|+|++||++.+| . ....+.--||.|...|++..+...||
T Consensus 40 ~Pmtl~Ei~E~lg-~----Sks~vS~~lkkL~~~~lV~~~~~~G~ 79 (177)
T COG1510 40 KPLTLDEIAEALG-M----SKSNVSMGLKKLQDWNLVKKVFEKGD 79 (177)
T ss_pred CCccHHHHHHHHC-C----CcchHHHHHHHHHhcchHHhhhccCc
Confidence 8999999999999 9 78889999999999999988766543
No 67
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=94.49 E-value=0.068 Score=39.16 Aligned_cols=49 Identities=22% Similarity=0.424 Sum_probs=43.8
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
|..|.++|.++| |-++-+||.+++| . ....+.|++|-|..+|+++.-+.
T Consensus 197 e~~il~~i~~~G--Gri~Q~eL~r~lg-l----sktTvsR~L~~LEk~GlIe~~K~ 245 (258)
T COG2512 197 EKEILDLIRERG--GRITQAELRRALG-L----SKTTVSRILRRLEKRGLIEKEKK 245 (258)
T ss_pred HHHHHHHHHHhC--CEEeHHHHHHhhC-C----ChHHHHHHHHHHHhCCceEEEEe
Confidence 567888999887 8899999999999 9 88899999999999999987643
No 68
>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=94.32 E-value=0.046 Score=31.01 Aligned_cols=41 Identities=22% Similarity=0.396 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 22 LHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 22 ~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+-.+|++|.++|-||.= ...|++|||+.+| + .+..+..-||
T Consensus 5 Q~e~L~~A~~~GYfd~P------R~~tl~elA~~lg-i----s~st~~~~LR 45 (53)
T PF04967_consen 5 QREILKAAYELGYFDVP------RRITLEELAEELG-I----SKSTVSEHLR 45 (53)
T ss_pred HHHHHHHHHHcCCCCCC------CcCCHHHHHHHhC-C----CHHHHHHHHH
Confidence 45689999999999742 5689999999999 9 6666555555
No 69
>PHA00738 putative HTH transcription regulator
Probab=94.16 E-value=0.15 Score=33.03 Aligned_cols=48 Identities=31% Similarity=0.295 Sum_probs=41.4
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
..+.|++.|.+. +++++.||++.++ . ....+.+=|+.|...|++....
T Consensus 13 tRr~IL~lL~~~---e~~~V~eLae~l~-l----SQptVS~HLKvLreAGLV~srK 60 (108)
T PHA00738 13 LRRKILELIAEN---YILSASLISHTLL-L----SYTTVLRHLKILNEQGYIELYK 60 (108)
T ss_pred HHHHHHHHHHHc---CCccHHHHHHhhC-C----CHHHHHHHHHHHHHCCceEEEE
Confidence 467888889863 4799999999999 9 7889999999999999998653
No 70
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=94.12 E-value=0.088 Score=35.50 Aligned_cols=47 Identities=17% Similarity=0.269 Sum_probs=41.5
Q ss_pred HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
.+|..|..+|.+. +.+|..|||+++| . .+..+.|=++-|...|+++.
T Consensus 14 ~~D~~IL~~Lq~d---~R~s~~eiA~~lg-l----S~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 14 RIDRNILNELQKD---GRISNVELSKRVG-L----SPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHhccC---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEE
Confidence 3788999999874 6899999999999 9 88899999999999999873
No 71
>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=94.04 E-value=0.11 Score=32.18 Aligned_cols=51 Identities=18% Similarity=0.272 Sum_probs=40.3
Q ss_pred HHHhChHHHHHh-cCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 29 VINLGLFEIIAK-AGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 29 av~LgIfd~l~~-~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-+.-.|++.|.. .....++++.+|+++++ . +..-++..++.|+..|.+=.+
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~-~----~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLG-M----SENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHST-S-----HHHHHHHHHHHHHTTSEEES
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHhC-c----CHHHHHHHHHHHHhCCeEecc
Confidence 345678888887 22347899999999998 9 899999999999999987644
No 72
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=93.95 E-value=0.14 Score=34.14 Aligned_cols=46 Identities=20% Similarity=0.373 Sum_probs=40.9
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
.|..|.+.|.+. +..|.+|||+++| . .+..+.|=++-|...|+++.
T Consensus 10 ~D~~Il~~Lq~d---~R~s~~eiA~~lg-l----S~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 10 LDRGILEALMEN---ARTPYAELAKQFG-V----SPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeee
Confidence 688899999874 6899999999999 9 88899999999999999873
No 73
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=93.91 E-value=0.14 Score=33.36 Aligned_cols=48 Identities=19% Similarity=0.366 Sum_probs=41.7
Q ss_pred HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.+|..|..+|.+. ++.|..|||+.+| . .+..+.+-++-|...|++...
T Consensus 8 ~~D~~IL~~L~~d---~r~~~~eia~~lg-l----S~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 8 DIDRRILRLLQED---ARISNAELAERVG-L----SPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred HHHHHHHHHHHHh---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCceeeE
Confidence 3677889999875 5799999999999 9 888999999999999988754
No 74
>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=93.88 E-value=0.14 Score=35.50 Aligned_cols=47 Identities=26% Similarity=0.340 Sum_probs=40.5
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+..|...|.++ +++|..|||+.++ . ++..+.|.++.|...|++....
T Consensus 145 ~~~IL~~l~~~---g~~s~~eia~~l~-i----s~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 145 ELKVLEVLKAE---GEKSVKNIAKKLG-K----SLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred HHHHHHHHHHc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEc
Confidence 45667777764 5799999999999 9 8889999999999999998765
No 75
>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=93.85 E-value=0.13 Score=30.51 Aligned_cols=50 Identities=22% Similarity=0.248 Sum_probs=43.1
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
++..+.+.|+.++. .+++..||+..++ . |+..+...++.|...|++....
T Consensus 3 ~~~~~Le~I~rsR~-~Gi~q~~L~~~~~-~----D~r~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 3 IQYCLLERIARSRY-NGITQSDLSKLLG-I----DPRSIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred hHHHHHHHHHhcCC-CCEehhHHHHHhC-C----CchHHHHHHHHHHHCCCEEEEE
Confidence 45567888988764 7899999999999 9 9999999999999999987543
No 76
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=93.78 E-value=0.31 Score=33.98 Aligned_cols=48 Identities=21% Similarity=0.039 Sum_probs=39.1
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD 89 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~ 89 (89)
|.-.|... +++|.+|||..+. . ++..+.|++.-|...|++....+.+|
T Consensus 50 iL~~L~~~---~~itq~eLa~~l~-l----~~sTvtr~l~rLE~kGlI~R~~~~~D 97 (185)
T PRK13777 50 ILWIAYHL---KGASISEIAKFGV-M----HVSTAFNFSKKLEERGYLTFSKKEDD 97 (185)
T ss_pred HHHHHHhC---CCcCHHHHHHHHC-C----CHhhHHHHHHHHHHCCCEEecCCCCC
Confidence 34445543 5899999999999 9 88899999999999999997765554
No 77
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=93.61 E-value=0.19 Score=30.69 Aligned_cols=52 Identities=23% Similarity=0.332 Sum_probs=40.1
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD 89 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~ 89 (89)
.+..+...|...+ +.+..+||+.++ . ++..+.|+++-|...|++....+.+|
T Consensus 23 ~q~~~L~~l~~~~---~~~~~~la~~l~-i----~~~~vt~~l~~Le~~glv~r~~~~~D 74 (126)
T COG1846 23 PQYQVLLALYEAG---GITVKELAERLG-L----DRSTVTRLLKRLEDKGLIERLRDPED 74 (126)
T ss_pred HHHHHHHHHHHhC---CCcHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeeecCCccc
Confidence 3444555666643 444499999999 9 99999999999999999997766544
No 78
>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=93.11 E-value=0.12 Score=27.76 Aligned_cols=23 Identities=30% Similarity=0.369 Sum_probs=17.8
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
++|..+||..++ + ....++|+++
T Consensus 21 G~si~~IA~~~g-v----sr~TvyR~l~ 43 (45)
T PF02796_consen 21 GMSIAEIAKQFG-V----SRSTVYRYLN 43 (45)
T ss_dssp T--HHHHHHHTT-S-----HHHHHHHHC
T ss_pred CCCHHHHHHHHC-c----CHHHHHHHHh
Confidence 399999999999 9 8888998875
No 79
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=93.09 E-value=0.27 Score=32.23 Aligned_cols=35 Identities=17% Similarity=0.226 Sum_probs=32.2
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
++.++++||..++ + ++..+.+.++.|...|++...
T Consensus 21 ~~~~~~ela~~l~-v----s~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 21 GYARVSDIAEALS-V----HPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred CCcCHHHHHHHhC-C----ChhHHHHHHHHHHHCCCEEEe
Confidence 7889999999999 9 888999999999999999743
No 80
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=93.05 E-value=0.33 Score=29.69 Aligned_cols=45 Identities=22% Similarity=0.324 Sum_probs=39.6
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|=|.|+.+ |-+++.+||.+.+ . ++..++=+|-.|+.+|-+++..
T Consensus 6 qlRd~l~~~---gr~s~~~Ls~~~~-~----p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 6 QVRDLLALR---GRMEAAQISQTLN-T----PQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHHc---CcccHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEeec
Confidence 355788876 5899999999999 9 8999999999999999998775
No 81
>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=93.02 E-value=0.14 Score=29.15 Aligned_cols=38 Identities=26% Similarity=0.371 Sum_probs=32.1
Q ss_pred CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
|..+ |..+||+..+ + ....+++.|+.|+..|++.....
T Consensus 21 g~~lps~~~la~~~~-v----sr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 21 GDRLPSERELAERYG-V----SRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp TSBE--HHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEETT
T ss_pred CCEeCCHHHHHHHhc-c----CCcHHHHHHHHHHHCCcEEEECC
Confidence 4678 9999999999 9 99999999999999999986543
No 82
>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=93.00 E-value=0.15 Score=29.51 Aligned_cols=35 Identities=34% Similarity=0.428 Sum_probs=32.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-++|-++||..+| + ....+.|+|+.|...|++.-.
T Consensus 27 ~~lt~~~iA~~~g-~----sr~tv~r~l~~l~~~g~I~~~ 61 (76)
T PF13545_consen 27 LPLTQEEIADMLG-V----SRETVSRILKRLKDEGIIEVK 61 (76)
T ss_dssp EESSHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred ecCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEc
Confidence 4689999999999 9 899999999999999999844
No 83
>PRK11050 manganese transport regulator MntR; Provisional
Probab=92.96 E-value=0.3 Score=32.66 Aligned_cols=44 Identities=27% Similarity=0.357 Sum_probs=37.1
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-|..++.. + ++.+..|||+.++ + ++..+.|.++.|...|++...
T Consensus 41 ~I~~~l~~-~--~~~t~~eLA~~l~-i----s~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 41 LIADLIAE-V--GEARQVDIAARLG-V----SQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred HHHHHHHh-c--CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence 35556654 2 6899999999999 9 999999999999999999754
No 84
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=92.96 E-value=0.22 Score=35.86 Aligned_cols=45 Identities=18% Similarity=0.256 Sum_probs=39.1
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
..|.+.|.+. +.+++.|||+.++ + .+..++|-|+.|...|++..+
T Consensus 8 ~~Il~~l~~~---~~~~~~ela~~l~-v----S~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 8 QILLELLAQL---GFVTVEKVIERLG-I----SPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHHHc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEe
Confidence 3477888874 6899999999999 9 899999999999999998753
No 85
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=92.81 E-value=0.2 Score=36.04 Aligned_cols=43 Identities=33% Similarity=0.524 Sum_probs=36.4
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|.-.|.+. +|+|+.|||+++| + .+..++|-|-.|...|++.-.
T Consensus 16 il~lL~~~---g~~sa~elA~~Lg-i----s~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 16 ILELLKKS---GPVSADELAEELG-I----SPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred HHHHHhcc---CCccHHHHHHHhC-C----CHHHHHHHHHHHHhCcceeee
Confidence 44455554 6999999999999 9 999999999999999988743
No 86
>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=92.80 E-value=0.27 Score=27.19 Aligned_cols=33 Identities=30% Similarity=0.329 Sum_probs=29.9
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.|..+||..++ + +...+.+.+..|...|++...
T Consensus 26 ~~~~~la~~~~-i----s~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 26 PSERELAEELG-V----SRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEec
Confidence 45999999999 9 899999999999999998754
No 87
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=92.73 E-value=0.31 Score=35.34 Aligned_cols=44 Identities=18% Similarity=0.203 Sum_probs=36.9
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
++.-.|-.. |++|+.||++.+| + ....++.+||.|...|++...
T Consensus 20 ~vY~aLl~~---g~~tA~eis~~sg-v----P~~kvY~vl~sLe~kG~v~~~ 63 (247)
T COG1378 20 KVYLALLCL---GEATAKEISEASG-V----PRPKVYDVLRSLEKKGLVEVI 63 (247)
T ss_pred HHHHHHHHh---CCccHHHHHHHcC-C----CchhHHHHHHHHHHCCCEEee
Confidence 344455554 6999999999999 9 778999999999999999865
No 88
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=92.71 E-value=0.2 Score=36.15 Aligned_cols=46 Identities=28% Similarity=0.356 Sum_probs=38.3
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-.|.+.+... +.+.|++|+|+.+| + .....+|-|-+|++.|++...
T Consensus 161 ~~i~~~~~~~--~~~~Taeela~~~g-i----SRvTaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 161 QKVREALKEP--DQELTAEELAQALG-I----SRVTARRYLEYLVSNGILEAE 206 (224)
T ss_pred HHHHHHHhCc--CCccCHHHHHHHhC-c----cHHHHHHHHHHHHhcCeeeEE
Confidence 3455667632 38999999999999 9 899999999999999998754
No 89
>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=92.42 E-value=0.37 Score=29.46 Aligned_cols=34 Identities=24% Similarity=0.411 Sum_probs=32.3
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
.|+...+||+.++ . ++..++-.|..|..+|++..
T Consensus 22 ~PVgSk~ia~~l~-~----s~aTIRN~M~~Le~lGlve~ 55 (78)
T PF03444_consen 22 EPVGSKTIAEELG-R----SPATIRNEMADLEELGLVES 55 (78)
T ss_pred CCcCHHHHHHHHC-C----ChHHHHHHHHHHHHCCCccC
Confidence 8999999999999 9 89999999999999999973
No 90
>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=92.10 E-value=1.1 Score=32.98 Aligned_cols=71 Identities=21% Similarity=0.290 Sum_probs=50.6
Q ss_pred hhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 6 RDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 6 ~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
++.....+.+++.+.....=+.++ + .|++.|... ++-++..+||+++| + .+..+++-+|.|.+.|++.-..
T Consensus 162 ee~Rkka~Vq~Ai~tLSySEleAv-~-~IL~~L~~~--egrlse~eLAerlG-V----SRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 162 EEARKKAAVQMAINTLSYSELEAV-E-HIFEELDGN--EGLLVASKIADRVG-I----TRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHHHHHHHHHHHhccHhHHHHH-H-HHHHHhccc--cccccHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecc
Confidence 334444455665544433333333 2 578888652 26899999999999 9 8999999999999999998544
No 91
>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=91.96 E-value=0.44 Score=32.72 Aligned_cols=51 Identities=22% Similarity=0.223 Sum_probs=38.9
Q ss_pred HHhChHHHHHhcC--CCCCCCHHHHHhhCCCCCCCCC-cchHHHHHHHHhccCceeeec
Q 045477 30 INLGLFEIIAKAG--PGAKLSASEIAAQLPATKNKDA-PTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 30 v~LgIfd~l~~~g--~~~~~t~~eLA~~~~~~~~~~d-~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.+..|++.|.+.. .+-|.|..|||+.++ . + +..+.+.|+.|...|++....
T Consensus 7 ~q~~iL~~l~~~~~~~~~~~~~~ela~~~~-~----~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 7 RQQEVLDLIRAHIESTGYPPSIREIARAVG-L----RSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred HHHHHHHHHHHHHHhcCCCCcHHHHHHHhC-C----CChHHHHHHHHHHHHCCCEecCC
Confidence 3445556555320 126789999999999 9 7 889999999999999998653
No 92
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=91.88 E-value=0.3 Score=35.25 Aligned_cols=45 Identities=18% Similarity=0.276 Sum_probs=39.5
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-.|.+.|.+. +.+++.|||+.++ + .+.-++|-|..|...|++..+
T Consensus 8 ~~Il~~l~~~---~~~~~~ela~~l~-v----S~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 8 DAIIELVKQQ---GYVSTEELVEHFS-V----SPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHc---CCEeHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence 4577888764 6899999999999 9 999999999999999998764
No 93
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=91.60 E-value=0.53 Score=28.00 Aligned_cols=43 Identities=19% Similarity=0.245 Sum_probs=31.7
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
+|+|..-. .++.+.++|+..++ . +...+.+.+..|...|+++.
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~~~-L----~~~~~~~yL~~L~~~gLI~~ 51 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYKAN-L----NYSTLKKYLKELEEKGLIKK 51 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTTST-------HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHH-cCCCCHHHHHHHhC-c----CHHHHHHHHHHHHHCcCeeC
Confidence 45554321 27899999999999 9 99999999999999999965
No 94
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=91.39 E-value=0.48 Score=33.04 Aligned_cols=46 Identities=20% Similarity=0.260 Sum_probs=39.5
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.-|++++-+. |.+|-+|||..++ . ...-++|+|+.|-..|++....
T Consensus 21 ~~v~~~l~~k---ge~tDeela~~l~-i----~~~~vrriL~~L~e~~li~~~k 66 (176)
T COG1675 21 VLVVDALLEK---GELTDEELAELLG-I----KKNEVRRILYALYEDGLISYRK 66 (176)
T ss_pred hHHHHHHHhc---CCcChHHHHHHhC-c----cHHHHHHHHHHHHhCCceEEEe
Confidence 3567888764 4799999999999 9 9999999999999999998543
No 95
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=91.35 E-value=0.38 Score=35.04 Aligned_cols=46 Identities=11% Similarity=0.210 Sum_probs=40.0
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
...|.+.|.+. +.+|+.|||+.++ + .+.-++|=|+.|...|++..+
T Consensus 19 ~~~Il~~L~~~---~~vtv~eLa~~l~-V----S~~TIRRDL~~Le~~G~l~r~ 64 (269)
T PRK09802 19 REQIIQRLRQQ---GSVQVNDLSALYG-V----STVTIRNDLAFLEKQGIAVRA 64 (269)
T ss_pred HHHHHHHHHHc---CCEeHHHHHHHHC-C----CHHHHHHHHHHHHhCCCeEEE
Confidence 34678888875 5799999999999 9 899999999999999998754
No 96
>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=91.30 E-value=0.56 Score=30.70 Aligned_cols=51 Identities=14% Similarity=0.254 Sum_probs=38.8
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.++.|..+|.+. +|.|+.||.+.++ -..+-+...+.++|+-|...|++...
T Consensus 5 ~E~~VM~vlW~~---~~~t~~eI~~~l~-~~~~~~~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 5 AEWEVMRVVWTL---GETTSRDIIRILA-EKKDWSDSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred HHHHHHHHHHcC---CCCCHHHHHHHHh-hccCCcHHHHHHHHHHHHHCCceeee
Confidence 466788888764 5899999877764 22222678899999999999999754
No 97
>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=91.25 E-value=0.28 Score=32.66 Aligned_cols=34 Identities=24% Similarity=0.377 Sum_probs=31.7
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|+|-+|||..+| + .+..+.|+|+.|...|++.-.
T Consensus 143 ~~t~~~iA~~lG-~----tretvsR~l~~l~~~g~I~~~ 176 (193)
T TIGR03697 143 RLSHQAIAEAIG-S----TRVTITRLLGDLRKKKLISIH 176 (193)
T ss_pred CCCHHHHHHHhC-C----cHHHHHHHHHHHHHCCCEEec
Confidence 689999999999 9 899999999999999999754
No 98
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=91.21 E-value=0.39 Score=36.24 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=39.7
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
-|.++|.++|. .++...+|..+++ . ....|.|+|+.|.+.+++.++++.
T Consensus 88 lvy~~I~~ag~-~GIw~~~i~~~t~-l----~~~~~~k~lk~Le~k~lIK~vksv 136 (327)
T PF05158_consen 88 LVYQLIEEAGN-KGIWTKDIKKKTN-L----HQTQLTKILKSLESKKLIKSVKSV 136 (327)
T ss_dssp HHHHHHHHHTT-T-EEHHHHHHHCT-------HHHHHHHHHHHHHTTSEEEE--S
T ss_pred HHHHHHHHhCC-CCCcHHHHHHHcC-C----CHHHHHHHHHHHHhCCCEEEecCc
Confidence 46788888874 8999999999999 9 899999999999999999998765
No 99
>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=91.07 E-value=0.46 Score=30.10 Aligned_cols=52 Identities=23% Similarity=0.376 Sum_probs=41.5
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|+.|.++|.+.| ++|+.||.+.++ -..+-.+..+.-+|+-|+..|+++...
T Consensus 4 ~E~~IM~~lW~~~---~~t~~eI~~~l~-~~~~~~~sTv~t~L~rL~~Kg~l~~~~ 55 (115)
T PF03965_consen 4 LELEIMEILWESG---EATVREIHEALP-EERSWAYSTVQTLLNRLVEKGFLTREK 55 (115)
T ss_dssp HHHHHHHHHHHHS---SEEHHHHHHHHC-TTSS--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHhCC---CCCHHHHHHHHH-hccccchhHHHHHHHHHHhCCceeEee
Confidence 4677889998874 699999999998 632335778999999999999998654
No 100
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=90.83 E-value=0.34 Score=30.11 Aligned_cols=49 Identities=14% Similarity=0.194 Sum_probs=39.2
Q ss_pred HhChHHHHHhc-CCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 31 NLGLFEIIAKA-GPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 31 ~LgIfd~l~~~-g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|-..+|.|.+. ..-.-+|...|+++++ + ...+-+++||.|...|++..+
T Consensus 25 dk~t~dkl~kEV~~~K~ITps~lserlk-I----~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 25 DEELLKRVAKEVKKEKIVTPYTLASKYG-I----KISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred CHHHHHHHHHHhccCcEEcHHHHHHHhc-c----hHHHHHHHHHHHHHCCCEEEE
Confidence 44466666542 2235689999999999 9 999999999999999999765
No 101
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=90.80 E-value=0.56 Score=32.34 Aligned_cols=45 Identities=20% Similarity=0.266 Sum_probs=37.5
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.|.+.+++.. ++.|.+|||++++ . .+..+++-+.+|+..|++...
T Consensus 166 ~Vl~~~~~g~--~g~s~~eIa~~l~-i----S~~Tv~~~~~~~~~~~~~~~~ 210 (225)
T PRK10046 166 AVRKLFKEPG--VQHTAETVAQALT-I----SRTTARRYLEYCASRHLIIAE 210 (225)
T ss_pred HHHHHHHcCC--CCcCHHHHHHHhC-c----cHHHHHHHHHHHHhCCeEEEE
Confidence 4566676521 4789999999999 9 999999999999999998765
No 102
>PRK00215 LexA repressor; Validated
Probab=90.72 E-value=0.78 Score=31.60 Aligned_cols=37 Identities=24% Similarity=0.276 Sum_probs=31.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.+.|..|||+.++ .+ +...+.|+++.|...|+++...
T Consensus 22 ~~~s~~ela~~~~-~~---~~~tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 22 YPPSRREIADALG-LR---SPSAVHEHLKALERKGFIRRDP 58 (205)
T ss_pred CCCCHHHHHHHhC-CC---ChHHHHHHHHHHHHCCCEEeCC
Confidence 7899999999999 62 3568999999999999997654
No 103
>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=90.66 E-value=0.6 Score=24.93 Aligned_cols=33 Identities=15% Similarity=0.351 Sum_probs=24.4
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHH
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~R 70 (89)
+|..|...|.+. +..|..+||+.+| . .+..+.+
T Consensus 4 ~D~~Il~~Lq~d---~r~s~~~la~~lg-l----S~~~v~~ 36 (42)
T PF13404_consen 4 LDRKILRLLQED---GRRSYAELAEELG-L----SESTVRR 36 (42)
T ss_dssp HHHHHHHHHHH----TTS-HHHHHHHHT-S-----HHHHHH
T ss_pred HHHHHHHHHHHc---CCccHHHHHHHHC-c----CHHHHHH
Confidence 577889999874 6899999999999 8 5555443
No 104
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=90.54 E-value=0.47 Score=34.22 Aligned_cols=45 Identities=27% Similarity=0.310 Sum_probs=39.5
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
..|.+.|.+. +.+++.|||+.++ + .+..++|=|+.|...|++..+
T Consensus 8 ~~Il~~L~~~---~~v~v~eLa~~l~-V----S~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 8 AAILEYLQKQ---GKTSVEELAQYFD-T----TGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHc---CCEEHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEE
Confidence 4577888875 6899999999999 9 899999999999999988764
No 105
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=90.51 E-value=0.78 Score=31.03 Aligned_cols=37 Identities=24% Similarity=0.349 Sum_probs=33.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+++...+||+.++ + .|..+..+++-|...|++.....
T Consensus 23 ~~~~~~diA~~L~-V----sp~sVt~ml~rL~~~GlV~~~~y 59 (154)
T COG1321 23 GFARTKDIAERLK-V----SPPSVTEMLKRLERLGLVEYEPY 59 (154)
T ss_pred CcccHHHHHHHhC-C----CcHHHHHHHHHHHHCCCeEEecC
Confidence 7999999999999 9 88899999999999999987644
No 106
>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=90.49 E-value=1.1 Score=27.96 Aligned_cols=48 Identities=21% Similarity=0.236 Sum_probs=39.8
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHH----------HHHhccCce
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRIL----------GLLASYGIV 81 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlL----------R~L~s~gi~ 81 (89)
.=+..+|+..|.+.-+ .++++.|||..++ + |+.-+.-.| +.|+.+|++
T Consensus 8 S~~R~~vl~~L~~~yp-~~~~~~eIar~v~-~----~~snV~GaL~G~g~rY~~e~SLv~lGLV 65 (90)
T PF07381_consen 8 SKVRKKVLEYLCSIYP-EPAYPSEIARSVG-S----DYSNVLGALRGDGKRYNKEDSLVGLGLV 65 (90)
T ss_pred HHHHHHHHHHHHHcCC-CcCCHHHHHHHHC-C----CHHHHHHHHhcCCCCcCcchhHHHcCCe
Confidence 5567889999988732 8999999999999 9 888777666 468899999
No 107
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=90.32 E-value=0.42 Score=32.34 Aligned_cols=35 Identities=23% Similarity=0.427 Sum_probs=32.1
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
++|-.|||+.+| + .+..+.|+|+.|...|+++-..
T Consensus 168 ~~t~~~lA~~lG-~----tr~tvsR~l~~l~~~gii~~~~ 202 (211)
T PRK11753 168 KITRQEIGRIVG-C----SREMVGRVLKMLEDQGLISAHG 202 (211)
T ss_pred CCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEecC
Confidence 789999999999 9 9999999999999999997543
No 108
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=90.25 E-value=0.48 Score=36.43 Aligned_cols=37 Identities=27% Similarity=0.319 Sum_probs=33.8
Q ss_pred CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 44 GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
++|.|.+||+++++ + ++..+++++..|...|++.+..
T Consensus 308 g~~~t~~~La~~l~-~----~~~~v~~iL~~L~~agLI~~~~ 344 (412)
T PRK04214 308 GKALDVDEIRRLEP-M----GYDELGELLCELARIGLLRRGE 344 (412)
T ss_pred CCCCCHHHHHHHhC-C----CHHHHHHHHHHHHhCCCeEecC
Confidence 37999999999999 9 9999999999999999998643
No 109
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=90.08 E-value=0.5 Score=34.10 Aligned_cols=44 Identities=20% Similarity=0.312 Sum_probs=39.8
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.|.+.|.+. |.++++|||+.++ + .+.-++|=|+.|...|++..+
T Consensus 9 ~Il~~l~~~---g~v~v~eLa~~~~-V----S~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 9 KILELLKEK---GKVSVEELAELFG-V----SEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHc---CcEEHHHHHHHhC-C----CHHHHHHhHHHHHHCCcEEEE
Confidence 577888875 6899999999999 9 999999999999999999875
No 110
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=89.90 E-value=0.99 Score=28.30 Aligned_cols=49 Identities=22% Similarity=0.266 Sum_probs=42.5
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
.++.|..+|... +|=++.-||..++ . +..-+.++++-|..+|++++...
T Consensus 8 l~~~IL~hl~~~---~~Dy~k~ia~~l~-~----~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 8 LDLKILQHLKKA---GPDYAKSIARRLK-I----PLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred hHHHHHHHHHHH---CCCcHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeEEecC
Confidence 356778888876 5788999999999 9 99999999999999999998754
No 111
>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=89.75 E-value=0.62 Score=26.80 Aligned_cols=45 Identities=18% Similarity=0.252 Sum_probs=36.1
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|++.|-+. |..|+.+|.+.++ . ++..+..-|-.|..+|++....
T Consensus 17 ~V~~~Ll~~---G~ltl~~i~~~t~-l----~~~~Vk~~L~~LiQh~~v~y~~ 61 (62)
T PF08221_consen 17 KVGEVLLSR---GRLTLREIVRRTG-L----SPKQVKKALVVLIQHNLVQYFE 61 (62)
T ss_dssp HHHHHHHHC----SEEHHHHHHHHT-------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHc---CCcCHHHHHHHhC-C----CHHHHHHHHHHHHHcCCeeeec
Confidence 467777765 6899999999999 9 8999999999999999987543
No 112
>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=89.67 E-value=0.47 Score=30.47 Aligned_cols=47 Identities=15% Similarity=0.215 Sum_probs=38.2
Q ss_pred ChHHHHHhc-CCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 33 GLFEIIAKA-GPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 33 gIfd~l~~~-g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
..+|.|... ..-.-+|...||++++ + .-.+-+++||.|...|++..+
T Consensus 45 ~~~~kl~kEV~~~K~ITp~~lserlk-I----~~SlAr~~Lr~L~~kG~Ik~V 92 (105)
T PF03297_consen 45 ETYDKLLKEVPKMKLITPSVLSERLK-I----NGSLARKALRELESKGLIKPV 92 (105)
T ss_dssp HHHHHHHHHCTTSSCECHHHHHHHHC-C----SCHHHHHHHHHHHHCCSSEEE
T ss_pred HHHHHHHHHhccCcEeeHHHHHHhHh-h----HHHHHHHHHHHHHHCCCEEEE
Confidence 456666543 2225689999999999 9 999999999999999999876
No 113
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=89.52 E-value=0.57 Score=28.20 Aligned_cols=32 Identities=34% Similarity=0.499 Sum_probs=29.2
Q ss_pred HHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 49 ASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 49 ~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
..|||+.++ + ++..+.|+++.|...|++....
T Consensus 2 ~~ela~~l~-i----s~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLN-V----SPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhC-C----ChHHHHHHHHHHHHCCCEEEcC
Confidence 579999999 9 9999999999999999998754
No 114
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=89.46 E-value=0.56 Score=37.69 Aligned_cols=42 Identities=31% Similarity=0.373 Sum_probs=33.3
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY 78 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~ 78 (89)
-.|-..+.+.+ ++.|++||+++++ . |++...++.|||+|+++
T Consensus 466 ~~~~~~~~~~~--~~~~~~~~~~~~~-~--~~~~~~~~~i~~~~~~n 507 (528)
T PRK14096 466 KKVEELLKEDG--GELSIEEIAAALG-A--PEQVETIYKILRHLAAN 507 (528)
T ss_pred HHHHHHHhccC--CCCCHHHHHHHcC-C--CccHHHHHHHHHHHhcC
Confidence 34555665544 8999999999999 5 44778999999999985
No 115
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=89.43 E-value=0.5 Score=31.79 Aligned_cols=34 Identities=18% Similarity=0.337 Sum_probs=31.3
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
-|+|-++||..+| + .+..+.|+|+.|...|++..
T Consensus 148 ~~~t~~~iA~~lG-~----tretvsR~l~~l~~~g~I~~ 181 (202)
T PRK13918 148 IYATHDELAAAVG-S----VRETVTKVIGELSREGYIRS 181 (202)
T ss_pred ecCCHHHHHHHhC-c----cHHHHHHHHHHHHHCCCEEc
Confidence 3689999999999 9 89999999999999999974
No 116
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=89.42 E-value=0.52 Score=32.60 Aligned_cols=35 Identities=17% Similarity=0.339 Sum_probs=32.0
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
|+|-++||+.+| + .+..+.|+|+.|...|++.-..
T Consensus 184 ~lt~~~iA~~lG-~----sr~tvsR~l~~l~~~g~I~~~~ 218 (235)
T PRK11161 184 TMTRGDIGNYLG-L----TVETISRLLGRFQKSGMLAVKG 218 (235)
T ss_pred cccHHHHHHHhC-C----cHHHHHHHHHHHHHCCCEEecC
Confidence 689999999999 9 9999999999999999998543
No 117
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=89.08 E-value=0.32 Score=33.60 Aligned_cols=45 Identities=16% Similarity=0.062 Sum_probs=38.9
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-.|.+.|.+. +.+++.||++.++ + .+..++|=++.|+..|++..+
T Consensus 10 ~~Il~~l~~~---~~~~~~~La~~~~-v----S~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 10 KALQELIEEN---PFITDEELAEKFG-V----SIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHC---CCEEHHHHHHHHC-c----CHHHHHHHHHHHhcchHHHHH
Confidence 3467778775 6899999999999 9 899999999999999988754
No 118
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=88.83 E-value=1 Score=31.51 Aligned_cols=44 Identities=23% Similarity=0.231 Sum_probs=36.9
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
|.+..+|+-. +|+|-.||++..| + ++ ..+++.|...|++.+.+.
T Consensus 93 LEtLaiIay~---qPiTr~eI~~irG-v----~~---~~ii~~L~~~gLI~e~gr 136 (188)
T PRK00135 93 LEVLAIIAYK---QPITRIEIDEIRG-V----NS---DGALQTLLAKGLIKEVGR 136 (188)
T ss_pred HHHHHHHHHc---CCcCHHHHHHHHC-C----CH---HHHHHHHHHCCCeEEcCc
Confidence 4567778764 7999999999999 8 54 889999999999988643
No 119
>PHA02943 hypothetical protein; Provisional
Probab=88.67 E-value=1 Score=30.99 Aligned_cols=44 Identities=23% Similarity=0.193 Sum_probs=37.1
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|.+.| +. |..|.+|||+.+| . .....+=+|..|...|.+.++.
T Consensus 15 eILE~L-k~---G~~TtseIAkaLG-l----S~~qa~~~LyvLErEG~VkrV~ 58 (165)
T PHA02943 15 KTLRLL-AD---GCKTTSRIANKLG-V----SHSMARNALYQLAKEGMVLKVE 58 (165)
T ss_pred HHHHHH-hc---CCccHHHHHHHHC-C----CHHHHHHHHHHHHHcCceEEEe
Confidence 455666 32 7899999999999 9 8888999999999999998764
No 120
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=88.62 E-value=1.2 Score=31.81 Aligned_cols=36 Identities=31% Similarity=0.387 Sum_probs=33.0
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
..+|.+|||+.++ . ++..+.|.++.|...|++....
T Consensus 20 ~~IS~~eLA~~L~-i----S~~Tvsr~Lk~LEe~GlI~R~~ 55 (217)
T PRK14165 20 VKISSSEFANHTG-T----SSKTAARILKQLEDEGYITRTI 55 (217)
T ss_pred CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEE
Confidence 5699999999999 9 9999999999999999998653
No 121
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=88.30 E-value=1.1 Score=35.37 Aligned_cols=47 Identities=17% Similarity=0.266 Sum_probs=38.9
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+..|...|... +++|..+||+.++ . ++..+.|++.-|.+.|++....
T Consensus 8 e~~vL~~L~~~---~~~s~~eLA~~l~-l----~~~tVt~~i~~Le~kGlV~~~~ 54 (489)
T PRK04172 8 EKKVLKALKEL---KEATLEELAEKLG-L----PPEAVMRAAEWLEEKGLVKVEE 54 (489)
T ss_pred HHHHHHHHHhC---CCCCHHHHHHHhC-c----CHHHHHHHHHHHHhCCCEEEEe
Confidence 34455566553 5899999999999 9 9999999999999999998653
No 122
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=88.07 E-value=0.65 Score=32.44 Aligned_cols=34 Identities=26% Similarity=0.325 Sum_probs=31.3
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
++|-++||..+| + .+..+.|+++.|...|++...
