Query 026766
Match_columns 233
No_of_seqs 142 out of 244
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 12:23:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026766.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026766hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05158 RNA_pol_Rpc34: RNA po 100.0 8.7E-78 1.9E-82 552.3 7.0 221 5-232 71-327 (327)
2 KOG3233 RNA polymerase III, su 100.0 1.2E-72 2.7E-77 500.9 16.7 211 3-231 69-296 (297)
3 COG5111 RPC34 DNA-directed RNA 100.0 4.7E-60 1E-64 412.5 15.6 209 6-232 73-301 (301)
4 PF04182 B-block_TFIIIC: B-blo 98.5 5.9E-07 1.3E-11 66.3 7.6 65 17-83 1-68 (75)
5 PF12802 MarR_2: MarR family; 98.3 2.8E-06 6E-11 59.0 7.7 59 15-75 2-60 (62)
6 COG2512 Predicted membrane-ass 98.3 1.8E-06 3.8E-11 77.9 7.5 55 14-71 191-245 (258)
7 PF01978 TrmB: Sugar-specific 98.2 3.7E-06 8.1E-11 60.1 6.1 62 15-84 5-66 (68)
8 PF13463 HTH_27: Winged helix 98.2 8.6E-06 1.9E-10 57.4 7.3 65 16-83 1-65 (68)
9 TIGR01889 Staph_reg_Sar staphy 98.2 9.7E-06 2.1E-10 63.3 8.1 64 15-80 22-87 (109)
10 PF13412 HTH_24: Winged helix- 98.2 7.4E-06 1.6E-10 54.8 6.2 48 16-67 1-48 (48)
11 PF01047 MarR: MarR family; I 98.1 1.5E-05 3.3E-10 55.0 7.3 57 16-76 1-57 (59)
12 TIGR02337 HpaR homoprotocatech 98.0 4.2E-05 9E-10 60.0 8.0 66 14-83 24-89 (118)
13 PRK10870 transcriptional repre 97.9 4.7E-05 1E-09 64.5 8.2 66 13-80 50-115 (176)
14 COG1846 MarR Transcriptional r 97.9 5.2E-05 1.1E-09 57.7 7.6 63 16-82 20-82 (126)
15 smart00550 Zalpha Z-DNA-bindin 97.9 5.3E-05 1.2E-09 54.8 6.5 50 17-68 5-54 (68)
16 PRK11512 DNA-binding transcrip 97.9 8.1E-05 1.7E-09 60.4 8.2 63 14-80 36-98 (144)
17 PF13730 HTH_36: Helix-turn-he 97.8 8.4E-05 1.8E-09 50.7 6.7 51 14-66 1-55 (55)
18 smart00347 HTH_MARR helix_turn 97.8 0.00014 3.1E-09 53.8 8.0 64 13-80 5-68 (101)
19 PRK03573 transcriptional regul 97.8 0.00013 2.9E-09 58.8 8.2 66 14-82 27-92 (144)
20 PRK13777 transcriptional regul 97.7 0.00014 3E-09 62.6 8.1 60 14-77 41-100 (185)
21 PF03965 Penicillinase_R: Peni 97.6 0.0023 5E-08 50.3 12.1 111 16-155 1-113 (115)
22 PF01726 LexA_DNA_bind: LexA D 97.5 0.00033 7.2E-09 50.6 6.2 57 13-71 1-61 (65)
23 COG3355 Predicted transcriptio 97.4 0.0008 1.7E-08 54.8 7.9 70 15-88 24-93 (126)
24 COG1522 Lrp Transcriptional re 97.2 0.0016 3.5E-08 52.7 7.8 71 13-87 3-78 (154)
25 TIGR02698 CopY_TcrY copper tra 97.2 0.0098 2.1E-07 48.2 12.3 112 15-155 1-114 (130)
26 PHA02943 hypothetical protein; 97.2 0.0072 1.6E-07 50.9 11.3 112 21-156 14-135 (165)
27 PF13601 HTH_34: Winged helix 97.1 0.0016 3.5E-08 48.6 6.5 54 23-80 5-58 (80)
28 TIGR00498 lexA SOS regulatory 97.1 0.0015 3.2E-08 55.7 6.8 56 13-70 1-60 (199)
29 TIGR01884 cas_HTH CRISPR locus 97.0 0.0031 6.7E-08 54.3 8.0 55 13-71 138-192 (203)
30 TIGR02702 SufR_cyano iron-sulf 97.0 0.0025 5.4E-08 54.8 7.5 129 20-165 3-140 (203)
31 PF12840 HTH_20: Helix-turn-he 96.9 0.0035 7.5E-08 43.9 6.4 49 18-70 10-58 (61)
32 cd00090 HTH_ARSR Arsenical Res 96.9 0.0076 1.6E-07 41.5 7.9 58 18-83 7-64 (78)
33 smart00344 HTH_ASNC helix_turn 96.9 0.0024 5.3E-08 48.9 5.5 54 16-73 1-54 (108)
34 TIGR01610 phage_O_Nterm phage 96.8 0.0057 1.2E-07 46.9 6.7 56 12-69 19-80 (95)
35 PRK00215 LexA repressor; Valid 96.7 0.0043 9.3E-08 53.1 6.6 53 16-70 2-58 (205)
36 smart00420 HTH_DEOR helix_turn 96.6 0.01 2.2E-07 39.0 6.4 47 20-70 2-48 (53)
37 PF02082 Rrf2: Transcriptional 96.6 0.012 2.6E-07 43.7 7.5 63 22-92 12-75 (83)
38 PF08784 RPA_C: Replication pr 96.5 0.0063 1.4E-07 46.7 5.6 51 15-67 44-96 (102)
39 PF01325 Fe_dep_repress: Iron 96.5 0.013 2.8E-07 41.5 6.4 45 21-69 11-55 (60)
40 COG3888 Predicted transcriptio 96.4 0.0092 2E-07 54.5 6.6 58 22-82 8-65 (321)
41 PF00325 Crp: Bacterial regula 96.4 0.0065 1.4E-07 38.2 3.9 30 35-66 3-32 (32)
42 PRK11169 leucine-responsive tr 96.4 0.0065 1.4E-07 50.7 5.2 59 13-75 9-67 (164)
43 smart00418 HTH_ARSR helix_turn 96.3 0.023 4.9E-07 38.1 6.9 43 23-70 2-44 (66)
44 PF05158 RNA_pol_Rpc34: RNA po 96.3 0.062 1.4E-06 50.1 11.7 127 15-167 6-136 (327)
45 PF09339 HTH_IclR: IclR helix- 96.2 0.011 2.3E-07 40.2 4.7 44 22-68 7-50 (52)
46 PRK04172 pheS phenylalanyl-tRN 96.2 0.018 3.9E-07 56.1 8.0 52 14-69 2-53 (489)
47 PF01022 HTH_5: Bacterial regu 96.1 0.023 5E-07 37.9 5.9 43 21-68 5-47 (47)
48 PF14947 HTH_45: Winged helix- 96.0 0.0087 1.9E-07 44.1 3.8 55 21-84 6-60 (77)
49 COG1378 Predicted transcriptio 96.0 0.024 5.2E-07 50.8 7.1 63 14-84 12-74 (247)
50 PRK06474 hypothetical protein; 95.9 0.1 2.2E-06 44.5 10.3 130 18-156 11-149 (178)
51 PRK11179 DNA-binding transcrip 95.9 0.022 4.7E-07 46.9 6.1 55 14-72 5-59 (153)
52 PF08220 HTH_DeoR: DeoR-like h 95.9 0.035 7.5E-07 38.7 6.1 46 21-70 3-48 (57)
53 PF02295 z-alpha: Adenosine de 95.9 0.039 8.5E-07 40.0 6.6 51 17-69 3-53 (66)
54 PF04703 FaeA: FaeA-like prote 95.9 0.029 6.3E-07 40.3 5.8 49 22-73 4-52 (62)
55 PF01638 HxlR: HxlR-like helix 95.8 0.04 8.6E-07 41.5 6.7 58 23-84 10-67 (90)
56 TIGR03433 padR_acidobact trans 95.8 0.028 6E-07 43.3 5.9 66 19-84 5-75 (100)
57 PRK14165 winged helix-turn-hel 95.8 0.036 7.7E-07 49.0 7.2 129 30-184 17-169 (217)
58 cd00092 HTH_CRP helix_turn_hel 95.6 0.041 8.8E-07 38.1 5.7 36 32-69 23-58 (67)
59 PRK09334 30S ribosomal protein 95.6 0.031 6.7E-07 42.8 5.2 57 22-82 27-85 (86)
60 PF09012 FeoC: FeoC like trans 95.5 0.036 7.9E-07 39.8 5.2 47 112-166 3-49 (69)
61 PRK12423 LexA repressor; Provi 95.4 0.057 1.2E-06 46.5 7.2 56 14-71 2-61 (202)
62 TIGR02944 suf_reg_Xantho FeS a 95.4 0.047 1E-06 43.5 6.1 51 17-69 8-58 (130)
63 PF10007 DUF2250: Uncharacteri 95.4 0.069 1.5E-06 41.3 6.6 72 16-97 5-79 (92)
64 COG1733 Predicted transcriptio 95.3 0.069 1.5E-06 42.9 6.9 49 35-85 37-86 (120)
65 PF06224 HTH_42: Winged helix 95.2 0.61 1.3E-05 42.3 13.6 124 20-167 87-217 (327)
66 COG3398 Uncharacterized protei 95.2 0.23 5.1E-06 44.3 10.2 122 18-165 101-222 (240)
67 PRK09954 putative kinase; Prov 95.2 0.069 1.5E-06 49.3 7.3 52 16-71 1-52 (362)
68 smart00346 HTH_ICLR helix_turn 95.1 0.076 1.6E-06 39.0 6.0 45 21-68 8-52 (91)
69 PF09012 FeoC: FeoC like trans 95.1 0.074 1.6E-06 38.2 5.8 48 22-73 4-51 (69)
70 smart00529 HTH_DTXR Helix-turn 95.0 0.38 8.2E-06 35.8 9.8 33 37-71 2-34 (96)
71 COG1725 Predicted transcriptio 95.0 0.17 3.7E-06 41.2 8.4 83 30-135 31-118 (125)
72 KOG2165 Anaphase-promoting com 94.9 0.19 4.2E-06 51.1 10.0 144 15-164 599-757 (765)
73 smart00345 HTH_GNTR helix_turn 94.9 0.11 2.4E-06 34.7 5.9 34 34-69 19-53 (60)
74 PF03297 Ribosomal_S25: S25 ri 94.9 0.069 1.5E-06 42.3 5.5 57 21-81 44-102 (105)
75 cd07153 Fur_like Ferric uptake 94.8 0.17 3.7E-06 39.1 7.6 59 21-82 4-65 (116)