T Consensus 179 ~lt~~~IA~~lG-i----sretlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 179 PMSRRDIADYLG-L----TIETVSRALSQLQDRGLIGLS 212 (230)
T ss_pred cCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCcEEec
Confidence 578999999999 9 999999999999999999743
No 123
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=88.03 E-value=1 Score=31.23 Aligned_cols=39 Identities=21% Similarity=0.215 Sum_probs=34.6
Q ss_pred CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+|..++..+||+..| + ....++--|+.|.+.|++.....
T Consensus 27 pG~~L~e~eLae~lg-V----SRtpVREAL~~L~~eGlv~~~~~ 65 (224)
T PRK11534 27 PDEKLRMSLLTSRYA-L----GVGPLREALSQLVAERLVTVVNQ 65 (224)
T ss_pred CCCcCCHHHHHHHHC-C----ChHHHHHHHHHHHHCCCEEEeCC
Confidence 457899999999999 9 88899999999999999986544
No 124
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=88.00 E-value=0.79 Score=29.60 Aligned_cols=38 Identities=13% Similarity=0.139 Sum_probs=33.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
.++|++|||+.+. | .+....++|+-|...|.+.=.+..
T Consensus 18 ~~vtl~elA~~l~-c----S~Rn~r~lLkkm~~~gWi~W~pg~ 55 (115)
T PF12793_consen 18 VEVTLDELAELLF-C----SRRNARTLLKKMQEEGWITWQPGR 55 (115)
T ss_pred cceeHHHHHHHhC-C----CHHHHHHHHHHHHHCCCeeeeCCC
Confidence 5689999999999 9 999999999999999998755443
No 125
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=87.84 E-value=1.2 Score=31.79 Aligned_cols=44 Identities=18% Similarity=0.289 Sum_probs=37.8
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
..|.+.|.+. +.++.+|||+.++ + .+..++|-|..|...|.+..
T Consensus 7 ~~Il~~l~~~---~~~~~~eLa~~l~-V----S~~TiRRdL~~L~~~~~l~r 50 (240)
T PRK10411 7 QAIVDLLLNH---TSLTTEALAEQLN-V----SKETIRRDLNELQTQGKILR 50 (240)
T ss_pred HHHHHHHHHc---CCCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEE
Confidence 3477788764 6899999999999 9 89999999999999887754
No 126
>PF13730 HTH_36: Helix-turn-helix domain
Probab=87.65 E-value=0.74 Score=25.08 Aligned_cols=30 Identities=20% Similarity=0.306 Sum_probs=27.5
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV 81 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~ 81 (89)
-|.+.||+.+| + ....+.|.++.|...|++
T Consensus 26 pS~~~la~~~g-~----s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 26 PSQETLAKDLG-V----SRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHC-c----CHHHHHHHHHHHHHCcCC
Confidence 38999999999 9 899999999999999874
No 127
>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=87.31 E-value=1.2 Score=32.11 Aligned_cols=36 Identities=17% Similarity=0.342 Sum_probs=32.2
Q ss_pred CCCCCHHHHHhhCCCCCCCCCcchHHHHHH-HHhccCceeee
Q 045477 44 GAKLSASEIAAQLPATKNKDAPTMLDRILG-LLASYGIVECS 84 (89)
Q Consensus 44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR-~L~s~gi~~e~ 84 (89)
+++.+++++|+.+| . ++..+.++++ .|...|++..+
T Consensus 253 ~~~~~~~~ia~~lg-~----~~~~~~~~~e~~Li~~~li~~~ 289 (305)
T TIGR00635 253 GGPVGLKTLAAALG-E----DADTIEDVYEPYLLQIGFLQRT 289 (305)
T ss_pred CCcccHHHHHHHhC-C----CcchHHHhhhHHHHHcCCcccC
Confidence 37899999999999 9 9999999999 79999999643
No 128
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=87.11 E-value=0.98 Score=24.11 Aligned_cols=24 Identities=29% Similarity=0.339 Sum_probs=17.2
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.++|..+||..+| . ++..+.|.++
T Consensus 19 ~G~s~~~IA~~lg-~----s~sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLG-R----SRSTVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT-------HHHHHHHHH
T ss_pred cCCCHHHHHHHHC-c----CcHHHHHHHh
Confidence 4699999999999 9 8999999876
No 129
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=86.89 E-value=1.3 Score=28.52 Aligned_cols=50 Identities=16% Similarity=0.202 Sum_probs=41.0
Q ss_pred HHhChHHHHHhc-CCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 30 INLGLFEIIAKA-GPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 30 v~LgIfd~l~~~-g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
++-.++|.+.+. +...-+|...||.+.| + +-..-+++||.|...|++...
T Consensus 42 vdee~~~ki~KEV~~~r~VTpy~la~r~g-I----~~SvAr~vLR~LeeeGvv~lv 92 (107)
T COG4901 42 VDEELLDKIRKEVPRERVVTPYVLASRYG-I----NGSVARIVLRHLEEEGVVQLV 92 (107)
T ss_pred ccHHHHHHHHHhcccceeecHHHHHHHhc-c----chHHHHHHHHHHHhCCceeee
Confidence 556778877653 2235689999999999 9 899999999999999998755
No 130
>PRK09954 putative kinase; Provisional
Probab=86.51 E-value=1.4 Score=32.80 Aligned_cols=44 Identities=16% Similarity=0.212 Sum_probs=38.6
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
+..|...|.++ +++|.+|||+.++ + ....+.+.++.|...|++.
T Consensus 5 ~~~il~~l~~~---~~~s~~~la~~l~-~----s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 5 EKEILAILRRN---PLIQQNEIADILQ-I----SRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHHC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCcC
Confidence 45678888874 5899999999999 9 8999999999999999875
No 131
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=86.11 E-value=2.7 Score=31.16 Aligned_cols=55 Identities=13% Similarity=0.321 Sum_probs=46.0
Q ss_pred HHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 21 VLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 21 ~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
-+..+|...+++.|.+.|+.. +|+.+.|||+.+| . ....+.-=+..|...|+++-
T Consensus 15 dv~kalaS~vRv~Il~lL~~k---~plNvneiAe~lg-L----pqst~s~~ik~Le~aGlirT 69 (308)
T COG4189 15 DVLKALASKVRVAILQLLHRK---GPLNVNEIAEALG-L----PQSTMSANIKVLEKAGLIRT 69 (308)
T ss_pred hHHHHHHHHHHHHHHHHHHHh---CCCCHHHHHHHhC-C----chhhhhhhHHHHHhcCceee
Confidence 355678888999999999985 6999999999999 8 66667777888888898874
No 132
>PRK01381 Trp operon repressor; Provisional
Probab=86.00 E-value=1.4 Score=28.13 Aligned_cols=41 Identities=20% Similarity=0.196 Sum_probs=34.9
Q ss_pred HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477 29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY 78 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~ 78 (89)
+..++|+..|-+ |++|-.|||+.+| + ....+.|.=|.|-..
T Consensus 42 ~~R~~I~~~L~~----g~~sQREIa~~lG-v----SiaTITRgsn~Lk~~ 82 (99)
T PRK01381 42 GTRVRIVEELLR----GELSQREIKQELG-V----GIATITRGSNSLKTA 82 (99)
T ss_pred HHHHHHHHHHHc----CCcCHHHHHHHhC-C----ceeeehhhHHHhccC
Confidence 567899998876 7899999999999 9 888899988887643
No 133
>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=85.93 E-value=1.6 Score=32.89 Aligned_cols=35 Identities=11% Similarity=0.220 Sum_probs=32.7
Q ss_pred CCCCHHHHHhh--CCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQ--LPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~--~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|+++.+|++. ++ + .+..++|-|..|...|++...
T Consensus 20 ~pv~s~~l~~~~~~~-v----S~aTiR~d~~~Le~~G~l~~~ 56 (337)
T TIGR00331 20 QPVGSKTLLEKYNLG-L----SSATIRNDMADLEDLGFIEKP 56 (337)
T ss_pred CCcCHHHHHhhcCCC-C----ChHHHHHHHHHHHHCCCccCC
Confidence 89999999999 88 8 888999999999999999765
No 134
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=85.84 E-value=1.6 Score=30.39 Aligned_cols=40 Identities=33% Similarity=0.471 Sum_probs=35.7
Q ss_pred CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
+|.+++-.+||+..| + ....++.-|+.|++-|++.-....
T Consensus 36 pG~~l~e~~La~~~g-v----SrtPVReAL~rL~~eGlv~~~p~r 75 (230)
T COG1802 36 PGERLSEEELAEELG-V----SRTPVREALRRLEAEGLVEIEPNR 75 (230)
T ss_pred CCCCccHHHHHHHhC-C----CCccHHHHHHHHHHCCCeEecCCC
Confidence 458999999999999 9 899999999999999999876544
No 135
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=85.77 E-value=1.6 Score=29.00 Aligned_cols=39 Identities=18% Similarity=0.228 Sum_probs=33.8
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
-|+|+|-.+ +.+|-++||..+| . +..-++++|..|-..+
T Consensus 5 ~v~d~L~~~---~~~~dedLa~~l~-i----~~n~vRkiL~~L~ed~ 43 (147)
T smart00531 5 LVLDALMRN---GCVTEEDLAELLG-I----KQKQLRKILYLLYDEK 43 (147)
T ss_pred eehHHHHhc---CCcCHHHHHHHhC-C----CHHHHHHHHHHHHhhh
Confidence 478888765 5899999999999 9 9999999999999833
No 136
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=85.72 E-value=1 Score=23.43 Aligned_cols=28 Identities=25% Similarity=0.374 Sum_probs=22.0
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
.++|+++||..+| . ++..+.|+.+....
T Consensus 7 ~~~~l~~iA~~~g-~----S~~~f~r~Fk~~~g 34 (42)
T PF00165_consen 7 QKLTLEDIAEQAG-F----SPSYFSRLFKKETG 34 (42)
T ss_dssp SS--HHHHHHHHT-S-----HHHHHHHHHHHTS
T ss_pred CCCCHHHHHHHHC-C----CHHHHHHHHHHHHC
Confidence 5799999999999 9 99999999987654
No 137
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=85.65 E-value=1.5 Score=29.96 Aligned_cols=39 Identities=33% Similarity=0.463 Sum_probs=34.4
Q ss_pred CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+|..++-.+||+..| + ....++.-|+.|.+.|++.....
T Consensus 31 pG~~L~e~~La~~lg-V----SRtpVReAL~~L~~eGlv~~~~~ 69 (212)
T TIGR03338 31 PGAKLNESDIAARLG-V----SRGPVREAFRALEEAGLVRNEKN 69 (212)
T ss_pred CCCEecHHHHHHHhC-C----ChHHHHHHHHHHHHCCCEEEecC
Confidence 347889999999999 9 89999999999999999986543
No 138
>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=84.42 E-value=1.6 Score=25.37 Aligned_cols=29 Identities=24% Similarity=0.477 Sum_probs=22.2
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHH
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~R 70 (89)
|++.-+++ |.++..|||+.++ + .+..+++
T Consensus 13 ~e~y~~~~--g~i~lkdIA~~Lg-v----s~~tIr~ 41 (60)
T PF10668_consen 13 FEIYKESN--GKIKLKDIAEKLG-V----SESTIRK 41 (60)
T ss_pred HHHHHHhC--CCccHHHHHHHHC-C----CHHHHHH
Confidence 55555554 8999999999999 9 7666553
No 139
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=84.35 E-value=1.7 Score=34.03 Aligned_cols=40 Identities=33% Similarity=0.361 Sum_probs=31.5
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|-..|.+ ||.|+.||++.++ + ....+.|.|+.| .|++...
T Consensus 5 ~~~~L~~----g~~~~~eL~~~l~-~----sq~~~s~~L~~L--~~~V~~~ 44 (442)
T PRK09775 5 LTTLLLQ----GPLSAAELAARLG-V----SQATLSRLLAAL--GDQVVRF 44 (442)
T ss_pred HHHHHhc----CCCCHHHHHHHhC-C----CHHHHHHHHHHh--hcceeEe
Confidence 3445554 7999999999999 9 788899999999 6666543
No 140
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=84.32 E-value=0.71 Score=32.26 Aligned_cols=50 Identities=16% Similarity=0.222 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 20 SVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 20 ~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
..+-.+|+.|.++|-||.= ...++.|||+.+| ++++.=...|+|-.|-|.
T Consensus 158 drQ~~vL~~A~~~GYFd~P------R~~~l~dLA~~lG-ISkst~~ehLRrAe~Kl~ 207 (215)
T COG3413 158 DRQLEVLRLAYKMGYFDYP------RRVSLKDLAKELG-ISKSTLSEHLRRAERKLI 207 (215)
T ss_pred HHHHHHHHHHHHcCCCCCC------ccCCHHHHHHHhC-CCHHHHHHHHHHHHHHHH
Confidence 4567899999999999752 5689999999999 943333334555555443
No 141
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=84.25 E-value=1.7 Score=32.01 Aligned_cols=43 Identities=16% Similarity=0.276 Sum_probs=37.0
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV 81 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~ 81 (89)
+..|.+.|.+. .+.+.+|||+.++ + ....+.|.++.|...|+.
T Consensus 6 ~~~il~~L~~~---~~~s~~~LA~~lg-v----sr~tV~~~l~~L~~~G~~ 48 (319)
T PRK11886 6 MLQLLSLLADG---DFHSGEQLGEELG-I----SRAAIWKHIQTLEEWGLD 48 (319)
T ss_pred HHHHHHHHHcC---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCc
Confidence 45677778752 6899999999999 9 899999999999999983
No 142
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=83.68 E-value=2.3 Score=32.08 Aligned_cols=35 Identities=11% Similarity=0.254 Sum_probs=32.2
Q ss_pred CCCCHHHHHhh--CCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQ--LPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~--~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|++..+|++. .+ + .+..++|-|..|...|++...
T Consensus 24 ~pv~s~~l~~~~~l~-~----S~aTIR~dm~~Le~~G~l~~~ 60 (339)
T PRK00082 24 EPVGSKTLSKRYGLG-V----SSATIRNDMADLEELGLLEKP 60 (339)
T ss_pred CCcCHHHHHHHhCCC-C----ChHHHHHHHHHHHhCCCcCCC
Confidence 89999999977 88 8 889999999999999999865
No 143
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=83.43 E-value=1.5 Score=30.38 Aligned_cols=36 Identities=17% Similarity=0.061 Sum_probs=32.0
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
-+.|-.|||+.+| + .+..|.|+|+-|...|++....
T Consensus 168 ~~~t~~~lA~~lG-~----sretvsR~L~~L~~~G~I~~~~ 203 (226)
T PRK10402 168 YHEKHTQAAEYLG-V----SYRHLLYVLAQFIQDGYLKKSK 203 (226)
T ss_pred ccchHHHHHHHHC-C----cHHHHHHHHHHHHHCCCEEeeC
Confidence 3578899999999 9 8999999999999999987543
No 144
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=83.32 E-value=2.4 Score=29.32 Aligned_cols=38 Identities=29% Similarity=0.317 Sum_probs=33.8
Q ss_pred CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+|..++..+||+..| + ....++--|+.|...|++.-..
T Consensus 31 pG~~L~e~~La~~lg-V----SRtpVREAL~~L~~eGLV~~~~ 68 (221)
T PRK11414 31 PGARLITKNLAEQLG-M----SITPVREALLRLVSVNALSVAP 68 (221)
T ss_pred CCCccCHHHHHHHHC-C----CchhHHHHHHHHHHCCCEEecC
Confidence 457899999999999 9 8889999999999999997543
No 145
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=83.32 E-value=2.3 Score=25.74 Aligned_cols=37 Identities=32% Similarity=0.492 Sum_probs=32.0
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
||..-.||.+.++++ .+..|.+-|+.|...|++....
T Consensus 17 g~~rf~el~~~l~~i----s~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 17 GPMRFSELQRRLPGI----SPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp SSEEHHHHHHHSTTS-----HHHHHHHHHHHHHTTSEEEEE
T ss_pred CCCcHHHHHHhcchh----HHHHHHHHHHHHHHcchhhccc
Confidence 799999999999438 8889999999999999998653
No 146
>PRK13239 alkylmercury lyase; Provisional
Probab=83.25 E-value=1.7 Score=30.94 Aligned_cols=39 Identities=23% Similarity=0.352 Sum_probs=31.2
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
-.-|+..|++ | +|.|.++||+.++ . +...+.++|+.|..
T Consensus 24 ~~~llr~la~-G--~pvt~~~lA~~~~-~----~~~~v~~~L~~l~~ 62 (206)
T PRK13239 24 LVPLLRLLAK-G--RPVSVTTLAAALG-W----PVEEVEAVLEAMPD 62 (206)
T ss_pred HHHHHHHHHc-C--CCCCHHHHHHHhC-C----CHHHHHHHHHhCCC
Confidence 3446777884 4 8999999999999 9 88888888887753
No 147
>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=83.24 E-value=1.3 Score=26.99 Aligned_cols=34 Identities=24% Similarity=0.370 Sum_probs=21.7
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHH
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLL 75 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L 75 (89)
|+..|++ | +|+|.++||..+| . ...-+..+|..+
T Consensus 29 LLr~LA~-G--~PVt~~~LA~a~g-~----~~e~v~~~L~~~ 62 (77)
T PF12324_consen 29 LLRLLAK-G--QPVTVEQLAAALG-W----PVEEVRAALAAM 62 (77)
T ss_dssp HHHHHTT-T--S-B-HHHHHHHHT-------HHHHHHHHHH-
T ss_pred HHHHHHc-C--CCcCHHHHHHHHC-C----CHHHHHHHHHhC
Confidence 6777876 4 8999999999999 8 555555555444
No 148
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=82.90 E-value=1.8 Score=24.43 Aligned_cols=28 Identities=21% Similarity=0.336 Sum_probs=23.0
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASY 78 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~ 78 (89)
++|+++||+.++ + ++..+.|+++.....
T Consensus 1 ~~~~~~la~~~~-~----s~~~l~~~f~~~~~~ 28 (84)
T smart00342 1 PLTLEDLAEALG-M----SPRHLQRLFKKETGT 28 (84)
T ss_pred CCCHHHHHHHhC-C----CHHHHHHHHHHHhCc
Confidence 478999999999 9 888898888866543
No 149
>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=82.88 E-value=2.5 Score=26.64 Aligned_cols=41 Identities=17% Similarity=0.165 Sum_probs=34.2
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
.+...||+..|-+ +++|=.|||+.+| + ....+.|.=|.|..
T Consensus 41 l~~R~~i~~~Ll~----~~~tQrEIa~~lG-i----S~atIsR~sn~lk~ 81 (94)
T TIGR01321 41 LGDRIRIVNELLN----GNMSQREIASKLG-V----SIATITRGSNNLKT 81 (94)
T ss_pred HHHHHHHHHHHHh----CCCCHHHHHHHhC-C----ChhhhhHHHhhccc
Confidence 3567788887766 6899999999999 9 88899998888764
No 150
>PF13518 HTH_28: Helix-turn-helix domain
Probab=82.23 E-value=3.4 Score=21.80 Aligned_cols=28 Identities=25% Similarity=0.260 Sum_probs=25.6
Q ss_pred CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477 48 SASEIAAQLPATKNKDAPTMLDRILGLLASYGI 80 (89)
Q Consensus 48 t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi 80 (89)
|..++|...+ + ++..++|.++..-..|+
T Consensus 14 s~~~~a~~~g-i----s~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 14 SVREIAREFG-I----SRSTVYRWIKRYREGGI 41 (52)
T ss_pred CHHHHHHHHC-C----CHhHHHHHHHHHHhcCH
Confidence 9999999999 9 88999999998888774
No 151
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=82.16 E-value=2.9 Score=30.83 Aligned_cols=37 Identities=16% Similarity=0.319 Sum_probs=33.3
Q ss_pred CCCCCHHHHHhhCCCCCCCCCcchHHHHHH-HHhccCceeeec
Q 045477 44 GAKLSASEIAAQLPATKNKDAPTMLDRILG-LLASYGIVECSV 85 (89)
Q Consensus 44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR-~L~s~gi~~e~~ 85 (89)
++|.+++.+|+.+| . ++..+.++++ +|...|++..+.
T Consensus 274 ~~~~~~~~~a~~lg-~----~~~~~~~~~e~~Li~~~li~~~~ 311 (328)
T PRK00080 274 GGPVGLDTLAAALG-E----ERDTIEDVYEPYLIQQGFIQRTP 311 (328)
T ss_pred CCceeHHHHHHHHC-C----CcchHHHHhhHHHHHcCCcccCC
Confidence 37999999999999 9 8999999999 999999997553
No 152
>PRK12423 LexA repressor; Provisional
Probab=82.13 E-value=4.2 Score=28.18 Aligned_cols=37 Identities=22% Similarity=0.236 Sum_probs=30.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
-+-|..|||+.+| .. .+..+++-|+.|+..|+++...
T Consensus 24 ~~Ps~~eia~~~g-~~---s~~~v~~~l~~L~~~G~l~~~~ 60 (202)
T PRK12423 24 QPPSLAEIAQAFG-FA---SRSVARKHVQALAEAGLIEVVP 60 (202)
T ss_pred CCCCHHHHHHHhC-CC---ChHHHHHHHHHHHHCCCEEecC
Confidence 4679999999999 73 3457899999999999998653
No 153
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=82.03 E-value=1.5 Score=24.39 Aligned_cols=31 Identities=26% Similarity=0.428 Sum_probs=20.8
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
|-..+.+ ..+|..+||+.+| . ++..+.|++.
T Consensus 2 L~~~m~~----~~it~~~La~~~g-i----s~~tl~~~~~ 32 (63)
T PF13443_consen 2 LKELMAE----RGITQKDLARKTG-I----SRSTLSRILN 32 (63)
T ss_dssp HHHHHHH----TT--HHHHHHHHT-------HHHHHHHHT
T ss_pred HHHHHHH----cCCCHHHHHHHHC-c----CHHHHHHHHh
Confidence 4566776 4679999999999 9 7877877764
No 154
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=81.82 E-value=3.1 Score=26.69 Aligned_cols=41 Identities=12% Similarity=0.125 Sum_probs=31.0
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
.+.+.|.++- ..+.|+++||+.++ + .+..+.|+++.-....
T Consensus 13 ~~~~~I~~~~-~~~~sl~~lA~~~g-~----S~~~l~r~Fk~~~G~s 53 (127)
T PRK11511 13 SILDWIEDNL-ESPLSLEKVSERSG-Y----SKWHLQRMFKKETGHS 53 (127)
T ss_pred HHHHHHHHhc-CCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCcC
Confidence 3455666553 26899999999999 9 9999999987665443
No 155
>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=81.61 E-value=1.2 Score=24.24 Aligned_cols=20 Identities=20% Similarity=0.396 Sum_probs=11.6
Q ss_pred CHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 48 SASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 48 t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
|+.|||+.+| + .+..+.|+|
T Consensus 1 Ti~dIA~~ag-v----S~~TVSr~l 20 (46)
T PF00356_consen 1 TIKDIAREAG-V----SKSTVSRVL 20 (46)
T ss_dssp CHHHHHHHHT-S----SHHHHHHHH
T ss_pred CHHHHHHHHC-c----CHHHHHHHH
Confidence 4566666666 6 555555544
No 156
>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=81.45 E-value=2.3 Score=25.08 Aligned_cols=43 Identities=21% Similarity=0.162 Sum_probs=26.7
Q ss_pred HhChHHHHHhcC-CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477 31 NLGLFEIIAKAG-PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY 78 (89)
Q Consensus 31 ~LgIfd~l~~~g-~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~ 78 (89)
+-.|++.|-++. .-..+|+.|||+.++ + .+..+.|+.+.|=-.
T Consensus 18 e~~Ia~yil~~~~~~~~~si~elA~~~~-v----S~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 18 EKKIADYILENPDEIAFMSISELAEKAG-V----SPSTIVRFCKKLGFS 61 (77)
T ss_dssp HHHHHHHHHH-HHHHCT--HHHHHHHCT-S-----HHHHHHHHHHCTTT
T ss_pred HHHHHHHHHhCHHHHHHccHHHHHHHcC-C----CHHHHHHHHHHhCCC
Confidence 334555554321 014689999999999 9 888999988876433
No 157
>PRK11642 exoribonuclease R; Provisional
Probab=81.12 E-value=2.9 Score=35.24 Aligned_cols=50 Identities=20% Similarity=0.215 Sum_probs=39.3
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|.+.|.+.+ +|++..+|++.++ .+...+...|.+.|+.|...|.+....
T Consensus 23 ~Il~~l~~~~--~~~~~~~L~~~l~-l~~~~~~~~l~~~L~~L~~~g~l~~~~ 72 (813)
T PRK11642 23 FILEHLTKRE--KPASREELAVELN-IEGEEQLEALRRRLRAMERDGQLVFTR 72 (813)
T ss_pred HHHHHHHhcC--CCCCHHHHHHHhC-CCChHHHHHHHHHHHHHHHCCCEEEcC
Confidence 4677776644 8999999999999 843334567999999999999987543
No 158
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=80.78 E-value=5.7 Score=23.88 Aligned_cols=44 Identities=23% Similarity=0.231 Sum_probs=36.9
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
..|...++. +..|++||-+.|| + +...|-..|--|+..|++...
T Consensus 8 ~~IL~~ls~----~c~TLeeL~ekTg-i----~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 8 QKILIILSK----RCCTLEELEEKTG-I----SKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHHh----ccCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeeee
Confidence 345556665 5899999999999 9 999999999999999998764
No 159
>PHA02591 hypothetical protein; Provisional
Probab=80.76 E-value=3.2 Score=25.56 Aligned_cols=33 Identities=18% Similarity=0.221 Sum_probs=26.5
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
.+...|.+ .++|.++||+.+| + +...+++.++-
T Consensus 50 ~vA~eL~e----qGlSqeqIA~~LG-V----sqetVrKYL~~ 82 (83)
T PHA02591 50 SVTHELAR----KGFTVEKIASLLG-V----SVRKVRRYLES 82 (83)
T ss_pred HHHHHHHH----cCCCHHHHHHHhC-C----CHHHHHHHHhc
Confidence 35556776 5799999999999 9 88888888763
No 160
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=80.75 E-value=2.6 Score=29.18 Aligned_cols=35 Identities=20% Similarity=0.168 Sum_probs=32.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.++|.+|||++++ . .+..++.-++.|+..|++.+.
T Consensus 177 ~g~s~~eIA~~l~-i----S~~Tv~~~~~~~~~~~~~~~~ 211 (239)
T PRK10430 177 YEFSTDELANAVN-I----SRVSCRKYLIWLVNCHILFTS 211 (239)
T ss_pred CCcCHHHHHHHhC-c----hHHHHHHHHHHHHhCCEEEEE
Confidence 6789999999999 9 999999999999999999544
No 161
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=80.24 E-value=1.3 Score=23.57 Aligned_cols=30 Identities=23% Similarity=0.243 Sum_probs=18.9
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGI 80 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi 80 (89)
+.|..+||+.+| + ++..++|.++-....|+
T Consensus 17 G~s~~~ia~~lg-v----s~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 17 GWSIREIAKRLG-V----SRSTVYRWIKRYREEGL 46 (50)
T ss_dssp T--HHHHHHHHT-S-----HHHHHHHHT-------
T ss_pred CCCHHHHHHHHC-c----CHHHHHHHHHHcccccc
Confidence 579999999999 9 99999999987766663
No 162
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=79.75 E-value=4.5 Score=24.82 Aligned_cols=39 Identities=13% Similarity=0.086 Sum_probs=28.9
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
.+.|.++- ..++|+++||+.++ . .+..|.|+++......
T Consensus 11 ~~~i~~~~-~~~~~~~~lA~~~~-~----S~~~l~r~f~~~~g~s 49 (107)
T PRK10219 11 IAWIDEHI-DQPLNIDVVAKKSG-Y----SKWYLQRMFRTVTHQT 49 (107)
T ss_pred HHHHHHhc-CCCCCHHHHHHHHC-C----CHHHHHHHHHHHHCcC
Confidence 34454442 26899999999999 9 8999998887665443
No 163
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=79.63 E-value=2.8 Score=29.08 Aligned_cols=59 Identities=15% Similarity=0.134 Sum_probs=41.1
Q ss_pred HHHHHHHHHHhChHHHHHhcCCCCC---CCHHHHHhhC-CCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 22 LHMTMKAVINLGLFEIIAKAGPGAK---LSASEIAAQL-PATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 22 ~~~aL~~av~LgIfd~l~~~g~~~~---~t~~eLA~~~-~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
...+|.+.+..==.+-|.+. +.| .|-.+|+..+ | . .+..|+|.++.|+..|++....|-
T Consensus 45 ~l~vL~aLls~~~~~d~~~~--~~piVfpSN~~La~r~~G-~----s~~tlrR~l~~LveaGLI~rrDS~ 107 (177)
T PF03428_consen 45 ALAVLDALLSFTPPDDWEPG--RRPIVFPSNAQLAERLNG-M----SERTLRRHLARLVEAGLIVRRDSP 107 (177)
T ss_pred HHHHHHHHHHhCCcccccCC--CCceeecCHHHHHHHHcC-C----CHHHHHHHHHHHHHCCCeeeccCC
Confidence 33444444444333444322 244 4889999999 8 9 899999999999999999876543
No 164
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=79.17 E-value=3.4 Score=27.28 Aligned_cols=34 Identities=32% Similarity=0.371 Sum_probs=30.7
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
=-|+.|+|..++ + +|..+.|..+.|...|++.-.
T Consensus 35 LPSvRelA~~~~-V----NpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 35 LPSVRELAKDLG-V----NPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred CCcHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence 349999999999 9 999999999999999988744
No 165
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=79.12 E-value=4.2 Score=26.85 Aligned_cols=52 Identities=17% Similarity=0.266 Sum_probs=39.9
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|--|.++|... ||.|+.||-+.++ ...--.+..+.-||+-|+-.|++....
T Consensus 7 aE~eVM~ilW~~---~~~t~~eI~~~l~-~~~ews~sTV~TLl~RL~KKg~l~~~k 58 (123)
T COG3682 7 AEWEVMEILWSR---GPATVREIIEELP-ADREWSYSTVKTLLNRLVKKGLLTRKK 58 (123)
T ss_pred HHHHHHHHHHHc---CCccHHHHHHHHh-hcccccHHHHHHHHHHHHhccchhhhh
Confidence 566778888876 6999999999998 621123456888999999999987654
No 166
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=79.10 E-value=8 Score=23.12 Aligned_cols=54 Identities=13% Similarity=0.188 Sum_probs=39.7
Q ss_pred HHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 24 MTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 24 ~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
......++=.|...+.... ++.+|.++--..+++. |...+.|+..+|...|++.
T Consensus 32 p~~Yl~iRn~il~~w~~n~-~~~lt~~~~~~~i~~~----d~~~~~ri~~FL~~~G~IN 85 (86)
T PF04433_consen 32 PEQYLKIRNTILAEWRKNP-NKYLTKTDARKLIKGI----DVNKIRRIYDFLERWGLIN 85 (86)
T ss_dssp HHHHHHHHHHHHHHHHHHT-TS---HHHHHHHTTSS----SHHHHHHHHHHHHHTTSSS
T ss_pred hHHHHHHHHHHHHHHHHCC-CCcccHHHHHHHcccc----CHHHHHHHHHHHHHcCccC
Confidence 3466677777888866543 3899999987776645 8999999999999999875
No 167
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=79.02 E-value=3.6 Score=29.08 Aligned_cols=38 Identities=34% Similarity=0.482 Sum_probs=33.6
Q ss_pred CCCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 43 PGAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 43 ~~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+|..+ |-.+||+..| + ....++--|+.|.+.|++.-..
T Consensus 29 pG~~LpsE~eLa~~~g-V----SRtpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 29 PGERLPPEREIAEMLD-V----TRTVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred CCCcCcCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 45788 6999999999 9 8999999999999999998554
No 168
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=78.68 E-value=5.7 Score=23.53 Aligned_cols=46 Identities=26% Similarity=0.333 Sum_probs=27.2
Q ss_pred HHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcch-------------HHHHHHHHhccCc
Q 045477 26 MKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTM-------------LDRILGLLASYGI 80 (89)
Q Consensus 26 L~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~-------------l~RlLR~L~s~gi 80 (89)
+|+..=.-|-+.+.+ ..+|-.|+|+.+| + .... +.++++++.+.|.
T Consensus 15 ~k~~l~~~i~~~~~~----~~ltQ~e~A~~lg-i----sq~~vS~l~~g~~~~~sl~~L~~~l~aLG~ 73 (80)
T PF13744_consen 15 AKAQLMAAIRELREE----RGLTQAELAERLG-I----SQPRVSRLENGKIDDFSLDTLLRYLEALGG 73 (80)
T ss_dssp HHHHHHHHHHHHHHC----CT--HHHHHHHHT-S-----HHHHHHHHTT-GCC--HHHHHHHHHHTTE
T ss_pred HHHHHHHHHHHHHHH----cCCCHHHHHHHHC-C----ChhHHHHHHcCcccCCCHHHHHHHHHHcCC
Confidence 333333336666665 6799999999999 8 4444 5556666666653
No 169
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=78.44 E-value=4.3 Score=28.27 Aligned_cols=38 Identities=26% Similarity=0.368 Sum_probs=33.9
Q ss_pred CCCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 43 PGAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 43 ~~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+|..+ |-.+||+..| + ....++--|+.|.+.|++.-..
T Consensus 26 pG~~LpsE~~La~~lg-V----SRtpVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 26 PGSILPAERELSELIG-V----TRTTLREVLQRLARDGWLTIQH 64 (235)
T ss_pred CCCcCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEeC
Confidence 45788 8999999999 9 8999999999999999998654
No 170
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=78.42 E-value=3.7 Score=29.46 Aligned_cols=40 Identities=20% Similarity=0.174 Sum_probs=34.4
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
-.|.+.|.+. +.+++.|||+.++ + .+..++|=|+.|...+
T Consensus 10 ~~I~~~l~~~---~~v~v~eLa~~~~-V----S~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 10 GQLLQALKRS---DKLHLKDAAALLG-V----SEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHc---CCCcHHHHHHHhC-C----CHHHHHHHHHHhhcCe
Confidence 3577888875 6899999999999 9 8999999999998654
No 171
>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=78.36 E-value=4.1 Score=27.87 Aligned_cols=37 Identities=14% Similarity=0.189 Sum_probs=31.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
|++|++|||.+.| + ....+.--|-.+++.|.+.....
T Consensus 5 Ga~T~eELA~~FG-v----ttRkvaStLa~~ta~Grl~Rv~q 41 (155)
T PF07789_consen 5 GAKTAEELAGKFG-V----TTRKVASTLAMVTATGRLIRVNQ 41 (155)
T ss_pred CcccHHHHHHHhC-c----chhhhHHHHHHHHhcceeEEecC
Confidence 7999999999999 9 88888888888888888776544
No 172
>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=78.32 E-value=3.7 Score=25.53 Aligned_cols=43 Identities=14% Similarity=0.120 Sum_probs=32.1
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
+..-+|.+.+++ +.+|+.|+|..++ + .+..|.++|| ..|++-.
T Consensus 11 Ka~~~d~~~~~~--~~~ti~~~AK~L~-i----~~~~l~~~Lr---~~g~l~~ 53 (111)
T PF03374_consen 11 KAEFYDAFVDSD--GLYTIREAAKLLG-I----GRNKLFQWLR---EKGWLYR 53 (111)
T ss_pred hhHHHHHHHcCC--CCccHHHHHHHhC-C----CHHHHHHHHH---hCCceEE
Confidence 345678887754 8999999999999 9 6666666665 4777654
No 173
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=77.54 E-value=4.5 Score=28.17 Aligned_cols=38 Identities=26% Similarity=0.368 Sum_probs=33.5
Q ss_pred CCCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 43 PGAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 43 ~~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+|..+ |-.|||++.| + ....++.-|+.|.+.|++....