76 PRK03902 manganese transport t 94.7 0.086 1.9E-06 42.7 5.9 47 19-69 9-55 (142)
77 smart00351 PAX Paired Box doma 94.6 0.62 1.3E-05 37.3 10.6 93 15-139 17-109 (125)
78 cd00131 PAX Paired Box domain 94.6 1.2 2.6E-05 35.9 12.3 109 14-154 16-126 (128)
79 COG0735 Fur Fe2+/Zn2+ uptake r 94.6 0.24 5.2E-06 40.8 8.3 58 15-73 18-78 (145)
80 smart00419 HTH_CRP helix_turn_ 94.5 0.085 1.9E-06 34.1 4.5 33 34-68 8-40 (48)
81 PF01475 FUR: Ferric uptake re 94.5 0.19 4E-06 39.4 7.1 92 16-115 6-105 (120)
82 PRK10402 DNA-binding transcrip 94.4 0.16 3.5E-06 43.7 7.3 60 15-82 148-209 (226)
83 TIGR03697 NtcA_cyano global ni 94.4 0.15 3.3E-06 42.0 6.8 51 16-68 113-175 (193)
84 PRK10141 DNA-binding transcrip 94.4 0.2 4.3E-06 40.2 7.2 57 11-71 8-65 (117)
85 PRK13509 transcriptional repre 94.4 0.42 9.2E-06 42.5 10.1 112 19-146 6-125 (251)
86 PRK11050 manganese transport r 94.2 1 2.2E-05 37.2 11.3 43 22-68 41-83 (152)
87 PF08279 HTH_11: HTH domain; 94.2 0.2 4.3E-06 33.8 5.9 41 21-64 3-43 (55)
88 PRK06266 transcription initiat 94.2 0.2 4.3E-06 42.9 7.2 50 17-70 21-70 (178)
89 COG3432 Predicted transcriptio 94.1 0.035 7.6E-07 43.2 2.1 60 21-85 18-77 (95)
90 PF03551 PadR: Transcriptional 94.0 0.12 2.6E-06 37.4 4.7 38 47-84 28-67 (75)
91 PRK10411 DNA-binding transcrip 93.9 0.68 1.5E-05 41.0 10.4 121 18-151 4-130 (240)
92 PRK09462 fur ferric uptake reg 93.9 0.44 9.5E-06 38.9 8.5 64 15-80 14-80 (148)
93 COG1321 TroR Mn-dependent tran 93.9 0.14 3.1E-06 42.8 5.6 110 20-157 12-122 (154)
94 PRK13918 CRP/FNR family transc 93.8 0.22 4.8E-06 41.4 6.8 52 15-68 118-181 (202)
95 PRK11161 fumarate/nitrate redu 93.8 0.17 3.8E-06 43.3 6.3 52 15-68 153-216 (235)
96 PRK09391 fixK transcriptional 93.8 0.16 3.5E-06 44.0 6.0 53 14-68 151-211 (230)
97 PF05732 RepL: Firmicute plasm 93.8 0.12 2.6E-06 43.7 5.0 46 22-69 60-108 (165)
98 PRK11014 transcriptional repre 93.7 0.27 5.9E-06 39.8 6.8 53 19-73 7-62 (141)
99 TIGR02719 repress_PhaQ poly-be 93.6 0.2 4.3E-06 41.4 5.9 66 19-84 25-93 (138)
100 PHA00738 putative HTH transcri 93.6 0.3 6.5E-06 38.9 6.6 50 18-71 12-61 (108)
101 PF08672 APC2: Anaphase promot 93.4 0.12 2.7E-06 36.8 3.8 51 114-164 2-54 (60)
102 PF02002 TFIIE_alpha: TFIIE al 93.3 0.15 3.3E-06 39.3 4.6 50 17-70 12-61 (105)
103 PRK10434 srlR DNA-bindng trans 93.2 0.85 1.8E-05 40.7 9.8 111 19-145 6-123 (256)
104 PF03444 HrcA_DNA-bdg: Winged 93.0 0.55 1.2E-05 35.4 7.0 55 16-72 2-59 (78)
105 PRK11753 DNA-binding transcrip 93.0 0.43 9.3E-06 39.9 7.3 32 35-68 169-200 (211)
106 smart00421 HTH_LUXR helix_turn 93.0 0.44 9.5E-06 31.1 5.9 43 14-62 2-44 (58)
107 PF13545 HTH_Crp_2: Crp-like h 93.0 0.32 6.9E-06 34.6 5.6 33 34-68 28-60 (76)
108 PRK05638 threonine synthase; V 93.0 0.32 7E-06 46.7 7.2 61 16-83 369-431 (442)
109 cd07377 WHTH_GntR Winged helix 92.9 0.19 4.1E-06 34.2 4.1 32 36-69 27-58 (66)
110 TIGR00738 rrf2_super rrf2 fami 92.7 0.32 6.9E-06 38.4 5.8 38 31-70 22-59 (132)
111 PF13936 HTH_38: Helix-turn-he 92.6 0.22 4.7E-06 32.9 3.9 42 13-59 2-43 (44)
112 PF13404 HTH_AsnC-type: AsnC-t 92.6 0.52 1.1E-05 31.0 5.7 42 16-61 1-42 (42)
113 PRK10430 DNA-binding transcrip 92.6 0.51 1.1E-05 40.6 7.3 64 14-80 157-222 (239)
114 TIGR02010 IscR iron-sulfur clu 92.5 0.37 8.1E-06 38.8 6.0 41 31-73 22-62 (135)
115 COG1654 BirA Biotin operon rep 92.3 0.49 1.1E-05 35.6 5.9 71 19-93 4-74 (79)
116 COG2345 Predicted transcriptio 92.1 3.6 7.9E-05 36.5 12.0 87 19-114 12-100 (218)
117 PF04545 Sigma70_r4: Sigma-70, 92.0 0.55 1.2E-05 31.2 5.4 43 13-60 2-44 (50)
118 COG1693 Repressor of nif and g 91.8 0.19 4.2E-06 46.4 3.9 55 15-70 3-60 (325)
119 TIGR00373 conserved hypothetic 91.3 0.72 1.6E-05 38.6 6.5 49 18-70 14-62 (158)
120 PF04703 FaeA: FaeA-like prote 91.3 0.38 8.1E-06 34.6 4.1 48 111-166 2-50 (62)
121 PRK11920 rirA iron-responsive 91.3 0.69 1.5E-05 38.4 6.4 46 26-73 16-61 (153)
122 PRK10906 DNA-binding transcrip 91.0 0.6 1.3E-05 41.7 6.1 115 18-148 5-126 (252)
123 PRK10046 dpiA two-component re 90.9 1.6 3.4E-05 37.3 8.5 57 16-77 162-218 (225)
124 COG1414 IclR Transcriptional r 90.9 0.57 1.2E-05 41.6 5.9 44 22-68 8-51 (246)
125 PRK10857 DNA-binding transcrip 90.7 0.64 1.4E-05 39.2 5.8 42 30-73 21-62 (164)
126 PF14394 DUF4423: Domain of un 90.7 2.3 4.9E-05 36.1 9.1 124 11-156 8-142 (171)
127 PRK09416 lstR lineage-specific 90.7 0.81 1.8E-05 37.8 6.1 68 14-84 39-109 (135)
128 PF13551 HTH_29: Winged helix- 90.6 4 8.6E-05 30.6 9.6 99 33-154 10-110 (112)
129 PF09202 Rio2_N: Rio2, N-termi 90.6 1.5 3.2E-05 33.1 7.0 58 13-73 1-60 (82)
130 PHA02701 ORF020 dsRNA-binding 90.3 0.72 1.6E-05 39.9 5.8 49 18-69 4-52 (183)
131 PRK00135 scpB segregation and 90.3 1.4 3E-05 38.2 7.5 52 14-72 86-137 (188)
132 PRK10163 DNA-binding transcrip 90.2 0.64 1.4E-05 41.6 5.6 44 22-68 29-72 (271)
133 PRK11569 transcriptional repre 90.2 0.89 1.9E-05 40.7 6.5 44 22-68 32-75 (274)
134 COG1349 GlpR Transcriptional r 90.1 3.4 7.4E-05 36.9 10.2 118 19-152 6-130 (253)
135 PRK09802 DNA-binding transcrip 90.1 3.5 7.6E-05 37.1 10.4 119 19-151 18-144 (269)
136 cd06170 LuxR_C_like C-terminal 90.1 1.2 2.5E-05 29.2 5.6 41 16-62 1-41 (57)
137 PF04492 Phage_rep_O: Bacterio 90.0 1.2 2.6E-05 34.8 6.2 54 13-68 27-86 (100)
138 TIGR02431 pcaR_pcaU beta-ketoa 89.8 0.67 1.5E-05 40.7 5.4 44 22-68 13-56 (248)
139 PRK13719 conjugal transfer tra 89.6 0.9 1.9E-05 40.3 5.9 54 4-63 132-185 (217)
140 PF05584 Sulfolobus_pRN: Sulfo 89.5 2.7 5.9E-05 31.2 7.4 51 15-71 3-53 (72)
141 smart00550 Zalpha Z-DNA-bindin 89.4 1.5 3.2E-05 31.5 6.0 49 108-164 5-55 (68)
142 cd07153 Fur_like Ferric uptake 89.2 2.2 4.8E-05 32.7 7.3 54 111-167 3-57 (116)
143 PF08221 HTH_9: RNA polymerase 89.1 1.4 3E-05 31.3 5.5 44 21-68 16-59 (62)
144 COG1959 Predicted transcriptio 89.1 1.3 2.8E-05 36.7 6.2 52 20-73 8-62 (150)
145 TIGR03879 near_KaiC_dom probab 88.9 0.4 8.6E-06 35.6 2.7 53 10-66 10-62 (73)
146 PRK09834 DNA-binding transcrip 88.8 1.1 2.5E-05 39.8 6.1 46 22-70 15-60 (263)
147 PF08784 RPA_C: Replication pr 88.5 0.96 2.1E-05 34.5 4.7 49 107-163 45-97 (102)
148 smart00420 HTH_DEOR helix_turn 88.3 2.9 6.3E-05 26.9 6.4 46 112-165 3-48 (53)
149 PF01475 FUR: Ferric uptake re 88.2 2.7 5.8E-05 32.8 7.2 57 108-167 7-64 (120)
150 PRK15090 DNA-binding transcrip 88.0 1 2.2E-05 39.8 5.3 43 22-68 18-60 (257)
151 cd06171 Sigma70_r4 Sigma70, re 87.9 1.5 3.3E-05 27.7 4.8 45 13-62 8-52 (55)
152 PRK09392 ftrB transcriptional 87.3 2.4 5.2E-05 36.3 7.1 50 15-66 146-203 (236)
153 COG3682 Predicted transcriptio 87.3 14 0.00031 30.0 12.6 112 15-155 3-116 (123)
154 COG4189 Predicted transcriptio 87.3 1.9 4.2E-05 39.1 6.5 55 21-80 26-82 (308)