T Consensus 27 pG~~LPsE~eLae~~g-V----SRt~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 27 PGSILPAERELSELIG-V----TRTTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred CCCcCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeC
Confidence 34778 7899999999 9 8999999999999999998653
No 174
>COG3695 Predicted methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=77.38 E-value=3.8 Score=26.29 Aligned_cols=41 Identities=22% Similarity=0.265 Sum_probs=32.5
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
.|++.++.-+.|.-+|-.+||+..| . |..+..+.|+|+.|.
T Consensus 10 ~v~~vv~~IP~GkV~TYGdIA~laG-~--p~~ARqVG~il~~l~ 50 (103)
T COG3695 10 RVLDVVAAIPEGKVSTYGDIAKLAG-L--PRAARQVGRILKHLP 50 (103)
T ss_pred HHHHHHHhCCCCceeeHHHHHHHhC-C--ChhHHHHHHHHhhCC
Confidence 5677777665557899999999999 5 445788999998765
No 175
>PRK05638 threonine synthase; Validated
Probab=77.14 E-value=6.4 Score=30.49 Aligned_cols=47 Identities=17% Similarity=0.228 Sum_probs=36.8
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
++.|...|.+ ++++..||++.++ . +-....+++.|+.|...|+++..
T Consensus 373 r~~IL~~L~~----~~~~~~el~~~l~-~--~~s~~~v~~hL~~Le~~GLV~~~ 419 (442)
T PRK05638 373 KLEILKILSE----REMYGYEIWKALG-K--PLKYQAVYQHIKELEELGLIEEA 419 (442)
T ss_pred HHHHHHHHhh----CCccHHHHHHHHc-c--cCCcchHHHHHHHHHHCCCEEEe
Confidence 4556667764 6899999999997 3 01566999999999999999753
No 176
>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=76.99 E-value=2.3 Score=24.70 Aligned_cols=33 Identities=15% Similarity=0.106 Sum_probs=24.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
.+-|..|||+.+| . ++.-+..+|+.......+.
T Consensus 19 r~Pt~eEiA~~lg-i----s~~~v~~~l~~~~~~~Sl~ 51 (78)
T PF04539_consen 19 REPTDEEIAEELG-I----SVEEVRELLQASRRPVSLD 51 (78)
T ss_dssp S--BHHHHHHHHT-S-----HHHHHHHHHHHSCCEESS
T ss_pred CCCCHHHHHHHHc-c----cHHHHHHHHHhCCCCeEEe
Confidence 6789999999999 9 9999999998765544443
No 177
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=76.87 E-value=4.8 Score=28.36 Aligned_cols=38 Identities=26% Similarity=0.381 Sum_probs=33.6
Q ss_pred CCCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 43 PGAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 43 ~~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+|..+ |-.+||+..| + ....++--|+.|.+.|++.-..
T Consensus 30 pG~~LpsE~eLa~~lg-V----SRtpVREAL~~L~~eGlv~~~~ 68 (254)
T PRK09464 30 PGEKLPPERELAKQFD-V----SRPSLREAIQRLEAKGLLLRRQ 68 (254)
T ss_pred CCCcCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 34778 8999999999 9 8999999999999999998654
No 178
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=76.60 E-value=5 Score=28.21 Aligned_cols=39 Identities=26% Similarity=0.338 Sum_probs=34.2
Q ss_pred CCCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 43 PGAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 43 ~~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+|..+ |-.+||+..| + ....++--|+.|...|++.-...
T Consensus 27 pG~~LPsE~eLa~~~g-V----SRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 27 VGQALPSERRLCEKLG-F----SRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred CCCcCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeCC
Confidence 45789 8899999999 9 89999999999999999986543
No 179
>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=76.53 E-value=4.5 Score=22.70 Aligned_cols=39 Identities=21% Similarity=0.288 Sum_probs=30.3
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
-++.|.+.|-+. +.+|..|||..++ + ....+.+-+..|-
T Consensus 6 rq~~Ll~~L~~~---~~~~~~ela~~l~-~----S~rti~~~i~~L~ 44 (59)
T PF08280_consen 6 RQLKLLELLLKN---KWITLKELAKKLN-I----SERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHH---TSBBHHHHHHHCT-S-----HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcC---CCCcHHHHHHHHC-C----CHHHHHHHHHHHH
Confidence 456788888773 6899999999999 9 7777777766654
No 180
>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=76.16 E-value=2.3 Score=25.61 Aligned_cols=33 Identities=27% Similarity=0.149 Sum_probs=28.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
..+|..|||+.++ + .+..+...++.+-..|++.
T Consensus 31 eGlS~kEIAe~LG-I----S~~TVk~~l~~~~~~~~~~ 63 (73)
T TIGR03879 31 AGKTASEIAEELG-R----TEQTVRNHLKGETKAGGLV 63 (73)
T ss_pred cCCCHHHHHHHHC-c----CHHHHHHHHhcCcccchHH
Confidence 4789999999999 9 8989999998877777653
No 181
>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=76.15 E-value=4.4 Score=24.66 Aligned_cols=32 Identities=13% Similarity=0.127 Sum_probs=25.0
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.|.+.|.+ | .+|+.+||+..| + ....++|.|+
T Consensus 10 ~I~e~l~~-~---~~ti~dvA~~~g-v----S~~TVsr~L~ 41 (80)
T TIGR02844 10 EIGKYIVE-T---KATVRETAKVFG-V----SKSTVHKDVT 41 (80)
T ss_pred HHHHHHHH-C---CCCHHHHHHHhC-C----CHHHHHHHhc
Confidence 45667776 4 789999999999 9 7778888653
No 182
>PRK03837 transcriptional regulator NanR; Provisional
Probab=76.04 E-value=5.9 Score=27.53 Aligned_cols=38 Identities=29% Similarity=0.388 Sum_probs=33.6
Q ss_pred CCCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 43 PGAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 43 ~~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+|..+ +-.+||+..+ + ....++--|+.|...|+++-..
T Consensus 33 pG~~Lp~E~~Lae~~g-V----SRt~VREAL~~L~~eGlv~~~~ 71 (241)
T PRK03837 33 PGDQLPSERELMAFFG-V----GRPAVREALQALKRKGLVQISH 71 (241)
T ss_pred CCCCCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 34678 8999999999 9 8999999999999999998643
No 183
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=75.98 E-value=5.1 Score=28.30 Aligned_cols=37 Identities=30% Similarity=0.387 Sum_probs=32.9
Q ss_pred CCCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 43 PGAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 43 ~~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|..+ |-.|||+..| + ....++.-|+.|.+.|++.-.
T Consensus 22 pG~~LpsE~eLae~~g-V----SRtpVREAL~~Le~~GlV~~~ 59 (253)
T PRK10421 22 AGMKLPAERQLAMQLG-V----SRNSLREALAKLVSEGVLLSR 59 (253)
T ss_pred CCCcCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence 44778 6899999999 9 899999999999999999754
No 184
>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=75.66 E-value=4.8 Score=26.92 Aligned_cols=35 Identities=11% Similarity=0.287 Sum_probs=27.1
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.|-+.|.+++ +...|+.||++.|+ + ++..+.+++|
T Consensus 34 kV~~yLr~~p-~~~ati~eV~e~tg-V----s~~~I~~~Ir 68 (137)
T TIGR03826 34 KVYKFLRKHE-NRQATVSEIVEETG-V----SEKLILKFIR 68 (137)
T ss_pred HHHHHHHHCC-CCCCCHHHHHHHHC-c----CHHHHHHHHH
Confidence 3445566654 25689999999999 9 8888888876
No 185
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=75.54 E-value=7.3 Score=31.23 Aligned_cols=50 Identities=8% Similarity=0.068 Sum_probs=41.4
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
...+..|...|.+.+ +..+..+||+.++ . ++..+.+.+..|.+.|+++-.
T Consensus 5 ~~~e~~iL~~l~~~~--~~~~~~~la~~~~-~----~~~~v~~~~~~L~~kg~v~~~ 54 (494)
T PTZ00326 5 ELEENTILSKLESEN--EIVNSLALAESLN-I----DHQKVVGAIKSLESANYITTE 54 (494)
T ss_pred hHHHHHHHHHHHhcC--CCCCHHHHHHHcC-C----CHHHHHHHHHHHHhCCCEEEE
Confidence 345667778887633 5799999999999 9 999999999999999988744
No 186
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=75.53 E-value=2.2 Score=30.45 Aligned_cols=44 Identities=14% Similarity=0.098 Sum_probs=32.1
Q ss_pred HHhChHHHHHhcCCC-CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477 30 INLGLFEIIAKAGPG-AKLSASEIAAQLPATKNKDAPTMLDRILGLLASY 78 (89)
Q Consensus 30 v~LgIfd~l~~~g~~-~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~ 78 (89)
.+..|.+.|-++... .-+|+.|||++++ + .+..+.|+.|.|=-.
T Consensus 17 ~e~~Ia~yil~n~~~v~~~si~~lA~~~~-v----S~aTv~Rf~kklG~~ 61 (284)
T PRK11302 17 SERKVAEVILASPQTAIHSSIATLAKMAN-V----SEPTVNRFCRSLDTK 61 (284)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhC-C----CHHHHHHHHHHcCCC
Confidence 355677777665321 3479999999999 9 888898888776433
No 187
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=75.42 E-value=3.5 Score=28.49 Aligned_cols=30 Identities=30% Similarity=0.392 Sum_probs=27.7
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGI 80 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi 80 (89)
|+|-++||..+| + .+..+.|+++.|...|+
T Consensus 173 ~~t~~~iA~~lG-~----tretvsR~l~~L~~~gl 202 (236)
T PRK09392 173 PYEKRVLASYLG-M----TPENLSRAFAALASHGV 202 (236)
T ss_pred eCCHHHHHHHhC-C----ChhHHHHHHHHHHhCCe
Confidence 567799999999 9 89999999999999996
No 188
>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=75.26 E-value=6.6 Score=21.81 Aligned_cols=38 Identities=21% Similarity=0.410 Sum_probs=26.5
Q ss_pred HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHH
Q 045477 27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70 (89)
Q Consensus 27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~R 70 (89)
|...=+.+...+.+.|. .-+|..|||+.+| + ++..++|
T Consensus 10 RL~~Y~r~L~~l~~~G~-~~vSS~~La~~~g-i----~~~qVRK 47 (50)
T PF06971_consen 10 RLPLYLRYLEQLKEEGV-ERVSSQELAEALG-I----TPAQVRK 47 (50)
T ss_dssp HHHHHHHHHHHHHHTT--SEE-HHHHHHHHT-S-----HHHHHH
T ss_pred HHHHHHHHHHHHHHcCC-eeECHHHHHHHHC-C----CHHHhcc
Confidence 34444566777877663 6789999999999 9 8887765
No 189
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=75.09 E-value=7.4 Score=20.69 Aligned_cols=24 Identities=21% Similarity=0.232 Sum_probs=21.4
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLL 75 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L 75 (89)
.|.+++|..+| + +...+.|+++..
T Consensus 28 ~s~~~vA~~~~-v----s~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELG-V----SWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHC-C----CHHHHHHHHHhh
Confidence 69999999999 9 999999998753
No 190
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=74.81 E-value=7 Score=31.33 Aligned_cols=49 Identities=10% Similarity=0.135 Sum_probs=40.7
Q ss_pred HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+++..|...|.+.+ ...+..+||+.++ . ++..+.+.+..|.+.|+++-.
T Consensus 3 ~~e~~iL~~l~~~~--~~~~~~~la~~~g-~----~~~~v~~~~~~L~~kg~v~~~ 51 (492)
T PLN02853 3 MAEEALLGALSNNE--EISDSGQFAASHG-L----DHNEVVGVIKSLHGFRYVDAQ 51 (492)
T ss_pred hHHHHHHHHHHhcC--CCCCHHHHHHHcC-C----CHHHHHHHHHHHHhCCCEEEE
Confidence 46677888887642 2389999999999 9 999999999999999988743
No 191
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=74.35 E-value=13 Score=25.36 Aligned_cols=54 Identities=19% Similarity=0.211 Sum_probs=41.8
Q ss_pred HhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhC--CCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 18 MGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQL--PATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 18 ~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~--~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+..|...+++..+++.= +.-...+||+++ + + .+.-+..-|..|...|+++...+
T Consensus 21 ~~~W~~~~ir~l~~l~~----------~~~d~~~iak~l~p~-i----s~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 21 YSSWYHPAIRELLPLMP----------FAPDPEWIAKRLRPK-I----SAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred HhhhHHHHHHHHhhcCC----------CCCCHHHHHHHhcCC-C----CHHHHHHHHHHHHHCCCeEECCC
Confidence 35666677777666431 233899999999 6 7 78889999999999999997765
No 192
>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=74.33 E-value=8.5 Score=23.79 Aligned_cols=40 Identities=15% Similarity=0.112 Sum_probs=32.8
Q ss_pred HHHHhChHH-HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 28 AVINLGLFE-IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 28 ~av~LgIfd-~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
.+-.+.|+. .|. +++|-.||++.+| + ....+.|+=|.|-.
T Consensus 35 l~~R~~va~~lL~-----~g~syreIa~~tg-v----S~aTItRvsr~Lk~ 75 (87)
T PF01371_consen 35 LAQRWQVAKELLD-----EGKSYREIAEETG-V----SIATITRVSRCLKY 75 (87)
T ss_dssp HHHHHHHHHHHHH-----TTSSHHHHHHHHT-S----THHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH-----CCCCHHHHHHHhC-C----CHHHHHHHHHHHHc
Confidence 456778888 665 4689999999999 9 88899999888863
No 193
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=74.28 E-value=2.7 Score=30.04 Aligned_cols=42 Identities=12% Similarity=0.122 Sum_probs=31.0
Q ss_pred HHhChHHHHHhcCC-CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 30 INLGLFEIIAKAGP-GAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 30 v~LgIfd~l~~~g~-~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
.|-.|++.|-++.. -..+|+.|||++++ + .+..+.|+.|.|=
T Consensus 13 ~e~~ia~yil~n~~~v~~~si~elA~~~~-v----S~aTv~Rf~kklG 55 (278)
T PRK11557 13 SDRKLADYLLLQPDTARHLSSQQLANEAG-V----SQSSVVKFAQKLG 55 (278)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhC-C----CHHHHHHHHHHcC
Confidence 35567777665431 13589999999999 9 8889999887664
No 194
>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=74.21 E-value=3.7 Score=21.04 Aligned_cols=22 Identities=23% Similarity=0.297 Sum_probs=18.7
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+|..|+|+.+| + .+..++++++
T Consensus 2 lt~~e~a~~lg-i----s~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLG-V----SKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHC-C----CHHHHHHHHH
Confidence 68999999999 9 8888887765
No 195
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=73.20 E-value=2.7 Score=24.41 Aligned_cols=35 Identities=29% Similarity=0.407 Sum_probs=28.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|-++++.||.+.| . -...+-.-||-|.+.|+++..
T Consensus 3 g~lvas~iAd~~G-i----TRSvIVNALRKleSaGvIesr 37 (61)
T PF08222_consen 3 GRLVASKIADRVG-I----TRSVIVNALRKLESAGVIESR 37 (61)
T ss_dssp EEE-HHHHHHHHT-------HHHHHHHHHHHHHTTSEEEE
T ss_pred ceehHHHHHHHhC-c----cHHHHHHHHHHHHhcCceeec
Confidence 4678999999999 9 788899999999999999853
No 196
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=73.07 E-value=5.2 Score=25.28 Aligned_cols=50 Identities=20% Similarity=0.242 Sum_probs=38.6
Q ss_pred HhChHHHHHhc--C---CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 31 NLGLFEIIAKA--G---PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 31 ~LgIfd~l~~~--g---~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+++|+..+... | +..-+|.+++++.++ . ++..+.+.+..|...|++...+
T Consensus 34 q~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg-~----~~~~V~~al~~Li~~~vI~~~g 88 (100)
T PF04492_consen 34 QLKILLAIIRKTYGWNKKMDRISNSQIAEMTG-L----SRDHVSKALNELIRRGVIIRDG 88 (100)
T ss_pred HHHHHHHHHHHccCCCCccceeeHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEeCC
Confidence 44555555431 1 225689999999999 9 8899999999999999997654
No 197
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=72.64 E-value=7.1 Score=27.56 Aligned_cols=38 Identities=26% Similarity=0.276 Sum_probs=33.1
Q ss_pred CCCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 43 PGAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 43 ~~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+|..+ |-.+||+..| + ....++--|+.|...|++.-..
T Consensus 28 pG~~LpsE~eLae~~g-V----SRtpVREAL~~L~~eGlV~~~~ 66 (253)
T PRK11523 28 VGDKLPAERFIADEKN-V----SRTVVREAIIMLEVEGYVEVRK 66 (253)
T ss_pred CCCCCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 34788 5789999999 9 8999999999999999997554
No 198
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=72.64 E-value=3 Score=25.41 Aligned_cols=27 Identities=26% Similarity=0.302 Sum_probs=19.5
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
.++|-.|||+++| - ++..+.+.++++.
T Consensus 2 ~G~tq~eIA~~lG-k----s~s~Vs~~l~Ll~ 28 (93)
T PF08535_consen 2 FGWTQEEIAKRLG-K----SRSWVSNHLALLD 28 (93)
T ss_dssp TT--HHHHHHHTT-------HHHHHHHHGGGS
T ss_pred CCCCHHHHHHHHC-C----CHHHHHHHHHHHc
Confidence 3689999999999 8 8889999988653
No 199
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=72.59 E-value=3.6 Score=26.78 Aligned_cols=33 Identities=24% Similarity=0.325 Sum_probs=24.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
..+|.+|+++..+ . ++..+..+...|.+.|+=.
T Consensus 46 k~Lt~~e~~~~~~-p----~~~~v~~V~~wL~~~G~~~ 78 (143)
T PF09286_consen 46 KYLTPEEFAALFA-P----SPEDVAAVKSWLKSHGLTV 78 (143)
T ss_dssp ----HHHHHHHHS-------HHHHHHHHHHHHHCT-EE
T ss_pred cCCCHHHHHHHHC-C----CHHHHHHHHHHHHHcCCce
Confidence 5699999999999 8 8889999999999999743
No 200
>PF12728 HTH_17: Helix-turn-helix domain
Probab=72.51 E-value=4.1 Score=21.73 Aligned_cols=22 Identities=23% Similarity=0.243 Sum_probs=18.7
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+|++|+|+.++ + .+..++++++
T Consensus 2 lt~~e~a~~l~-i----s~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLG-I----SRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHC-c----CHHHHHHHHH
Confidence 68999999999 9 8887777765
No 201
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=71.46 E-value=11 Score=26.47 Aligned_cols=47 Identities=23% Similarity=0.234 Sum_probs=35.4
Q ss_pred HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
-++..|.|.|...| ..+|+.+||.+++ . +..-+.|-|=-|-..|.+.
T Consensus 4 ~~~~~i~~~l~~~~--~~~~a~~i~k~l~-i----~k~~vNr~LY~L~~~~~v~ 50 (183)
T PHA02701 4 DCASLILTLLSSSG--DKLPAKRIAKELG-I----SKHEANRCLYRLLESDAVS 50 (183)
T ss_pred hHHHHHHHHHHhcC--CCCcHHHHHHHhC-c----cHHHHHHHHHHHhhcCcEe
Confidence 35678999999865 4699999999999 9 7766777665555555553
No 202
>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=71.25 E-value=20 Score=22.04 Aligned_cols=35 Identities=17% Similarity=0.255 Sum_probs=27.0
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
..|+..+. .+.|..|||+.++ + ....++|+.|.|.
T Consensus 41 ~~I~~ll~-----~G~S~~eIA~~Lg-I----SrsTIyRi~R~~n 75 (88)
T TIGR02531 41 LQVAKMLK-----QGKTYSDIEAETG-A----STATISRVKRCLN 75 (88)
T ss_pred HHHHHHHH-----CCCCHHHHHHHHC-c----CHHHHHHHHHhcc
Confidence 34455454 3579999999999 9 8999999888543
No 203
>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=71.04 E-value=4.8 Score=20.43 Aligned_cols=22 Identities=32% Similarity=0.442 Sum_probs=17.8
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+|..|+|+.++ + ++..+.+..+
T Consensus 1 ~s~~e~a~~lg-v----s~~tl~~~~~ 22 (49)
T cd04762 1 LTTKEAAELLG-V----SPSTLRRWVK 22 (49)
T ss_pred CCHHHHHHHHC-c----CHHHHHHHHH
Confidence 47899999999 9 8877776655
No 204
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=70.87 E-value=5.9 Score=29.93 Aligned_cols=35 Identities=34% Similarity=0.421 Sum_probs=32.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.++|=+|||+++| . ....+.|++......|+++=.
T Consensus 25 ~gltQ~eIA~~Lg-i----SR~~v~rlL~~Ar~~GiV~I~ 59 (321)
T COG2390 25 EGLTQSEIAERLG-I----SRATVSRLLAKAREEGIVKIS 59 (321)
T ss_pred cCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCeEEEE
Confidence 5899999999999 9 899999999999999998743
No 205
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=70.43 E-value=10 Score=19.65 Aligned_cols=24 Identities=25% Similarity=0.264 Sum_probs=18.6
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
++|..|||+.++ + .+..+++.++.
T Consensus 18 g~s~~eia~~l~-i----s~~tv~~~~~~ 41 (58)
T smart00421 18 GLTNKEIAERLG-I----SEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHC-C----CHHHHHHHHHH
Confidence 579999999999 9 67666655543
No 206
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=70.11 E-value=4.2 Score=29.33 Aligned_cols=42 Identities=19% Similarity=0.307 Sum_probs=30.9
Q ss_pred HHhChHHHHHhcCC-CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 30 INLGLFEIIAKAGP-GAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 30 v~LgIfd~l~~~g~-~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
.|..|++.+-++.. -..+|+.+||+.++ + .+..+.|+.|.|=
T Consensus 29 ~e~~Ia~yil~~~~~v~~~si~~lA~~~~-v----S~aTi~Rf~kkLG 71 (292)
T PRK11337 29 LESRVVEWLLKPGDLSEATALKDIAEALA-V----SEAMIVKVAKKLG 71 (292)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhC-C----ChHHHHHHHHHcC
Confidence 35677777765431 13489999999999 9 8888888887664
No 207
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=69.54 E-value=5.5 Score=27.03 Aligned_cols=26 Identities=31% Similarity=0.282 Sum_probs=22.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLL 75 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L 75 (89)
.++|.+|||+.+| + .+..++|-++..
T Consensus 150 ~Gls~~EIA~~lg-i----S~~tV~r~l~~a 175 (185)
T PF07638_consen 150 EGLSVEEIAERLG-I----SERTVRRRLRRA 175 (185)
T ss_pred CCCCHHHHHHHHC-c----CHHHHHHHHHHH
Confidence 4789999999999 9 898999888764
No 208
>smart00526 H15 Domain in histone families 1 and 5.
Probab=69.53 E-value=14 Score=20.88 Aligned_cols=50 Identities=20% Similarity=0.157 Sum_probs=33.1
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCc----chHHHHHHHHhccCceeee
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAP----TMLDRILGLLASYGIVECS 84 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~----~~l~RlLR~L~s~gi~~e~ 84 (89)
|.++|..-.+.++.|...|...+. ...+.++ .+|.+-|+.++..|.|..+
T Consensus 11 I~eAI~~l~er~GsS~~aI~kyi~-~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~ 64 (66)
T smart00526 11 ITEAISALKERKGSSLQAIKKYIE-ANYKVLPNNFRSLLKLALKKLVASGKLVQV 64 (66)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHH-HhCCCChHHHHHHHHHHHHHHHhcCceeec
Confidence 455555443346789999998877 5322222 3466778888999988765
No 209
>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=69.44 E-value=4.2 Score=21.76 Aligned_cols=24 Identities=29% Similarity=0.382 Sum_probs=18.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
..+|..|+|+.+| + ++..+.|+.+
T Consensus 8 ~gls~~~la~~~g-i----s~~~i~~~~~ 31 (55)
T PF01381_consen 8 KGLSQKELAEKLG-I----SRSTISRIEN 31 (55)
T ss_dssp TTS-HHHHHHHHT-S-----HHHHHHHHT
T ss_pred cCCCHHHHHHHhC-C----CcchhHHHhc
Confidence 5789999999999 9 7878877765
No 210
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=69.14 E-value=14 Score=25.63 Aligned_cols=47 Identities=15% Similarity=0.340 Sum_probs=37.4
Q ss_pred HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
+.-....|.+.|.+.|. ..+|++|||+..+ + ++..++|=|+.|-..|
T Consensus 14 r~~~~~~il~~l~~~~~-~~vs~~~L~~~~~-v----~~~tirrDl~~l~~~G 60 (213)
T PRK05472 14 RLPLYYRYLKELKEEGV-ERVSSKELAEALG-V----DSAQIRKDLSYFGEFG 60 (213)
T ss_pred HhHHHHHHHHHHHHcCC-cEEeHHHHHHHhC-c----CHHHHHHHHHHHHhcC
Confidence 45566778888887531 3899999999999 9 8889999888887666
No 211
>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=68.82 E-value=5.5 Score=21.22 Aligned_cols=25 Identities=32% Similarity=0.384 Sum_probs=19.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
.++|..|||+.+| . ....+.++.+-
T Consensus 19 ~~~t~~eIa~~lg-~----s~~~V~~~~~~ 43 (50)
T PF04545_consen 19 EGLTLEEIAERLG-I----SRSTVRRILKR 43 (50)
T ss_dssp ST-SHHHHHHHHT-S----CHHHHHHHHHH
T ss_pred CCCCHHHHHHHHC-C----cHHHHHHHHHH
Confidence 6899999999999 9 78777777653
No 212
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=68.58 E-value=11 Score=25.26 Aligned_cols=46 Identities=20% Similarity=0.258 Sum_probs=37.9
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCC-CCCCCCcchHHHHHHHHhccCceeee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPA-TKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~-~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-|.+.|.... .|.|+.+|..-+++ + ....+.+.|..|+..|-+.+-
T Consensus 5 ~Il~y~~~qN--RPys~~di~~nL~~~~----~K~~v~k~Ld~L~~~g~i~~K 51 (169)
T PF07106_consen 5 AILEYMKEQN--RPYSAQDIFDNLHNKV----GKTAVQKALDSLVEEGKIVEK 51 (169)
T ss_pred HHHHHHHHcC--CCCcHHHHHHHHHhhc----cHHHHHHHHHHHHhCCCeeee
Confidence 4678887764 99999999999974 5 567899999999999987653
No 213
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=67.84 E-value=10 Score=27.38 Aligned_cols=40 Identities=18% Similarity=0.120 Sum_probs=30.9
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
+.+.|.++- ..++|+++||+.++ . ++..+.|+++..+...
T Consensus 10 ~~~~i~~~~-~~~~~l~~lA~~~~-~----S~~~l~r~F~~~~g~s 49 (289)
T PRK15121 10 LLIWLEGHL-DQPLSLDNVAAKAG-Y----SKWHLQRMFKDVTGHA 49 (289)
T ss_pred HHHHHHhcc-cCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCcC
Confidence 445565543 26899999999999 9 9999999998776543
No 214
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=67.46 E-value=8.7 Score=28.59 Aligned_cols=42 Identities=19% Similarity=0.349 Sum_probs=34.4
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV 81 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~ 81 (89)
+.|..+|.... . +|+.+||+..+ + ....++|=++.|...|+=
T Consensus 11 ~~ii~~L~~~~--~-vta~~lA~~~~-V----S~RTi~RDi~~L~~~gvP 52 (311)
T COG2378 11 LQIIQILRAKE--T-VTAAELADEFE-V----SVRTIYRDIATLRAAGVP 52 (311)
T ss_pred HHHHHHHHhCc--c-chHHHHHHhcC-C----CHHHHHHHHHHHHHCCCC
Confidence 34555666542 4 99999999999 9 999999999999998874
No 215
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=67.09 E-value=7.1 Score=30.92 Aligned_cols=37 Identities=14% Similarity=0.246 Sum_probs=33.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
..+|++|||+.+. | .++..+++|+.|...|.+.=...
T Consensus 22 ~~~~l~~la~~l~-c----s~R~~~~~l~~~~~~gwl~w~~~ 58 (552)
T PRK13626 22 QETTLNELAELLN-C----SRRHMRTLLNTMQQRGWLTWQAE 58 (552)
T ss_pred ceeeHHHHHHHhc-C----ChhHHHHHHHHHHHCCCeeeecC
Confidence 6789999999999 9 99999999999999998875443
No 216
>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=66.70 E-value=12 Score=21.93 Aligned_cols=41 Identities=15% Similarity=0.221 Sum_probs=31.0
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV 81 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~ 81 (89)
.|+++|.+. +++|++||+..++ . +...+..-+--|+.-+=+
T Consensus 12 ~Vw~~L~~~---~~~s~~el~k~~~-l----~~~~~~~AiGWLarE~KI 52 (65)
T PF10771_consen 12 KVWQLLNEN---GEWSVSELKKATG-L----SDKEVYLAIGWLARENKI 52 (65)
T ss_dssp HHHHHHCCS---SSEEHHHHHHHCT------SCHHHHHHHHHHHCTTSE
T ss_pred HHHHHHhhC---CCcCHHHHHHHhC-c----CHHHHHHHHHHHhccCce
Confidence 367888763 7999999999999 8 777777777777765433
No 217
>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=66.26 E-value=7.2 Score=20.59 Aligned_cols=22 Identities=18% Similarity=0.169 Sum_probs=18.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRI 71 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~Rl 71 (89)
..+|+.+||++++ + ....++|-
T Consensus 15 ~~~s~~~Ia~~~g-v----s~~~~y~~ 36 (47)
T PF00440_consen 15 EAVSIRDIARRAG-V----SKGSFYRY 36 (47)
T ss_dssp TTSSHHHHHHHHT-S----CHHHHHHH
T ss_pred HhCCHHHHHHHHc-c----chhhHHHH
Confidence 6899999999999 9 77777653
No 218
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=66.05 E-value=43 Score=23.52 Aligned_cols=65 Identities=18% Similarity=0.164 Sum_probs=46.7
Q ss_pred HHHhHHHHHHHHHHHHhCh-------HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 16 VTMGSVLHMTMKAVINLGL-------FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 16 l~~~~~~~~aL~~av~LgI-------fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
..|+.|.-.|+.+|.+.++ ..+|...+ .|.++.+|+..++ .. |.-.+.=-+|-|-.-|+++.+++
T Consensus 63 ~Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrd--R~K~laDic~~ln-~e---Dth~itYslrKL~k~gLit~t~~ 134 (199)
T COG5631 63 EAFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRD--RPKSLADICQMLN-RE---DTHNITYSLRKLLKGGLITRTGS 134 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcC--chhhHHHHHHHhc-cc---cchhHHHHHHHHHhccceecCCC
Confidence 4667787777777765543 22344334 8999999999999 62 55567777899999999987654
No 219
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=65.67 E-value=10 Score=26.17 Aligned_cols=39 Identities=8% Similarity=0.074 Sum_probs=28.6
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcch----HHHHHHHHh
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTM----LDRILGLLA 76 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~----l~RlLR~L~ 76 (89)
+--|..|+..+++ +.|.+|||++++ . .+.. +.|+++.|-
T Consensus 139 T~RE~eVL~lla~-----G~snkeIA~~L~-i----S~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 139 SRTESSMLRMWMA-----GQGTIQISDQMN-I----KAKTVSSHKGNIKRKIK 181 (207)
T ss_pred CHHHHHHHHHHHc-----CCCHHHHHHHcC-C----CHHHHHHHHHHHHHHhC
Confidence 3456677777774 689999999999 9 5554 566776654
No 220
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=65.55 E-value=12 Score=26.58 Aligned_cols=40 Identities=10% Similarity=0.173 Sum_probs=31.4
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
+.+.|..+- .+++|+++||+.++ . .+..+.|+.|--+...
T Consensus 188 ~~~~i~~~~-~~~isl~~lA~~~~-l----S~~~l~r~Fk~~~G~t 227 (290)
T PRK10572 188 ACQYISDHL-ASEFDIESVAQHVC-L----SPSRLAHLFRQQLGIS 227 (290)
T ss_pred HHHHHHhcc-cCCCCHHHHHHHHC-C----CHHHHHHHHHHHHCcC
Confidence 455665553 37999999999999 9 8999999998765544
No 221
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=65.39 E-value=3.1 Score=31.15 Aligned_cols=47 Identities=19% Similarity=0.325 Sum_probs=35.4
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
.++|.++| +.++...+|-.+++ . +...+.|+|+-|-+.+++..+++.
T Consensus 90 y~lIe~sg-~~GIW~k~ik~ksn-L----p~~~v~K~LkSLEsKkLIKsVKsv 136 (297)
T KOG3233|consen 90 YSLIEESG-NEGIWSKEIKRKSN-L----PQTVVNKILKSLESKKLIKSVKSV 136 (297)
T ss_pred HHHHHHcC-CCceeeehhhhccC-C----CHHHHHHHHHHHHHHHHHHHHHhh
Confidence 33444444 36677777777777 7 778899999999999998887765
No 222
>PF13551 HTH_29: Winged helix-turn helix
Probab=65.34 E-value=12 Score=22.60 Aligned_cols=27 Identities=26% Similarity=0.233 Sum_probs=25.2
Q ss_pred CHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 48 SASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 48 t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
|..++|..+| + ++..++|.++.....|
T Consensus 14 ~~~~ia~~lg-~----s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLG-I----SRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHC-c----CHHHHHHHHHHHHccc
Confidence 7999999999 9 9999999999988877
No 223
>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=65.31 E-value=8.6 Score=27.69 Aligned_cols=33 Identities=21% Similarity=0.457 Sum_probs=26.6
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
...|+...+ ...|+..||+.-+ + .|..++|||+
T Consensus 19 ir~L~~~~p-~~~t~~~Lae~F~-v----spe~irrILk 51 (225)
T PF06413_consen 19 IRYLHKEDP-EEWTVERLAESFK-V----SPEAIRRILK 51 (225)
T ss_pred HHHHHHhCc-cccCHHHHHhhCC-C----CHHHHHHHHh
Confidence 345666543 4579999999999 9 9999999997
No 224
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=64.82 E-value=5.6 Score=23.83 Aligned_cols=35 Identities=31% Similarity=0.445 Sum_probs=23.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV 81 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~ 81 (89)
|.+|..||...++ - ...++..+..|+..|...||=
T Consensus 20 G~lT~~eI~~~L~-~-~~~~~e~id~i~~~L~~~gI~ 54 (82)
T PF03979_consen 20 GYLTYDEINDALP-E-DDLDPEQIDEIYDTLEDEGIE 54 (82)
T ss_dssp SS-BHHHHHHH-S---S---HHHHHHHHHHHHTT---
T ss_pred CcCCHHHHHHHcC-c-cCCCHHHHHHHHHHHHHCCCE
Confidence 6899999999999 3 123788999999999999873
No 225
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=64.50 E-value=13 Score=25.80 Aligned_cols=38 Identities=18% Similarity=0.130 Sum_probs=30.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
|..|.+||.+++. ..- .+..+..+++.|...|++.+..
T Consensus 41 G~rt~~eI~~~l~-~~~--p~~~v~~~L~~L~~~G~l~~~~ 78 (193)
T TIGR03882 41 GRRTLDEIIAALA-GRF--PAEEVLYALDRLERRGYLVEDA 78 (193)
T ss_pred CCCCHHHHHHHhh-ccC--CHHHHHHHHHHHHHCCCEeccC
Confidence 7899999999987 411 3556999999999999998753
No 226
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=64.44 E-value=5.9 Score=22.83 Aligned_cols=17 Identities=12% Similarity=0.362 Sum_probs=11.0
Q ss_pred CcchHHHHHHHHhccCc
Q 045477 64 APTMLDRILGLLASYGI 80 (89)
Q Consensus 64 d~~~l~RlLR~L~s~gi 80 (89)
.+..-.|+.+.+..+|+
T Consensus 28 ~~~t~~~i~~~~~~~gy 44 (70)
T smart00354 28 SEETREKVLAAMEELGY 44 (70)
T ss_pred CHHHHHHHHHHHHHhCC
Confidence 44566677777776665
No 227
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=64.04 E-value=9.7 Score=30.34 Aligned_cols=45 Identities=20% Similarity=0.327 Sum_probs=38.0
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
++..+.+. +++|..+|+..++ . +...+.|.+..|...|++...++
T Consensus 407 il~~~~en---~~~T~~~L~~~l~-i----s~~~i~r~i~~Lv~~g~~~~~g~ 451 (467)
T COG2865 407 ILELIKEN---GKVTARELREILG-I----SSETIRRRIANLVKRGLLKQLGS 451 (467)
T ss_pred HHHHHhhc---cccCHHHHHHHhC-c----chhhHHHHHHHHhcccHHHHhCc
Confidence 45555553 6999999999999 9 89999999999999999987654
No 228
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=63.86 E-value=22 Score=24.78 Aligned_cols=46 Identities=20% Similarity=0.232 Sum_probs=37.6
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
.|.+.-+|+=+ +|+|-.||-+.-| + ..+++++.|..+|++.+.+..