155 PF00392 GntR: Bacterial regul 87.2 1.3 2.8E-05 31.0 4.4 35 34-70 23-58 (64)
156 cd04781 HTH_MerR-like_sg6 Heli 87.2 7.9 0.00017 30.5 9.4 70 35-137 1-70 (120)
157 PRK09483 response regulator; P 87.1 2.1 4.6E-05 35.0 6.4 46 12-63 145-190 (217)
158 cd04780 HTH_MerR-like_sg5 Heli 87.1 11 0.00023 28.8 9.8 72 35-137 1-72 (95)
159 COG5625 Predicted transcriptio 87.1 0.85 1.9E-05 36.1 3.7 70 14-88 17-86 (113)
160 PRK15431 ferrous iron transpor 87.0 4.4 9.4E-05 30.5 7.3 45 113-165 6-50 (78)
161 PF00538 Linker_histone: linke 86.7 3.4 7.4E-05 30.1 6.6 55 17-71 3-66 (77)
162 PF07106 TBPIP: Tat binding pr 86.6 8.9 0.00019 31.9 9.9 108 20-136 3-121 (169)
163 cd04787 HTH_HMRTR_unk Helix-Tu 86.5 12 0.00027 30.0 10.3 70 35-136 1-70 (133)
164 PRK00082 hrcA heat-inducible t 86.4 1.6 3.6E-05 40.8 5.9 51 14-68 2-59 (339)
165 PF08461 HTH_12: Ribonuclease 86.3 2.1 4.6E-05 30.7 5.2 46 22-68 2-50 (66)
166 PRK09462 fur ferric uptake reg 86.2 3.8 8.2E-05 33.4 7.3 55 109-166 17-73 (148)
167 PRK10840 transcriptional regul 86.0 2 4.4E-05 36.0 5.8 45 13-63 148-192 (216)
168 PF13412 HTH_24: Winged helix- 85.6 3.9 8.4E-05 26.7 5.8 47 108-162 2-48 (48)
169 COG1777 Predicted transcriptio 85.4 1.2 2.7E-05 39.4 4.2 48 35-84 29-78 (217)
170 PF06163 DUF977: Bacterial pro 85.2 2.1 4.6E-05 35.0 5.2 42 22-67 16-57 (127)
171 PRK00411 cdc6 cell division co 84.5 3.7 8E-05 38.0 7.2 58 12-71 290-360 (394)
172 PRK04424 fatty acid biosynthes 84.3 0.74 1.6E-05 39.3 2.3 72 19-94 8-89 (185)
173 PF01978 TrmB: Sugar-specific 84.0 4.1 8.9E-05 28.6 5.8 50 109-166 8-57 (68)
174 COG5340 Predicted transcriptio 84.0 1.1 2.3E-05 40.4 3.3 55 13-71 11-65 (269)
175 PF04967 HTH_10: HTH DNA bindi 83.7 5.2 0.00011 27.8 6.0 46 16-63 1-50 (53)
176 PF00196 GerE: Bacterial regul 83.6 2.8 6.1E-05 28.6 4.6 44 14-63 2-45 (58)
177 PRK11639 zinc uptake transcrip 83.3 4.5 9.7E-05 34.0 6.7 56 15-71 23-81 (169)
178 COG1695 Predicted transcriptio 83.0 3.8 8.3E-05 32.6 5.9 67 18-84 9-80 (138)
179 PTZ00326 phenylalanyl-tRNA syn 82.9 4.7 0.0001 39.9 7.5 60 17-83 5-64 (494)
180 PRK00135 scpB segregation and 82.5 22 0.00048 30.7 10.7 126 19-164 5-134 (188)
181 PHA02943 hypothetical protein; 82.4 6.5 0.00014 33.4 7.1 51 107-166 9-59 (165)
182 cd01105 HTH_GlnR-like Helix-Tu 82.4 17 0.00038 27.0 8.9 72 34-137 1-72 (88)
183 smart00531 TFIIE Transcription 82.3 1.3 2.8E-05 36.4 3.0 79 21-119 4-85 (147)
184 PRK11886 bifunctional biotin-- 82.3 3.7 8.1E-05 37.5 6.2 46 20-69 6-52 (319)
185 PRK11402 DNA-binding transcrip 82.1 2.9 6.3E-05 36.4 5.2 54 21-81 12-73 (241)
186 COG0640 ArsR Predicted transcr 81.8 8.4 0.00018 27.1 6.8 43 22-68 29-71 (110)
187 TIGR00122 birA_repr_reg BirA b 81.8 4.1 8.8E-05 28.7 5.1 43 21-68 3-45 (69)
188 PF08222 HTH_CodY: CodY helix- 81.5 6.2 0.00013 28.3 5.7 38 36-76 6-43 (61)
189 PRK11083 DNA-binding response 81.5 4.7 0.0001 32.9 6.1 47 14-62 153-208 (228)
190 cd04770 HTH_HMRTR Helix-Turn-H 81.3 24 0.00052 27.6 10.2 71 35-137 1-71 (123)
191 COG2188 PhnF Transcriptional r 81.3 3.2 6.9E-05 36.5 5.2 56 22-84 11-74 (236)
192 TIGR02787 codY_Gpos GTP-sensin 81.1 3.4 7.3E-05 37.5 5.4 57 12-70 173-232 (251)
193 PRK10336 DNA-binding transcrip 81.1 4.2 9.2E-05 33.1 5.6 55 15-71 149-211 (219)
194 PRK10651 transcriptional regul 81.0 4.8 0.0001 32.4 5.9 46 13-64 153-198 (216)
195 PF13384 HTH_23: Homeodomain-l 81.0 2.8 6E-05 27.5 3.7 30 34-65 17-46 (50)
196 COG5647 Cullin, a subunit of E 80.7 13 0.00028 38.5 9.8 140 19-164 609-763 (773)
197 TIGR02325 C_P_lyase_phnF phosp 80.4 2.6 5.5E-05 36.3 4.3 55 21-82 11-73 (238)
198 PF13411 MerR_1: MerR HTH fami 80.3 14 0.00031 25.5 7.4 67 36-135 2-68 (69)
199 TIGR02277 PaaX_trns_reg phenyl 80.3 3.4 7.4E-05 37.6 5.2 47 34-83 17-64 (280)
200 TIGR00721 tfx DNA-binding prot 80.1 4.1 8.8E-05 33.7 5.1 43 14-62 5-51 (137)
201 PF09397 Ftsk_gamma: Ftsk gamm 80.1 5.9 0.00013 28.7 5.4 54 22-81 10-63 (65)
202 COG2390 DeoR Transcriptional r 79.9 4.1 9E-05 38.1 5.7 49 18-68 10-58 (321)
203 PRK11475 DNA-binding transcrip 79.7 5.1 0.00011 34.6 5.9 45 13-63 132-176 (207)
204 COG0735 Fur Fe2+/Zn2+ uptake r 79.6 9.9 0.00021 31.2 7.3 55 111-168 23-78 (145)
205 PHA03103 double-strand RNA-bin 79.3 5.3 0.00011 34.6 5.8 49 21-71 13-62 (183)
206 TIGR02404 trehalos_R_Bsub treh 79.1 4.7 0.0001 34.8 5.5 33 36-70 26-58 (233)
207 PRK03975 tfx putative transcri 78.8 5.8 0.00013 32.9 5.7 41 13-59 4-44 (141)
208 PF13034 DUF3895: Protein of u 78.7 14 0.00031 27.8 7.2 60 109-168 4-70 (78)
209 PRK15201 fimbriae regulatory p 78.5 5.5 0.00012 34.8 5.6 45 13-63 131-175 (198)
210 PLN02853 Probable phenylalanyl 78.2 7.6 0.00016 38.5 7.2 59 19-84 4-62 (492)
211 COG1675 TFA1 Transcription ini 77.8 9.8 0.00021 32.8 7.0 52 18-73 18-69 (176)
212 cd01107 HTH_BmrR Helix-Turn-He 77.8 29 0.00062 26.8 9.1 71 36-137 2-72 (108)
213 PRK10100 DNA-binding transcrip 77.8 5.8 0.00013 34.5 5.7 45 13-63 153-197 (216)
214 COG2865 Predicted transcriptio 77.8 4.8 0.0001 39.6 5.6 67 15-87 399-465 (467)
215 PRK14999 histidine utilization 77.8 5.6 0.00012 34.6 5.7 39 36-81 38-76 (241)
216 COG3388 Predicted transcriptio 77.3 2.1 4.7E-05 33.4 2.5 43 21-67 17-59 (101)
217 COG1386 scpB Chromosome segreg 77.2 8.6 0.00019 33.2 6.5 57 14-77 88-144 (184)
218 PRK09764 DNA-binding transcrip 77.1 6.1 0.00013 34.4 5.7 53 22-81 9-69 (240)
219 PRK15002 redox-sensitivie tran 77.1 32 0.0007 28.7 9.7 95 35-163 12-108 (154)
220 cd04776 HTH_GnyR Helix-Turn-He 77.1 34 0.00074 27.0 10.1 68 36-137 2-69 (118)
221 TIGR02147 Fsuc_second hypothet 77.0 30 0.00065 31.6 10.3 122 11-155 106-239 (271)
222 cd04789 HTH_Cfa Helix-Turn-Hel 76.9 19 0.00041 27.6 7.8 68 35-135 2-69 (102)
223 PF08461 HTH_12: Ribonuclease 76.7 8.6 0.00019 27.5 5.4 48 113-163 2-50 (66)
224 TIGR02392 rpoH_proteo alternat 76.4 5.6 0.00012 35.5 5.3 48 12-62 215-266 (270)
225 COG1510 Predicted transcriptio 76.4 17 0.00037 31.4 7.9 91 22-136 30-120 (177)
226 PF08220 HTH_DeoR: DeoR-like h 76.3 8.7 0.00019 26.5 5.2 46 112-165 3-48 (57)
227 PRK15411 rcsA colanic acid cap 75.8 5.8 0.00013 34.0 5.1 43 15-63 137-179 (207)
228 PRK11920 rirA iron-responsive 75.7 19 0.00041 29.8 8.0 37 122-166 23-59 (153)
229 TIGR00331 hrcA heat shock gene 75.6 5.9 0.00013 37.1 5.4 42 25-70 14-57 (337)
230 PRK04217 hypothetical protein; 75.6 6.3 0.00014 31.3 4.9 45 12-61 39-83 (110)
231 PF09904 HTH_43: Winged helix- 75.4 12 0.00027 28.9 6.2 74 21-114 10-86 (90)
232 PRK15369 two component system 75.2 12 0.00025 29.6 6.4 45 13-63 147-191 (211)
233 COG3398 Uncharacterized protei 75.2 6.1 0.00013 35.5 5.1 46 20-69 176-221 (240)
234 TIGR02044 CueR Cu(I)-responsiv 74.8 40 0.00087 26.7 10.0 69 35-135 1-69 (127)
235 PF08281 Sigma70_r4_2: Sigma-7 74.8 9 0.0002 25.4 4.9 42 13-59 8-49 (54)
236 TIGR02018 his_ut_repres histid 74.7 4.7 0.0001 34.8 4.3 39 36-81 27-65 (230)
237 PRK10736 hypothetical protein; 74.6 7.3 0.00016 37.2 5.9 50 15-69 305-354 (374)
238 KOG3095 Transcription initiati 74.2 21 0.00045 33.0 8.4 100 22-150 143-249 (284)
239 cd04783 HTH_MerR1 Helix-Turn-H 74.2 41 0.0009 26.5 10.3 71 35-137 1-71 (126)
240 PF13613 HTH_Tnp_4: Helix-turn 74.0 11 0.00024 25.4 5.2 44 15-62 2-45 (53)
241 PF13744 HTH_37: Helix-turn-he 73.9 5.6 0.00012 29.2 4.0 36 21-58 18-53 (80)
242 KOG3233 RNA polymerase III, su 73.9 17 0.00037 33.7 7.7 127 15-166 7-135 (297)
243 PRK11639 zinc uptake transcrip 73.7 13 0.00028 31.2 6.6 54 110-166 27-81 (169)
244 cd04773 HTH_TioE_rpt2 Second H 73.5 40 0.00087 26.1 10.3 70 35-136 1-70 (108)
245 PRK04984 fatty acid metabolism 73.4 8 0.00017 33.4 5.4 46 22-69 11-64 (239)
246 PRK10512 selenocysteinyl-tRNA- 73.3 49 0.0011 33.5 11.7 103 33-165 438-540 (614)
247 PF14502 HTH_41: Helix-turn-he 73.2 7.8 0.00017 26.6 4.1 39 31-71 3-41 (48)
248 PF04218 CENP-B_N: CENP-B N-te 73.2 11 0.00023 25.8 4.9 41 14-59 5-45 (53)
249 PRK15092 DNA-binding transcrip 72.9 8.5 0.00018 34.7 5.7 57 1-68 1-60 (310)
250 PF00126 HTH_1: Bacterial regu 72.7 13 0.00028 25.5 5.4 43 20-68 3-48 (60)
251 PRK10710 DNA-binding transcrip 72.7 7 0.00015 32.4 4.7 47 14-62 159-214 (240)
252 cd04774 HTH_YfmP Helix-Turn-He 72.4 32 0.0007 26.1 8.0 70 36-137 2-71 (96)
253 PRK10360 DNA-binding transcrip 72.3 11 0.00024 30.2 5.7 44 14-63 136-179 (196)
254 COG1497 Predicted transcriptio 72.1 15 0.00034 33.3 7.0 51 21-81 13-64 (260)
255 cd01282 HTH_MerR-like_sg3 Heli 71.8 45 0.00097 25.9 9.1 69 35-136 1-69 (112)
256 cd01108 HTH_CueR Helix-Turn-He 71.7 49 0.0011 26.3 10.0 69 35-135 1-69 (127)
257 PF01726 LexA_DNA_bind: LexA D 71.6 15 0.00033 26.2 5.6 46 112-164 13-59 (65)
258 PRK15481 transcriptional regul 71.4 9.2 0.0002 36.0 5.7 48 20-69 7-62 (431)
259 COG2186 FadR Transcriptional r 71.2 11 0.00024 33.3 5.8 70 36-113 36-106 (241)
260 COG5631 Predicted transcriptio 70.8 12 0.00026 32.3 5.6 63 12-80 77-140 (199)
261 PRK10079 phosphonate metabolis 70.8 6.4 0.00014 34.3 4.2 40 36-82 37-76 (241)
262 PRK09958 DNA-binding transcrip 70.7 15 0.00032 29.6 6.1 48 13-66 141-188 (204)
263 smart00843 Ftsk_gamma This dom 70.6 13 0.00028 26.8 5.0 53 22-80 9-61 (63)
264 cd04782 HTH_BltR Helix-Turn-He 70.5 44 0.00095 25.3 9.4 69 36-136 2-70 (97)
265 PF07574 SMC_Nse1: Nse1 non-SM 70.4 69 0.0015 27.5 11.2 106 54-165 51-186 (200)
266 COG4190 Predicted transcriptio 70.3 14 0.0003 30.7 5.8 60 15-78 61-120 (144)
267 COG4742 Predicted transcriptio 70.2 17 0.00036 33.2 6.8 57 17-85 12-68 (260)
268 cd04788 HTH_NolA-AlbR Helix-Tu 70.0 45 0.00097 25.2 8.4 71 35-137 1-71 (96)
269 COG3682 Predicted transcriptio 69.5 13 0.00027 30.4 5.3 55 109-167 6-60 (123)
270 KOG1767 40S ribosomal protein 69.4 4 8.7E-05 32.4 2.3 44 33-80 59-102 (110)
271 TIGR03020 EpsA transcriptional 69.3 15 0.00033 32.9 6.4 45 13-63 188-232 (247)
272 TIGR03338 phnR_burk phosphonat 69.3 8.1 0.00017 32.6 4.4 46 22-69 15-67 (212)
273 PF04079 DUF387: Putative tran 69.2 9.3 0.0002 32.1 4.7 61 13-80 77-138 (159)
274 PRK15431 ferrous iron transpor 69.1 21 0.00045 26.9 6.0 45 22-70 6-50 (78)
275 TIGR02154 PhoB phosphate regul 69.1 4.8 0.0001 32.7 2.9 47 15-61 154-203 (226)
276 PF10007 DUF2250: Uncharacteri 68.8 18 0.00038 28.0 5.8 48 110-165 8-55 (92)
277 TIGR02812 fadR_gamma fatty aci 68.8 12 0.00026 32.3 5.5 47 22-70 10-64 (235)
278 PRK09514 zntR zinc-responsive 68.8 62 0.0013 26.3 10.4 69 35-135 2-70 (140)
279 TIGR00637 ModE_repress ModE mo 68.7 18 0.00039 27.8 5.9 41 16-62 2-42 (99)
280 PF02082 Rrf2: Transcriptional 68.6 34 0.00073 24.9 7.2 35 123-165 25-59 (83)
281 PRK11302 DNA-binding transcrip 68.6 6.5 0.00014 34.7 3.9 52 12-65 10-63 (284)
282 PRK10403 transcriptional regul 68.5 18 0.00039 28.9 6.2 45 13-63 151-195 (215)
283 PRK09333 30S ribosomal protein 68.5 12 0.00027 31.4 5.2 45 22-70 57-115 (150)
284 PRK04214 rbn ribonuclease BN/u 68.2 12 0.00025 35.8 5.8 44 23-68 297-342 (412)
285 TIGR02036 dsdC D-serine deamin 68.1 16 0.00036 32.3 6.4 52 11-68 3-57 (302)
286 TIGR02928 orc1/cdc6 family rep 68.0 22 0.00048 32.4 7.3 60 12-71 282-352 (365)
287 COG2865 Predicted transcriptio 67.7 11 0.00023 37.2 5.4 104 53-168 350-453 (467)
288 PF12802 MarR_2: MarR family; 67.6 24 0.00052 23.6 5.8 48 111-166 7-56 (62)
289 cd04767 HTH_HspR-like_MBC Heli 67.5 28 0.0006 28.1 6.9 28 35-68 2-29 (120)
290 PF03979 Sigma70_r1_1: Sigma-7 67.5 10 0.00022 28.1 4.1 38 117-159 15-52 (82)
291 TIGR01321 TrpR trp operon repr 67.3 12 0.00026 29.1 4.6 44 16-61 33-80 (94)
292 PRK10188 DNA-binding transcrip 67.0 16 0.00035 32.2 6.0 44 14-63 178-221 (240)
293 PF00292 PAX: 'Paired box' dom 66.8 67 0.0015 26.2 9.1 106 16-153 18-125 (125)
294 cd04769 HTH_MerR2 Helix-Turn-H 66.8 59 0.0013 25.3 9.7 70 35-137 1-70 (116)
295 PRK08301 sporulation sigma fac 66.7 13 0.00029 32.0 5.3 48 13-62 176-228 (234)
296 PRK10216 DNA-binding transcrip 66.5 16 0.00035 32.6 6.0 45 12-62 4-48 (319)
297 PRK10227 DNA-binding transcrip 66.1 70 0.0015 25.9 10.0 69 35-135 1-69 (135)
298 COG2524 Predicted transcriptio 66.1 17 0.00036 33.6 5.9 86 13-100 1-92 (294)
299 PF10264 Stork_head: Winged he 66.1 32 0.00069 26.0 6.5 57 107-163 13-69 (80)
300 PRK10512 selenocysteinyl-tRNA- 65.8 77 0.0017 32.1 11.2 111 15-162 486-597 (614)
301 PF06207 DUF1002: Protein of u 65.1 1E+02 0.0022 27.5 11.0 58 99-156 147-205 (225)
302 TIGR03541 reg_near_HchA LuxR f 65.1 20 0.00044 31.2 6.2 46 12-63 168-213 (232)
303 PF09106 SelB-wing_2: Elongati 65.0 6.8 0.00015 27.1 2.6 39 32-70 15-54 (59)
304 COG1339 Transcriptional regula 64.9 17 0.00036 32.2 5.5 36 31-68 16-51 (214)
305 PF00538 Linker_histone: linke 64.9 39 0.00085 24.5 6.8 49 118-168 16-68 (77)
306 PF10576 EndIII_4Fe-2S: Iron-s 64.8 2.3 5.1E-05 23.0 0.2 11 203-213 7-17 (17)
307 cd00592 HTH_MerR-like Helix-Tu 64.7 56 0.0012 24.3 10.3 70 35-137 1-70 (100)
308 TIGR02937 sigma70-ECF RNA poly 64.7 13 0.00029 28.1 4.5 45 13-62 108-152 (158)
309 PRK10225 DNA-binding transcrip 64.7 10 0.00022 33.2 4.3 47 22-70 13-67 (257)
310 TIGR02702 SufR_cyano iron-sulf 64.4 35 0.00077 29.1 7.5 47 111-165 3-49 (203)
311 PRK03837 transcriptional regul 64.3 11 0.00024 32.5 4.3 46 22-69 17-70 (241)
312 PRK15418 transcriptional regul 64.3 9.8 0.00021 35.2 4.3 50 16-68 12-61 (318)
313 COG4565 CitB Response regulato 64.2 47 0.001 29.7 8.3 65 13-80 152-217 (224)