T Consensus 94 alEtLAiIAY~---QPiTR~eI~~iRG-v-------~~~~~i~~L~e~glI~~~g~~ 139 (184)
T COG1386 94 ALETLAIIAYK---QPVTRSEIEEIRG-V-------AVSQVISTLLERGLIREVGRR 139 (184)
T ss_pred HHHHHHHHHHc---CCccHHHHHHHhC-c-------cHHHHHHHHHHCCCeEecCCC
Confidence 34566677753 7999999999989 8 556799999999999998754
No 229
>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=63.71 E-value=20 Score=21.74 Aligned_cols=52 Identities=12% Similarity=0.218 Sum_probs=35.2
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHH-HHHHhccCceeeecc
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRI-LGLLASYGIVECSVD 86 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~Rl-LR~L~s~gi~~e~~~ 86 (89)
.|..+...|.+.=.+||..++-||..++ - ++..+.-+ =-+|...|++..+.+
T Consensus 9 ~D~~yL~~l~~~f~ggPvGl~tlA~~l~-e----d~~Tie~v~EPyLiq~G~I~RT~r 61 (76)
T PF05491_consen 9 LDRRYLKTLIENFKGGPVGLDTLAAALG-E----DKETIEDVIEPYLIQIGFIQRTPR 61 (76)
T ss_dssp HHHHHHHHHHHCSTTS-B-HHHHHHHTT-S-----HHHHHHTTHHHHHHTTSEEEETT
T ss_pred HHHHHHHHHHHHcCCCCeeHHHHHHHHC-C----CHhHHHHHhhHHHHHhhhHhhCcc
Confidence 3556667777631249999999999999 8 77766644 467888888887743
No 230
>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=62.94 E-value=15 Score=23.32 Aligned_cols=25 Identities=24% Similarity=0.324 Sum_probs=19.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
..+|..|||+.++ + .+..+.|.|.-
T Consensus 70 pd~tl~Ela~~l~-V----s~~ti~~~Lkr 94 (119)
T PF01710_consen 70 PDATLRELAERLG-V----SPSTIWRALKR 94 (119)
T ss_pred CCcCHHHHHHHcC-C----CHHHHHHHHHH
Confidence 4789999999999 9 77777766543
No 231
>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=62.90 E-value=23 Score=20.91 Aligned_cols=39 Identities=18% Similarity=0.168 Sum_probs=26.2
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
.|++.+.+-+.|.-.|..+||+.++ . |..+..+.+.|+.
T Consensus 4 ~V~~~v~~IP~G~v~TYg~iA~~~g-~--p~~~R~Vg~al~~ 42 (79)
T cd06445 4 RVWEALRQIPYGEVTTYGQIAKLAG-T--PKAARAVGSALAR 42 (79)
T ss_pred HHHHHHhcCCCCCcCcHHHHHHHHC-C--CCcHHHHHHHHHh
Confidence 4667776555558899999999999 4 2234455555544
No 232
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=62.54 E-value=8.6 Score=32.28 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=33.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
...|.+|+++.++ . .+..|+|-|-....+|++.+.+
T Consensus 615 ~twt~eelse~l~-i----p~~~lrrrL~fWi~~GvL~e~~ 650 (765)
T KOG2165|consen 615 NTWTLEELSESLG-I----PVPALRRRLSFWIQKGVLREEP 650 (765)
T ss_pred ccccHHHHHHHhC-C----CHHHHHHHHHHHHHcCeeecCC
Confidence 5799999999999 9 8899999999999999999876
No 233
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=62.19 E-value=11 Score=28.11 Aligned_cols=34 Identities=26% Similarity=0.316 Sum_probs=31.0
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
..+|=+|||+++| + ....+.|+|..--..|+++-
T Consensus 28 ~g~tQ~eIA~~lg-i----SR~~VsRlL~~Ar~~GiV~I 61 (318)
T PRK15418 28 DGLTQSEIGERLG-L----TRLKVSRLLEKGRQSGIIRV 61 (318)
T ss_pred cCCCHHHHHHHhC-C----CHHHHHHHHHHHHHcCcEEE
Confidence 5799999999999 9 88899999999999999873
No 234
>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=62.11 E-value=3.5 Score=22.58 Aligned_cols=29 Identities=31% Similarity=0.458 Sum_probs=18.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc-cCce
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLAS-YGIV 81 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s-~gi~ 81 (89)
.++++.|||..++ . ++ ..|++.|-. .|+.
T Consensus 2 ~~i~V~elAk~l~-v----~~---~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 2 EKIRVSELAKELG-V----PS---KEIIKKLFKELGIM 31 (54)
T ss_dssp -EE-TTHHHHHHS-S----SH---HHHHHHH-HHHTS-
T ss_pred CceEHHHHHHHHC-c----CH---HHHHHHHHHhCCcC
Confidence 4789999999999 8 44 456666633 6766
No 235
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=62.02 E-value=7.1 Score=24.66 Aligned_cols=43 Identities=12% Similarity=0.220 Sum_probs=34.4
Q ss_pred hHHHHH-hcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 34 LFEIIA-KAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 34 Ifd~l~-~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
|||+|. ..+ +++...-|.-.++ . +-....+++..|+..|++..
T Consensus 20 i~dIL~~~~~--~~~~~Tri~y~aN-l----ny~~~~~yi~~L~~~Gli~~ 63 (95)
T COG3432 20 IFDILKAISE--GGIGITRIIYGAN-L----NYKRAQKYIEMLVEKGLIIK 63 (95)
T ss_pred HHHHHHHhcC--CCCCceeeeeecC-c----CHHHHHHHHHHHHhCCCEEe
Confidence 577777 333 6788888888888 8 88899999999999995543
No 236
>PRK04217 hypothetical protein; Provisional
Probab=61.82 E-value=14 Score=23.80 Aligned_cols=32 Identities=13% Similarity=0.167 Sum_probs=23.5
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.++..+.. ..+|.+|||+.++ + ....+++.++
T Consensus 49 eai~l~~~----eGlS~~EIAk~LG-I----S~sTV~r~L~ 80 (110)
T PRK04217 49 EALRLVDY----EGLTQEEAGKRMG-V----SRGTVWRALT 80 (110)
T ss_pred HHHHHHHH----cCCCHHHHHHHHC-c----CHHHHHHHHH
Confidence 44544443 4689999999999 9 7777776664
No 237
>PHA00542 putative Cro-like protein
Probab=61.62 E-value=13 Score=22.17 Aligned_cols=24 Identities=25% Similarity=0.245 Sum_probs=17.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.++|..|+|+.+| + ....+.|+.+
T Consensus 30 ~glTq~elA~~lg-I----s~~tIsr~e~ 53 (82)
T PHA00542 30 AGWSQEQIADATD-V----SQPTICRIYS 53 (82)
T ss_pred CCCCHHHHHHHHC-c----CHHHHHHHHc
Confidence 4689999999999 8 5656665553
No 238
>PF08721 Tn7_Tnp_TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The C-terminal domain of TnsA binds DNA. ; PDB: 1F1Z_B 1T0F_B.
Probab=61.44 E-value=25 Score=19.98 Aligned_cols=41 Identities=12% Similarity=0.223 Sum_probs=31.5
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhC----CCCCCCCCcchHHHHHHHHhccCcee
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQL----PATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~----~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
+...+.+. ++.|+.++.+.+ + . ++...-.++|+|.+.+.+.
T Consensus 32 i~~~l~~~---~~~tl~~l~~~~d~~~~-l----~~g~~L~~l~~LiA~k~i~ 76 (79)
T PF08721_consen 32 ILARLRKN---PTMTLRDLCKELDKDYE-L----EPGTALPLLRHLIATKRIK 76 (79)
T ss_dssp HHHHHHHT---TTSBHHHHHHHHHHHCT-------TTHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHc---CCCCHHHHHHHHHHhcC-C----CcCChHHHHHHHHhCChhc
Confidence 56677765 469999999887 5 6 7777888999999988775
No 239
>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=61.14 E-value=21 Score=19.67 Aligned_cols=37 Identities=27% Similarity=0.369 Sum_probs=30.9
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
++.+|..+.+.| |...-|+.++ . .+..+.|-++.|-.
T Consensus 3 ~l~~f~~v~~~g-----s~~~AA~~l~-i----s~~~vs~~i~~LE~ 39 (60)
T PF00126_consen 3 QLRYFLAVAETG-----SISAAAEELG-I----SQSAVSRQIKQLEE 39 (60)
T ss_dssp HHHHHHHHHHHS-----SHHHHHHHCT-S----SHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhC-----CHHHHHHHhh-c----cchHHHHHHHHHHH
Confidence 467888888865 7899999999 9 88899998888764
No 240
>PF13814 Replic_Relax: Replication-relaxation
Probab=61.12 E-value=19 Score=23.98 Aligned_cols=44 Identities=23% Similarity=0.251 Sum_probs=33.2
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 37 IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 37 ~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|.+. +.+|..+|+.... .+ ...+..++|.|+-|...|++....
T Consensus 3 ~L~~~---r~lt~~Qi~~l~~-~~-~~~~~~~~rrL~~L~~~glv~~~~ 46 (191)
T PF13814_consen 3 LLARH---RFLTTDQIARLLF-PS-SKSERTARRRLKRLRELGLVDRFR 46 (191)
T ss_pred hHHHh---cCcCHHHHHHHHc-CC-CcchHHHHHHHHHHhhCCcEEeec
Confidence 45555 5899999999999 61 111237999999999999997553
No 241
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=61.00 E-value=6.4 Score=22.15 Aligned_cols=37 Identities=22% Similarity=0.340 Sum_probs=20.3
Q ss_pred CCCCHHHHHhhCCCCCCCCCcc----hHHHHHHHHhccCcee
Q 045477 45 AKLSASEIAAQLPATKNKDAPT----MLDRILGLLASYGIVE 82 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~----~l~RlLR~L~s~gi~~ 82 (89)
++.|+.||++.+. ..-+.++. -+..++..|...|+++
T Consensus 28 g~~t~~ei~~~l~-~~y~~~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 28 GPRTVEEIVDALA-EEYDVDPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp SSS-HHHHHHHHH-HHTT--HHHHHHHHHHHHHHHHHTT---
T ss_pred CCCCHHHHHHHHH-HHcCCCHHHHHHHHHHHHHHHHHCcCcC
Confidence 6788888877654 21111443 3677888888888763
No 242
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=60.96 E-value=13 Score=28.32 Aligned_cols=38 Identities=18% Similarity=0.201 Sum_probs=28.7
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
+.+.+..+- +.|+|++|||...+ . .+..+.|+.|.-..
T Consensus 225 ~i~~me~nl-e~plsl~~LA~~~~-~----S~R~leRlF~~~lG 262 (328)
T COG4977 225 AIELMEANL-EEPLSLEELADRAG-L----SRRQLERLFRAELG 262 (328)
T ss_pred HHHHHHHhh-cCCcCHHHHHHHhC-C----CHHHHHHHHHHHhC
Confidence 344454432 37999999999999 9 89999999876543
No 243
>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=60.94 E-value=12 Score=20.48 Aligned_cols=31 Identities=23% Similarity=0.375 Sum_probs=22.7
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHH
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~R 70 (89)
-|..|+..+.. +.|..|||..++ + .+..++.
T Consensus 7 ~E~~vl~~l~~-----G~~~~eIA~~l~-i----s~~tV~~ 37 (58)
T PF00196_consen 7 RELEVLRLLAQ-----GMSNKEIAEELG-I----SEKTVKS 37 (58)
T ss_dssp HHHHHHHHHHT-----TS-HHHHHHHHT-S----HHHHHHH
T ss_pred HHHHHHHHHHh-----cCCcchhHHhcC-c----chhhHHH
Confidence 46667777774 689999999999 9 7766543
No 244
>PRK15482 transcriptional regulator MurR; Provisional
Probab=60.80 E-value=8 Score=27.83 Aligned_cols=42 Identities=12% Similarity=0.109 Sum_probs=30.5
Q ss_pred HHhChHHHHHhcCC-CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 30 INLGLFEIIAKAGP-GAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 30 v~LgIfd~l~~~g~-~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
.|-.|.+.|-++.. -.-+|+.|||++++ + .+..+.|+-|.|=
T Consensus 17 ~e~~Ia~yIl~n~~~v~~~si~elA~~~~-v----S~aTv~Rf~kkLG 59 (285)
T PRK15482 17 NEQKIADFLRANVSELKSVSSRKMAKQLG-I----SQSSIVKFAQKLG 59 (285)
T ss_pred HHHHHHHHHHhCHHHHHhcCHHHHHHHhC-C----CHHHHHHHHHHhC
Confidence 35567777665431 13589999999999 9 8888888877654
No 245
>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=60.41 E-value=14 Score=25.27 Aligned_cols=27 Identities=15% Similarity=0.352 Sum_probs=23.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
.+.|.++||+.+| . ++..+.|.|+++.
T Consensus 119 ~g~s~~~iA~~lg-~----s~~~V~r~l~l~~ 145 (187)
T TIGR00180 119 FSMTQEDLAKKIG-K----SRAHITNLLRLLK 145 (187)
T ss_pred hCCCHHHHHHHHC-c----CHHHHHHHHHHHc
Confidence 3679999999999 9 8999999998764
No 246
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=60.34 E-value=17 Score=29.91 Aligned_cols=50 Identities=24% Similarity=0.332 Sum_probs=38.3
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.|.+.|.+.. +.|++..+|++.++ .....+...+.++|+.|...|.+...
T Consensus 6 ~il~~l~~~~-~~~~~~~~l~~~l~-~~~~~~~~~l~~~l~~l~~~g~l~~~ 55 (709)
T TIGR02063 6 LILEFLKSKK-GKPISLKELAKAFH-LKGADEKKALRKRLRALEDDGLVKKN 55 (709)
T ss_pred HHHHHHHhCC-CCCCCHHHHHHHhC-CCChHHHHHHHHHHHHHHHCCCEEEc
Confidence 3666776532 38999999999999 83323556799999999999998754
No 247
>PRK13503 transcriptional activator RhaS; Provisional
Probab=60.30 E-value=18 Score=25.42 Aligned_cols=38 Identities=16% Similarity=0.152 Sum_probs=29.4
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
+.+.|.++- ..++|+++||+.++ . ++..+.|+.+.-..
T Consensus 176 ~~~~I~~~~-~~~~tl~~lA~~~~-l----S~~~l~r~Fk~~~G 213 (278)
T PRK13503 176 LLAWLEDHF-AEEVNWEALADQFS-L----SLRTLHRQLKQQTG 213 (278)
T ss_pred HHHHHHHhh-cCCCCHHHHHHHHC-C----CHHHHHHHHHHHhC
Confidence 555666553 26999999999999 9 99999998865443
No 248
>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=59.69 E-value=22 Score=18.44 Aligned_cols=23 Identities=22% Similarity=0.157 Sum_probs=17.7
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
++|..|||+.++ . .+..+++.++
T Consensus 15 ~~s~~eia~~l~-~----s~~tv~~~~~ 37 (57)
T cd06170 15 GKTNKEIADILG-I----SEKTVKTHLR 37 (57)
T ss_pred CCCHHHHHHHHC-C----CHHHHHHHHH
Confidence 589999999999 8 6666555544
No 249
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=59.28 E-value=34 Score=19.95 Aligned_cols=51 Identities=12% Similarity=0.179 Sum_probs=38.0
Q ss_pred HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
..+....+.|+...... ..++.++|++.++ . +..-+.+++.-+...|.+.-
T Consensus 6 l~~~~~~~~l~~l~~~y---~~i~~~~i~~~~~-l----~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00088 6 LQRKIRLTNLLQLSEPY---SSISLSDLAKLLG-L----SVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHHHHHHHHHHHHhHHh---ceeeHHHHHHHhC-c----CHHHHHHHHHHHHHCCCeEE
Confidence 34445555666666543 6899999999999 8 66678999988888887753
No 250
>smart00753 PAM PCI/PINT associated module.
Probab=59.28 E-value=34 Score=19.95 Aligned_cols=51 Identities=12% Similarity=0.179 Sum_probs=38.0
Q ss_pred HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
..+....+.|+...... ..++.++|++.++ . +..-+.+++.-+...|.+.-
T Consensus 6 l~~~~~~~~l~~l~~~y---~~i~~~~i~~~~~-l----~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00753 6 LQRKIRLTNLLQLSEPY---SSISLSDLAKLLG-L----SVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHHHHHHHHHHHHhHHh---ceeeHHHHHHHhC-c----CHHHHHHHHHHHHHCCCeEE
Confidence 34445555666666543 6899999999999 8 66678999988888887753
No 251
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=59.18 E-value=39 Score=20.68 Aligned_cols=47 Identities=15% Similarity=0.156 Sum_probs=33.6
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCC-C--CCCCCcchHHHHHHHHhccCceeee
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPA-T--KNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~-~--~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|.-+|.+ +|++--||.+.+.. . .-+.++..++++|+-|...|++...
T Consensus 9 iL~~L~~----~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~ 58 (100)
T TIGR03433 9 ILKTLSL----GPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAE 58 (100)
T ss_pred HHHHHhc----CCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEE
Confidence 4445554 68898888888641 0 0122677899999999999999873
No 252
>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=58.98 E-value=31 Score=20.71 Aligned_cols=40 Identities=15% Similarity=0.161 Sum_probs=28.1
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
..|++.+.+-+.|.-.|-.+||+.+| . |..+..+.+.|+.
T Consensus 5 ~~V~~~l~~IP~G~v~TYg~iA~~~g-~--p~~~RaVg~al~~ 44 (80)
T TIGR00589 5 QRVWQALRTIPYGETKSYGQLAARIG-N--PKAVRAVGGANGR 44 (80)
T ss_pred HHHHHHHhCCCCCCcCCHHHHHHHhC-C--CChHHHHHHHHHh
Confidence 46778887665558899999999999 3 2244556666544
No 253
>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=58.79 E-value=18 Score=25.50 Aligned_cols=40 Identities=18% Similarity=0.164 Sum_probs=30.9
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
+-+.|.++- ..++|++++|+.++ . .+..|.|+.+..+.+.
T Consensus 191 ~~~~I~~~~-~~~~sl~~lA~~~~-~----S~~~l~r~Fk~~~G~t 230 (287)
T TIGR02297 191 FNFLIEENY-KQHLRLPEYADRLG-I----SESRLNDICRRFSALS 230 (287)
T ss_pred HHHHHHHhh-ccCCCHHHHHHHHC-C----CHHHHHHHHHHHhCCC
Confidence 334565543 26899999999999 9 9999999998766544
No 254
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=58.34 E-value=7.9 Score=23.67 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=22.3
Q ss_pred HHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477 51 EIAAQLPATKNKDAPTMLDRILGLLASYGI 80 (89)
Q Consensus 51 eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi 80 (89)
+.++..- ++||.=...|++||-.|+.+||
T Consensus 57 ~av~~FE-~~HP~l~~~lr~i~~sLa~MGI 85 (85)
T PF14357_consen 57 EAVERFE-ASHPKLAGILRNIMDSLANMGI 85 (85)
T ss_pred HHHHHHH-HhCCcHHHHHHHHHHHHHHCCC
Confidence 3444444 6688777889999999999997
No 255
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=58.29 E-value=22 Score=26.64 Aligned_cols=35 Identities=26% Similarity=0.355 Sum_probs=32.7
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+++-.+|||..++ - ||..++-.|-.|-+.|+++-.
T Consensus 24 r~IKgeeIA~~l~-r----npGTVRNqmq~LkaLgLVegv 58 (294)
T COG2524 24 RPIKGEEIAEVLN-R----NPGTVRNQMQSLKALGLVEGV 58 (294)
T ss_pred CCcchHHHHHHHc-c----CcchHHHHHHHHHhcCccccc
Confidence 7999999999999 9 999999999999999998754
No 256
>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=58.27 E-value=11 Score=19.82 Aligned_cols=23 Identities=9% Similarity=0.138 Sum_probs=17.3
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
..+|..++|..++ + .+..+.++.
T Consensus 14 ~gltq~~lA~~~g-v----s~~~vs~~e 36 (58)
T TIGR03070 14 LGLTQADLADLAG-V----GLRFIRDVE 36 (58)
T ss_pred cCCCHHHHHHHhC-C----CHHHHHHHH
Confidence 4688899999998 8 666666554
No 257
>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=58.23 E-value=17 Score=23.57 Aligned_cols=33 Identities=33% Similarity=0.386 Sum_probs=20.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
.|.|+.|||+.++ . ....++=++--|...|.+.
T Consensus 54 ~~~SVAEiAA~L~-l----PlgVvrVLvsDL~~~G~v~ 86 (114)
T PF05331_consen 54 RPLSVAEIAARLG-L----PLGVVRVLVSDLADAGLVR 86 (114)
T ss_pred CCccHHHHHHhhC-C----CchhhhhhHHHHHhCCCEE
Confidence 4778888888877 5 3333444445566666655
No 258
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=58.19 E-value=6.4 Score=28.65 Aligned_cols=45 Identities=22% Similarity=0.178 Sum_probs=32.8
Q ss_pred HHhChHHHHHhcCC-CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 30 INLGLFEIIAKAGP-GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 30 v~LgIfd~l~~~g~-~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
.|.+|++.|-++++ -.-+|+.|||+.++ + .+..+.|+-|.|=-.|
T Consensus 19 ~er~iA~yil~~~~~~~~~si~elA~~a~-V----S~aTv~Rf~~kLGf~G 64 (281)
T COG1737 19 SERKIADYILANPDEVALLSIAELAERAG-V----SPATVVRFARKLGFEG 64 (281)
T ss_pred HHHHHHHHHHhCHHHHHHHHHHHHHHHhC-C----CHHHHHHHHHHcCCCC
Confidence 45667777765431 13479999999999 9 8888888888775444
No 259
>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=58.04 E-value=12 Score=19.97 Aligned_cols=23 Identities=30% Similarity=0.329 Sum_probs=14.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
.++|..|||+.+| . .+..+.+.+
T Consensus 25 ~g~s~~eIa~~l~-~----s~~~v~~~l 47 (54)
T PF08281_consen 25 QGMSYAEIAEILG-I----SESTVKRRL 47 (54)
T ss_dssp S---HHHHHHHCT-S-----HHHHHHHH
T ss_pred HCcCHHHHHHHHC-c----CHHHHHHHH
Confidence 5789999999999 9 676655444
No 260
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=57.84 E-value=14 Score=21.70 Aligned_cols=50 Identities=22% Similarity=0.111 Sum_probs=34.1
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCC--CCc----chHHHHHHHHhccCceeeec
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNK--DAP----TMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~--~d~----~~l~RlLR~L~s~gi~~e~~ 85 (89)
.++|.+-++..+.|...|...+. ...+ .++ ..|.+-|+.++..|.|..+.
T Consensus 10 ~eAI~~l~er~GsS~~aI~kyI~-~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 10 LEAIKALKERKGSSLQAIKKYIK-AKYKVDLNPANFKSRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHHCCSSSSEEHHHHHHHHH-HHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECS
T ss_pred HHHHHHcCCCCCCCHHHHHHHHH-HhcCcCCChHHHHHHHHHHHHHHHHCCcEEeec
Confidence 44454433336789999888766 4332 122 46889999999999998775
No 261
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=57.42 E-value=15 Score=22.14 Aligned_cols=31 Identities=23% Similarity=0.304 Sum_probs=23.6
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+|..|++..++ + ++. .++.|+..|++.....
T Consensus 1 is~~e~~~~~~-i----~~~----~l~~lve~Gli~p~~~ 31 (84)
T PF13591_consen 1 ISLEEFCEACG-I----EPE----FLRELVEEGLIEPEGE 31 (84)
T ss_pred CCHHHHHHHHC-c----CHH----HHHHHHHCCCeeecCC
Confidence 47889999999 8 776 5666778888876543
No 262
>PRK15340 transcriptional regulator InvF; Provisional
Probab=57.11 E-value=41 Score=24.08 Aligned_cols=42 Identities=7% Similarity=-0.043 Sum_probs=33.0
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGI 80 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi 80 (89)
+|...|-++. ..+.|+++||+.+| . .+..+.|+.+.....+.
T Consensus 113 ~l~~~Ll~~~-~~~~sleeLA~~~g-v----S~r~f~RlFk~~~G~tp 154 (216)
T PRK15340 113 WLVGYLLAQS-TSGNTMRMLGEDYG-V----SYTHFRRLCSRALGGKA 154 (216)
T ss_pred HHHHHHHhCc-cCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCcCH
Confidence 5566665543 37889999999999 9 99999999988776553
No 263
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=56.86 E-value=25 Score=20.36 Aligned_cols=49 Identities=20% Similarity=0.278 Sum_probs=36.7
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.+-.|.+.|.+.| +.+.+.-+++..++ . ...-+.|+|-.|-..|.+...
T Consensus 5 ~ee~Il~~L~~~g-~~~a~~ia~~~~L~-~----~kk~VN~~LY~L~k~g~v~k~ 53 (66)
T PF02295_consen 5 LEEKILDFLKELG-GSTATAIAKALGLS-V----PKKEVNRVLYRLEKQGKVCKE 53 (66)
T ss_dssp HHHHHHHHHHHHT-SSEEEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhcC-CccHHHHHHHhCcc-h----hHHHHHHHHHHHHHCCCEeeC
Confidence 4567889998876 35666666776776 5 567899999999999988754
No 264
>PRK13558 bacterio-opsin activator; Provisional
Probab=56.85 E-value=10 Score=30.20 Aligned_cols=51 Identities=14% Similarity=0.109 Sum_probs=35.6
Q ss_pred hHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 19 GSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 19 ~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
-.-+--+|++|.+.|-||.= ...|.+|||+.++ +++|.=...|+|-.|-|.
T Consensus 609 t~~q~e~l~~a~~~gyf~~p------r~~~~~e~a~~l~-is~~t~~~~lr~a~~~l~ 659 (665)
T PRK13558 609 TDRQLTALQKAYVSGYFEWP------RRVEGEELAESMG-ISRSTFHQHLRAAERKLV 659 (665)
T ss_pred CHHHHHHHHHHHHcCCCCCC------ccCCHHHHHHHhC-CCHHHHHHHHHHHHHHHH
Confidence 35567799999999999742 5689999999999 943333334444444443
No 265
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=56.55 E-value=11 Score=22.78 Aligned_cols=25 Identities=28% Similarity=0.348 Sum_probs=18.0
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCC
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPAT 59 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~ 59 (89)
+...++.++++ ..++..||++.+| .
T Consensus 3 i~~~l~~~l~~----r~~~~~eLa~~ig-i 27 (73)
T COG3655 3 IAVRLDVMLAD----RKISLKELAEAIG-I 27 (73)
T ss_pred chHhHHHHHHH----HhhhHHHHHHHHc-c
Confidence 34456667776 5678888888888 7
No 266
>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=56.52 E-value=12 Score=19.25 Aligned_cols=27 Identities=19% Similarity=0.348 Sum_probs=20.6
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
+|+.|+|+.+| + .+. -+|.....|++.
T Consensus 1 ~~~~e~a~~~g-v----~~~----tlr~~~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTG-V----SPS----TLRYYERIGLLS 27 (49)
T ss_pred CcHHHHHHHHC-c----CHH----HHHHHHHCCCCC
Confidence 57899999999 8 665 455667778776
No 267
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=56.27 E-value=12 Score=26.31 Aligned_cols=31 Identities=19% Similarity=0.311 Sum_probs=21.7
Q ss_pred CCCCHHHHHhhCCCCCCCC---------Ccc--hHHHHHHHHh
Q 045477 45 AKLSASEIAAQLPATKNKD---------APT--MLDRILGLLA 76 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~---------d~~--~l~RlLR~L~ 76 (89)
=++|-+|||..+| +++|- ||. .+.|++|+|.
T Consensus 17 LGitQ~dLA~~aG-VSQ~~IArlE~G~vdPrlSt~k~Il~aL~ 58 (187)
T COG3620 17 LGITQKDLARRAG-VSQPYIARLEAGKVDPRLSTVKRILEALE 58 (187)
T ss_pred cCCCHHHHHHHcC-ccHHHHHHHhcCCCCccHHHHHHHHHHHH
Confidence 4577778887777 65442 554 3889999986
No 268
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=56.27 E-value=21 Score=26.08 Aligned_cols=39 Identities=13% Similarity=0.181 Sum_probs=30.1
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
.+.+.|.++- ..++|+++||+.++ . ++..+.|+++.-+.
T Consensus 195 ~~~~~i~~~~-~~~~tl~~lA~~~~-~----S~~~l~r~Fk~~~G 233 (302)
T PRK10371 195 QMLGFIAENY-DQALTINDVAEHVK-L----NANYAMGIFQRVMQ 233 (302)
T ss_pred HHHHHHHHhh-cCCCCHHHHHHHHC-c----CHHHHHHHHHHHhC
Confidence 4555666543 26899999999999 9 99999999886543
No 269
>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=55.94 E-value=25 Score=19.31 Aligned_cols=34 Identities=18% Similarity=0.314 Sum_probs=23.0
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
-++.|.+.+.+ |+ +..+||...| + ....+..++.
T Consensus 11 eK~~iI~~~e~----g~-s~~~ia~~fg-v----~~sTv~~I~K 44 (53)
T PF04218_consen 11 EKLEIIKRLEE----GE-SKRDIAREFG-V----SRSTVSTILK 44 (53)
T ss_dssp HHHHHHHHHHC----TT--HHHHHHHHT-------CCHHHHHHH
T ss_pred HHHHHHHHHHc----CC-CHHHHHHHhC-C----CHHHHHHHHH
Confidence 45566666643 44 9999999999 9 8888888774
No 270
>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=55.66 E-value=12 Score=22.26 Aligned_cols=23 Identities=13% Similarity=0.231 Sum_probs=19.2
Q ss_pred CCCCcchHHHHHHHHhccCceee
Q 045477 61 NKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 61 ~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
.++.|.+|.++.|.|...|+--.
T Consensus 8 a~DRpGLL~~i~~~l~~~gl~I~ 30 (72)
T cd04895 8 SARKPGILLEAVQVLTDLDLCIT 30 (72)
T ss_pred ECCcCCHHHHHHHHHHHCCcEEE
Confidence 45688999999999999997543
No 271
>PRK15044 transcriptional regulator SirC; Provisional
Probab=55.65 E-value=33 Score=25.79 Aligned_cols=44 Identities=25% Similarity=0.279 Sum_probs=33.7
Q ss_pred HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
+...-..-++.+.|.++- ..+.|+++||+.++ . .+..+.|.++.
T Consensus 188 ~~~is~~~kV~~~I~~nl-~~~~SLeeLA~~lg-m----S~~tL~R~Fk~ 231 (295)
T PRK15044 188 AIKITTKEKVYNIIISDL-TRKWSQAEVAGKLF-M----SVSSLKRKLAA 231 (295)
T ss_pred HhhhhHHHHHHHHHHhCc-ccCCCHHHHHHHhC-C----CHHHHHHHHHH
Confidence 333333456777887653 37999999999999 9 89999998875
No 272
>PRK00118 putative DNA-binding protein; Validated
Probab=55.23 E-value=13 Score=23.66 Aligned_cols=23 Identities=17% Similarity=0.185 Sum_probs=18.7
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
..+|.+|||+.+| + .+..+.+.+
T Consensus 32 eg~S~~EIAe~lG-I----S~~TV~r~L 54 (104)
T PRK00118 32 DDYSLGEIAEEFN-V----SRQAVYDNI 54 (104)
T ss_pred cCCCHHHHHHHHC-c----CHHHHHHHH
Confidence 5799999999999 9 776666554
No 273
>PHA01976 helix-turn-helix protein
Probab=55.21 E-value=12 Score=20.80 Aligned_cols=23 Identities=13% Similarity=0.138 Sum_probs=16.3
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
..+|..|+|+.++ + .+..+.++.
T Consensus 14 ~glt~~~lA~~~g-v----s~~~v~~~e 36 (67)
T PHA01976 14 RAWSAPELSRRAG-V----RHSLIYDFE 36 (67)
T ss_pred cCCCHHHHHHHhC-C----CHHHHHHHH
Confidence 4688888888888 7 555555543
No 274
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=55.13 E-value=20 Score=19.92 Aligned_cols=40 Identities=18% Similarity=0.328 Sum_probs=30.0
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
.+++-+||-+++. . +..++.....++..|+..|.+...+.
T Consensus 16 ~G~~keeLrsrl~-~-~~l~~k~~~~ll~~l~~~g~l~~~g~ 55 (59)
T PF09106_consen 16 PGMPKEELRSRLF-K-PRLPPKLFNALLEALVAEGRLKVEGD 55 (59)
T ss_dssp S-EEHHHHHHHCS-T--TS-HCCHHHHHHHHHHTTSEEEESS
T ss_pred cCcCHHHHHHHHh-h-ccCCHHHHHHHHHHHHHCCCeeeECC
Confidence 5789999998884 1 11178899999999999999987653
No 275
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=55.11 E-value=19 Score=26.56 Aligned_cols=36 Identities=22% Similarity=0.273 Sum_probs=28.9
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
.|.+.|..+. ..+.|+++||+.++ . .+..+.|.++.
T Consensus 185 ~i~~~I~~~~-~~~~sl~~lA~~~g-m----S~stl~R~Fk~ 220 (291)
T PRK15186 185 NIYNIIISDI-SRKWALKDISDSLY-M----SCSTLKRKLKQ 220 (291)
T ss_pred HHHHHHHhCc-cCCCCHHHHHHHHC-c----CHHHHHHHHHH
Confidence 3456666553 37999999999999 9 88899998876
No 276
>PRK13824 replication initiation protein RepC; Provisional
Probab=54.96 E-value=17 Score=28.27 Aligned_cols=36 Identities=19% Similarity=0.186 Sum_probs=31.4
Q ss_pred CCHHHHHhhC-CCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 47 LSASEIAAQL-PATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 47 ~t~~eLA~~~-~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
.|-.+|+.++ | . .+..|+|.++.|+..|++....|-
T Consensus 83 pSN~~La~r~~G-m----s~~tlrRhla~LveaGLI~rrDSp 119 (404)
T PRK13824 83 PSNAQLSLRAHG-M----AGATLRRHLAALVEAGLIIRRDSP 119 (404)
T ss_pred hhHHHHHHHHcC-C----CHHHHHHHHHHHHHCCCeEeecCC
Confidence 4889999985 8 9 899999999999999999876553
No 277
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=54.93 E-value=46 Score=24.44 Aligned_cols=44 Identities=30% Similarity=0.416 Sum_probs=36.2
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
.||+-|. |++|-+.++-||.++| + -...+---||-|-+.|+++.
T Consensus 193 ~I~eELd--G~EG~lvASkiADrvG-I----TRSVIVNALRKlESAGvIeS 236 (261)
T COG4465 193 HIFEELD--GNEGLLVASKIADRVG-I----TRSVIVNALRKLESAGVIES 236 (261)
T ss_pred HHHHhcC--CccceeeehhhhhhhC-c----hHHHHHHHHHHhhhcCceee
Confidence 4566663 3458899999999999 9 77788899999999999864
No 278
>PRK10736 hypothetical protein; Provisional
Probab=54.86 E-value=18 Score=28.01 Aligned_cols=35 Identities=11% Similarity=-0.020 Sum_probs=31.7
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.|++++||+.+++ . ++..+..+|-.|.-.|++.+.
T Consensus 320 ~~~~iD~L~~~~~-l----~~~~v~~~L~~LEl~G~v~~~ 354 (374)
T PRK10736 320 EVTPVDVVAERAG-Q----PVPEVVTQLLELELAGWIAAV 354 (374)
T ss_pred CCCCHHHHHHHHC-c----CHHHHHHHHHHHHhCCcEEEc
Confidence 6899999999999 9 888999999999999998765
No 279
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.77 E-value=15 Score=23.11 Aligned_cols=24 Identities=38% Similarity=0.433 Sum_probs=21.7
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.++|.++||..++ . .+..|.++|.
T Consensus 22 ~~LS~~~iA~~Ln-~----t~~~lekil~ 45 (97)
T COG4367 22 CPLSDEEIATALN-W----TEVKLEKILQ 45 (97)
T ss_pred ccccHHHHHHHhC-C----CHHHHHHHHH
Confidence 6899999999999 9 8889999983
No 280
>PRK13501 transcriptional activator RhaR; Provisional
Probab=54.71 E-value=22 Score=25.36 Aligned_cols=40 Identities=8% Similarity=0.174 Sum_probs=31.1
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
+.+.|.++- ..++|++++|+.++ . .+..|.|+.+......
T Consensus 181 i~~~I~~~~-~e~~sl~~lA~~~~-l----S~~~l~r~Fk~~~G~T 220 (290)
T PRK13501 181 IMSALQQSL-GAYFDMADFCHKNQ-L----VERSLKQLFRQQTGMS 220 (290)
T ss_pred HHHHHHHhh-ccCCCHHHHHHHHC-c----CHHHHHHHHHHHHCcC
Confidence 466666543 26899999999999 9 9999999998665443
No 281
>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=54.56 E-value=12 Score=22.43 Aligned_cols=22 Identities=23% Similarity=0.099 Sum_probs=18.4
Q ss_pred CCCCcchHHHHHHHHhccCcee
Q 045477 61 NKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 61 ~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
.++.|.+|+++.|.+...|+--
T Consensus 7 a~DRpGLL~~i~~~l~~~~l~i 28 (75)
T cd04896 7 CVDQKGLLYDILRTSKDCNIQI 28 (75)
T ss_pred eCCcccHHHHHHHHHHHCCeEE
Confidence 3568899999999999988754
No 282
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=54.36 E-value=38 Score=19.05 Aligned_cols=53 Identities=21% Similarity=0.365 Sum_probs=43.0
Q ss_pred HHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 24 MTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 24 ~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.++.....+.|...+.+. .+.++.+|+..++ . ....+.+-|+.|...|++...
T Consensus 20 ~~l~~~~r~~il~~l~~~---~~~~~~~l~~~~~-~----~~~~v~~hL~~L~~~glv~~~ 72 (110)
T COG0640 20 KALADPTRLEILSLLAEG---GELTVGELAEALG-L----SQSTVSHHLKVLREAGLVELR 72 (110)
T ss_pred HHhCCHHHHHHHHHHHhc---CCccHHHHHHHHC-C----ChhHHHHHHHHHHHCCCeEEE
Confidence 345555778888888763 4788999999998 8 888999999999999998863
No 283
>PRK13502 transcriptional activator RhaR; Provisional
Probab=54.32 E-value=22 Score=25.13 Aligned_cols=39 Identities=10% Similarity=0.106 Sum_probs=30.8
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
.+.+.|.++- ..+++++++|+.++ . .+..|.|+.+.-+.
T Consensus 180 ~~~~~I~~~~-~~~~~~~~lA~~~~-i----S~~~L~r~fk~~~G 218 (282)
T PRK13502 180 KLITALANSL-ECPFALDAFCQQEQ-C----SERVLRQQFRAQTG 218 (282)
T ss_pred HHHHHHHhcc-cCCCCHHHHHHHHC-c----CHHHHHHHHHHHHC
Confidence 5666676653 26899999999999 9 99999999876543
No 284
>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=54.26 E-value=17 Score=18.30 Aligned_cols=25 Identities=28% Similarity=0.203 Sum_probs=20.2
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
..+|..+||+.++ + ....+.|.++.
T Consensus 25 ~~~~~~~ia~~~~-~----s~~~i~~~~~~ 49 (55)
T cd06171 25 EGLSYEEIAEILG-I----SRSTVRQRLHR 49 (55)
T ss_pred cCCCHHHHHHHHC-c----CHHHHHHHHHH
Confidence 4689999999999 9 77777776653
No 285
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=54.06 E-value=24 Score=25.71 Aligned_cols=40 Identities=13% Similarity=0.143 Sum_probs=30.3
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY 78 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~ 78 (89)
.+.+.|.++- ..++|+++||+.++ . .+..+.|+++.....
T Consensus 222 ~~~~~i~~~~-~~~~sl~~lA~~~~-~----S~~~l~r~fk~~~g~ 261 (322)
T PRK09393 222 PLIDWMRAHL-AEPHTVASLAARAA-M----SPRTFLRRFEAATGM 261 (322)
T ss_pred HHHHHHHhcc-CCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCc
Confidence 3445565542 37899999999999 9 899999998876543
No 286
>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=53.62 E-value=4.3 Score=27.67 Aligned_cols=24 Identities=21% Similarity=0.307 Sum_probs=0.0
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.|+|..|||..+| . ++..+.|..+
T Consensus 48 ~PLt~~~iA~~lg-l----~~STVSRav~ 71 (160)
T PF04552_consen 48 KPLTMKDIADELG-L----HESTVSRAVK 71 (160)
T ss_dssp -----------------------------
T ss_pred cCCCHHHHHHHhC-C----CHhHHHHHHc
Confidence 7999999999999 9 8999999875
No 287
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=53.25 E-value=18 Score=24.26 Aligned_cols=40 Identities=15% Similarity=0.079 Sum_probs=29.4
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
.-+|.+.++. |-++..|+|..++ + -+..|.+.|| ..|++-
T Consensus 36 ~f~D~v~~~~--gli~~re~AK~lk-i----ge~~l~~~L~---e~~~l~ 75 (135)
T COG3645 36 EFADAVVEAS--GLILFRELAKLLK-I----GENRLFAWLR---ENKYLI 75 (135)
T ss_pred HHHHHHhcCc--cceeHHHHHHHHc-c----CHHHHHHHHH---HCCEEE
Confidence 4578888875 7899999999999 9 6655555554 455544
No 288
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=53.22 E-value=21 Score=26.10 Aligned_cols=36 Identities=14% Similarity=0.118 Sum_probs=28.9
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
.+.+++..+- .++.|+++||+.++ . .+..+.|.++.
T Consensus 138 kv~~~I~~~~-~~~~tl~~LA~~~g-m----S~s~l~R~FK~ 173 (253)
T PRK09940 138 KVRNIVNMKL-AHPWKLKDICDCLY-I----SESLLKKKLKQ 173 (253)
T ss_pred HHHHHHHHhh-cCCCCHHHHHHHHC-c----CHHHHHHHHHH
Confidence 4556666553 37899999999999 9 89899999875
No 289
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=53.12 E-value=11 Score=20.95 Aligned_cols=24 Identities=29% Similarity=0.389 Sum_probs=16.5
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
..+|..++|+.+| + ++..+.|+.+
T Consensus 13 ~gls~~~lA~~~g-~----s~s~v~~iE~ 36 (64)
T PF13560_consen 13 AGLSQAQLADRLG-V----SQSTVSRIER 36 (64)
T ss_dssp HTS-HHHHHHHHT-S-----HHHHHHHHT
T ss_pred cCCCHHHHHHHHC-c----CHHHHHHHHC
Confidence 4689999999999 8 6666666543
No 290
>KOG4062 consensus 6-O-methylguanine-DNA methyltransferase MGMT/MGT1, involved in DNA repair [Replication, recombination and repair]
Probab=53.02 E-value=24 Score=24.61 Aligned_cols=48 Identities=10% Similarity=0.173 Sum_probs=33.9
Q ss_pred HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477 27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGI 80 (89)
Q Consensus 27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi 80 (89)
.....+.+++.|-+-.-|.-.|-.|||+..| +|...+-+=+++..+++
T Consensus 87 ~t~F~~kVw~al~~i~~Gev~tY~~iA~~iG------~PsaaRaVg~A~~~n~l 134 (178)
T KOG4062|consen 87 GTDFQRKVWDALCEIPYGEVSTYGQIARRIG------NPSAARAVGSAMAHNNL 134 (178)
T ss_pred cchHHHHHHHHHhccCCCceeeHHHHHHHhC------CcHHHHHHHHHHccCCC
Confidence 3445667888887644347789999999999 56666666666655543
No 291
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=52.89 E-value=36 Score=25.12 Aligned_cols=50 Identities=14% Similarity=0.126 Sum_probs=39.5
Q ss_pred HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
....+.+|.=.|.+ ||.|.+||-..++ + .+..+..=++-|...|++.+..
T Consensus 11 ~SekRk~lLllL~e----gPkti~EI~~~l~-v----s~~ai~pqiKkL~~~~LV~~~~ 60 (260)
T COG4742 11 LSEKRKDLLLLLKE----GPKTIEEIKNELN-V----SSSAILPQIKKLKDKGLVVQEG 60 (260)
T ss_pred ccHHHHHHHHHHHh----CCCCHHHHHHHhC-C----CcHHHHHHHHHHhhCCCEEecC
Confidence 33456677777876 7999999999999 9 7777777778888888887663
No 292
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=52.88 E-value=28 Score=24.37 Aligned_cols=37 Identities=19% Similarity=0.271 Sum_probs=32.6
Q ss_pred CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
|..+ |=.|||+..+ + ....+++-|..|+..|++....
T Consensus 26 G~~LPsE~eL~~~~~-V----SR~TvR~Al~~L~~eGli~r~~ 63 (240)
T PRK09764 26 GDALPTESALQTEFG-V----SRVTVRQALRQLVEQQILESIQ 63 (240)
T ss_pred CCcCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 3567 7799999999 9 8999999999999999998654
No 293
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=52.70 E-value=16 Score=22.40 Aligned_cols=29 Identities=10% Similarity=0.149 Sum_probs=23.1
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
++..|+|+.+| + .+ +-+|+....|++...
T Consensus 1 m~I~eva~~~g-v----s~----~tlR~Ye~~GLl~p~ 29 (95)
T cd04780 1 MRMSELSKRSG-V----SV----ATIKYYLREGLLPEG 29 (95)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 57899999999 7 44 377888889998764
No 294
>COG3177 Fic family protein [Function unknown]
Probab=52.62 E-value=23 Score=26.67 Aligned_cols=38 Identities=32% Similarity=0.276 Sum_probs=35.2
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
+..|+.++....+ + ......|-+..|+..|++.+.+..
T Consensus 303 ~~~t~~~~~~~~~-~----s~~Ta~r~l~~l~~~g~l~~~~~~ 340 (348)
T COG3177 303 GYLTAAEIEAILG-V----SKATATRDLKELLELGILEEVKGR 340 (348)
T ss_pred CCccHHHHHHHhC-c----cHHHHHHHHHHHHhCCCeeecCCC
Confidence 7899999999999 9 888999999999999999988654
No 295
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=52.46 E-value=15 Score=22.86 Aligned_cols=32 Identities=13% Similarity=0.175 Sum_probs=25.0
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
.+|..|+++.++ + ++. ++.-|+..|++....+
T Consensus 7 ~lt~~Elc~~~g-i----~~~----~l~eLve~GlIep~~~ 38 (101)
T PRK10265 7 TFTITEFCLHTG-V----SEE----ELNEIVGLGVIEPREI 38 (101)
T ss_pred EeeHHHHHHHHC-c----CHH----HHHHHHHCCCeecCCC
Confidence 579999999999 9 777 5556678899885433
No 296
>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=52.37 E-value=7.7 Score=30.38 Aligned_cols=35 Identities=23% Similarity=0.199 Sum_probs=29.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
..+|.+||++.++ . ++..+.|.|..|+..|++...
T Consensus 533 ~~~t~~ei~~~~~-~----~~~~l~~~L~~l~~~~~l~~~ 567 (588)
T PF00888_consen 533 DSLTVEEISEKTG-I----SEEELKRALKSLVKSKILILL 567 (588)
T ss_dssp SEEEHHHHHHHC--------HHHHHHHHHCCCTTTTCSEE
T ss_pred CCccHHHHHHHHC-c----CHHHHHHHHHHHHhCCcceee
Confidence 6899999999999 9 999999999999999999743
No 297
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=52.14 E-value=15 Score=20.41 Aligned_cols=28 Identities=14% Similarity=0.142 Sum_probs=20.8
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
+|+.|+|+.+| + ++..|++. ...|++..
T Consensus 1 ~s~~eva~~~g-v----s~~tlr~~----~~~gli~~ 28 (70)
T smart00422 1 YTIGEVAKLAG-V----SVRTLRYY----ERIGLLPP 28 (70)
T ss_pred CCHHHHHHHHC-c----CHHHHHHH----HHCCCCCC
Confidence 47899999999 9 77655544 55888764
No 298
>PRK15185 transcriptional regulator HilD; Provisional
Probab=52.09 E-value=23 Score=26.75 Aligned_cols=36 Identities=17% Similarity=0.325 Sum_probs=29.9
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
.+.+.|.++. ..+.|++++|+.++ . .+..|.|.++.
T Consensus 210 rV~~~I~~n~-~~~~SledLA~~lg-m----S~~tL~R~FK~ 245 (309)
T PRK15185 210 RVYNIISSSP-SRQWKLTDVADHIF-M----STSTLKRKLAE 245 (309)
T ss_pred HHHHHHHhCc-cCCCCHHHHHHHHC-c----CHHHHHHHHHH
Confidence 4777777653 47899999999999 9 89899998874
No 299
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=51.94 E-value=35 Score=24.99 Aligned_cols=47 Identities=26% Similarity=0.304 Sum_probs=40.0
Q ss_pred HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
-...+|+..+..+ .++++.|+.+..+ . +...++=.+|.|-+.+.++-
T Consensus 101 s~R~~Iy~~i~~n---PG~~lsEl~~nl~-i----~R~TlRyhlriLe~~~li~a 147 (240)
T COG3398 101 SKRDGIYNYIKPN---PGFSLSELRANLY-I----NRSTLRYHLRILESNPLIEA 147 (240)
T ss_pred hhHHHHHHHhccC---CCccHHHHHHhcC-C----ChHHHHHHHHHHHhCcchhh
Confidence 3457788888875 4899999999999 9 88899999999999988763
No 300
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=51.30 E-value=20 Score=23.04 Aligned_cols=23 Identities=9% Similarity=0.242 Sum_probs=14.7
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
.++|.+|+|+.+| + ....+.|+.
T Consensus 17 ~Glsq~eLA~~~G-i----s~~~is~iE 39 (120)
T PRK13890 17 RHMTKKELSERSG-V----SISFLSDLT 39 (120)
T ss_pred cCCCHHHHHHHHC-c----CHHHHHHHH
Confidence 4678888888877 6 444444433
No 301
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=51.26 E-value=22 Score=25.11 Aligned_cols=43 Identities=14% Similarity=0.217 Sum_probs=26.7
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.+.|.+......+|+++|++.|+ + ...-|+..|-.+|++....
T Consensus 139 ~~~L~~~~~~~~isi~~is~~Tg-i-------~~~DIi~tL~~l~~l~~~~ 181 (188)
T PF01853_consen 139 LEYLLEFKGKKSISIKDISQETG-I-------RPEDIISTLQQLGMLKYYK 181 (188)
T ss_dssp HHHHHHTSSE--EEHHHHHHHH--B-------THHHHHHHHHHTT-EEEET
T ss_pred HHHHHhcCCCCeEEHHHHHHHHC-C-------CHHHHHHHHHHCCCEEEEC
Confidence 44444433112699999999999 9 3455777888888887653
No 302
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=51.23 E-value=23 Score=25.44 Aligned_cols=38 Identities=16% Similarity=0.330 Sum_probs=29.3
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
++++-|+..+. .-.|.+|||++++ + |+..++|=+-++=
T Consensus 20 R~le~l~a~~v-~rvsS~els~~~~-v----dsatIRrDfSYFG 57 (211)
T COG2344 20 RVLERLHASGV-ERVSSKELSEALG-V----DSATIRRDFSYFG 57 (211)
T ss_pred HHHHHHHHcCC-ceecHHHHHHHhC-C----CHHHHhhhhHHHH
Confidence 45677777653 5689999999999 9 9998888665543
No 303
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=51.19 E-value=65 Score=23.72 Aligned_cols=53 Identities=11% Similarity=0.156 Sum_probs=37.2
Q ss_pred hHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCC-CCCCCCcchHHHHHHHHhccCceeeec
Q 045477 19 GSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPA-TKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 19 ~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~-~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
..|...+++..+.+. + +.....+||..+++ + ...-+..-|..|...|+++..+
T Consensus 120 ~~W~~~virel~~~~--------~--~~~~~~~ia~~l~p~i----s~~ev~~sL~~L~~~glikk~~ 173 (271)
T TIGR02147 120 RHWYNSVIRELLGVM--------P--FADDPEELAKRCFPKI----SAEQVKESLDLLERLGLIKKNE 173 (271)
T ss_pred HHHHHHHHHHHhhcC--------C--CCCCHHHHHHHhCCCC----CHHHHHHHHHHHHHCCCeeECC
Confidence 455555555554432 1 34468899999983 3 5666889999999999998764
No 304
>PF02387 IncFII_repA: IncFII RepA protein family; InterPro: IPR003446 These proteins are plasmid encoded and essential for plasmid replication, they are also involved in copy control functions [].; GO: 0006276 plasmid maintenance
Probab=51.04 E-value=27 Score=25.98 Aligned_cols=40 Identities=23% Similarity=0.429 Sum_probs=26.0
Q ss_pred CCCCHHHHHhhCCCCCCCCCc-----chHHHHH-HHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAP-----TMLDRIL-GLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~-----~~l~RlL-R~L~s~gi~~e~~ 85 (89)
-.+|+++||..+| .++-++. ..+.|++ .+|..+|++++..
T Consensus 94 V~~sie~LA~ecG-Lst~s~~Gn~sitRasR~i~e~le~~Gli~~~~ 139 (281)
T PF02387_consen 94 VQASIEQLADECG-LSTKSAAGNKSITRASRLISEFLEPLGLITCEK 139 (281)
T ss_pred eeecHHHHHHHhC-CcccCCCCCeeHHHHHHHHHHHHHhcCCeeeee
Confidence 5689999999988 7532221 2244555 4456799987654
No 305
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=51.03 E-value=21 Score=24.28 Aligned_cols=33 Identities=21% Similarity=0.252 Sum_probs=30.3
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|-.+||+.++ + ....+.|.+..|...+++...
T Consensus 76 ~t~~~ia~~l~-i----S~~Tv~r~ik~L~e~~iI~k~ 108 (165)
T PF05732_consen 76 ATQKEIAEKLG-I----SKPTVSRAIKELEEKNIIKKI 108 (165)
T ss_pred eeHHHHHHHhC-C----CHHHHHHHHHHHHhCCcEEEc
Confidence 58999999999 9 888999999999999999865
No 306
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=50.72 E-value=25 Score=25.97 Aligned_cols=36 Identities=19% Similarity=0.310 Sum_probs=29.5
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
.+.+.|.++- ..++|+++||..++ . .+..+.|+++.
T Consensus 146 ~v~~yI~~~~-~~~lsl~~lA~~~g-~----S~~~L~R~Fk~ 181 (274)
T PRK09978 146 RVCTVINNNI-AHEWTLARIASELL-M----SPSLLKKKLRE 181 (274)
T ss_pred HHHHHHHhcc-cCCCCHHHHHHHHC-c----CHHHHHHHHHh
Confidence 4666777653 37899999999999 9 89999999874
No 307
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=50.67 E-value=30 Score=26.19 Aligned_cols=37 Identities=19% Similarity=0.288 Sum_probs=32.4
Q ss_pred CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
|..+ |..+||+.++ + ....+.+-++.|.+.|++....
T Consensus 26 g~~lps~r~la~~~~-v----sr~tv~~a~~~L~~~g~i~~~~ 63 (431)
T PRK15481 26 GDSLPPVRELASELG-V----NRNTVAAAYKRLVTAGLAQSQG 63 (431)
T ss_pred CCcCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeC
Confidence 3566 8899999999 9 9999999999999999987543
No 308
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=50.65 E-value=13 Score=25.13 Aligned_cols=37 Identities=16% Similarity=0.159 Sum_probs=26.4
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcc----hHHHHHHHHh
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT----MLDRILGLLA 76 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~----~l~RlLR~L~ 76 (89)
-|..|...+. ++.|..|||+.++ . .+. .+.|++|-|-
T Consensus 154 rE~evl~~~~-----~G~s~~eIA~~l~-i----S~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 154 KESEVLRLFA-----EGFLVTEIAKKLN-R----SIKTISSQKKSAMMKLG 194 (216)
T ss_pred HHHHHHHHHH-----CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHHcC
Confidence 4556666665 3689999999999 8 554 3667776664
No 309
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=50.22 E-value=20 Score=24.29 Aligned_cols=31 Identities=23% Similarity=0.355 Sum_probs=19.8
Q ss_pred HHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 36 EIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 36 d~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+.+...| +-.|.+|||+.+| + ++..|+|-..
T Consensus 26 e~~~~~~--~r~T~~eiAee~G-i----s~~tLYrWr~ 56 (142)
T PF13022_consen 26 ELMPENG--ERRTQAEIAEEVG-I----SRSTLYRWRQ 56 (142)
T ss_dssp HHS--------S-HHHHHHHHT-S-----HHHHHHHHH
T ss_pred HHhhhcc--ccchHHHHHHHhC-C----CHHHHHHHHh
Confidence 5555544 6899999999999 9 9999998764
No 310
>PRK14999 histidine utilization repressor; Provisional
Probab=50.08 E-value=31 Score=24.14 Aligned_cols=36 Identities=22% Similarity=0.240 Sum_probs=32.2
Q ss_pred CCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
..+ |=.|||+..+ + ....++|-|..|+..|++....
T Consensus 34 ~~LPsE~eLa~~~g-V----SR~TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 34 DRIPSEAELVAQYG-F----SRMTINRALRELTDEGWLVRLQ 70 (241)
T ss_pred CcCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 556 8999999999 9 8999999999999999998653
No 311
>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=50.02 E-value=22 Score=23.62 Aligned_cols=30 Identities=20% Similarity=0.114 Sum_probs=21.4
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHH
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~R 70 (89)
.+.+.+.|- ...|+.+||++.| + .+..+++
T Consensus 18 ~~lf~e~G~-~~~s~~~IA~~ag-v----s~~~lY~ 47 (202)
T TIGR03613 18 LDTFSRFGF-HGTSLEQIAELAG-V----SKTNLLY 47 (202)
T ss_pred HHHHHHhCc-ccCCHHHHHHHhC-C----CHHHHHH
Confidence 345666653 6789999999999 9 6655443
No 312
>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=49.97 E-value=10 Score=21.87 Aligned_cols=48 Identities=15% Similarity=0.263 Sum_probs=24.9
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCC---CCC-CCCc-chHH-HHHHHHh-ccCceeee
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPA---TKN-KDAP-TMLD-RILGLLA-SYGIVECS 84 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~---~~~-~~d~-~~l~-RlLR~L~-s~gi~~e~ 84 (89)
..+|.+.| +|+|..||.+.... .+. ..+| ..|. +|-+.+- ..+.|..+
T Consensus 8 ~~vL~~~~--~pm~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~~~d~~F~~v 62 (72)
T PF05066_consen 8 YEVLEEAG--RPMTFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIKNEDSRFVKV 62 (72)
T ss_dssp HHHHHHH---S-EEHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH-T-SS-EES
T ss_pred HHHHHhcC--CCcCHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcccCCCCEEEe
Confidence 45677776 89999999987541 110 1122 2344 5555554 55666554
No 313
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=49.88 E-value=13 Score=26.82 Aligned_cols=38 Identities=18% Similarity=0.176 Sum_probs=27.6
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcch----HHHHHHHH
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTM----LDRILGLL 75 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~----l~RlLR~L 75 (89)
..-|..|+..+++ ++|.+|||++++ . .+.. +.++++.|
T Consensus 145 S~RE~eVL~Lia~-----G~SnkEIA~~L~-I----S~~TVk~hvs~I~~KL 186 (217)
T PRK13719 145 TKYQNDVFILYSF-----GFSHEYIAQLLN-I----TVGSSKNKISEILKFF 186 (217)
T ss_pred CHHHHHHHHHHHC-----CCCHHHHHHHhC-C----CHHHHHHHHHHHHHHh
Confidence 3456778888874 699999999999 8 5544 55566554
No 314
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=49.73 E-value=26 Score=24.31 Aligned_cols=36 Identities=22% Similarity=0.272 Sum_probs=31.8
Q ss_pred CCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
..+ |=.|||+..| + ....++|-|+.|+..|++....
T Consensus 22 ~~LPsE~eLa~~~g-V----SR~TVR~Al~~L~~eGli~r~~ 58 (233)
T TIGR02404 22 DYLPSEHELMDQYG-A----SRETVRKALNLLTEAGYIQKIQ 58 (233)
T ss_pred CCCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeC
Confidence 444 8899999999 9 8999999999999999998654
No 315
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=49.60 E-value=32 Score=23.85 Aligned_cols=37 Identities=27% Similarity=0.395 Sum_probs=32.5
Q ss_pred CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
|..+ |=.|||+..+ + ....++|-|..|+..|++....
T Consensus 22 g~~LPsE~eLa~~~~-V----SR~TVR~Al~~L~~eGli~r~~ 59 (230)
T TIGR02018 22 GHRIPSEHELVAQYG-C----SRMTVNRALRELTDAGLLERRQ 59 (230)
T ss_pred CCcCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 3556 8889999999 9 8999999999999999988654
No 316
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=49.31 E-value=14 Score=26.38 Aligned_cols=21 Identities=19% Similarity=0.203 Sum_probs=12.5
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
+|..|||+..| + ....+.|+|
T Consensus 1 ~ti~dIA~~aG-V----S~~TVSrvL 21 (328)
T PRK11303 1 MKLDEIARLAG-V----SRTTASYVI 21 (328)
T ss_pred CCHHHHHHHhC-C----CHHHHHHHH
Confidence 46677777777 6 444444444
No 317
>PF14502 HTH_41: Helix-turn-helix domain
Probab=48.99 E-value=35 Score=18.94 Aligned_cols=34 Identities=15% Similarity=0.215 Sum_probs=30.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
.-.|++|++++.+ + ....+..-|++|...|.+.-
T Consensus 5 Ri~tI~e~~~~~~-v----s~GtiQ~Alk~Le~~gaI~L 38 (48)
T PF14502_consen 5 RIPTISEYSEKFG-V----SRGTIQNALKFLEENGAIKL 38 (48)
T ss_pred ccCCHHHHHHHhC-c----chhHHHHHHHHHHHCCcEEe
Confidence 4568999999999 9 88899999999999998763
No 318
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=48.85 E-value=73 Score=21.81 Aligned_cols=49 Identities=22% Similarity=0.269 Sum_probs=36.7
Q ss_pred hChHHHHHhcC--CCCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 32 LGLFEIIAKAG--PGAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 32 LgIfd~l~~~g--~~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
-.|.+.|.+.+ +|..+ |-.|||++.+ + ....+++=|+.|...|++....
T Consensus 8 ~~l~~~I~~g~~~~g~~lPsE~eLa~~~~-V----sr~Tvr~Al~~L~~eGli~~~~ 59 (231)
T TIGR03337 8 DHLSYQIRAGALLPGDKLPSERDLGERFN-T----TRVTIREALQQLEAEGLIYRED 59 (231)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCeEEEeC
Confidence 34555554421 22344 7899999999 9 8889999999999999988653
No 319
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=48.73 E-value=41 Score=20.25 Aligned_cols=50 Identities=18% Similarity=0.016 Sum_probs=33.3
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCC----cchHHHHHHHHhccCceeeec
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDA----PTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d----~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.+.|..-.+..+.|...|...+. ...+.+ ..+|.+-|+-++..|.|..+.
T Consensus 12 ~eAI~~l~er~GsS~~aI~kyI~-~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~k 65 (88)
T cd00073 12 TEAIKALKERKGSSLQAIKKYIE-AKYKVDDENFNKLLKLALKKGVAKGKLVQVK 65 (88)
T ss_pred HHHHHHcCCCCCcCHHHHHHHHH-HHCCcchHHHHHHHHHHHHHHHHCCCeEeec
Confidence 34443322236789999998877 543333 345778888899999988765
No 320
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=48.62 E-value=40 Score=26.89 Aligned_cols=46 Identities=15% Similarity=0.263 Sum_probs=33.6
Q ss_pred hHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 19 GSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 19 ~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
+||....++.. .+.. +.+|+.+|++.|+ . ...-|+..|-.+|++..
T Consensus 358 ~YW~~~i~~~L---------~~~~--~~~si~~is~~T~-i-------~~~Dii~tL~~l~~l~~ 403 (450)
T PLN00104 358 GYWTRVLLEIL---------KKHK--GNISIKELSDMTA-I-------KAEDIVSTLQSLNLIQY 403 (450)
T ss_pred HHHHHHHHHHH---------HhcC--CCccHHHHHHHhC-C-------CHHHHHHHHHHCCCEEe
Confidence 56666655553 3433 6899999999999 8 44558888888888764
No 321
>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=48.50 E-value=36 Score=21.10 Aligned_cols=37 Identities=19% Similarity=0.194 Sum_probs=30.3
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
++.+|..+.+.| |...-|+.++ + .+..+.|-++.|-.
T Consensus 6 ~l~~~~av~~~g-----Sis~AA~~L~-i----S~stvs~~I~~LE~ 42 (99)
T TIGR00637 6 RVALLKAIARMG-----SISQAAKDAG-I----SYKSAWDYIRAMNN 42 (99)
T ss_pred HHHHHHHHHHhC-----CHHHHHHHHC-C----CHHHHHHHHHHHHH
Confidence 567888888865 7888899999 9 78888888887764
No 322
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=48.35 E-value=54 Score=21.11 Aligned_cols=36 Identities=28% Similarity=0.347 Sum_probs=32.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|+..-.||-..++++ .+..|.+=||.|...|++..+
T Consensus 35 g~~RF~eL~r~i~~I----s~k~Ls~~Lk~Le~~Glv~R~ 70 (120)
T COG1733 35 GPKRFNELRRSIGGI----SPKMLSRRLKELEEDGLVERV 70 (120)
T ss_pred CCCcHHHHHHHcccc----CHHHHHHHHHHHHHCCCEEee
Confidence 688999999998877 788999999999999999865
No 323
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=48.19 E-value=40 Score=20.12 Aligned_cols=41 Identities=15% Similarity=0.199 Sum_probs=29.8
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
.+.+.|...- ..+.+++++|..++ . .+..|.|.++......
T Consensus 24 ~~~~~i~~~~-~~~~~l~~la~~~g-~----S~~~l~r~f~~~~g~s 64 (127)
T COG2207 24 RALDYIEENL-AEPLTLEDLARRLG-M----SRRTLSRLFKKETGTS 64 (127)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHC-C----CHHHHHHHHHHHHCCC
Confidence 4455555422 26799999999999 9 8989999888555443
No 324
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=48.14 E-value=51 Score=24.84 Aligned_cols=31 Identities=13% Similarity=0.219 Sum_probs=24.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
+.+|+.+|+..|+ . ...-|+..|..+|++..
T Consensus 222 ~~isi~~is~~T~-i-------~~~Dii~tL~~l~~l~~ 252 (290)
T PLN03238 222 GDVSIKDLSLATG-I-------RGEDIVSTLQSLNLIKY 252 (290)
T ss_pred CCccHHHHHHHhC-C-------CHHHHHHHHHHCCcEEE
Confidence 6899999999999 8 33447788888888764
No 325
>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=47.99 E-value=14 Score=28.82 Aligned_cols=24 Identities=21% Similarity=0.349 Sum_probs=22.2
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.|+|..+||+.+| . ++..+.|+.+
T Consensus 317 kPLtlkdiA~~lg-l----heSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELG-L----HESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhC-C----Cccchhhhhc
Confidence 7999999999999 9 9999999873
No 326
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=47.86 E-value=30 Score=27.93 Aligned_cols=36 Identities=11% Similarity=-0.010 Sum_probs=31.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|-+..|+++.++ . ++..+.+++|+|+..|.+....
T Consensus 487 ~~~~~~~~~~~~~-~----~~~~~~~~l~~l~~~g~~~~~~ 522 (581)
T TIGR00475 487 KGAWVREFAEEVN-G----DEKVMLKRVRKAGHRGGETLIV 522 (581)
T ss_pred CCCCHHHHHhhhC-C----CHHHHHHHHHHHHhCCCEEEEe
Confidence 6889999999999 9 8889999999999999776554
No 327
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=47.52 E-value=12 Score=21.80 Aligned_cols=37 Identities=30% Similarity=0.428 Sum_probs=30.3
Q ss_pred CCCCHHHHHhhC---CCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQL---PATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~---~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+.+++.++|..+ + .+ .....++-+.-+|.+.|+++..
T Consensus 23 ~~i~l~~ia~~l~~~~-~k--~~~RRlYDI~NVLealgli~K~ 62 (71)
T PF02319_consen 23 KSISLNEIADKLISEN-VK--TQRRRLYDIINVLEALGLIEKQ 62 (71)
T ss_dssp TEEEHHHHHHHCHHHC-CH--HHCHHHHHHHHHHHHCTSEEEE
T ss_pred CcccHHHHHHHHcccc-cc--cccchhhHHHHHHHHhCceeec
Confidence 799999999999 6 30 0356788999999999999874
No 328
>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=47.46 E-value=30 Score=19.63 Aligned_cols=23 Identities=30% Similarity=0.378 Sum_probs=15.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
..+|..++|+.+| + ....+.+++
T Consensus 17 ~~~t~~~lA~~~g-i----s~~tis~~~ 39 (78)
T TIGR02607 17 LGLSIRALAKALG-V----SRSTLSRIV 39 (78)
T ss_pred cCCCHHHHHHHhC-C----CHHHHHHHH
Confidence 4577788888877 7 555555554
No 329
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=47.43 E-value=19 Score=19.98 Aligned_cols=40 Identities=20% Similarity=0.338 Sum_probs=27.0
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
|-+-.|.+.+ .++|..|||..++ - .-..++|.++--..+|
T Consensus 9 Eqaqid~m~q----lG~s~~~isr~i~-R----Sr~~Ir~yl~dP~~yg 48 (50)
T PF11427_consen 9 EQAQIDVMHQ----LGMSLREISRRIG-R----SRTCIRRYLKDPVNYG 48 (50)
T ss_dssp HHHHHHHHHH----TT--HHHHHHHHT-------HHHHHHHHHSCCCTT
T ss_pred HHHHHHHHHH----hchhHHHHHHHhC-c----cHHHHHHHhcChhhcc
Confidence 3345677776 4689999999999 8 7888888887655554
No 330
>PRK13500 transcriptional activator RhaR; Provisional
Probab=47.30 E-value=37 Score=24.76 Aligned_cols=40 Identities=8% Similarity=0.097 Sum_probs=31.0
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY 78 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~ 78 (89)
.+.+.|.++- ..++|++++|+..+ . .+..|.|+.+.-+..