314 PRK06266 transcription initiat 64.2 21 0.00046 30.4 6.0 44 113-164 26-69 (178)
315 PF13518 HTH_28: Helix-turn-he 64.0 18 0.00039 23.4 4.4 30 34-65 12-41 (52)
316 COG4189 Predicted transcriptio 63.8 38 0.00081 31.0 7.7 51 105-163 19-69 (308)
317 PRK11062 nhaR transcriptional 63.7 19 0.0004 31.8 5.8 43 14-62 2-44 (296)
318 PRK05803 sporulation sigma fac 63.7 14 0.0003 32.0 4.9 43 13-57 173-216 (233)
319 PRK10086 DNA-binding transcrip 63.7 19 0.00041 32.0 5.9 44 13-62 11-54 (311)
320 PF06648 DUF1160: Protein of u 63.7 13 0.00029 30.1 4.4 65 96-164 25-89 (122)
321 smart00418 HTH_ARSR helix_turn 63.5 24 0.00052 22.9 5.1 43 114-165 2-44 (66)
322 PF01418 HTH_6: Helix-turn-hel 63.5 15 0.00032 26.7 4.3 50 13-64 11-62 (77)
323 PRK11557 putative DNA-binding 63.5 8.8 0.00019 34.0 3.7 52 12-65 6-59 (278)
324 PRK09645 RNA polymerase sigma 63.3 17 0.00037 29.4 5.1 45 13-62 116-164 (173)
325 PF13443 HTH_26: Cro/C1-type H 63.2 7.6 0.00016 26.5 2.6 26 31-58 7-32 (63)
326 PF06971 Put_DNA-bind_N: Putat 63.1 16 0.00035 25.0 4.1 34 22-57 16-49 (50)
327 TIGR00281 segregation and cond 63.0 36 0.00078 29.4 7.2 59 15-80 84-143 (186)
328 TIGR03337 phnR transcriptional 62.8 19 0.0004 30.8 5.5 33 36-70 27-59 (231)
329 TIGR00635 ruvB Holliday juncti 62.8 20 0.00044 31.9 5.9 53 13-67 233-287 (305)
330 COG4738 Predicted transcriptio 62.7 20 0.00043 29.1 5.1 35 32-68 39-73 (124)
331 cd01106 HTH_TipAL-Mta Helix-Tu 62.6 66 0.0014 24.4 9.8 70 36-137 2-71 (103)
332 PF13814 Replic_Relax: Replica 62.6 22 0.00047 29.4 5.7 35 35-71 10-47 (191)
333 cd04775 HTH_Cfa-like Helix-Tur 62.5 67 0.0015 24.5 8.5 69 35-136 2-70 (102)
334 PRK11534 DNA-binding transcrip 62.4 13 0.00029 31.7 4.5 46 22-69 11-63 (224)
335 PRK00118 putative DNA-binding 62.3 25 0.00053 27.7 5.6 42 13-59 15-56 (104)
336 PF10557 Cullin_Nedd8: Cullin 62.1 37 0.00081 24.1 6.1 60 105-164 4-63 (68)
337 PRK11642 exoribonuclease R; Pr 62.1 25 0.00055 36.8 7.2 50 15-68 17-70 (813)
338 COG0789 SoxR Predicted transcr 62.0 54 0.0012 25.2 7.6 70 36-137 2-71 (124)
339 PRK09986 DNA-binding transcrip 62.0 14 0.00031 32.0 4.7 51 12-68 3-56 (294)
340 PRK14137 recX recombination re 61.8 31 0.00066 30.0 6.6 54 103-162 35-88 (195)
341 PRK09508 leuO leucine transcri 61.6 22 0.00047 31.7 5.9 44 13-62 19-62 (314)
342 PRK12427 flagellar biosynthesi 61.5 16 0.00034 32.0 4.8 46 12-62 180-225 (231)
343 TIGR02846 spore_sigmaK RNA pol 61.5 18 0.00038 31.3 5.2 48 13-62 172-224 (227)
344 PRK10421 DNA-binding transcrip 61.3 13 0.00028 32.5 4.3 34 35-70 26-60 (253)
345 cd04777 HTH_MerR-like_sg1 Heli 61.3 33 0.00071 26.3 6.1 67 35-135 1-67 (107)
346 PF10711 DUF2513: Hypothetical 61.2 17 0.00037 27.9 4.5 64 21-87 8-71 (102)
347 cd04763 HTH_MlrA-like Helix-Tu 61.0 29 0.00062 24.2 5.3 27 36-68 2-29 (68)
348 PF03965 Penicillinase_R: Peni 60.9 30 0.00066 26.8 5.9 53 110-166 4-56 (115)
349 PRK11523 DNA-binding transcrip 60.7 13 0.00029 32.4 4.3 47 22-70 12-66 (253)
350 PRK10082 cell density-dependen 60.7 22 0.00047 31.5 5.7 45 12-62 7-51 (303)
351 TIGR01529 argR_whole arginine 60.7 42 0.00091 27.6 7.0 54 22-83 6-62 (146)
352 PF04539 Sigma70_r3: Sigma-70 60.5 23 0.0005 25.1 4.9 42 106-155 2-44 (78)
353 TIGR02063 RNase_R ribonuclease 60.4 21 0.00047 36.5 6.3 48 19-68 3-54 (709)
354 PRK09652 RNA polymerase sigma 59.9 19 0.00041 28.8 4.8 41 13-58 126-166 (182)
355 PRK11013 DNA-binding transcrip 59.9 25 0.00055 31.2 6.0 49 14-68 2-53 (309)
356 COG4465 CodY Pleiotropic trans 59.6 5.2 0.00011 35.9 1.5 59 12-73 179-240 (261)
357 PRK09464 pdhR transcriptional 59.4 15 0.00032 32.1 4.3 53 22-81 14-74 (254)
358 smart00753 PAM PCI/PINT associ 59.2 25 0.00054 25.5 4.9 51 106-164 6-57 (88)
359 smart00088 PINT motif in prote 59.2 25 0.00054 25.5 4.9 51 106-164 6-57 (88)
360 PF10771 DUF2582: Protein of u 59.1 17 0.00037 26.3 3.9 44 21-68 11-54 (65)
361 CHL00148 orf27 Ycf27; Reviewed 59.0 18 0.00038 29.9 4.6 47 15-61 161-216 (240)
362 PRK09990 DNA-binding transcrip 58.7 15 0.00034 31.9 4.3 47 22-70 11-65 (251)
363 TIGR02051 MerR Hg(II)-responsi 58.6 89 0.0019 24.7 10.1 68 37-136 2-69 (124)
364 PF09382 RQC: RQC domain; Int 58.6 50 0.0011 24.8 6.7 54 112-165 7-76 (106)
365 PRK10681 DNA-binding transcrip 58.5 84 0.0018 27.8 9.0 115 19-150 8-129 (252)
366 cd05029 S-100A6 S-100A6: S-100 58.5 43 0.00094 25.0 6.2 54 105-159 7-64 (88)
367 PF04157 EAP30: EAP30/Vps36 fa 58.3 9.9 0.00022 33.2 3.0 61 100-160 89-150 (223)
368 COG3415 Transposase and inacti 58.3 1.1E+02 0.0023 25.4 11.3 92 33-157 20-112 (138)
369 smart00422 HTH_MERR helix_turn 58.2 57 0.0012 22.3 8.2 27 36-68 2-28 (70)
370 TIGR01950 SoxR redox-sensitive 58.2 1E+02 0.0022 25.2 10.2 68 35-135 2-69 (142)
371 COG1420 HrcA Transcriptional r 58.2 26 0.00057 33.1 6.0 55 14-68 2-59 (346)
372 PF01047 MarR: MarR family; I 58.1 25 0.00055 23.4 4.5 46 113-166 7-52 (59)
373 COG1167 ARO8 Transcriptional r 57.9 1.8E+02 0.004 28.0 12.6 142 21-164 7-184 (459)
374 PRK09642 RNA polymerase sigma 57.7 25 0.00054 28.0 5.1 44 14-62 105-152 (160)
375 COG2771 CsgD DNA-binding HTH d 57.7 39 0.00084 22.5 5.4 44 14-63 3-46 (65)
376 PRK11414 colanic acid/biofilm 57.6 16 0.00034 31.3 4.1 52 15-69 9-67 (221)
377 COG2197 CitB Response regulato 57.5 26 0.00056 30.2 5.5 44 14-63 147-190 (211)
378 PRK11242 DNA-binding transcrip 57.4 25 0.00054 30.5 5.4 40 17-62 2-41 (296)
379 TIGR02479 FliA_WhiG RNA polyme 57.4 23 0.0005 30.4 5.1 40 13-57 173-212 (224)
380 PRK11482 putative DNA-binding 57.3 21 0.00045 32.2 5.0 52 11-68 24-78 (317)
381 PRK10857 DNA-binding transcrip 57.3 40 0.00087 28.3 6.4 38 120-165 22-59 (164)
382 PRK09791 putative DNA-binding 57.1 29 0.00064 30.4 5.9 42 15-62 4-45 (302)
383 PRK06288 RNA polymerase sigma 56.9 20 0.00044 31.8 4.9 44 13-61 210-257 (268)
384 PRK11337 DNA-binding transcrip 56.9 14 0.0003 33.0 3.8 51 13-65 23-75 (292)
385 smart00346 HTH_ICLR helix_turn 56.8 40 0.00087 24.3 5.7 43 114-164 10-53 (91)
386 COG0664 Crp cAMP-binding prote 56.5 34 0.00073 27.6 5.8 51 16-68 141-203 (214)
387 TIGR02844 spore_III_D sporulat 56.5 27 0.00058 26.2 4.7 33 20-57 8-40 (80)
388 PRK13752 putative transcriptio 56.3 1.1E+02 0.0024 25.0 9.3 69 35-135 8-76 (144)
389 PRK10094 DNA-binding transcrip 56.3 29 0.00064 30.9 5.8 41 16-62 2-42 (308)
390 cd08767 Cdt1_c The C-terminal 56.3 47 0.001 26.7 6.4 47 106-156 46-92 (126)
391 cd01279 HTH_HspR-like Helix-Tu 56.2 87 0.0019 23.8 9.0 70 35-136 2-71 (98)
392 PF08280 HTH_Mga: M protein tr 56.0 33 0.0007 23.7 4.8 39 20-62 7-45 (59)
393 PF09279 EF-hand_like: Phospho 55.9 29 0.00064 25.0 4.8 46 110-156 2-47 (83)
394 PF04695 Pex14_N: Peroxisomal 55.9 34 0.00073 27.8 5.6 47 108-159 3-51 (136)
395 KOG2587 RNA polymerase III (C) 55.9 1.5E+02 0.0033 29.8 10.9 108 24-137 25-133 (551)
396 PF11313 DUF3116: Protein of u 55.8 64 0.0014 24.7 6.7 56 18-73 4-64 (85)
397 PF06970 RepA_N: Replication i 55.7 31 0.00067 25.5 4.9 48 11-60 14-76 (76)
398 PF07106 TBPIP: Tat binding pr 55.7 38 0.00082 28.1 6.0 47 111-163 3-50 (169)
399 PF04552 Sigma54_DBD: Sigma-54 55.5 8.7 0.00019 32.4 2.1 87 32-138 47-136 (160)
400 smart00526 H15 Domain in histo 55.4 58 0.0013 22.7 6.1 53 18-70 6-65 (66)
401 smart00049 DEP Domain found in 55.4 50 0.0011 23.4 5.9 56 123-184 20-75 (77)
402 TIGR02989 Sig-70_gvs1 RNA poly 55.4 24 0.00052 27.9 4.6 44 13-61 109-152 (159)
403 PRK06811 RNA polymerase factor 55.2 30 0.00065 28.7 5.4 49 12-65 128-180 (189)
404 PRK09935 transcriptional regul 55.1 46 0.001 26.6 6.3 44 14-63 148-191 (210)
405 PRK06986 fliA flagellar biosyn 54.9 24 0.00051 30.6 4.8 45 13-62 182-230 (236)
406 PF13565 HTH_32: Homeodomain-l 54.8 39 0.00084 23.8 5.2 44 109-152 34-77 (77)
407 PRK05572 sporulation sigma fac 54.5 24 0.00053 30.9 4.9 43 12-59 199-241 (252)
408 PF13833 EF-hand_8: EF-hand do 54.5 23 0.00049 23.2 3.7 37 121-159 2-38 (54)
409 PRK01381 Trp operon repressor; 54.2 20 0.00044 28.2 3.8 44 16-61 33-80 (99)
410 PRK13919 putative RNA polymera 54.2 25 0.00054 28.8 4.7 44 13-61 133-180 (186)
411 PRK07670 RNA polymerase sigma 54.1 39 0.00084 29.6 6.1 110 13-154 1-148 (251)
412 TIGR02394 rpoS_proteo RNA poly 53.9 26 0.00056 31.5 5.1 45 12-58 219-264 (285)
413 TIGR02393 RpoD_Cterm RNA polym 53.9 26 0.00057 30.4 5.0 45 12-58 173-218 (238)
414 cd04786 HTH_MerR-like_sg7 Heli 53.6 1.2E+02 0.0025 24.5 10.3 70 35-136 1-70 (131)
415 PF01454 MAGE: MAGE family; I 53.5 1.1E+02 0.0024 25.6 8.7 139 25-165 5-166 (195)
416 TIGR03787 marine_sort_RR prote 53.3 31 0.00068 28.3 5.2 46 14-61 155-202 (227)
417 PRK11511 DNA-binding transcrip 53.2 24 0.00051 27.9 4.2 41 21-63 12-52 (127)
418 PRK03601 transcriptional regul 53.1 36 0.00078 29.7 5.8 40 17-62 2-41 (275)
419 PRK03911 heat-inducible transc 53.1 25 0.00054 32.2 4.7 37 32-68 20-56 (260)
420 PRK15479 transcriptional regul 53.1 30 0.00066 27.9 5.0 47 15-63 148-199 (221)
421 PRK10161 transcriptional regul 53.0 26 0.00056 28.9 4.6 46 15-60 154-202 (229)
422 cd00090 HTH_ARSR Arsenical Res 53.0 64 0.0014 21.3 6.3 47 110-165 8-54 (78)
423 PF01381 HTH_3: Helix-turn-hel 53.0 16 0.00035 24.0 2.8 26 32-59 7-32 (55)
424 PRK14997 LysR family transcrip 52.9 34 0.00074 30.0 5.6 47 16-68 2-51 (301)
425 PRK12529 RNA polymerase sigma 52.2 30 0.00066 28.4 4.9 42 12-58 124-165 (178)
426 TIGR02424 TF_pcaQ pca operon t 52.2 39 0.00084 29.5 5.8 47 16-68 3-52 (300)
427 TIGR02944 suf_reg_Xantho FeS a 52.0 1.1E+02 0.0023 24.0 7.8 36 122-165 24-59 (130)
428 PF08100 Dimerisation: Dimeris 51.8 25 0.00054 24.1 3.6 40 20-60 8-50 (51)
429 PRK10014 DNA-binding transcrip 51.5 32 0.00068 30.6 5.2 25 33-59 5-29 (342)
430 PF06479 Ribonuc_2-5A: Ribonuc 51.5 6.6 0.00014 32.0 0.8 57 88-152 32-88 (129)
431 PF07381 DUF1495: Winged helix 51.5 79 0.0017 24.3 6.7 61 20-84 11-81 (90)
432 PRK14135 recX recombination re 51.2 66 0.0014 28.4 7.2 36 31-66 68-104 (263)
433 COG3413 Predicted DNA binding 51.1 44 0.00096 28.7 5.9 47 15-63 155-205 (215)
434 PRK11151 DNA-binding transcrip 51.0 38 0.00083 29.8 5.6 40 17-62 2-41 (305)
435 cd00569 HTH_Hin_like Helix-tur 50.9 41 0.00089 18.4 4.8 22 33-56 20-41 (42)
436 COG0478 RIO-like serine/threon 50.9 48 0.001 31.0 6.3 61 10-73 5-67 (304)
437 COG1959 Predicted transcriptio 50.7 95 0.0021 25.5 7.6 44 115-166 14-60 (150)
438 PF01090 Ribosomal_S19e: Ribos 50.7 17 0.00037 30.2 3.1 46 23-70 57-114 (139)
439 PRK14135 recX recombination re 50.6 55 0.0012 28.9 6.6 74 84-163 19-106 (263)
440 PF07848 PaaX: PaaX-like prote 50.6 81 0.0017 22.9 6.3 51 30-83 16-67 (70)
441 PRK07037 extracytoplasmic-func 50.6 33 0.00071 27.4 4.7 41 13-58 107-147 (163)
442 TIGR02835 spore_sigmaE RNA pol 50.3 33 0.00073 29.7 5.0 44 13-58 176-220 (234)
443 COG1802 GntR Transcriptional r 50.1 49 0.0011 28.4 6.0 52 17-70 15-73 (230)
444 COG4901 Ribosomal protein S25 49.9 43 0.00093 26.6 5.0 60 19-82 43-103 (107)
445 PRK09906 DNA-binding transcrip 49.8 37 0.0008 29.6 5.3 38 19-62 4-41 (296)
446 TIGR02980 SigBFG RNA polymeras 49.7 35 0.00075 29.2 5.0 42 13-59 176-217 (227)
447 smart00344 HTH_ASNC helix_turn 49.7 54 0.0012 24.5 5.6 49 109-165 3-51 (108)
448 COG0826 Collagenase and relate 49.6 67 0.0015 30.3 7.3 95 47-164 45-167 (347)
449 COG2411 Uncharacterized conser 49.5 41 0.00088 29.2 5.2 50 13-66 135-188 (188)
450 TIGR00738 rrf2_super rrf2 fami 49.3 54 0.0012 25.5 5.7 36 122-165 24-59 (132)
451 TIGR03303 OM_YaeT outer membra 49.2 1E+02 0.0022 30.7 8.9 99 26-124 73-211 (741)
452 PRK15421 DNA-binding transcrip 49.0 43 0.00094 30.1 5.8 41 16-62 2-42 (317)
453 cd01109 HTH_YyaN Helix-Turn-He 48.9 1.2E+02 0.0026 23.3 10.8 69 36-136 2-70 (113)
454 PF09079 Cdc6_C: CDC6, C termi 48.7 52 0.0011 23.9 5.2 60 30-89 11-78 (85)
455 PF11994 DUF3489: Protein of u 48.6 81 0.0017 23.4 6.0 59 20-82 12-71 (72)
456 cd04765 HTH_MlrA-like_sg2 Heli 48.6 1.2E+02 0.0026 23.1 7.6 70 36-137 2-72 (99)
457 PRK11924 RNA polymerase sigma 48.5 36 0.00077 27.1 4.6 43 12-59 122-164 (179)
458 cd04764 HTH_MlrA-like_sg1 Heli 48.4 88 0.0019 21.5 7.8 65 36-133 2-66 (67)
459 cd04761 HTH_MerR-SF Helix-Turn 48.1 41 0.00088 21.4 4.1 27 36-68 2-28 (49)
460 PF09107 SelB-wing_3: Elongati 48.0 82 0.0018 21.5 5.6 43 25-71 3-45 (50)
461 KOG4603 TBP-1 interacting prot 47.9 1.4E+02 0.0031 26.0 8.3 60 18-81 7-67 (201)
462 PF01399 PCI: PCI domain; Int 47.8 31 0.00067 25.1 3.9 46 108-161 45-90 (105)
463 TIGR02885 spore_sigF RNA polym 47.7 35 0.00077 29.3 4.8 43 12-59 180-222 (231)
464 PRK10906 DNA-binding transcrip 47.6 49 0.0011 29.5 5.8 49 109-165 5-53 (252)
465 PF02796 HTH_7: Helix-turn-hel 47.6 20 0.00042 23.4 2.4 27 30-58 17-43 (45)
466 PRK10837 putative DNA-binding 47.6 46 0.001 28.7 5.5 47 16-68 3-52 (290)
467 cd08768 Cdc6_C Winged-helix do 47.5 1E+02 0.0022 22.1 8.0 53 19-71 3-67 (87)
468 PRK10411 DNA-binding transcrip 47.3 62 0.0013 28.6 6.3 46 111-164 6-51 (240)
469 PRK12547 RNA polymerase sigma 47.3 41 0.00088 27.1 4.8 42 13-59 110-151 (164)
470 TIGR02952 Sig70_famx2 RNA poly 47.2 43 0.00094 26.7 5.0 43 12-59 119-161 (170)
471 PF03672 UPF0154: Uncharacteri 47.1 83 0.0018 22.8 5.8 44 110-156 18-61 (64)
472 PF04157 EAP30: EAP30/Vps36 fa 47.1 39 0.00085 29.4 5.0 50 15-66 171-220 (223)
473 COG3177 Fic family protein [Fu 47.1 42 0.0009 31.4 5.4 41 29-71 299-339 (348)