T Consensus 210 ~i~~yI~~~~-~e~isl~~lA~~~~-i----S~~~L~r~FK~~tG~ 249 (312)
T PRK13500 210 KLITRLAASL-KSPFALDKFCDEAS-C----SERVLRQQFRQQTGM 249 (312)
T ss_pred HHHHHHHHcc-cCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCc
Confidence 3566676652 26899999999999 9 999999998765543
No 331
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=46.83 E-value=19 Score=25.33 Aligned_cols=32 Identities=25% Similarity=0.268 Sum_probs=28.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV 81 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~ 81 (89)
+++|+.+|++.++ . .+....-.|..+...|++
T Consensus 189 g~vt~~~l~~~~~-w----s~~~a~~~L~~~~~~G~l 220 (223)
T PF04157_consen 189 GGVTASELAEKLG-W----SVERAKEALEELEREGLL 220 (223)
T ss_dssp SEEEHHHHHHHHT-B-----HHHHHHHHHHHHHTTSE
T ss_pred CCCCHHHHHHHhC-C----CHHHHHHHHHHHHhCCCE
Confidence 8999999999999 9 899999999999999876
No 332
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=46.76 E-value=21 Score=22.25 Aligned_cols=24 Identities=42% Similarity=0.618 Sum_probs=20.3
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.++|.++||+.++ . ++..|.++|-
T Consensus 22 ~~ls~~~ia~dL~-~----s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLG-T----SPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhC-C----CHHHHHHHHc
Confidence 4689999999999 9 8888888874
No 333
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=46.51 E-value=33 Score=24.42 Aligned_cols=36 Identities=19% Similarity=0.214 Sum_probs=27.3
Q ss_pred ChHHHHHhcCCCCC-CCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 33 GLFEIIAKAGPGAK-LSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 33 gIfd~l~~~g~~~~-~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
.+.+.|.++=. .| +|+++||+.++ + .+..|.|+.+-
T Consensus 201 ~~~~~I~~~l~-~~~ls~~~lA~~~g-i----S~r~L~r~Fk~ 237 (302)
T PRK09685 201 KVVALIDQSIQ-EEILRPEWIAGELG-I----SVRSLYRLFAE 237 (302)
T ss_pred HHHHHHHHhcC-CCCCCHHHHHHHHC-C----CHHHHHHHHHH
Confidence 45556665421 45 99999999999 9 88888888763
No 334
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=46.42 E-value=29 Score=24.10 Aligned_cols=38 Identities=16% Similarity=0.194 Sum_probs=27.8
Q ss_pred HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcch----HHHHHHHHh
Q 045477 29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTM----LDRILGLLA 76 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~----l~RlLR~L~ 76 (89)
--|..|...+.+ +.|.+|||++++ . .+.. +.++|+-|-
T Consensus 137 ~RE~eVL~ll~~-----G~snkeIA~~L~-i----S~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 137 PTEREILRFMSR-----GYSMPQIAEQLE-R----NIKTIRAHKFNVMSKLG 178 (207)
T ss_pred HHHHHHHHHHHC-----CCCHHHHHHHHC-C----CHHHHHHHHHHHHHHcC
Confidence 356777778874 689999999999 8 5543 556666553
No 335
>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=46.34 E-value=29 Score=22.57 Aligned_cols=27 Identities=15% Similarity=0.318 Sum_probs=19.6
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHH
Q 045477 37 IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLD 69 (89)
Q Consensus 37 ~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~ 69 (89)
.+.+.|- ...|+.+||+..| + +...++
T Consensus 20 lf~~~G~-~~~s~~~IA~~ag-v----sk~~ly 46 (189)
T TIGR03384 20 SIGERGS-LDVTIAQIARRAG-V----SSGIIS 46 (189)
T ss_pred HHHhcCc-ccCCHHHHHHHhC-C----CHHHHH
Confidence 4566553 6799999999999 8 554444
No 336
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=46.24 E-value=25 Score=21.08 Aligned_cols=29 Identities=24% Similarity=0.205 Sum_probs=22.7
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|..|+|..+| + .+. .+|+....|++...
T Consensus 2 ~~i~e~A~~~g-v----s~~----tLr~ye~~Gli~p~ 30 (91)
T cd04766 2 YVISVAAELSG-M----HPQ----TLRLYERLGLLSPS 30 (91)
T ss_pred cCHHHHHHHHC-c----CHH----HHHHHHHCCCcCCC
Confidence 58899999999 8 554 66777778998753
No 337
>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=46.17 E-value=39 Score=19.58 Aligned_cols=24 Identities=25% Similarity=0.225 Sum_probs=17.3
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCC
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPAT 59 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~ 59 (89)
.+.+.|.+.+ .|+|++||...+. .
T Consensus 9 ~~VeymK~r~--~Plt~~eI~d~l~-~ 32 (65)
T PF02186_consen 9 KAVEYMKKRD--HPLTLEEILDYLS-L 32 (65)
T ss_dssp HHHHHHHHH---S-B-HHHHHHHHT-S
T ss_pred HHHHHHHhcC--CCcCHHHHHHHHc-C
Confidence 3556777765 8999999999999 7
No 338
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=46.13 E-value=39 Score=21.95 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=32.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-|.|.++||..++ - +...+..-|-+|...|+++..
T Consensus 52 ipy~~e~LA~~~~-~----~~~~V~~AL~~f~k~glIe~~ 86 (121)
T PF09681_consen 52 IPYTAEMLALEFD-R----PVDTVRLALAVFQKLGLIEID 86 (121)
T ss_pred CCCcHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence 6999999999999 8 888999999999999999864
No 339
>PRK09526 lacI lac repressor; Reviewed
Probab=45.74 E-value=18 Score=25.90 Aligned_cols=24 Identities=13% Similarity=0.199 Sum_probs=19.5
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+..|..|||+..| + ....+.|+|.
T Consensus 4 ~~~ti~dIA~~aG-V----S~~TVSrvLn 27 (342)
T PRK09526 4 KPVTLYDVARYAG-V----SYQTVSRVLN 27 (342)
T ss_pred CCCcHHHHHHHhC-C----CHHHHHHHhc
Confidence 4679999999999 9 7777777775
No 340
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=45.71 E-value=37 Score=22.09 Aligned_cols=36 Identities=22% Similarity=0.287 Sum_probs=32.2
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
-++|-.+||..+| . ....+.|++.-|...|++....
T Consensus 170 ~~~~~~~ia~~~g-~----~~~~vsr~l~~l~~~g~i~~~~ 205 (214)
T COG0664 170 LPLTHKDLAEYLG-L----SRETVSRILKELRKDGLISVRG 205 (214)
T ss_pred ccCCHHHHHHHhC-C----chhhHHHHHHHHHhCCcEeeCC
Confidence 4799999999999 9 8889999999999999987554
No 341
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=45.37 E-value=33 Score=23.69 Aligned_cols=36 Identities=14% Similarity=0.268 Sum_probs=31.8
Q ss_pred CCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
..+ |=.|||++.+ + ....++|-|..|+..|++....
T Consensus 30 ~~LPsE~eLa~~~~-V----SR~TvR~Al~~L~~eGli~r~~ 66 (238)
T TIGR02325 30 DYLPAEMQLAERFG-V----NRHTVRRAIAALVERGLLRAEQ 66 (238)
T ss_pred CcCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 455 7889999999 9 8999999999999999998653
No 342
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=45.24 E-value=27 Score=24.62 Aligned_cols=32 Identities=22% Similarity=0.287 Sum_probs=29.6
Q ss_pred CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 48 SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 48 t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|=.|||++.+ + ....++|-|+.|+..|++...
T Consensus 33 sE~eLa~~f~-V----SR~TvRkAL~~L~~eGli~r~ 64 (236)
T COG2188 33 SERELAEQFG-V----SRMTVRKALDELVEEGLIVRR 64 (236)
T ss_pred CHHHHHHHHC-C----cHHHHHHHHHHHHHCCcEEEE
Confidence 6789999999 9 999999999999999999765
No 343
>PRK09492 treR trehalose repressor; Provisional
Probab=45.08 E-value=19 Score=25.43 Aligned_cols=24 Identities=25% Similarity=0.365 Sum_probs=18.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+.+|..|||+..| + ....+.|+|+
T Consensus 3 ~~~ti~dIA~~ag-V----S~~TVSrvLn 26 (315)
T PRK09492 3 NKLTIKDIARLSG-V----GKSTVSRVLN 26 (315)
T ss_pred CCCcHHHHHHHhC-C----CHHHHhHHhC
Confidence 3578999999999 8 6667777664
No 344
>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=45.01 E-value=40 Score=24.21 Aligned_cols=41 Identities=15% Similarity=0.245 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhChHHHHHh-cCCCCCCCHHHHHhhCCCCCCCCCcchHH
Q 045477 20 SVLHMTMKAVINLGLFEIIAK-AGPGAKLSASEIAAQLPATKNKDAPTMLD 69 (89)
Q Consensus 20 ~~~~~aL~~av~LgIfd~l~~-~g~~~~~t~~eLA~~~~~~~~~~d~~~l~ 69 (89)
=|...+-.++.+|. ..+.+ .| ..+|..||...++ + |+.+|+
T Consensus 178 Kwr~~~q~~l~eL~--~~~~~~e~--~~~TM~eL~~~l~-I----D~~LI~ 219 (221)
T PF10376_consen 178 KWRSASQEALYELQ--SEMSEEEG--EKFTMGELIKRLG-I----DYDLIH 219 (221)
T ss_pred HHHHHHHHHHHHHH--HHHhhccc--cCccHHHHHHHhC-C----CccccC
Confidence 45566667777654 55665 44 7899999999999 9 887763
No 345
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=44.99 E-value=33 Score=22.97 Aligned_cols=28 Identities=14% Similarity=0.100 Sum_probs=19.6
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHH
Q 045477 37 IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70 (89)
Q Consensus 37 ~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~R 70 (89)
.+.+.|- ..+|+++||+..| + ++..+++
T Consensus 23 lf~~~G~-~~~ti~~Ia~~ag-v----sk~t~Y~ 50 (213)
T PRK09975 23 QFALRGV-SNTTLNDIADAAN-V----TRGAIYW 50 (213)
T ss_pred HHHHcCc-ccCCHHHHHHHcC-C----CHHHHHH
Confidence 3555442 5799999999999 9 6655443
No 346
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=44.62 E-value=20 Score=25.70 Aligned_cols=24 Identities=13% Similarity=0.250 Sum_probs=19.3
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+..|..|||+..| + ....+.|+|+
T Consensus 5 ~~~Ti~dIA~~ag-V----S~~TVSr~Ln 28 (342)
T PRK10014 5 KKITIHDVALAAG-V----SVSTVSLVLS 28 (342)
T ss_pred CCCcHHHHHHHhC-C----CHHHHHHHHC
Confidence 4679999999999 8 7777777764
No 347
>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=44.28 E-value=23 Score=25.41 Aligned_cols=24 Identities=25% Similarity=0.313 Sum_probs=20.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.++|..|||+.+| + .+..++++.+
T Consensus 235 ~~~t~~eIA~~lg-v----S~~~V~q~~~ 258 (270)
T TIGR02392 235 DKLTLQELAAEYG-V----SAERIRQIEK 258 (270)
T ss_pred CCcCHHHHHHHHC-C----CHHHHHHHHH
Confidence 5899999999999 9 8888876654
No 348
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=44.19 E-value=14 Score=23.91 Aligned_cols=35 Identities=14% Similarity=0.235 Sum_probs=31.5
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.-+|.+=|..++. + +..+-++.||.|...|++..+
T Consensus 59 k~it~svl~dRlk-I----ngsLAr~alr~L~~kG~Ik~V 93 (110)
T KOG1767|consen 59 KLITPSVLSDRLK-I----NGSLARAALRELSNKGVIKQV 93 (110)
T ss_pred eeecHHHhhhhhh-h----chHHHHHHHHHHHhcchHHHH
Confidence 4589999999999 9 899999999999999998765
No 349
>PRK10130 transcriptional regulator EutR; Provisional
Probab=44.17 E-value=40 Score=25.50 Aligned_cols=38 Identities=11% Similarity=0.137 Sum_probs=28.6
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
+-+.|.++- ..|+|+.+||+.++ + .+..|.|..+....
T Consensus 245 ~~~~i~~~~-~~~ltv~~lA~~~g-v----S~r~L~r~Fk~~~G 282 (350)
T PRK10130 245 AREYVLENM-SEPVTVLDLCNQLH-V----SRRTLQNAFHAILG 282 (350)
T ss_pred HHHHHHhhh-cCCCCHHHHHHHHC-C----CHHHHHHHHHHHHC
Confidence 335555543 37899999999999 9 89888888865543
No 350
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=43.77 E-value=39 Score=24.01 Aligned_cols=37 Identities=30% Similarity=0.273 Sum_probs=27.5
Q ss_pred HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcch----HHHHHHHH
Q 045477 29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTM----LDRILGLL 75 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~----l~RlLR~L 75 (89)
--|..|+..+++ +.|.+|||+.++ . .+.. +.|+++-|
T Consensus 136 pRErEVLrLLAq-----GkTnKEIAe~L~-I----S~rTVkth~srImkKL 176 (198)
T PRK15201 136 VTERHLLKLIAS-----GYHLSETAALLS-L----SEEQTKSLRRSIMRKL 176 (198)
T ss_pred HHHHHHHHHHHC-----CCCHHHHHHHhC-C----CHHHHHHHHHHHHHHh
Confidence 357788888874 689999999999 8 5544 45566554
No 351
>cd00131 PAX Paired Box domain
Probab=43.57 E-value=12 Score=24.39 Aligned_cols=53 Identities=17% Similarity=0.223 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 20 SVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 20 ~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
|..+.++-.-....|....+ .++|..+||+.++ + ....+.|++.-....|=+.
T Consensus 12 ~~m~~~lS~d~R~rIv~~~~-----~G~s~~~iA~~~~-V----s~~tV~r~i~r~~e~G~v~ 64 (128)
T cd00131 12 FVNGRPLPDSIRQRIVELAQ-----SGIRPCDISRQLR-V----SHGCVSKILNRYYETGSIR 64 (128)
T ss_pred ccCCCcCCHHHHHHHHHHHH-----cCCCHHHHHHHHC-c----CHHHHHHHHHHHHHcCCcC
Confidence 33333444445556665553 3689999999999 9 8889999998777666554
No 352
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=43.46 E-value=20 Score=25.56 Aligned_cols=22 Identities=9% Similarity=0.276 Sum_probs=15.4
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.|+.|||+..| + .+..+.|+|+
T Consensus 2 ~ti~dIA~~ag-v----S~~TVSrvLn 23 (329)
T TIGR01481 2 VTIYDVAREAG-V----SMATVSRVVN 23 (329)
T ss_pred CcHHHHHHHhC-C----CHHHHHHHhC
Confidence 47788888888 7 6666666654
No 353
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=43.32 E-value=41 Score=16.28 Aligned_cols=14 Identities=29% Similarity=0.399 Sum_probs=9.5
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
..+|..++|+.++ +
T Consensus 9 ~~~s~~~la~~~~-i 22 (56)
T smart00530 9 KGLTQEELAEKLG-V 22 (56)
T ss_pred cCCCHHHHHHHhC-C
Confidence 3567777777776 6
No 354
>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=43.32 E-value=32 Score=22.30 Aligned_cols=26 Identities=23% Similarity=0.309 Sum_probs=17.7
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLL 75 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L 75 (89)
.++|++||.+.|+ + ||=.|.++-+..
T Consensus 22 rG~sveeI~e~T~-I----D~wFL~~i~~Iv 47 (123)
T PF02787_consen 22 RGYSVEEIHELTK-I----DPWFLEQIKNIV 47 (123)
T ss_dssp TTB-HHHHHHHH--------HHHHHHHHHHH
T ss_pred cCCCHHHHHHHHC-c----cHHHHHHHHHHH
Confidence 4689999999999 9 998888776544
No 355
>cd04900 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD is the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=43.14 E-value=24 Score=20.07 Aligned_cols=19 Identities=37% Similarity=0.714 Sum_probs=16.5
Q ss_pred CCCcchHHHHHHHHhccCc
Q 045477 62 KDAPTMLDRILGLLASYGI 80 (89)
Q Consensus 62 ~~d~~~l~RlLR~L~s~gi 80 (89)
++.|.++.++.+.|+.+|+
T Consensus 9 ~Dr~gLl~~i~~~l~~~~l 27 (73)
T cd04900 9 PDRPGLFARIAGALDQLGL 27 (73)
T ss_pred cCCCCHHHHHHHHHHHCCC
Confidence 5578899999999998875
No 356
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.01 E-value=34 Score=29.00 Aligned_cols=50 Identities=22% Similarity=0.203 Sum_probs=42.5
Q ss_pred HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-.+..+.||+...++ ..+|.+||.+.|+ . ...-+.|+|+-|+...++...
T Consensus 606 ~s~~q~~vfll~n~~---e~lt~eei~e~T~-l----~~~dl~~~L~sl~~ak~~~l~ 655 (773)
T COG5647 606 FSVYQLLVFLLFNDH---EELTFEEILELTK-L----STDDLKRVLQSLSCAKLVVLL 655 (773)
T ss_pred HHHHHHHHHHHhcCc---cceeHHHHHhhcC-C----ChhhHHHHHHHHHhhheeeec
Confidence 456788899988764 6899999999999 9 888999999999988877644
No 357
>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=42.92 E-value=31 Score=20.48 Aligned_cols=36 Identities=17% Similarity=0.154 Sum_probs=22.2
Q ss_pred CCCCHHHHHhhCCC---CCCCCCcchHHHHHHHHhccCce
Q 045477 45 AKLSASEIAAQLPA---TKNKDAPTMLDRILGLLASYGIV 81 (89)
Q Consensus 45 ~~~t~~eLA~~~~~---~~~~~d~~~l~RlLR~L~s~gi~ 81 (89)
|+.|++||++.+.. + ...-..-+..+++.|...|++
T Consensus 42 g~~tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~L~~~gli 80 (81)
T TIGR03859 42 GKRSLAEIIQELAQRFPA-AEEIEDDVIAFLAVARAKHWL 80 (81)
T ss_pred CCCcHHHHHHHHHHHcCC-hhhHHHHHHHHHHHHHHCcCc
Confidence 67899999988731 3 111123355666777677775
No 358
>smart00351 PAX Paired Box domain.
Probab=42.71 E-value=36 Score=21.83 Aligned_cols=44 Identities=18% Similarity=0.240 Sum_probs=33.5
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
....|..... ++.|..+||+.++ + .+..++|+++-....|.+..
T Consensus 22 ~R~riv~~~~-----~G~s~~~iA~~~g-v----s~~tV~kwi~r~~~~G~~~p 65 (125)
T smart00351 22 ERQRIVELAQ-----NGVRPCDISRQLC-V----SHGCVSKILGRYYETGSIRP 65 (125)
T ss_pred HHHHHHHHHH-----cCCCHHHHHHHHC-c----CHHHHHHHHHHHHHcCCcCC
Confidence 4445554443 3579999999999 9 89999999988777777654
No 359
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=42.40 E-value=62 Score=26.46 Aligned_cols=36 Identities=19% Similarity=0.179 Sum_probs=32.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.|-+..||+..++ . ++.....+|++|+..|.+....
T Consensus 505 ~p~~~~~~~~~l~-~----~~~~~~~~l~~l~~~g~lv~l~ 540 (614)
T PRK10512 505 EPWWVRDLAKETG-T----DEQAMRLTLRQAAQQGIITAIV 540 (614)
T ss_pred CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 6889999999999 9 8999999999999999776654
No 360
>PF13309 HTH_22: HTH domain
Probab=42.11 E-value=23 Score=20.24 Aligned_cols=43 Identities=14% Similarity=0.076 Sum_probs=26.1
Q ss_pred HHHHHHhChHHHHHhcCC-CCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 26 MKAVINLGLFEIIAKAGP-GAKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 26 L~~av~LgIfd~l~~~g~-~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+.-.-++.|...|.+.|- .-.=++..+|+.++ + ....++|-||
T Consensus 21 l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~-i----S~~TVY~YLr 64 (64)
T PF13309_consen 21 LSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLG-I----SRATVYRYLR 64 (64)
T ss_pred CCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHC-C----CHHHHHHHcC
Confidence 333444444444444320 01126899999999 9 7888888775
No 361
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=42.04 E-value=25 Score=20.19 Aligned_cols=41 Identities=24% Similarity=0.324 Sum_probs=29.9
Q ss_pred CCCCHHHHHhhCCCCC--C--CCCcchHHHHHHHHhccCceeeecc
Q 045477 45 AKLSASEIAAQLPATK--N--KDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~--~--~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+|++--||.+.+. -. + ..++..|++.|+-|...|+++....
T Consensus 8 ~~~~Gyei~~~l~-~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~ 52 (75)
T PF03551_consen 8 GPMHGYEIKQELE-ERTGGFWKISPGSLYPALKRLEEEGLIESRWE 52 (75)
T ss_dssp S-EEHHHHHHHHH-HCSTTTEETTHHHHHHHHHHHHHTTSEEEEEE
T ss_pred CCCcHHHHHHHHH-HHhCCCcccChhHHHHHHHHHHhCCCEEEeee
Confidence 5788888877765 31 0 1267789999999999999986643
No 362
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=41.98 E-value=30 Score=21.93 Aligned_cols=31 Identities=19% Similarity=0.207 Sum_probs=24.8
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+|+.|+|+.+| + .+ +.+|+-...|++....+
T Consensus 1 m~IgevA~~~g-v----s~----~tlRyYe~~GLl~p~~~ 31 (120)
T cd04781 1 LDIAEVARQSG-L----PA----STLRYYEEKGLIASIGR 31 (120)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCCcC
Confidence 57899999999 7 44 47899999999986543
No 363
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=41.90 E-value=20 Score=28.24 Aligned_cols=23 Identities=22% Similarity=0.277 Sum_probs=21.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
.|+|..|||+.+| . ++..+.|..
T Consensus 342 kPLtlkdvAe~lg-l----heSTVSRav 364 (455)
T PRK05932 342 KPLVLKDIAEELG-M----HESTISRAT 364 (455)
T ss_pred cCccHHHHHHHhC-C----Cccchhhhh
Confidence 7999999999999 9 999999986
No 364
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=41.63 E-value=22 Score=25.83 Aligned_cols=40 Identities=25% Similarity=0.243 Sum_probs=28.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+--|++||..--. +.-|.|+....|.|+.|...|+++-..
T Consensus 120 ~i~si~DL~~Gk~-IAip~d~~n~~r~L~lL~~~Gli~l~~ 159 (271)
T PRK11063 120 KIKSLDELQDGSQ-VAVPNDPTNLGRSLLLLQKVGLIKLKD 159 (271)
T ss_pred CCCCHHHhcCCCE-EEecCCCccHHHHHHHHHHCCCEEecC
Confidence 3557888862222 334668999999999999999977543
No 365
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.34 E-value=31 Score=21.70 Aligned_cols=31 Identities=16% Similarity=0.237 Sum_probs=24.9
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+|+.|+|+.+| + .+ +-+|+-...|++....+
T Consensus 1 ~~ige~a~~~g-v----s~----~tLryYe~~GLi~p~~~ 31 (116)
T cd04769 1 MYIGELAQQTG-V----TI----KAIRLYEEKGLLPSPKR 31 (116)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCCCC
Confidence 57899999999 8 44 47899999999986543
No 366
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=41.34 E-value=25 Score=28.49 Aligned_cols=44 Identities=11% Similarity=0.043 Sum_probs=31.4
Q ss_pred HhChHHHHHhcCC-CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 31 NLGLFEIIAKAGP-GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 31 ~LgIfd~l~~~g~-~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
|-.|.+.|-++.. -.-+|+.|||++++ + .+..+.|+.|.|=-.|
T Consensus 358 E~~IA~yIl~n~~~v~~~si~eLA~~~~-v----S~aTV~Rf~kkLGf~G 402 (638)
T PRK14101 358 ERRVADLALNHPRSIINDPIVDIARKAD-V----SQPTVIRFCRSLGCQG 402 (638)
T ss_pred HHHHHHHHHhCHHHHHhccHHHHHHHhC-C----CHHHHHHHHHHhCCCC
Confidence 4566676655431 13579999999999 9 8889999887764333
No 367
>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=41.29 E-value=87 Score=19.46 Aligned_cols=49 Identities=14% Similarity=0.088 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 20 SVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 20 ~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
+..|.+.+.-..+.=-.+..+. .+.++.|||.+.+ . ....+++|++..-
T Consensus 49 iyiP~~~~~~~~~R~~~I~~~f---~G~n~~eLA~kyg-l----S~r~I~~Ii~~~~ 97 (108)
T PF08765_consen 49 IYIPKCDRLLRALRNREIRREF---NGMNVRELARKYG-L----SERQIYRIIKRVR 97 (108)
T ss_dssp -----SHHHHHHHHHHHHHHH-----SS-HHHHHHHHT-------HHHHHHHHHHHH
T ss_pred EEeeCccHHHHHHHHHHHHHHh---CCCCHHHHHHHHC-c----CHHHHHHHHHHHH
Confidence 5566654443333333444443 2578999999999 9 8889999987543
No 368
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=41.25 E-value=21 Score=25.59 Aligned_cols=22 Identities=9% Similarity=0.280 Sum_probs=17.2
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.|..|||+.+| + ....+.|+|+
T Consensus 2 ~Ti~dIA~~ag-V----S~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAG-V----STTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhC-C----CHHHHHHHHc
Confidence 47889999998 8 7777777774
No 369
>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=41.14 E-value=52 Score=19.74 Aligned_cols=39 Identities=21% Similarity=0.203 Sum_probs=24.0
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
..|++.+.+-+.|.-.|..|||+.++ - |..+..+.+.|+
T Consensus 5 ~~V~~~v~~IP~G~v~TYg~iA~~~g-~--p~~ar~Vg~al~ 43 (85)
T PF01035_consen 5 RRVWEAVRQIPYGKVTTYGEIARLLG-R--PKAARAVGSALA 43 (85)
T ss_dssp HHHHHHHTTS-TT-BEEHHHHHHHTT----TTCHHHHHHHHH
T ss_pred HHHHHHHHcCCCCceEeHHHHHHHHh-h--cccHHHHHHHhc
Confidence 34566666544457899999999999 2 334445555554
No 370
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=40.83 E-value=23 Score=19.65 Aligned_cols=30 Identities=20% Similarity=0.290 Sum_probs=21.4
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+|+.|+|+.+| + .+. .+|+....|++....
T Consensus 1 yti~eva~~~g-v----s~~----tlr~y~~~gll~~~~ 30 (69)
T PF13411_consen 1 YTIKEVAKLLG-V----SPS----TLRYYEREGLLPPPR 30 (69)
T ss_dssp EEHHHHHHHTT-T----THH----HHHHHHHTTSSTTBE
T ss_pred CcHHHHHHHHC-c----CHH----HHHHHHHhcCccccc
Confidence 47899999999 8 665 556666677765443
No 371
>PRK09480 slmA division inhibitor protein; Provisional
Probab=40.82 E-value=40 Score=22.08 Aligned_cols=14 Identities=14% Similarity=0.458 Sum_probs=13.1
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
...|+++||++.| +
T Consensus 29 ~~~ti~~Ia~~ag-v 42 (194)
T PRK09480 29 ERITTAKLAARVG-V 42 (194)
T ss_pred CccCHHHHHHHhC-C
Confidence 6889999999999 9
No 372
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=40.78 E-value=31 Score=22.06 Aligned_cols=30 Identities=7% Similarity=0.246 Sum_probs=24.3
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
|++.|+|+.+| + .+ +-+|+--..|++....
T Consensus 1 m~I~e~a~~~g-v----s~----~tlRyYe~~GLl~p~~ 30 (127)
T TIGR02044 1 MNIGQVAKLTG-L----SS----KMIRYYEEKGLIPPPL 30 (127)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCCC
Confidence 57899999999 8 54 4788999999997643
No 373
>cd04897 ACT_ACR_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=40.51 E-value=27 Score=20.85 Aligned_cols=24 Identities=21% Similarity=0.295 Sum_probs=19.9
Q ss_pred CCCCcchHHHHHHHHhccCceeee
Q 045477 61 NKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 61 ~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.++-|.+|+++-|.|+.+|+.-..
T Consensus 8 ~~DRpGLL~~i~~~l~~~~l~I~~ 31 (75)
T cd04897 8 CRDRPKLLFDVVCTLTDMDYVVFH 31 (75)
T ss_pred eCCcCcHHHHHHHHHHhCCeEEEE
Confidence 466899999999999999986543
No 374
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=40.41 E-value=36 Score=25.88 Aligned_cols=49 Identities=20% Similarity=0.210 Sum_probs=38.4
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCC----CCCCCCcchHHHHHHHHhccCceeeec
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPA----TKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~----~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
...|.++|++++ .|+.+..||..+.+ . ..+.++=-||.|--+|+.+.+.
T Consensus 8 ~ieIl~il~esd--~plgak~Ia~el~kRGy~i----geRavRYhlk~lderglt~kvg 60 (325)
T COG1693 8 LIEILRILAESD--EPLGAKIIALELRKRGYNI----GERAVRYHLKKLDERGLTRKVG 60 (325)
T ss_pred HHHHHHHHHhcC--CccchHHHHHHHHhcccch----hHHHHHHHHHHHhhccchhhcc
Confidence 345888999986 89999999998763 3 4566777888898888877654
No 375
>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=40.40 E-value=35 Score=19.11 Aligned_cols=25 Identities=32% Similarity=0.275 Sum_probs=20.1
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHH
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLL 75 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L 75 (89)
.++..|-|..+| + ....|.|+.|.+
T Consensus 15 hlp~~eAA~~Lg-v----~~T~LKr~CR~~ 39 (52)
T PF02042_consen 15 HLPIKEAAKELG-V----SVTTLKRRCRRL 39 (52)
T ss_pred CCCHHHHHHHhC-C----CHHHHHHHHHHc
Confidence 467888899999 8 888888888743
No 376
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.13 E-value=35 Score=20.54 Aligned_cols=27 Identities=19% Similarity=0.260 Sum_probs=19.9
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
+|+.|+|+.+| + .+. -+|+....|++.
T Consensus 1 ~~~~eva~~~g-i----~~~----tlr~~~~~Gll~ 27 (100)
T cd00592 1 YTIGEVAKLLG-V----SVR----TLRYYEEKGLLP 27 (100)
T ss_pred CCHHHHHHHHC-c----CHH----HHHHHHHCCCcC
Confidence 47889999999 8 665 445556678876
No 377
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=39.97 E-value=23 Score=25.33 Aligned_cols=24 Identities=13% Similarity=0.243 Sum_probs=18.7
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+..|..|||+..| + ....+.|+|+
T Consensus 4 ~~~ti~dIA~~ag-V----S~~TVSrvLn 27 (331)
T PRK14987 4 KRPVLQDVADRVG-V----TKMTVSRFLR 27 (331)
T ss_pred CCCcHHHHHHHhC-C----CHHHhhhhhC
Confidence 4579999999999 8 6767777663
No 378
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=39.96 E-value=28 Score=24.17 Aligned_cols=41 Identities=32% Similarity=0.401 Sum_probs=26.8
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
-|..|...|+ .+.|-+|||.+++ .+...=...+.++||-|-
T Consensus 152 RE~eVL~lla-----~G~snkeIA~~L~-iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 152 RELEVLRLLA-----EGLSNKEIAEELN-LSEKTVKTHVSNILRKLG 192 (211)
T ss_pred HHHHHHHHHH-----CCCCHHHHHHHHC-CCHhHHHHHHHHHHHHcC
Confidence 3455666666 4789999999999 821111224677887664
No 379
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=39.57 E-value=90 Score=21.75 Aligned_cols=44 Identities=18% Similarity=0.126 Sum_probs=35.2
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
...-+|+=. +|+|-.||-+.-| + + -+.+++.|..+|++++.++.
T Consensus 91 EtLAIIAY~---QPITr~eIe~IRG-v----~---s~~~l~~L~ergLI~~~Gr~ 134 (186)
T TIGR00281 91 EVLAIIAYK---QPITRARINEIRG-V----K---SYQIVDDLVEKGLVVELGRK 134 (186)
T ss_pred HHHHHHHHc---CCcCHHHHHHHcC-C----C---HHHHHHHHHHCCCeEecCcC
Confidence 345566643 7999999999999 8 5 36799999999999988654
No 380
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=39.56 E-value=56 Score=24.80 Aligned_cols=28 Identities=18% Similarity=0.333 Sum_probs=23.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
.++|+++||+.++ . ++..+.|+.+....
T Consensus 98 ~~lsl~eLA~~lG-~----S~~~L~R~Fkk~~G 125 (353)
T PRK15435 98 TPVTLEALADQVA-M----SPFHLHRLFKATTG 125 (353)
T ss_pred CCCCHHHHHHHHC-C----CHHHHHHHHHHHHC
Confidence 6899999999999 9 88889988876543
No 381
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=39.32 E-value=99 Score=22.45 Aligned_cols=50 Identities=12% Similarity=0.187 Sum_probs=36.5
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCC----CCCCcchHHHHHHHHhccCceeeecc
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATK----NKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~----~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
-|.+.|... ||+|.+||.+.+. .. .+.......++|+.|...|.+....+
T Consensus 89 ~v~~~L~~~---gplt~~eL~~~l~-~~~~~~~~~~~~~~~~~l~~l~~~G~l~~~~~ 142 (327)
T PF06224_consen 89 AVLDALRAD---GPLTRAELREALA-EAGWWGWGGPSSPWKHLLEYLWYRGLLCVGPR 142 (327)
T ss_pred HHHHHHHhc---CCCCHHHHHHHhh-hccccCCCCCCchHHHHHHHHHhCCeEEEecc
Confidence 356667442 7999999999987 52 11134478999999999999886653
No 382
>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=39.10 E-value=35 Score=20.78 Aligned_cols=24 Identities=33% Similarity=0.252 Sum_probs=19.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.+.|..|||+.+| + .+..+++.+.
T Consensus 125 ~g~s~~eIA~~l~-~----s~~~v~~~~~ 148 (158)
T TIGR02937 125 EGLSYKEIAEILG-I----SVGTVKRRLK 148 (158)
T ss_pred cCCCHHHHHHHHC-C----CHHHHHHHHH
Confidence 4689999999999 9 7777665554
No 383
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.94 E-value=32 Score=21.91 Aligned_cols=28 Identities=14% Similarity=0.180 Sum_probs=23.1
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
++..|+|+.+| + .+. -+|+.-..|++..
T Consensus 1 m~I~e~a~~~g-v----s~~----tlR~Ye~~GLl~~ 28 (126)
T cd04783 1 LTIGELAKAAG-V----NVE----TIRYYQRRGLLPE 28 (126)
T ss_pred CCHHHHHHHHC-c----CHH----HHHHHHHCCCCCC
Confidence 57899999999 8 664 4599999999974
No 384
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=38.91 E-value=57 Score=21.32 Aligned_cols=49 Identities=10% Similarity=0.084 Sum_probs=33.3
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCC--CCC---cchHHHHHHHHhcc
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKN--KDA---PTMLDRILGLLASY 78 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~--~~d---~~~l~RlLR~L~s~ 78 (89)
+..|..|...|.++. +..+|-+||++.+. ... +.. ...+.||+|.|...
T Consensus 156 t~~E~~il~~l~~~~-~~~~s~~~i~~~l~-~~~~~~~~~tv~~~i~~l~~Kl~~~ 209 (228)
T PRK11083 156 TRYEFLLLKTLLLSP-GRVFSRQQLMDIVW-EDAQDSYDRTVDTHIKTLRAKLRAI 209 (228)
T ss_pred CHHHHHHHHHHHhCC-CceECHHHHHHHhc-CCCCCCCccCHHHHHHHHHHHhccC
Confidence 345667778888753 47899999999988 521 001 23588999998643
No 385
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=38.84 E-value=34 Score=22.00 Aligned_cols=22 Identities=23% Similarity=0.404 Sum_probs=17.1
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRI 71 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~Rl 71 (89)
.++|.+|||+.+| + .+..+.+.
T Consensus 124 ~~~s~~EIA~~lg-i----s~~tV~~~ 145 (163)
T PRK07037 124 HGETQKDIARELG-V----SPTLVNFM 145 (163)
T ss_pred cCCCHHHHHHHHC-C----CHHHHHHH
Confidence 4789999999999 9 66555443
No 386
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=38.73 E-value=40 Score=23.49 Aligned_cols=27 Identities=30% Similarity=0.407 Sum_probs=22.4
Q ss_pred CC-CCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 45 AK-LSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 45 ~~-~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
.| +|+.+|++.++ . ++.-+..++..|.
T Consensus 18 ~pgls~~~La~~l~-~----~~~~v~~~l~~L~ 45 (188)
T PRK00135 18 EEGLSLEQLAEILE-L----EPTEVQQLLEELQ 45 (188)
T ss_pred CCCCCHHHHHHHHC-C----CHHHHHHHHHHHH
Confidence 66 99999999999 8 7777777777774
No 387
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=38.66 E-value=50 Score=23.71 Aligned_cols=39 Identities=13% Similarity=0.231 Sum_probs=28.1
Q ss_pred HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
++..++...+.|..-. .-.|.+||++.+| . .+..|.|--
T Consensus 6 ~~~~~~~~v~~lr~lk--~~~ty~el~~~~g-~----p~~~l~RYv 44 (238)
T PRK08558 6 KVRLQLRAVRVLRSLK--KTYTYEELSSITG-L----PESVLNRYV 44 (238)
T ss_pred hHHHHHHHHHHHHHHh--cccCHHHHHHHHC-C----CHHHHHHHH
Confidence 3455666677776543 5689999999999 8 777776654
No 388
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=38.58 E-value=39 Score=24.05 Aligned_cols=35 Identities=29% Similarity=0.414 Sum_probs=30.4
Q ss_pred CCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 45 AKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 45 ~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
..+ +=.||+++.| + .-..|+--|+.|.+.|++.-.