474 TIGR02985 Sig70_bacteroi1 RNA 47.0 43 0.00093 26.1 4.8 43 13-60 111-153 (161)
475 cd04779 HTH_MerR-like_sg4 Heli 47.0 1.6E+02 0.0034 24.0 10.7 69 36-137 2-70 (134)
476 PF03428 RP-C: Replication pro 47.0 92 0.002 26.7 7.1 59 14-73 39-108 (177)
477 TIGR02607 antidote_HigA addict 46.9 61 0.0013 22.7 5.2 38 16-58 3-40 (78)
478 TIGR03418 chol_sulf_TF putativ 46.8 48 0.001 28.8 5.5 38 19-62 4-41 (291)
479 PF13542 HTH_Tnp_ISL3: Helix-t 46.6 63 0.0014 21.0 4.9 36 21-59 15-50 (52)
480 PRK12519 RNA polymerase sigma 46.6 34 0.00074 28.2 4.4 44 14-62 140-187 (194)
481 PF07524 Bromo_TP: Bromodomain 46.4 70 0.0015 23.0 5.5 38 101-138 23-73 (77)
482 TIGR03298 argP transcriptional 46.4 54 0.0012 28.5 5.8 44 18-67 3-49 (292)
483 PRK15320 transcriptional activ 45.9 46 0.001 29.8 5.2 48 15-68 164-211 (251)
484 COG1867 TRM1 N2,N2-dimethylgua 45.9 2.6E+02 0.0055 27.1 10.5 55 54-114 228-291 (380)
485 PRK10341 DNA-binding transcrip 45.9 50 0.0011 29.3 5.6 42 15-62 6-47 (312)
486 KOG2593 Transcription initiati 45.5 37 0.00081 33.1 4.9 54 17-74 28-81 (436)
487 PRK13348 chromosome replicatio 45.4 54 0.0012 28.6 5.7 41 16-62 2-42 (294)
488 PRK00117 recX recombination re 45.2 55 0.0012 26.6 5.3 54 104-163 7-60 (157)
489 PRK06930 positive control sigm 45.2 41 0.00088 28.4 4.6 44 13-61 112-155 (170)
490 PRK04158 transcriptional repre 45.1 24 0.00052 32.2 3.4 60 12-74 176-238 (256)
491 PRK11074 putative DNA-binding 45.0 57 0.0012 28.7 5.8 41 16-62 2-42 (300)
492 TIGR02043 ZntR Zn(II)-responsi 45.0 1.6E+02 0.0034 23.5 10.4 69 35-135 2-70 (131)
493 PRK04280 arginine repressor; P 45.0 85 0.0018 26.0 6.4 57 20-84 6-65 (148)
494 TIGR02531 yecD_yerC TrpR-relat 45.0 52 0.0011 25.1 4.7 37 15-58 36-72 (88)
495 TIGR02948 SigW_bacill RNA poly 44.7 39 0.00084 27.5 4.4 43 13-60 134-176 (187)
496 TIGR02984 Sig-70_plancto1 RNA 44.6 51 0.0011 26.8 5.0 42 13-59 138-179 (189)
497 PRK06596 RNA polymerase factor 44.6 49 0.0011 29.9 5.3 44 12-58 227-270 (284)
498 COG2963 Transposase and inacti 44.3 84 0.0018 24.1 6.0 51 13-67 5-56 (116)
499 smart00345 HTH_GNTR helix_turn 44.2 86 0.0019 20.2 5.7 35 123-165 20-54 (60)
500 PRK12683 transcriptional regul 44.1 54 0.0012 29.2 5.6 39 18-62 3-42 (309)
No 1
>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=100.00 E-value=8.7e-78 Score=552.31 Aligned_cols=221 Identities=43% Similarity=0.812 Sum_probs=63.4
Q ss_pred CCCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026766 5 KRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE 84 (233)
Q Consensus 5 ~~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~ 84 (233)
+.++.++++++|+++|++||++|++|||+|||++|||++| |||+++|+|+||+||+|+|||+||||++++||+|||||
T Consensus 71 ~~~~~a~k~~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t--~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml~~ 148 (327)
T PF05158_consen 71 VSEEEAKKLKGLSDEERLVYQLIEEAGNKGIWTKDIKKKT--NLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYMLYD 148 (327)
T ss_dssp --SSS-----SSSCCHHHHHHHHHHHTTT-EEHHHHHHHC--T--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEESS
T ss_pred eCHHHHhhhcCCCHHHHHHHHHHHHhCCCCCcHHHHHHHc--CCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEEcc
Confidence 5678899999999999999999999999999999999999 99999999999999999999999999999999999999
Q ss_pred cccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhhCCC-----------------------------CCHHHHHHHHHH
Q 026766 85 FEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKV-----------------------------ATLEGISDSIKR 135 (233)
Q Consensus 85 lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~-----------------------------~T~~~I~~~I~~ 135 (233)
||||+|||||+||+||+||+|||+.|+++|++||++++. ||+++|++||++
T Consensus 149 l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~eI~~fI~~ 228 (327)
T PF05158_consen 149 LEPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEEIAEFINK 228 (327)
T ss_dssp S-------------------------------------------------------------------------------
T ss_pred CCcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHHHHHHHHH
Confidence 999999999999999999999999999999999986544 999999999999
Q ss_pred hCCcccccCHHHHHHHHHHHhcCCeEEEEeeCCCCCcccccCccee-------eecccCCCCCCCCCCCCCCCCCCCCCC
Q 026766 136 SGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVC-------YKNVSKGGGGGEPKTGSLASIPCGVCP 208 (233)
Q Consensus 136 ~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~~~g~f~~~~~g~~~-------Yr~~~~~~~~~~p~~~~l~~vPCg~CP 208 (233)
+||++++||++||++||++|||||+||++.+++.+++.....+..+ ||.+ .+.+..++++++|||+||
T Consensus 229 sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~PCg~CP 303 (327)
T PF05158_consen 229 SGISNVELSEEDIESLLDTLVYDGKIEEVRSGDGYEYYRAPGQSVLYCSKRRYYRAV-----GPEPSASGLTEVPCGVCP 303 (327)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cCCCceecCHHHHHHHHHHHhhCceeEEEeccCCceeeeeecccceeeecccccccc-----ccccCCCCccCCCCCCCC
Confidence 9999999999999999999999999999987643333322222222 3322 133457789999999999
Q ss_pred ccccCCCCCccCcccccchHhhhc
Q 026766 209 QINICKPDGVISPKTCVYYTKWLD 232 (233)
Q Consensus 209 v~~~C~~~G~IsP~~C~Y~~~WL~ 232 (233)
||+.|.+||+|||++|+||++||+
T Consensus 304 Vf~~C~~~G~IsP~~C~Yf~~WL~ 327 (327)
T PF05158_consen 304 VFDQCSPGGPISPKTCVYFDEWLD 327 (327)
T ss_dssp ------------------------
T ss_pred ccceeCCCCCCCchhchHHHHhhC
Confidence 999999999999999999999996
No 2
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=100.00 E-value=1.2e-72 Score=500.85 Aligned_cols=211 Identities=37% Similarity=0.776 Sum_probs=198.3
Q ss_pred CCCCCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 3 KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 3 ~~~~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
++|+|+.|...+.++++|++||++|+++||+|||.++||.++ |||+++|+|+||+||+|+|||+||||++++||+|||
T Consensus 69 r~~d~~~a~~~~~~e~eEk~vy~lIe~sg~~GIW~k~ik~ks--nLp~~~v~K~LkSLEsKkLIKsVKsv~n~~~KvYmL 146 (297)
T KOG3233|consen 69 RAKDPKSASKGKGMENEEKLVYSLIEESGNEGIWSKEIKRKS--NLPQTVVNKILKSLESKKLIKSVKSVKNSRKKVYML 146 (297)
T ss_pred eccCchhhcccccCChHHHHHHHHHHHcCCCceeeehhhhcc--CCCHHHHHHHHHHHHHHHHHHHHHhhcCCCceEEEE
Confidence 467888888999999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred eccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhh-----------------CCCCCHHHHHHHHHHhCCcccccCH
Q 026766 83 VEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIK-----------------LKVATLEGISDSIKRSGAFKVDLTK 145 (233)
Q Consensus 83 ~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~-----------------~~~~T~~~I~~~I~~~~i~~~~Ls~ 145 (233)
|+|+||.|+|||+||+||+||.|||+.|.++|++|+++ .+++|++||++||++.+|++|.|+.