T Consensus 32 ~~LP~EreLae~fg-V----SR~~vREAl~~L~a~Glve~r 67 (241)
T COG2186 32 DRLPSERELAERFG-V----SRTVVREALKRLEAKGLVEIR 67 (241)
T ss_pred CCCCCHHHHHHHHC-C----CcHHHHHHHHHHHHCCCeeec
Confidence 444 6889999999 9 888999999999999998743
No 389
>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=38.38 E-value=31 Score=17.73 Aligned_cols=26 Identities=27% Similarity=0.439 Sum_probs=19.5
Q ss_pred CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 48 SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 48 t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
|..|+|+.+| + .+ +-||+.-..|++.
T Consensus 1 ti~e~A~~~g-v----s~----~tlR~ye~~Gll~ 26 (38)
T PF00376_consen 1 TIGEVAKLLG-V----SP----RTLRYYEREGLLP 26 (38)
T ss_dssp EHHHHHHHHT-S-----H----HHHHHHHHTTSS-
T ss_pred CHHHHHHHHC-C----CH----HHHHHHHHCCCCC
Confidence 4689999999 8 55 4778888889884
No 390
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.28 E-value=55 Score=20.70 Aligned_cols=39 Identities=10% Similarity=0.174 Sum_probs=32.2
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
.|-.+.+...|.+ +-|-.+|-..+| + ....+.|+=|.|-
T Consensus 43 laqRlqVa~mL~e-----g~tY~~I~~eTG-a----StaTIsRVkRcl~ 81 (100)
T COG4496 43 LAQRLQVAKMLKE-----GRTYRDIEDETG-A----STATISRVKRCLN 81 (100)
T ss_pred HHHHHHHHHHHHc-----CCCcchhhhccC-c----chhhHHHHHHHHH
Confidence 4567888888875 467889999999 9 8889999999874
No 391
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=38.26 E-value=37 Score=21.38 Aligned_cols=29 Identities=14% Similarity=0.284 Sum_probs=23.7
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|..|+|+.+| + .+ +.+|+--..|++...
T Consensus 1 ~~I~eva~~~g-v----s~----~tLRyYe~~GLl~p~ 29 (123)
T cd04770 1 MKIGELAKAAG-V----SP----DTIRYYERIGLLPPP 29 (123)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 57899999999 8 54 367899999999854
No 392
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=38.21 E-value=49 Score=26.42 Aligned_cols=36 Identities=19% Similarity=0.350 Sum_probs=27.9
Q ss_pred HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHH
Q 045477 31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLL 75 (89)
Q Consensus 31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L 75 (89)
...|.+.|.+ +++|.++||+.++ + ....++|=+..+
T Consensus 6 ~~~iL~~L~~----~~~t~~~LA~~l~-V----S~RTIr~dI~~i 41 (584)
T PRK09863 6 ELKIVDLLEQ----QDRSGGELAQQLG-V----SRRTIVRDIAYI 41 (584)
T ss_pred HHHHHHHHHc----CCCCHHHHHHHhC-C----CHHHHHHHHHHH
Confidence 3456777743 6899999999999 9 888888777644
No 393
>PRK09726 antitoxin HipB; Provisional
Probab=37.80 E-value=31 Score=20.58 Aligned_cols=14 Identities=21% Similarity=0.285 Sum_probs=11.9
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
..+|..|+|+.+| +
T Consensus 24 ~gltq~elA~~~g-v 37 (88)
T PRK09726 24 NGWTQSELAKKIG-I 37 (88)
T ss_pred cCCCHHHHHHHHC-c
Confidence 5688999999988 7
No 394
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=37.55 E-value=65 Score=22.24 Aligned_cols=36 Identities=14% Similarity=0.228 Sum_probs=27.2
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL 74 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~ 74 (89)
.+-.|++.+.. ++.|+.++|++.| + +...+.=|+|+
T Consensus 21 ~r~~Iy~~~~~----~~~sv~~vS~~yg-i----~~~RV~AIvrL 56 (172)
T PF12298_consen 21 LREQIYEDVMQ----DGKSVREVSQKYG-I----KIQRVEAIVRL 56 (172)
T ss_pred HHHHHHHHHHh----CCCCHHHHHHHhC-C----CHHHHHHHHHH
Confidence 45567777766 5679999999999 9 77776666664
No 395
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=37.52 E-value=53 Score=22.91 Aligned_cols=34 Identities=12% Similarity=0.161 Sum_probs=30.7
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
-|=.|||+..+ + .-..+++-|..|+..|++....
T Consensus 34 PsE~eLa~~~~-V----SR~TvR~Al~~L~~eGli~r~~ 67 (241)
T PRK11402 34 PTENELCTQYN-V----SRITIRKAISDLVADGVLIRWQ 67 (241)
T ss_pred cCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 48899999999 9 8999999999999999998653
No 396
>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=37.26 E-value=66 Score=23.70 Aligned_cols=41 Identities=10% Similarity=0.130 Sum_probs=32.9
Q ss_pred hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
-.|-|-|..+| |-+++.||+..++ + |...+.|..+.++...
T Consensus 58 ~EI~~el~~~g--GRv~~~dL~~~Ln-V----d~~~ie~~~~~i~~~~ 98 (272)
T PF09743_consen 58 KEIKDELYVHG--GRVNLVDLAQALN-V----DLDHIERRAQEIVKSD 98 (272)
T ss_pred HHHHHHHHHcC--CceEHHHHHHhcC-c----CHHHHHHHHHHHHhCC
Confidence 34556665565 8999999999999 9 9999999998877543
No 397
>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=37.01 E-value=44 Score=20.97 Aligned_cols=23 Identities=22% Similarity=0.183 Sum_probs=17.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
.++|..|||+.+| + .+..++..+
T Consensus 128 ~~~~~~eIA~~lg-i----s~~tv~~~~ 150 (161)
T TIGR02985 128 EGKSYKEIAEELG-I----SVKTVEYHI 150 (161)
T ss_pred cCCCHHHHHHHHC-C----CHHHHHHHH
Confidence 4789999999999 9 666655443
No 398
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=36.81 E-value=56 Score=23.05 Aligned_cols=35 Identities=23% Similarity=0.393 Sum_probs=27.6
Q ss_pred HHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 36 EIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 36 d~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
..|..+. .+.++++||..++ . +|..++|+.+.-..
T Consensus 89 ~~ie~~~--~~~~le~la~~lg-~----sp~~~~R~FK~~~G 123 (187)
T COG2169 89 RLIEQNP--EKRWLEELADELG-V----SPSTLHRLFKAITG 123 (187)
T ss_pred HHHHcCC--CcccHHHHHHHhC-C----ChHHHHHHHHHHhC
Confidence 4455543 7899999999999 9 99999998875443
No 399
>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=36.79 E-value=26 Score=18.85 Aligned_cols=23 Identities=22% Similarity=0.309 Sum_probs=18.4
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
-++..|+++.+| + ....++|+++
T Consensus 3 ll~~~ev~~~~g-~----s~~ti~~~~k 25 (51)
T PF05930_consen 3 LLRIKEVAELLG-V----SRSTIYRLIK 25 (51)
T ss_dssp EE-HHHHHHHHS-S-----HHHHHHHHH
T ss_pred cccHHHHHHHHC-C----CHHHHHHHHh
Confidence 367899999999 9 8889999887
No 400
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=36.77 E-value=27 Score=25.17 Aligned_cols=22 Identities=18% Similarity=0.374 Sum_probs=15.6
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.|..|||+..| + ....+.|+|+
T Consensus 2 ~ti~dIA~~aG-V----S~~TVSrvLn 23 (346)
T PRK10401 2 ITIRDVARQAG-V----SVATVSRVLN 23 (346)
T ss_pred CCHHHHHHHhC-C----CHHHHHHHHC
Confidence 47788888888 7 6666666664
No 401
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=36.74 E-value=53 Score=22.06 Aligned_cols=21 Identities=19% Similarity=0.290 Sum_probs=16.3
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCC
Q 045477 37 IIAKAGPGAKLSASEIAAQLPAT 59 (89)
Q Consensus 37 ~l~~~g~~~~~t~~eLA~~~~~~ 59 (89)
.+.+.|- ...|+++||+..| +
T Consensus 23 lf~e~G~-~~~t~~~Ia~~ag-v 43 (215)
T PRK10668 23 LFSQQGV-SATSLADIAKAAG-V 43 (215)
T ss_pred HHHHcCc-ccCCHHHHHHHhC-C
Confidence 3566552 5689999999999 8
No 402
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=36.45 E-value=46 Score=19.61 Aligned_cols=26 Identities=23% Similarity=0.418 Sum_probs=21.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLL 75 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L 75 (89)
.++|+.|.|..+| . ++..+.+-.|..
T Consensus 12 ~~~s~~~Aa~~lG-~----~~~~v~~wv~~f 37 (65)
T PF05344_consen 12 QQISVAQAADRLG-T----DPGTVRRWVRMF 37 (65)
T ss_pred ccccHHHHHHHHC-c----CHHHHHHHHHHH
Confidence 6899999999999 9 888887766543
No 403
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.36 E-value=42 Score=20.91 Aligned_cols=29 Identities=14% Similarity=0.171 Sum_probs=22.6
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|..|+|+.+| + .+ +-+|+....|++...
T Consensus 1 ~~i~e~a~~~g-v----s~----~tlr~ye~~gll~~~ 29 (113)
T cd01109 1 YTIKEVAEKTG-L----SA----DTLRYYEKEGLLPPV 29 (113)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 47899999999 8 55 367788888998543
No 404
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=36.27 E-value=41 Score=21.52 Aligned_cols=29 Identities=10% Similarity=0.226 Sum_probs=23.4
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|..|+|+.+| + .+ +-+|+-...|++...
T Consensus 1 m~I~e~a~~~g-v----s~----~tlRyYe~~GLl~~~ 29 (127)
T cd01108 1 MNIGEAAKLTG-L----SA----KMIRYYEEIGLIPPP 29 (127)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 57899999999 8 55 477888889999744
No 405
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=35.93 E-value=28 Score=25.10 Aligned_cols=21 Identities=10% Similarity=0.240 Sum_probs=14.0
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
.|+.|||+..| + ....+.|+|
T Consensus 2 ~ti~dIA~~aG-V----S~~TVSrvL 22 (343)
T PRK10727 2 ATIKDVARLAG-V----SVATVSRVI 22 (343)
T ss_pred CCHHHHHHHhC-C----CHHHHHHHh
Confidence 36778888877 7 555555555
No 406
>COG3703 ChaC Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]
Probab=35.83 E-value=51 Score=23.36 Aligned_cols=36 Identities=28% Similarity=0.290 Sum_probs=26.3
Q ss_pred CCCCHHHHHh----hCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 45 AKLSASEIAA----QLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 45 ~~~t~~eLA~----~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
++.+.+++|. .+| - ++++...|.+.+.+|..+||=.
T Consensus 130 g~l~~~~~A~~ia~a~G-~-sG~n~eYL~~t~~hL~~~gi~d 169 (190)
T COG3703 130 GDLDAEQIAAIIAAAVG-L-SGPNAEYLFNTLQHLRKLGIRD 169 (190)
T ss_pred CCCcHHHHHHHHHHHhC-C-CCCcHHHHHHHHHHHHhcCCcc
Confidence 4566655554 444 3 5558899999999999999744
No 407
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=35.79 E-value=32 Score=27.47 Aligned_cols=23 Identities=17% Similarity=0.250 Sum_probs=21.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
.|++..+||+.+| . ++..+.|+.
T Consensus 368 kPLtlkdVAe~lg-l----HeSTVSRa~ 390 (481)
T PRK12469 368 KPLVLRDVAEELG-L----HESTISRAT 390 (481)
T ss_pred cCCcHHHHHHHhC-C----CcchhhHHh
Confidence 7999999999999 9 999999986
No 408
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=35.70 E-value=66 Score=22.48 Aligned_cols=56 Identities=27% Similarity=0.313 Sum_probs=38.8
Q ss_pred HhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCC------CCCCCCcchHH-----HHHHHHhcc
Q 045477 18 MGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPA------TKNKDAPTMLD-----RILGLLASY 78 (89)
Q Consensus 18 ~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~------~~~~~d~~~l~-----RlLR~L~s~ 78 (89)
.||...+.--.||++|-.|.|++ |..+++|-..+.. ...|.+|..+. +|-|.|...
T Consensus 88 TGy~sIATAV~AvKlGA~~YLaK-----PAdaDdi~aAl~~~~~d~~~~~~~~pmS~~rl~WEhIqrvl~e~ 154 (182)
T COG4567 88 TGYASIATAVEAVKLGACDYLAK-----PADADDILAALLRREPDEDTAPPENPMSADRLRWEHIQRVLEEC 154 (182)
T ss_pred ecchHHHHHHHHHHhhhhhhcCC-----CCChHHHHHHHhhcCCCcccCCCCCCCchhHhhHHHHHHHHHHh
Confidence 47888888888999999999974 8888888776541 12444555444 455666543
No 409
>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=35.63 E-value=38 Score=19.13 Aligned_cols=14 Identities=36% Similarity=0.325 Sum_probs=12.4
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
.+.+..|||+.+| +
T Consensus 12 ~G~~~~eIA~~Lg-~ 25 (58)
T PF06056_consen 12 QGWSIKEIAEELG-V 25 (58)
T ss_pred cCCCHHHHHHHHC-C
Confidence 3689999999999 8
No 410
>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=35.62 E-value=34 Score=15.08 Aligned_cols=21 Identities=33% Similarity=0.305 Sum_probs=15.5
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHH
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRI 71 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~Rl 71 (89)
+.|..++|+..+ . ....+++.
T Consensus 21 ~~s~~~ia~~~~-i----s~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLG-V----SRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHC-C----CHHHHHHh
Confidence 458999999998 8 56555553
No 411
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=35.62 E-value=38 Score=18.12 Aligned_cols=19 Identities=32% Similarity=0.588 Sum_probs=15.3
Q ss_pred CCCcchHHHHHHHHhccCc
Q 045477 62 KDAPTMLDRILGLLASYGI 80 (89)
Q Consensus 62 ~~d~~~l~RlLR~L~s~gi 80 (89)
|+.|..|.++++.+...|+
T Consensus 6 ~d~~G~L~~i~~~i~~~~~ 24 (73)
T cd04886 6 PDRPGQLAKLLAVIAEAGA 24 (73)
T ss_pred CCCCChHHHHHHHHHHcCC
Confidence 4578889999999987665
No 412
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=35.49 E-value=29 Score=24.04 Aligned_cols=34 Identities=29% Similarity=0.289 Sum_probs=23.8
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
..++|.++-...++|-+|||++++ . ++..|.|+=
T Consensus 80 Y~e~Ir~ARE~~G~SqedLA~ki~-e----k~svI~~iE 113 (165)
T COG1813 80 YGERIREAREKRGLSQEDLAAKLK-E----KVSVIRRIE 113 (165)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhc-c----cHHHHHHHH
Confidence 345555433237899999999999 8 777766653
No 413
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=35.36 E-value=29 Score=18.52 Aligned_cols=19 Identities=37% Similarity=0.614 Sum_probs=16.2
Q ss_pred CCCcchHHHHHHHHhccCc
Q 045477 62 KDAPTMLDRILGLLASYGI 80 (89)
Q Consensus 62 ~~d~~~l~RlLR~L~s~gi 80 (89)
|+.|..|.++...|+.+|+
T Consensus 8 ~drpG~l~~v~~~la~~~i 26 (66)
T PF01842_consen 8 PDRPGILADVTEILADHGI 26 (66)
T ss_dssp ETSTTHHHHHHHHHHHTTE
T ss_pred CCCCCHHHHHHHHHHHcCC
Confidence 4578899999999998886
No 414
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=35.33 E-value=57 Score=19.09 Aligned_cols=34 Identities=18% Similarity=0.230 Sum_probs=22.8
Q ss_pred HHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 49 ASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 49 ~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-.+|++..+ + .|-....+..+++-|...|++.-.
T Consensus 25 Y~~lc~~~~-~-~pls~~r~~~~l~eL~~~gli~~~ 58 (85)
T PF09079_consen 25 YEELCESLG-V-DPLSYRRFSDYLSELEMLGLIESE 58 (85)
T ss_dssp HHHHHHHTT-S-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHcC-C-CCCCHHHHHHHHHHHHhCCCeEEE
Confidence 356788888 7 333455677778888899998744
No 415
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=35.33 E-value=37 Score=22.40 Aligned_cols=22 Identities=14% Similarity=0.237 Sum_probs=17.4
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
||.+|||..+| . ....+.|-.|
T Consensus 1 MT~eELA~~tG-~----srQTINrWvR 22 (122)
T PF07037_consen 1 MTPEELAELTG-Y----SRQTINRWVR 22 (122)
T ss_pred CCHHHHHHHhC-c----cHHHHHHHHH
Confidence 68899999999 8 6666766655
No 416
>PRK15320 transcriptional activator SprB; Provisional
Probab=35.25 E-value=46 Score=24.27 Aligned_cols=43 Identities=14% Similarity=0.174 Sum_probs=29.7
Q ss_pred HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
.-|..|+..|++ +.|-+|||++++ .+...=...+.|++..|-.
T Consensus 167 dREIEVL~LLAk-----G~SNKEIAekL~-LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 167 QAKYALLILLSS-----GHPAIELAKKFG-LGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred HHHHHHHHHHHc-----CCCHHHHHHHhc-cchhhHHHHHHHHHHHcCC
Confidence 357778888875 689999999999 7322223346677766643
No 417
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=35.17 E-value=43 Score=21.77 Aligned_cols=29 Identities=14% Similarity=0.242 Sum_probs=23.8
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
|+..|+|+.+| + .+ +-+|+--..|++...
T Consensus 1 m~Ige~a~~~g-v----s~----~tLRyYE~~GLl~p~ 29 (131)
T cd04786 1 MKIGELAKRSG-M----AA----SRIRFYEAEGLLSSV 29 (131)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 57899999999 8 44 478999999999754
No 418
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=35.15 E-value=88 Score=21.10 Aligned_cols=30 Identities=17% Similarity=0.201 Sum_probs=25.0
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCC
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLP 57 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~ 57 (89)
+..+..|++.|.+-+.|...|..|||+.+|
T Consensus 72 t~fq~~Vw~~l~~Ip~G~t~tY~~lA~~~g 101 (155)
T PRK00901 72 TEFQKKVWKALQEIPYGETRSYKEIAVNIG 101 (155)
T ss_pred ChHHHHHHHHHccCCCCCcCCHHHHHHHHC
Confidence 456678888888766668899999999999
No 419
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=34.81 E-value=41 Score=24.50 Aligned_cols=24 Identities=21% Similarity=0.214 Sum_probs=20.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.++|..|||+.+| + .+..++++.+
T Consensus 247 ~~~Tl~EIA~~lg-v----S~~rVrqi~~ 270 (284)
T PRK06596 247 DKSTLQELAAEYG-V----SAERVRQIEK 270 (284)
T ss_pred CCcCHHHHHHHHC-C----CHHHHHHHHH
Confidence 5899999999999 9 8888777765
No 420
>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=34.69 E-value=86 Score=20.31 Aligned_cols=25 Identities=16% Similarity=0.232 Sum_probs=19.2
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCC
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPAT 59 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~ 59 (89)
-.++.+.+.| =..+|++||+++.| +
T Consensus 11 a~~~Ll~~k~-~~~ITV~~I~~~Ag-v 35 (176)
T TIGR02366 11 AFKDLMEVQA-FSKISVSDIMSTAQ-I 35 (176)
T ss_pred HHHHHHHHCC-CccCCHHHHHHHhC-C
Confidence 3455677655 36799999999999 9
No 421
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.65 E-value=50 Score=20.34 Aligned_cols=28 Identities=18% Similarity=0.252 Sum_probs=22.8
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
++..|+|+.+| + .+. -+|+-...|++..
T Consensus 2 ~~i~eva~~~g-v----s~~----tlR~ye~~Gll~~ 29 (102)
T cd04789 2 YTISELAEKAG-I----SRS----TLLYYEKLGLITG 29 (102)
T ss_pred CCHHHHHHHHC-c----CHH----HHHHHHHCCCCCC
Confidence 58899999999 8 554 6778888899875
No 422
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=34.53 E-value=27 Score=25.01 Aligned_cols=22 Identities=18% Similarity=0.300 Sum_probs=15.1
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.|..|||+..| + ....+.|+|+
T Consensus 2 ~ti~dIA~~ag-V----S~~TVSrvln 23 (327)
T PRK10339 2 ATLKDIAIEAG-V----SLATVSRVLN 23 (327)
T ss_pred CCHHHHHHHhC-C----CHHhhhhhhc
Confidence 37788888888 7 5556666553
No 423
>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=34.50 E-value=33 Score=19.11 Aligned_cols=19 Identities=16% Similarity=0.284 Sum_probs=14.3
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDR 70 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~R 70 (89)
+|..|+|+.+| + .+..|++
T Consensus 1 ~~i~evA~~~g-v----s~~tlR~ 19 (67)
T cd04764 1 YTIKEVSEIIG-V----KPHTLRY 19 (67)
T ss_pred CCHHHHHHHHC-c----CHHHHHH
Confidence 47899999999 8 6664443
No 424
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=34.44 E-value=56 Score=22.16 Aligned_cols=27 Identities=19% Similarity=0.047 Sum_probs=19.3
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHH
Q 045477 37 IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLD 69 (89)
Q Consensus 37 ~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~ 69 (89)
.+.+.|- ...|+.+||+..| + ....++
T Consensus 30 lf~e~Gy-~~~s~~dIA~~aG-v----s~gtiY 56 (212)
T PRK15008 30 TFSQFGF-HGTRLEQIAELAG-V----SKTNLL 56 (212)
T ss_pred HHHHhCc-ccCCHHHHHHHhC-c----CHHHHH
Confidence 3566552 5689999999999 9 554443
No 425
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=34.29 E-value=57 Score=22.21 Aligned_cols=24 Identities=42% Similarity=0.403 Sum_probs=19.6
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
++.|..+||..+| + ....++|++.
T Consensus 171 ~g~s~~~iak~lg-i----s~~Tv~r~~k 194 (200)
T PRK13413 171 KGTSKSEIARKLG-V----SRTTLARFLK 194 (200)
T ss_pred CCCCHHHHHHHHC-C----CHHHHHHHHH
Confidence 3589999999999 9 7777777765
No 426
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=34.14 E-value=27 Score=22.91 Aligned_cols=14 Identities=36% Similarity=0.344 Sum_probs=12.8
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
.++|.+|||+.+| .
T Consensus 151 ~g~s~~eIA~~lg-i 164 (187)
T TIGR02948 151 EDLSLKEISEILD-L 164 (187)
T ss_pred cCCCHHHHHHHHC-C
Confidence 4689999999999 8
No 427
>PRK13698 plasmid-partitioning protein; Provisional
Probab=34.11 E-value=77 Score=24.18 Aligned_cols=41 Identities=12% Similarity=0.174 Sum_probs=29.9
Q ss_pred HHHHhCh-H-HHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477 28 AVINLGL-F-EIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76 (89)
Q Consensus 28 ~av~LgI-f-d~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~ 76 (89)
-.+|.+. + ..|-+. ...|-+|||+.+| . +...+.|.||++.
T Consensus 159 s~iE~A~ay~~~L~~~---~~~tQeeLA~~lG-~----SRs~Vsn~Lrla~ 201 (323)
T PRK13698 159 SAYERGLRYASRLQNE---FAGNISALADAEN-I----SRKIITRCINTAK 201 (323)
T ss_pred CHHHHHHHHHHHHHHh---cCCCHHHHHHHHC-C----CHHHHHHHHHHHc
Confidence 3345554 3 335432 4589999999999 9 8999999999864
No 428
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=34.05 E-value=91 Score=18.15 Aligned_cols=50 Identities=24% Similarity=0.273 Sum_probs=36.2
Q ss_pred HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
..+...... +-.+... -..++.++||+.++ . +..-+..++--+...|.+.
T Consensus 42 l~~~i~~~~-l~~l~~~--y~~i~~~~ia~~l~-~----~~~~vE~~l~~~I~~~~i~ 91 (105)
T PF01399_consen 42 LKEKIRRRN-LRQLSKP--YSSISISEIAKALQ-L----SEEEVESILIDLISNGLIK 91 (105)
T ss_dssp HHHHHHHHH-HHHHHHC---SEEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSSE
T ss_pred HHHHHHHHH-HHHHHHH--hcccchHHHHHHhc-c----chHHHHHHHHHHHHCCCEE
Confidence 333344444 4444432 26899999999999 9 8889999999888888876
No 429
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=34.02 E-value=59 Score=22.53 Aligned_cols=27 Identities=19% Similarity=0.268 Sum_probs=19.1
Q ss_pred HHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHH
Q 045477 38 IAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70 (89)
Q Consensus 38 l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~R 70 (89)
+.+.|- ..+|..+||+++| + .+..|++
T Consensus 17 ~~e~G~-~~lsmr~lA~~lg-v----~~~slY~ 43 (205)
T PRK13756 17 LNEVGI-EGLTTRKLAQKLG-V----EQPTLYW 43 (205)
T ss_pred HHHcCc-ccCCHHHHHHHhC-C----CchHHHH
Confidence 444442 5789999999999 9 5555443
No 430
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=34.01 E-value=25 Score=22.72 Aligned_cols=14 Identities=36% Similarity=0.366 Sum_probs=12.9
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
.++|.+|||+.+| +
T Consensus 128 ~g~s~~EIA~~l~-i 141 (161)
T PRK12528 128 DGLGYGEIATELG-I 141 (161)
T ss_pred cCCCHHHHHHHHC-C
Confidence 5799999999999 8
No 431
>PRK13749 transcriptional regulator MerD; Provisional
Probab=34.00 E-value=47 Score=21.57 Aligned_cols=32 Identities=13% Similarity=0.064 Sum_probs=26.0
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
.+|+.|+|+.+| + .+ +-+|+.-..|++....+
T Consensus 3 ~~tIgelA~~~g-v----S~----~tiR~YE~~GLl~p~~r 34 (121)
T PRK13749 3 AYTVSRLALDAG-V----SV----HIVRDYLLRGLLRPVAC 34 (121)
T ss_pred CCcHHHHHHHHC-C----CH----HHHHHHHHCCCCCCCCc
Confidence 479999999999 8 44 47899999999976543
No 432
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=34.00 E-value=88 Score=21.59 Aligned_cols=48 Identities=15% Similarity=0.274 Sum_probs=38.6
Q ss_pred HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+......-+||+.|.+ +=+|..||.+..| - |. .+=|.+|-.-|++++.
T Consensus 13 ~f~s~~~kkV~~~Ls~----~W~T~~El~e~~G-~----d~---~~~L~~LkK~gLiE~q 60 (160)
T PF09824_consen 13 TFNSEVYKKVYDELSK----GWMTEEELEEKYG-K----DV---RESLLILKKGGLIESQ 60 (160)
T ss_pred HhCCHHHHHHHHHHHh----ccCCHHHHHHHHC-c----CH---HHHHHHHHHcCchhhc
Confidence 3444566789999987 7899999999999 6 44 8888888888888754
No 433
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=33.98 E-value=31 Score=24.58 Aligned_cols=10 Identities=30% Similarity=0.179 Sum_probs=5.4
Q ss_pred HHHHHhhCCCC
Q 045477 49 ASEIAAQLPAT 59 (89)
Q Consensus 49 ~~eLA~~~~~~ 59 (89)
..|||+..| +
T Consensus 2 i~dIA~~aG-V 11 (327)
T TIGR02417 2 LSDIAKLAG-V 11 (327)
T ss_pred HHHHHHHhC-C
Confidence 455555555 5
No 434
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=33.91 E-value=24 Score=20.53 Aligned_cols=32 Identities=19% Similarity=0.186 Sum_probs=24.0
Q ss_pred HHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 49 ASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 49 ~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
++.++..++ . +++..+.|+.|.|-.+|+...-
T Consensus 18 ie~~~~~~~-~---~~~e~~~rf~~~L~~~Gv~~~L 49 (69)
T PF09269_consen 18 IERLVAMTN-F---DDEESLRRFQRKLKKMGVEKAL 49 (69)
T ss_dssp HHHHHTTEE-E----TGGGHHHHHHHHHHTTHHHHH
T ss_pred HHHHHHhcC-C---CCHHHHHHHHHHHHHCCHHHHH
Confidence 456666666 4 2778999999999999987643
No 435
>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=33.76 E-value=44 Score=18.68 Aligned_cols=27 Identities=19% Similarity=0.294 Sum_probs=18.4
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc-Ccee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASY-GIVE 82 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~-gi~~ 82 (89)
+++.|+|+.+| + ++..|+ +.... |++.
T Consensus 1 ~~i~e~A~~~g-V----s~~tlr----~ye~~~gl~~ 28 (68)
T cd04763 1 YTIGEVALLTG-I----KPHVLR----AWEREFGLLK 28 (68)
T ss_pred CCHHHHHHHHC-c----CHHHHH----HHHHhcCCCC
Confidence 47889999999 9 776554 44442 6664
No 436
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=33.75 E-value=50 Score=20.07 Aligned_cols=30 Identities=20% Similarity=0.196 Sum_probs=23.5
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
+|+.|+|+.+| + .+ +-+|+-...|++....
T Consensus 1 ~ti~eva~~~g-v----s~----~tLRyye~~Gll~p~~ 30 (96)
T cd04768 1 LTIGEFAKLAG-V----SI----RTLRHYDDIGLFKPAK 30 (96)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCCc
Confidence 47899999999 8 54 3778888889997653
No 437
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=33.70 E-value=48 Score=20.74 Aligned_cols=29 Identities=17% Similarity=0.123 Sum_probs=23.2
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|..|+|+.+| + .+ +-+|+....|++...
T Consensus 1 y~Ige~A~~~g-v----s~----~tlR~ye~~GLl~p~ 29 (107)
T cd01111 1 YSISQLALDAG-V----SV----HIVRDYLLRGLLHPV 29 (107)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 47889999999 8 54 478888889999764
No 438
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=33.69 E-value=24 Score=20.74 Aligned_cols=25 Identities=12% Similarity=0.161 Sum_probs=17.5
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRI 71 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~Rl 71 (89)
.+.+++||++.|+ . +.....+|.+|
T Consensus 43 ~Ga~~~el~~~Cg-L-~~aEAeLl~~L 67 (70)
T PF10975_consen 43 QGASVEELMEECG-L-SRAEAELLLSL 67 (70)
T ss_pred cCCCHHHHHHHcC-C-CHHHHHHHHHH
Confidence 3589999999999 7 33345555554
No 439
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=33.58 E-value=47 Score=20.43 Aligned_cols=27 Identities=11% Similarity=0.272 Sum_probs=22.1
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
+|..|+|+.+| + .+. -+|+....|++.
T Consensus 2 ~~i~eva~~~g-v----s~~----tLR~ye~~Gll~ 28 (102)
T cd04775 2 YTIGQMSRKFG-V----SRS----TLLYYESIGLIP 28 (102)
T ss_pred CCHHHHHHHHC-c----CHH----HHHHHHHCCCCC
Confidence 57899999999 8 554 458888899994
No 440
>PRK00767 transcriptional regulator BetI; Validated
Probab=33.28 E-value=62 Score=21.20 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=16.1
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCC
Q 045477 37 IIAKAGPGAKLSASEIAAQLPAT 59 (89)
Q Consensus 37 ~l~~~g~~~~~t~~eLA~~~~~~ 59 (89)
.+.+.|- ...|..+||+.+| +
T Consensus 21 lf~~~G~-~~~s~~~Ia~~aG-v 41 (197)
T PRK00767 21 AIGEVGL-LDATIAQIARRAG-V 41 (197)
T ss_pred HHHHcCc-ccCCHHHHHHHhC-C
Confidence 3555553 5689999999999 8
No 441
>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=33.25 E-value=87 Score=17.08 Aligned_cols=29 Identities=21% Similarity=0.146 Sum_probs=23.0
Q ss_pred HHHHHHHHhHHHHHHHHHHHHhChHHHHH
Q 045477 11 AYAFEVTMGSVLHMTMKAVINLGLFEIIA 39 (89)
Q Consensus 11 ~~~~~l~~~~~~~~aL~~av~LgIfd~l~ 39 (89)
..+..+..+.....+++...++|+++.|-
T Consensus 29 ~El~kil~~~~~~~~~~~l~~~gll~~if 57 (64)
T PF12627_consen 29 EELEKILSSPNPSRAFKLLDELGLLEYIF 57 (64)
T ss_dssp HHHHHHHTSTTHHHHHHHHHHTTCHHHHS
T ss_pred HHHHHHHcCCCHHHHHHHHHHcCCHHHHC
Confidence 34555666778888999999999999873
No 442
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=33.20 E-value=51 Score=20.05 Aligned_cols=29 Identities=14% Similarity=0.128 Sum_probs=22.7
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|..|+|+.+| + .+ +-+|+-...|++...
T Consensus 1 ~~i~eva~~~g-v----s~----~tlR~ye~~Gll~p~ 29 (97)
T cd04782 1 FTTGEFAKLCG-I----SK----QTLFHYDKIGLFKPE 29 (97)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 47889999999 8 54 367888888998654
No 443
>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=33.10 E-value=35 Score=18.82 Aligned_cols=21 Identities=14% Similarity=0.131 Sum_probs=15.4
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRIL 72 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlL 72 (89)
+|..|+|+.+| + .+..|++.-
T Consensus 1 ~s~~eva~~~g-v----s~~tlr~w~ 21 (68)
T cd01104 1 YTIGAVARLTG-V----SPDTLRAWE 21 (68)
T ss_pred CCHHHHHHHHC-c----CHHHHHHHH
Confidence 46889999999 8 776666543
No 444
>PRK04158 transcriptional repressor CodY; Validated
Probab=33.09 E-value=80 Score=23.35 Aligned_cols=44 Identities=30% Similarity=0.416 Sum_probs=36.6
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
.||+-|. |.+|-+.++-||.+.| + -...+---||-|-|.|+++.
T Consensus 190 hIf~eL~--g~EG~lvASkiADrvg-I----TRSVIVNALRK~ESAGvIES 233 (256)
T PRK04158 190 HIFEELD--GNEGLLVASKIADRVG-I----TRSVIVNALRKLESAGVIES 233 (256)
T ss_pred HHHHhcC--CCcceEEeeecccccC-C----chhhhhhhhhhhhcccceee
Confidence 5777773 4458899999999999 8 67788889999999999874
No 445
>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=32.98 E-value=33 Score=14.02 Aligned_cols=8 Identities=63% Similarity=1.095 Sum_probs=5.5
Q ss_pred ChHHHHHh
Q 045477 33 GLFEIIAK 40 (89)
Q Consensus 33 gIfd~l~~ 40 (89)
|+||++.+
T Consensus 1 Gl~Di~Kk 8 (13)
T PF08256_consen 1 GLFDIAKK 8 (13)
T ss_pred CHHHHHHH
Confidence 67777754
No 446
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=32.94 E-value=27 Score=22.75 Aligned_cols=14 Identities=21% Similarity=0.083 Sum_probs=12.9
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
.++|.+|||+.+| +
T Consensus 127 ~g~s~~eIA~~lg-i 140 (164)
T PRK12547 127 SGFSYEDAAAICG-C 140 (164)
T ss_pred cCCCHHHHHHHhC-C
Confidence 5789999999999 9
No 447
>PF15467 SGIII: Secretogranin-3
Probab=32.92 E-value=42 Score=26.30 Aligned_cols=50 Identities=18% Similarity=0.345 Sum_probs=36.8
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCC-CCCCCCcchHHHHHHHHhccCceeeec
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPA-TKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~-~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
||-|++-+ |.|+|+.+|.+++.+ +=--+|.....||.--|-..|+++++.
T Consensus 120 PdglhQlD-GTPLTAeDIVqKIAtrIYEEnDRGVFDkIVSKLLnLGLITeSQ 170 (453)
T PF15467_consen 120 PDGLHQLD-GTPLTAEDIVQKIATRIYEENDRGVFDKIVSKLLNLGLITESQ 170 (453)
T ss_pred chhhhccC-CCCCcHHHHHHHHHHHHHhcccchHHHHHHHHHHhccccchhh
Confidence 45666543 489999999998763 112236678899999999999998763
No 448
>PRK09483 response regulator; Provisional
Probab=32.90 E-value=76 Score=20.66 Aligned_cols=36 Identities=25% Similarity=0.336 Sum_probs=23.9
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcch----HHHHHHHH
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTM----LDRILGLL 75 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~----l~RlLR~L 75 (89)
-|..|...+. .+.|.+|||+.++ . .+.. +.|+++-|
T Consensus 152 rE~~vl~~~~-----~G~~~~~Ia~~l~-i----s~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 152 RELQIMLMIT-----KGQKVNEISEQLN-L----SPKTVNSYRYRMFSKL 191 (217)
T ss_pred HHHHHHHHHH-----CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHHc
Confidence 4445555554 3589999999999 8 5544 55555554
No 449
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=32.70 E-value=50 Score=21.32 Aligned_cols=30 Identities=10% Similarity=0.095 Sum_probs=24.9
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.+|+.|+|+.+| + .+ +-+|+-...|++...
T Consensus 3 ~~tI~elA~~~g-v----s~----~tlR~Ye~~GLL~p~ 32 (120)
T TIGR02054 3 AYTISRLAEDAG-V----SV----HVVRDYLLRGLLHPV 32 (120)
T ss_pred CCcHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 579999999999 8 44 478888999999765
No 450
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=32.68 E-value=52 Score=19.98 Aligned_cols=29 Identities=21% Similarity=0.208 Sum_probs=23.2
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
++..|+|+.+| + .+ +-+|+-...|++...
T Consensus 1 m~i~eva~~~g-v----s~----~tlR~ye~~Gll~p~ 29 (96)
T cd04788 1 WKIGELARRTG-L----SV----RTLHHYDHIGLLSPS 29 (96)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 57899999999 8 44 467888889998764
No 451
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=32.66 E-value=1.5e+02 Score=19.68 Aligned_cols=61 Identities=11% Similarity=0.014 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCC-CCCCCcchHHHHHHHHhccCceeee
Q 045477 20 SVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPAT-KNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 20 ~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~-~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
-+.....+-.+++=|.-+|.+ +|++-=||.+.+... --..++..|+++|+-|...|++...
T Consensus 15 ~~~~ql~kg~l~~~IL~~L~~----~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~ 76 (138)
T TIGR02719 15 KQINGAPKNFLVPFLLLCLKD----WNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQ 76 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHcc----CCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEE
Confidence 334455666777777777865 578877777765410 0122677899999999999999853
No 452
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=32.55 E-value=1.3e+02 Score=21.11 Aligned_cols=34 Identities=24% Similarity=0.269 Sum_probs=28.2
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
++.|+.+||.+++ . +..-+.|.|=-|-..|.+..
T Consensus 26 ~~~~a~~i~~~l~-~----~k~~vNr~LY~l~~~~~v~~ 59 (183)
T PHA03103 26 EGITAIEISRKLN-I----EKSEVNKQLYKLQREGMVYM 59 (183)
T ss_pred CCccHHHHHHHhC-C----CHHHHHHHHHHHHhcCceec
Confidence 7999999999999 9 77778888877777776643
No 453
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=32.53 E-value=45 Score=19.36 Aligned_cols=20 Identities=15% Similarity=0.272 Sum_probs=16.9
Q ss_pred CCCcchHHHHHHHHhccCce
Q 045477 62 KDAPTMLDRILGLLASYGIV 81 (89)
Q Consensus 62 ~~d~~~l~RlLR~L~s~gi~ 81 (89)
++.|.++.++.+.|...|+=
T Consensus 8 ~Dr~gLfa~i~~~l~~~~l~ 27 (76)
T cd04927 8 SDRKGLLHDVTEVLYELELT 27 (76)
T ss_pred CCCCCHHHHHHHHHHHCCCe
Confidence 45788999999999998863
No 454
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=32.48 E-value=31 Score=23.19 Aligned_cols=14 Identities=14% Similarity=0.285 Sum_probs=12.8
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
..+|.+|||+.+| +
T Consensus 156 eg~s~~EIA~~lg-i 169 (194)
T PRK12531 156 EELPHQQVAEMFD-I 169 (194)
T ss_pred cCCCHHHHHHHhC-c
Confidence 4689999999999 8
No 455
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=32.48 E-value=48 Score=18.79 Aligned_cols=14 Identities=21% Similarity=0.266 Sum_probs=10.1
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
..+|.+|+|..++ +
T Consensus 9 ~glsl~~va~~t~-I 22 (62)
T PF13413_consen 9 KGLSLEDVAEETK-I 22 (62)
T ss_dssp TT--HHHHHHHCS--
T ss_pred cCCCHHHHHHHhC-C
Confidence 6899999999999 8
No 456
>cd02758 MopB_Tetrathionate-Ra The MopB_Tetrathionate-Ra CD contains tetrathionate reductase, subunit A, (TtrA) and other related proteins. The Salmonella enterica tetrathionate reductase catalyses the reduction of trithionate but not sulfur or thiosulfate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=32.38 E-value=63 Score=26.95 Aligned_cols=39 Identities=13% Similarity=0.122 Sum_probs=32.8
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
-|+.|.+.- .+.|.++.++.|| + ++..|.++-|.+++.+
T Consensus 328 gfe~l~e~~--~~~Tpe~~a~icG-V----p~~~I~~lAr~fa~~~ 366 (735)
T cd02758 328 ALQLLKEEA--FSYSLEEYAEICG-V----PEAKIIELAKEFTSHG 366 (735)
T ss_pred HHHHHHHHh--hcCCHHHHHHHHC-c----CHHHHHHHHHHHHhcC
Confidence 477777654 6799999999999 9 9999999999998754
No 457
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=32.37 E-value=43 Score=22.11 Aligned_cols=14 Identities=29% Similarity=0.344 Sum_probs=12.9
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
.++|.+|||+.+| +
T Consensus 152 ~g~s~~eIA~~lg-i 165 (187)
T PRK12534 152 EGITYEELAARTD-T 165 (187)
T ss_pred cCCCHHHHHHHhC-C
Confidence 4799999999999 8
No 458
>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=32.37 E-value=43 Score=22.35 Aligned_cols=36 Identities=25% Similarity=0.451 Sum_probs=27.4
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
.|...+.+ ...+..+|++.+. - ||.+..+|||..=+
T Consensus 10 ~l~~~l~~----~~~~~~~l~~~i~-~----Dp~L~~~lL~~aNs 45 (196)
T PF08668_consen 10 RLLSLLND----PEASIDELAELIE-S----DPALAARLLRLANS 45 (196)
T ss_dssp HHHHHHHS----TTS-HHHHHHHHH-T----SHHHHHHHHHHHHS
T ss_pred HHHHHHcC----CCCCHHHHHHHHH-H----CHHHHHHHHHHHhh
Confidence 34455543 4679999999999 8 99999999998654
No 459
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=32.29 E-value=51 Score=23.18 Aligned_cols=26 Identities=19% Similarity=0.170 Sum_probs=20.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLL 75 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L 75 (89)
.++|.+|||+.+| + ....++|+.+.+
T Consensus 198 ~~~t~~EIA~~lg-i----s~~~V~q~~~~~ 223 (231)
T PRK12427 198 HEMSLKEIALVLD-L----TEARICQLNKKI 223 (231)
T ss_pred cCCCHHHHHHHHC-c----CHHHHHHHHHHH
Confidence 5799999999999 9 777777665443
No 460
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=32.26 E-value=54 Score=21.69 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=15.0
Q ss_pred HHHhcCCCCCCCHHHHHhhCCCC
Q 045477 37 IIAKAGPGAKLSASEIAAQLPAT 59 (89)
Q Consensus 37 ~l~~~g~~~~~t~~eLA~~~~~~ 59 (89)
.+.+.|- ...|+++||++.| +
T Consensus 20 lf~e~G~-~~tSi~~Ia~~aG-v 40 (192)
T PRK14996 20 VALAEGF-AAMTVRRIASEAQ-V 40 (192)
T ss_pred HHHhcCh-hhccHHHHHHHhC-C
Confidence 3455542 5678999999999 8
No 461
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=32.18 E-value=41 Score=23.89 Aligned_cols=22 Identities=23% Similarity=0.368 Sum_probs=16.3
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
+|..|||+..| + ....+.|+|.
T Consensus 2 ~ti~dIA~~ag-V----S~sTVSr~Ln 23 (311)
T TIGR02405 2 LTIKDIARLAG-V----GKSTVSRVLN 23 (311)
T ss_pred CcHHHHHHHhC-C----CHHHHHHHhC
Confidence 47888888888 8 6666766663
No 462
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=31.83 E-value=53 Score=20.88 Aligned_cols=29 Identities=10% Similarity=0.219 Sum_probs=23.8
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
++..|+|+.+| + .+ +-+|+--..|++...
T Consensus 1 m~IgevA~~~g-v----s~----~tLRyYe~~GLl~p~ 29 (127)
T cd04784 1 MKIGELAKKTG-C----SV----ETIRYYEKEGLLPAP 29 (127)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 57899999999 8 44 478999999999754
No 463
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=31.65 E-value=1.4e+02 Score=22.14 Aligned_cols=30 Identities=23% Similarity=0.172 Sum_probs=26.4
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
.|.|+.||+..++ + ++.-+.|..|+++...
T Consensus 156 ~prtl~eIa~a~~-V----~~kei~rtyr~~~~~L 185 (285)
T COG1405 156 VPRTLDEIAKALG-V----SKKEIGRTYRLLVREL 185 (285)
T ss_pred CCccHHHHHHHHC-C----CHHHHHHHHHHHHHhc
Confidence 7999999999999 9 8888999999777644
No 464
>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=31.48 E-value=28 Score=18.20 Aligned_cols=35 Identities=17% Similarity=0.236 Sum_probs=19.8
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV 81 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~ 81 (89)
++|.+.+...+. -.....+....|++..+..+|+-
T Consensus 8 gvs~~tvs~~l~-g~~~vs~~~~~~i~~~~~~l~~~ 42 (52)
T cd01392 8 GVSVATVSRVLN-GKPRVSEETRERVLAAAEELGYR 42 (52)
T ss_pred CcCHHHHHHHHc-CCCCCCHHHHHHHHHHHHHhCCC
Confidence 355555555555 31111455677777777777753
No 465
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=31.44 E-value=95 Score=21.11 Aligned_cols=30 Identities=17% Similarity=0.216 Sum_probs=25.4
Q ss_pred HHHHhChHHHHHhcCCCCCCCHHHHHhhCC
Q 045477 28 AVINLGLFEIIAKAGPGAKLSASEIAAQLP 57 (89)
Q Consensus 28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~ 57 (89)
+.-...|++.|.+-+-|...|-.|||++++
T Consensus 87 t~Fq~~Vw~aL~~IP~Get~TY~eiA~~ig 116 (168)
T COG0350 87 TGFQGRVWQALREIPYGETVTYGEIARRLG 116 (168)
T ss_pred ChHHHHHHHHHhcCCCCCcEeHHHHHHHhC
Confidence 466778999998776557899999999999
No 466
>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=31.23 E-value=36 Score=23.53 Aligned_cols=14 Identities=36% Similarity=0.309 Sum_probs=11.3
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
.+.|++|+|+..| +
T Consensus 68 aGas~eeVA~~~G-~ 81 (170)
T PF11268_consen 68 AGASAEEVAEEAG-V 81 (170)
T ss_pred CCCCHHHHHHHhC-C
Confidence 4678888888888 7
No 467
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=31.18 E-value=58 Score=19.88 Aligned_cols=28 Identities=14% Similarity=0.190 Sum_probs=20.7
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
+|..|+|+.+| + .+. -+|+....|++..
T Consensus 1 ~ti~eva~~~g-v----s~~----tlR~ye~~Gll~~ 28 (103)
T cd01106 1 YTVGEVAKLTG-V----SVR----TLHYYDEIGLLKP 28 (103)
T ss_pred CCHHHHHHHHC-c----CHH----HHHHHHHCCCCCC
Confidence 47889999999 8 654 5566677888754
No 468
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=30.77 E-value=1.1e+02 Score=19.90 Aligned_cols=37 Identities=22% Similarity=0.155 Sum_probs=33.2
Q ss_pred CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 44 GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
.-|.+.++||..++ - +...+..-|-++...|++....
T Consensus 49 ~ipy~~e~LA~~~~-~----~~~~V~~Al~~f~k~glIe~~d 85 (119)
T TIGR01714 49 LAPYNAEMLATMFN-R----NVGDIRITLQTLESLGLIEKKN 85 (119)
T ss_pred CCCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 37999999999999 8 8889999999999999998763
No 469
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=30.70 E-value=83 Score=18.98 Aligned_cols=33 Identities=18% Similarity=0.157 Sum_probs=28.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
.+.|-++||+.+| + ....+-.-+..|-..|+=-
T Consensus 18 ~~~SGe~La~~Lg-i----SRtaVwK~Iq~Lr~~G~~I 50 (79)
T COG1654 18 NFVSGEKLAEELG-I----SRTAVWKHIQQLREEGVDI 50 (79)
T ss_pred CcccHHHHHHHHC-c----cHHHHHHHHHHHHHhCCce
Confidence 6999999999999 9 8888999999888888643
No 470
>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=30.67 E-value=50 Score=18.60 Aligned_cols=31 Identities=29% Similarity=0.425 Sum_probs=15.9
Q ss_pred CCCCHHHHHhhC---CC-CCCCCCcchHHHHHHHHhccCcee
Q 045477 45 AKLSASEIAAQL---PA-TKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 45 ~~~t~~eLA~~~---~~-~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
...|+.||+..+ |. + ....+.|.|+ ..|+..
T Consensus 12 p~~s~~~i~~~l~~~~~~v----S~~TI~r~L~---~~g~~~ 46 (72)
T PF01498_consen 12 PRISAREIAQELQEAGISV----SKSTIRRRLR---EAGLKK 46 (72)
T ss_dssp ----HHHHHHHT---T--S-----HHHHHHHHH---HT-EEE
T ss_pred CCCCHHHHHHHHHHccCCc----CHHHHHHHHH---HcCccc
Confidence 468999999988 41 4 4555555554 456544
No 471
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=30.57 E-value=66 Score=19.67 Aligned_cols=28 Identities=25% Similarity=0.265 Sum_probs=21.1
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
+|+.|+|+.+| + .+. .+|+....|++..
T Consensus 2 ~~i~eva~~~g-V----s~~----tLR~ye~~Gli~p 29 (98)
T cd01279 2 YPISVAAELLG-I----HPQ----TLRVYDRLGLVSP 29 (98)
T ss_pred cCHHHHHHHHC-c----CHH----HHHHHHHCCCCCC
Confidence 57899999999 8 554 5566677888764
No 472
>cd02762 MopB_1 The MopB_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=30.54 E-value=1.7e+02 Score=23.03 Aligned_cols=37 Identities=14% Similarity=0.167 Sum_probs=29.6
Q ss_pred HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477 35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY 78 (89)
Q Consensus 35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~ 78 (89)
||.+.+.= .+.|.++.++.|| + ++..+.++-|.++..
T Consensus 248 f~~~~~~~--~~~t~e~~~~~tG-v----~~~~I~~lA~~~a~~ 284 (539)
T cd02762 248 LDEVRAAL--AEFTPEAYAPRCG-V----PAETIRRLAREFAAA 284 (539)
T ss_pred HHHHHHHH--hcCCHHHHHHHHC-c----CHHHHHHHHHHHhcC
Confidence 56665543 5789999999999 9 888899999988753
No 473
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=30.48 E-value=60 Score=20.19 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=22.1
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+|+.|+|+.+| + .+. .+|+-...|++...
T Consensus 1 ~~i~eva~~~g-v----s~~----tlR~ye~~Gll~p~ 29 (108)
T cd04773 1 MTIGELAHLLG-V----PPS----TLRHWEKEGLLSPD 29 (108)
T ss_pred CCHHHHHHHHC-c----CHH----HHHHHHHCCCCCCC
Confidence 57899999999 8 554 66777778888643
No 474
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=30.47 E-value=1e+02 Score=17.05 Aligned_cols=48 Identities=17% Similarity=0.217 Sum_probs=31.0
Q ss_pred HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCC-CCcc----hHHHHHHHHhcc
Q 045477 29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNK-DAPT----MLDRILGLLASY 78 (89)
Q Consensus 29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~-~d~~----~l~RlLR~L~s~ 78 (89)
..+..|+..|..+. +.++|-++|.+.+- -... .+.. .+.||=+.|...
T Consensus 8 ~~e~~lL~~L~~~~-~~~vs~~~l~~~~w-~~~~~~~~~~l~~~I~rLR~kL~~~ 60 (77)
T PF00486_consen 8 PKEFRLLELLLRNP-GRVVSREELIEALW-GDEEDVSDNSLDVHISRLRKKLEDA 60 (77)
T ss_dssp HHHHHHHHHHHHTT-TSEEEHHHHHHHHT-SSSSTTCTHHHHHHHHHHHHHHHSS
T ss_pred HHHHHHHHHHHhCC-CCCCCHHHhCChhh-hcccccchhhHHHHHHHHHHHHhhc
Confidence 35677888888764 48999999999987 4222 1222 255555555553
No 475
>PRK00441 argR arginine repressor; Provisional
Probab=30.40 E-value=87 Score=20.93 Aligned_cols=39 Identities=21% Similarity=0.235 Sum_probs=29.6
Q ss_pred ChHHHHHhcCCCCCCCHHHHHhhC-----CCCCCCCCcchHHHHHHHHhccC
Q 045477 33 GLFEIIAKAGPGAKLSASEIAAQL-----PATKNKDAPTMLDRILGLLASYG 79 (89)
Q Consensus 33 gIfd~l~~~g~~~~~t~~eLA~~~-----~~~~~~~d~~~l~RlLR~L~s~g 79 (89)
.|.++|.+. +..|..||++.+ + + ....++|-++.|-...
T Consensus 8 ~I~~ll~~~---~~~~q~eL~~~L~~~G~~-v----SqaTisRDl~~L~lvK 51 (149)
T PRK00441 8 KILEIINSK---EIETQEELAEELKKMGFD-V----TQATVSRDIKELKLIK 51 (149)
T ss_pred HHHHHHHHc---CCCcHHHHHHHHHhcCCC-c----CHHHHHHHHHHcCcEE
Confidence 355777774 588999999997 7 7 6778999888776443
No 476
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=30.37 E-value=76 Score=22.12 Aligned_cols=33 Identities=21% Similarity=0.270 Sum_probs=30.0
Q ss_pred CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 48 SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 48 t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
|=.|||+..+ + ....++|-|..|+..|++....
T Consensus 37 sE~eLa~~~~-V----SR~TVR~Al~~L~~eGli~r~~ 69 (241)
T PRK10079 37 AEQQLAARYE-V----NRHTLRRAIDQLVEKGWVQRRQ 69 (241)
T ss_pred CHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence 7889999999 9 8999999999999999987653
No 477
>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=30.20 E-value=75 Score=15.39 Aligned_cols=21 Identities=29% Similarity=0.480 Sum_probs=12.5
Q ss_pred CCCHHHHHhhCCCCCCCCCcchHHHH
Q 045477 46 KLSASEIAAQLPATKNKDAPTMLDRI 71 (89)
Q Consensus 46 ~~t~~eLA~~~~~~~~~~d~~~l~Rl 71 (89)
.+|..++|..++ . .+..+.++
T Consensus 12 ~~s~~~~a~~~~-~----~~~~v~~~ 32 (58)
T cd00093 12 GLTQEELAEKLG-V----SRSTISRI 32 (58)
T ss_pred CCCHHHHHHHHC-C----CHHHHHHH
Confidence 466677777776 6 44444443
No 478
>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=30.18 E-value=1.1e+02 Score=17.30 Aligned_cols=36 Identities=22% Similarity=0.367 Sum_probs=26.5
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s 77 (89)
+.|.+-..+ -+|+.-+++.++ + .+....|+++-|-.
T Consensus 4 Lidll~~~P---~Vsa~mva~~L~-v----T~~~A~~li~eLg~ 39 (54)
T PF11972_consen 4 LIDLLLSRP---LVSAPMVAKELG-V----TPQAAQRLIAELGL 39 (54)
T ss_pred HHHHHHhCc---cccHHHHHHHhC-C----CHHHHHHHHHHhhc
Confidence 566666532 369999999999 9 78888888766543
No 479
>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=30.16 E-value=57 Score=21.35 Aligned_cols=20 Identities=30% Similarity=0.350 Sum_probs=16.0
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLD 69 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~ 69 (89)
.++|.+|||+.+| + .+..+.
T Consensus 149 ~g~s~~EIA~~lg-i----s~~tVk 168 (183)
T TIGR02999 149 AGLTVEEIAELLG-V----SVRTVE 168 (183)
T ss_pred cCCCHHHHHHHhC-C----CHHHHH
Confidence 5799999999999 8 565544
No 480
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=30.14 E-value=96 Score=18.88 Aligned_cols=22 Identities=27% Similarity=0.182 Sum_probs=17.3
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRI 71 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~Rl 71 (89)
..+|+.+||++.| + .+..++|-
T Consensus 31 ~~~t~~~Ia~~ag-v----s~~~~Y~~ 52 (201)
T COG1309 31 AATTVDEIAKAAG-V----SKGTLYRH 52 (201)
T ss_pred CCCCHHHHHHHhC-C----CcchhHHH
Confidence 4789999999999 9 66665543
No 481
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=30.12 E-value=56 Score=20.93 Aligned_cols=19 Identities=26% Similarity=0.113 Sum_probs=15.7
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTML 68 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l 68 (89)
.++|.+|||+.+| + .+..+
T Consensus 121 ~g~s~~EIA~~lg-i----s~~tV 139 (160)
T PRK09642 121 EEKSYQEIALQEK-I----EVKTV 139 (160)
T ss_pred hCCCHHHHHHHHC-C----CHHHH
Confidence 5799999999999 9 56554
No 482
>PF09645 F-112: F-112 protein; InterPro: IPR018601 This entry is represented by Sulfolobus virus-like particle SSV1, p11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2VQC_A.
Probab=29.96 E-value=59 Score=20.81 Aligned_cols=40 Identities=18% Similarity=0.355 Sum_probs=24.8
Q ss_pred hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477 34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY 78 (89)
Q Consensus 34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~ 78 (89)
+|.+|.+. +.+|+.+|-.... + +|+-.-.+.|++|..+..
T Consensus 12 l~kiLq~K---~Eit~eDIlaqfe-I-S~s~Ay~I~~~lr~iCe~ 51 (110)
T PF09645_consen 12 LYKILQEK---KEITLEDILAQFE-I-SYSRAYNIQRVLRKICEQ 51 (110)
T ss_dssp HHHHHHHH---SEE-HHHHHHHH-----HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHc---CcCcHHHHHHHhc-c-chhhhhHHHHHHHHHHHh
Confidence 47778764 6899999999988 8 222233466777777653
No 483
>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=29.90 E-value=34 Score=21.76 Aligned_cols=14 Identities=29% Similarity=0.304 Sum_probs=12.9
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
.++|.+|||+.+| +
T Consensus 126 ~g~~~~eIA~~l~-i 139 (159)
T TIGR02989 126 RGVSLTALAEQLG-R 139 (159)
T ss_pred cCCCHHHHHHHhC-C
Confidence 4789999999999 8
No 484
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=29.73 E-value=60 Score=20.81 Aligned_cols=29 Identities=10% Similarity=0.220 Sum_probs=23.4
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+++.|+|+.+| + .+ +-+|+-...|++...
T Consensus 1 m~I~e~a~~~g-v----s~----~tlR~Ye~~GLl~~~ 29 (127)
T TIGR02047 1 MKIGELAQKTG-V----SV----ETIRFYEKQGLLPPP 29 (127)
T ss_pred CcHHHHHHHHC-c----CH----HHHHHHHHCCCCCCC
Confidence 57899999999 8 44 478888999999743
No 485
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=29.65 E-value=76 Score=26.06 Aligned_cols=37 Identities=14% Similarity=0.129 Sum_probs=32.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
-++|+.|||+.+. | .+...+++|+.+-..|-++-...
T Consensus 22 ~~~tl~eLA~~lf-C----S~Rh~R~lL~q~q~~gWL~W~p~ 58 (564)
T COG4533 22 VETTLNELADILF-C----SRRHARTLLRQMQEAGWLTWQPQ 58 (564)
T ss_pred ceeeHHHHHHHhc-c----CHHHHHHHHHHHHHcCCEEeccC
Confidence 5689999999999 9 99999999999999998875543
No 486
>PF02746 MR_MLE_N: Mandelate racemase / muconate lactonizing enzyme, N-terminal domain; InterPro: IPR013341 Mandelate racemase 5.1.2.2 from EC (MR) and muconate lactonizing enzyme 5.5.1.1 from EC (MLE) are two bacterial enzymes involved in aromatic acid catabolism. They catalyse mechanistically distinct reactions yet they are related at the level of their primary, quaternary (homooctamer) and tertiary structures [, ]. A number of other proteins also seem to be evolutionary related to these two enzymes. These include, various plasmid-encoded chloromuconate cycloisomerases 5.5.1.7 from EC, Escherichia coli protein rspA [], E. coli bifunctional DGOA protein, E. coli hypothetical proteins ycjG, yfaW and yidU and a hypothetical protein from Streptomyces ambofaciens []. This entry represents the N-terminal region of these proteins.; PDB: 2OX4_F 3T9P_A 2QQ6_A 3CYJ_C 3GY1_A 3S47_B 3RRA_B 3RR1_A 3STP_A 3T8Q_A ....
Probab=29.47 E-value=1.2e+02 Score=18.62 Aligned_cols=19 Identities=26% Similarity=0.574 Sum_probs=16.7
Q ss_pred HHHHHHHHHhChHHHHHhc
Q 045477 23 HMTMKAVINLGLFEIIAKA 41 (89)
Q Consensus 23 ~~aL~~av~LgIfd~l~~~ 41 (89)
....++|+|+=++|++++.
T Consensus 89 ~~~a~aaid~AlwDl~gK~ 107 (117)
T PF02746_consen 89 NPAAKAAIDMALWDLLGKI 107 (117)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 5677899999999999985
No 487
>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=29.23 E-value=56 Score=20.75 Aligned_cols=24 Identities=29% Similarity=0.270 Sum_probs=14.9
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILG 73 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR 73 (89)
.-+|++|||+..+ + ....++-.++
T Consensus 32 eDlSlsEIAe~~~-i----SRqaV~d~ik 55 (101)
T PF04297_consen 32 EDLSLSEIAEELG-I----SRQAVYDSIK 55 (101)
T ss_dssp S---HHHHHHHCT-S-----HHHHHHHHH
T ss_pred cCCCHHHHHHHHC-C----CHHHHHHHHH
Confidence 4689999999999 9 6655554443
No 488
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=29.21 E-value=50 Score=24.78 Aligned_cols=22 Identities=9% Similarity=0.101 Sum_probs=19.3
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHH
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRI 71 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~Rl 71 (89)
.|+|..|||+.+| + ....+++|
T Consensus 281 ~~~Tl~eIa~~lg-v----S~eRVrQI 302 (324)
T PRK07921 281 QPRTLDQIGKLFG-L----SRERVRQI 302 (324)
T ss_pred CCcCHHHHHHHHC-C----CHHHHHHH
Confidence 6899999999999 9 78777766
No 489
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=29.05 E-value=67 Score=19.81 Aligned_cols=32 Identities=19% Similarity=0.234 Sum_probs=25.1
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD 87 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~ 87 (89)
+|+.|+|+.+| + .+ |-+|+-...|++....++
T Consensus 1 ~~I~eva~~~g-v----s~----~tLRyYE~~GLl~p~~~~ 32 (124)
T COG0789 1 YTIGEVAKLTG-V----SV----RTLRFYERKGLLSPERRD 32 (124)
T ss_pred CcHHHHHHHhC-C----CH----HHHHHHHHcCCCCCcccC
Confidence 47899999999 8 44 578999999998766443
No 490
>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=28.94 E-value=32 Score=22.59 Aligned_cols=14 Identities=29% Similarity=0.271 Sum_probs=12.9
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
.++|.+|||+.+| +
T Consensus 153 ~~~s~~EIA~~lg-i 166 (190)
T TIGR02939 153 EGLSYEDIARIMD-C 166 (190)
T ss_pred cCCCHHHHHHHHC-c
Confidence 5789999999999 8
No 491
>PLN03239 histone acetyltransferase; Provisional
Probab=28.90 E-value=1.5e+02 Score=23.00 Aligned_cols=50 Identities=22% Similarity=0.235 Sum_probs=34.3
Q ss_pred hHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 19 GSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 19 ~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+||....++...+. .+++..+|+.+|+..|+ . ...-|+-.|..+|++...
T Consensus 265 ~YW~~~il~~L~~~--------~~~~~~~si~dis~~Tg-i-------~~~DIi~tL~~l~~l~~~ 314 (351)
T PLN03239 265 PYWGSTIVDFLLNH--------SGNDSSLSIMDIAKKTS-I-------MAEDIVFALNQLGILKFI 314 (351)
T ss_pred HHHHHHHHHHHHhc--------cCCCCCccHHHHHHHhC-C-------CHHHHHHHHHHCCcEEEE
Confidence 56766666654331 12125799999999999 9 445578888888888754
No 492
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.78 E-value=51 Score=21.79 Aligned_cols=14 Identities=36% Similarity=0.332 Sum_probs=12.9
Q ss_pred CCCCHHHHHhhCCCC
Q 045477 45 AKLSASEIAAQLPAT 59 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~ 59 (89)
.++|.+|||+.+| +
T Consensus 148 ~~~s~~eIA~~lg-i 161 (182)
T PRK12537 148 DGCSHAEIAQRLG-A 161 (182)
T ss_pred cCCCHHHHHHHHC-C
Confidence 5799999999999 8
No 493
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=28.69 E-value=73 Score=29.11 Aligned_cols=34 Identities=21% Similarity=0.309 Sum_probs=31.8
Q ss_pred CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477 45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC 83 (89)
Q Consensus 45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e 83 (89)
||.|+.++|+..| . .+..+...|+.|+..|.+-+
T Consensus 988 gp~~~~~~a~~~g-l----~~~~~~~~l~~l~~~g~~~~ 1021 (1490)
T PRK09751 988 ALVTAEQLAHEFS-L----GIAIVEEQLQQLREQGLVMN 1021 (1490)
T ss_pred CCCcHHHHHHHhC-C----CHHHHHHHHHHHHhCCCEEe
Confidence 7999999999999 9 89999999999999998776
No 494
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=28.69 E-value=1.1e+02 Score=19.38 Aligned_cols=51 Identities=18% Similarity=0.327 Sum_probs=37.1
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCC---CCCcchHHHHHHHHhccCceeee
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKN---KDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~---~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
.++-|.-+|.. +|.+--||.+.+....+ ..++..++.+|+-|...|++...
T Consensus 10 l~~~iL~~L~~----~~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~ 63 (138)
T COG1695 10 LELLILSLLSE----KPSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESR 63 (138)
T ss_pred HHHHHHHHHhc----CCchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEE
Confidence 44556666765 58888888887662112 23788999999999999999864
No 495
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=28.68 E-value=68 Score=19.70 Aligned_cols=29 Identities=7% Similarity=0.060 Sum_probs=23.5
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS 84 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~ 84 (89)
+++.|+|+.+| + .+ +-+|+--..|++...
T Consensus 1 m~Ige~a~~~g-v----s~----~tlRyYe~~GLl~p~ 29 (107)
T cd04777 1 MKIGKFAKKNN-I----TI----DTVRHYIDLGLLIPE 29 (107)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCcCCc
Confidence 57899999999 7 44 478999999998753
No 496
>PF00395 SLH: S-layer homology domain; InterPro: IPR001119 S-layers are paracrystalline mono-layered assemblies of (glyco)proteins which coat the surface of bacteria [, ]. Several S-layer proteins and some other cell wall proteins contain one or more copies of a domain of about 50-60 residues, which has been called SLH (for S-layer homology). Although it was originally proposed that SLH domains bind to peptidoglycan, it is now evident that pyruvylated secondary cell wall polymers (SCWPs), which are either teichoic acids, teichuronic acids, lipoteichoic acids or lipoglycans, serve as the anchoring structures for SLH motifs in the Gram-positive cell wall [, ]. However, the study of S-layer protein SbpA of Bacillus sphaericus revealed that SLH motifs are not sufficient for specific binding to SCWPs. Thus, the molecular basis explaining SLH affinity and specificity of interaction with cell wall polymers are not completely elucidated [].; PDB: 3PYW_A.
Probab=28.66 E-value=49 Score=16.99 Aligned_cols=30 Identities=17% Similarity=0.333 Sum_probs=19.3
Q ss_pred HHHHHHHHhChHHHHHhc--CCCCCCCHHHHH
Q 045477 24 MTMKAVINLGLFEIIAKA--GPGAKLSASEIA 53 (89)
Q Consensus 24 ~aL~~av~LgIfd~l~~~--g~~~~~t~~eLA 53 (89)
..+..++++||+.-..+. .+++++|-.|+|
T Consensus 14 ~~i~~~~~~gi~~G~~~~~f~P~~~iTR~e~A 45 (45)
T PF00395_consen 14 EAIQWLYQLGIISGYSDGTFNPNDPITRAEAA 45 (45)
T ss_dssp HHHHHHHHTTSS---TTS---TTSB-BHHHHH
T ss_pred HHHHHHHHcCCcccCCCCeECCCCCcCHHHhC
Confidence 678999999999877642 245788888875
No 497
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=28.55 E-value=65 Score=21.03 Aligned_cols=30 Identities=13% Similarity=0.259 Sum_probs=24.1
Q ss_pred CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477 47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV 85 (89)
Q Consensus 47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~ 85 (89)
|+..|+|+.+| + .+ +-+|+--..|+|....
T Consensus 1 m~Ige~a~~~g-v----s~----~tlRyYE~~GLl~p~~ 30 (135)
T PRK10227 1 MNISDVAKITG-L----TS----KAIRFYEEKGLVTPPM 30 (135)
T ss_pred CCHHHHHHHHC-c----CH----HHHHHHHHCCCCCCcc
Confidence 57899999999 7 44 4789999999997653
No 498
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=28.43 E-value=60 Score=19.59 Aligned_cols=23 Identities=13% Similarity=0.131 Sum_probs=18.3
Q ss_pred CcchHHHHHHHHhccCceeeecc
Q 045477 64 APTMLDRILGLLASYGIVECSVD 86 (89)
Q Consensus 64 d~~~l~RlLR~L~s~gi~~e~~~ 86 (89)
+..-+.|++|.|...|++.++..
T Consensus 55 ~~~~~~~li~~Li~~g~L~~~~~ 77 (106)
T PF09382_consen 55 SKDDWERLIRQLILEGYLSEDNG 77 (106)
T ss_dssp -HHHHHHHHHHHHHTTSEEEEEC
T ss_pred CHHHHHHHHHHHHHcCCceecCC
Confidence 45569999999999999976643
No 499
>cd04913 ACT_AKii-LysC-BS-like_1 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins. This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is fee
Probab=28.34 E-value=61 Score=17.48 Aligned_cols=19 Identities=37% Similarity=0.583 Sum_probs=14.7
Q ss_pred CCCcchHHHHHHHHhccCc
Q 045477 62 KDAPTMLDRILGLLASYGI 80 (89)
Q Consensus 62 ~~d~~~l~RlLR~L~s~gi 80 (89)
++.+..+.|+++.|...|+
T Consensus 10 ~~~~g~~~~i~~~L~~~~I 28 (75)
T cd04913 10 PDKPGVAAKIFGALAEANI 28 (75)
T ss_pred CCCCcHHHHHHHHHHHcCC
Confidence 4467789999999987665
No 500
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=28.32 E-value=42 Score=26.23 Aligned_cols=46 Identities=15% Similarity=0.172 Sum_probs=33.6
Q ss_pred HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477 30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE 82 (89)
Q Consensus 30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~ 82 (89)
....+.+.|.=++ |..|+-|||++++ . +...+.-..+.|...|+++
T Consensus 341 ~~~~~l~~L~~~D--G~~slldIA~~~~-~----~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 341 QQMAMLWVLNYSD--GKNSLLDIAERIG-L----PFDELADAARKLLEAGLLK 386 (386)
T ss_dssp -HHHHHHHHHH-E--EEEEHHHHHHHHT-------HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHhcc--CCCcHHHHHHHHC-c----CHHHHHHHHHHHHHcCCCC
Confidence 3445677776544 7899999999999 9 8888888999999888864
Done!