T Consensus 147 y~leP~~elTGG~WytDqdlDvEfIe~L~~~c~~fl~~~~~~~~~~~~gp~~~~~~~~~t~~ei~~~i~~l~I~nV~Lsl 226 (297)
T KOG3233|consen 147 YDLEPDSELTGGTWYTDQDLDVEFIEVLKQICVRFLESKRFPAEKNVEGPMFVRNESYPTVQEIKEFIRNLNILNVELSL 226 (297)
T ss_pred ecccccccccCCcccccccccHHHHHHHHHHHHHHHHhcccchhhccccchhhhhccCCCHHHHHHHHHHcCcccccccH
Confidence 99999999999999999999999999999999999973 4789999999999999999999999
Q ss_pred HHHHHHHHHHhcCCeEEEEeeCCCCCcccccCcceeeecccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCccccc
Q 026766 146 QQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCV 225 (233)
Q Consensus 146 ~di~~il~~Lv~Dg~ie~v~~~~~g~f~~~~~g~~~Yr~~~~~~~~~~p~~~~l~~vPCg~CPv~~~C~~~G~IsP~~C~ 225 (233)
+|++.|+++|||||+||... +| .+||++.. +.|..+.+.++|||.|||++.|+++|.|||.||+
T Consensus 227 ~dleti~~vlvyDGkvE~r~-dG-----------~~yra~~~----~~~~~~~~~~~Pcg~cPv~~dC~~~g~isP~tC~ 290 (297)
T KOG3233|consen 227 EDLETILDVLVYDGKVEKRH-DG-----------PRYRAFGP----NIPRAGLVAGIPCGICPVIDDCSPGGVISPITCV 290 (297)
T ss_pred HHHHHHhHHheecceeeeee-cC-----------ceeeecCC----CCCCcCccCCCcccCCcchhccCCCCccCchhhH
Confidence 99999999999999999843 32 27998653 3567788889999999999999999999999999
Q ss_pred chHhhh
Q 026766 226 YYTKWL 231 (233)
Q Consensus 226 Y~~~WL 231 (233)
||++||
T Consensus 291 Ym~~WL 296 (297)
T KOG3233|consen 291 YMDKWL 296 (297)
T ss_pred HHHhhc
Confidence 999999
No 3
>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]
Probab=100.00 E-value=4.7e-60 Score=412.45 Aligned_cols=209 Identities=25% Similarity=0.426 Sum_probs=191.7
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc
Q 026766 6 RPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF 85 (233)
Q Consensus 6 ~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l 85 (233)
+.++|+..+.|+++|..||++|+.+|++|||.+.|+.+| |||.+.|-||||+||+|++||+||||++|+||+||||+|
T Consensus 73 ~~~ea~~~~tm~~~E~~vYs~i~~SG~EGiW~Ktik~rT--Nlh~~vV~kcLkSlESkr~vKSvKsvKnptRKiYmLYdl 150 (301)
T COG5111 73 LESEASPINTMDDYELTVYSLISQSGGEGIWLKTIKDRT--NLHHNVVGKCLKSLESKRIVKSVKSVKNPTRKIYMLYDL 150 (301)
T ss_pred ecccCCcccccchHHHHHHHHHHhcCCCceehhhhhhhc--cCcHHHHHHHHHHHHHHHHHHHhhhhcCCCceEEEEecc
Confidence 346788889999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred ccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhh--------------------CCCCCHHHHHHHHHHhCCcccccCH
Q 026766 86 EPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIK--------------------LKVATLEGISDSIKRSGAFKVDLTK 145 (233)
Q Consensus 86 ePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~--------------------~~~~T~~~I~~~I~~~~i~~~~Ls~ 145 (233)
.||+||||||||||||+|.|||+.|..++++||.+ .+|||++||++||+..+|.+|+|+.
T Consensus 151 vPS~eiTGGpWFtD~elDvEfi~~ll~ii~rf~~~n~fp~kn~~~gpnv~~~P~y~~ypT~~~I~n~vr~~ni~~v~L~l 230 (301)
T COG5111 151 VPSEEITGGPWFTDNELDVEFIARLLEIIERFLEKNLFPRKNFEEGPNVFYAPKYEDYPTLEDIMNYVRNVNILSVPLRL 230 (301)
T ss_pred cccccccCCCccccCcccHHHHHHHHHHHHHHHHhccCCccchhcCCccccCCccCCCccHHHHHHHHHhceeeeccccH
Confidence 99999999999999999999999999999999974 3699999999999999999999999
Q ss_pred HHHHHHHHHHhcCCeEEEEeeCCCCCcccccCcceeeecccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCccccc
Q 026766 146 QQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCV 225 (233)
Q Consensus 146 ~di~~il~~Lv~Dg~ie~v~~~~~g~f~~~~~g~~~Yr~~~~~~~~~~p~~~~l~~vPCg~CPv~~~C~~~G~IsP~~C~ 225 (233)
++++++.++|||||++|++.++ ..||...-... ..+..++-|||.||+-|+|...-.++|.+|+
T Consensus 231 ~n~~sL~dvLvyDgKvEK~~~g------------~~yR~~~~~~~----~~nq~~~ep~gn~~led~~e~s~km~p~s~~ 294 (301)
T COG5111 231 DNLESLADVLVYDGKVEKLHSG------------PIYRYRAFKPY----AKNQGEGEPAGNKALEDEEEFSFKMFPASVV 294 (301)
T ss_pred HHHHHHhHheeecCeeeeeccC------------cceeeeecChh----hhcccCCCCCCCCcccchHhhhcccCceeEE
Confidence 9999999999999999998643 23665332111 2457789999999999999999999999999
Q ss_pred chHhhhc
Q 026766 226 YYTKWLD 232 (233)
Q Consensus 226 Y~~~WL~ 232 (233)
||++|+.
T Consensus 295 y~dew~~ 301 (301)
T COG5111 295 YFDEWTI 301 (301)
T ss_pred eehhhcC
Confidence 9999973
No 4
>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=98.49 E-value=5.9e-07 Score=66.26 Aligned_cols=65 Identities=25% Similarity=0.306 Sum_probs=56.7
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc---cCCCeeeEEee
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI---HSKGKKHLMAV 83 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV---~~~~rK~Yml~ 83 (233)
|+.+..|++.|-.++..|||+.||.+.+ +++++.+.+.+|.|+++|||.....+ ..++...++++
T Consensus 1 t~~~~~~Le~I~rsR~~Gi~q~~L~~~~--~~D~r~i~~~~k~L~~~gLI~k~~~~~~~~~~~~~t~ll~ 68 (75)
T PF04182_consen 1 TDIQYCLLERIARSRYNGITQSDLSKLL--GIDPRSIFYRLKKLEKKGLIVKQSVISSSNSKGTRTNLLH 68 (75)
T ss_pred CchHHHHHHHHHhcCCCCEehhHHHHHh--CCCchHHHHHHHHHHHCCCEEEEEeccccCCCceEEEEEE
Confidence 5678999999999999999999999999 99999999999999999999986662 33566666654
No 5
>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=98.35 E-value=2.8e-06 Score=58.97 Aligned_cols=59 Identities=14% Similarity=0.249 Sum_probs=53.9
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK 75 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~ 75 (233)
+|++.|..|+..|...+..++...+|...+ ++++..++++++.||++|||...++-+++
T Consensus 2 glt~~q~~vL~~l~~~~~~~~t~~~la~~l--~~~~~~vs~~v~~L~~~Glv~r~~~~~D~ 60 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPGEELTQSELAERL--GISKSTVSRIVKRLEKKGLVERERDPGDR 60 (62)
T ss_dssp TSTHHHHHHHHHHHHSTTSGEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEE-SSST
T ss_pred ccCHHHHHHHHHHHHCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEeCCCCCC
Confidence 689999999999999999999999999999 99999999999999999999998887754
No 6
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=98.31 E-value=1.8e-06 Score=77.88 Aligned_cols=55 Identities=25% Similarity=0.477 Sum_probs=51.9
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
.+|+++|+.|..+|.+.|+. |.|+||++++ |+|.+++.|+|+.||++|||+..|.
T Consensus 191 ~~L~~~e~~il~~i~~~GGr-i~Q~eL~r~l--glsktTvsR~L~~LEk~GlIe~~K~ 245 (258)
T COG2512 191 YDLNEDEKEILDLIRERGGR-ITQAELRRAL--GLSKTTVSRILRRLEKRGLIEKEKK 245 (258)
T ss_pred CCCCHHHHHHHHHHHHhCCE-EeHHHHHHhh--CCChHHHHHHHHHHHhCCceEEEEe
Confidence 58999999999999998874 9999999999 9999999999999999999999885
No 7
>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=98.21 E-value=3.7e-06 Score=60.14 Aligned_cols=62 Identities=23% Similarity=0.339 Sum_probs=53.2
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE 84 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~ 84 (233)
+|++.|..||..+-..|. +..++|.+.+ +++.+++.++|+.|+++|||..... +.++|...+
T Consensus 5 gLs~~E~~vy~~Ll~~~~--~t~~eIa~~l--~i~~~~v~~~L~~L~~~GlV~~~~~----~~~~Y~a~~ 66 (68)
T PF01978_consen 5 GLSENEAKVYLALLKNGP--ATAEEIAEEL--GISRSTVYRALKSLEEKGLVEREEG----RPKVYRAVP 66 (68)
T ss_dssp CHHHHHHHHHHHHHHHCH--EEHHHHHHHH--TSSHHHHHHHHHHHHHTTSEEEEEE----CCEEEEEE-
T ss_pred CcCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEcC----ceEEEEEeC
Confidence 688999999999986665 9999999999 9999999999999999999988772 256776554
No 8
>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=98.18 E-value=8.6e-06 Score=57.41 Aligned_cols=65 Identities=22% Similarity=0.322 Sum_probs=52.1
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV 83 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~ 83 (233)
||..|..|+..|. ..+.++..++|...+ +++...++++|++|+++|||....+-++++.++|-|.
T Consensus 1 lt~~q~~vL~~l~-~~~~~~t~~~l~~~~--~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT 65 (68)
T PF13463_consen 1 LTRPQWQVLRALA-HSDGPMTQSDLAERL--GISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLT 65 (68)
T ss_dssp --HHHHHHHHHHT---TS-BEHHHHHHHT--T--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-
T ss_pred CCHHHHHHHHHHH-ccCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeC
Confidence 5788999999998 556679999999999 9999999999999999999999999988777777654
No 9
>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=98.17 E-value=9.7e-06 Score=63.29 Aligned_cols=64 Identities=17% Similarity=0.229 Sum_probs=57.2
Q ss_pred CCChHHHHHHHHHH--hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026766 15 SLTDHERLIYDVIR--SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL 80 (233)
Q Consensus 15 ~L~~~e~lVy~~I~--~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y 80 (233)
+|+..|..|+.+|. .+.+.|+.+++|...+ +++...|+++++.||++|+|++.++-.++++...
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l--~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i 87 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEI--LIKQSALVKIIKKLSKKGYLSKERSEDDERKVII 87 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEE
Confidence 78999999999998 6666789999999999 9999999999999999999999999997544433
No 10
>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=98.16 E-value=7.4e-06 Score=54.77 Aligned_cols=48 Identities=25% Similarity=0.497 Sum_probs=41.4
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCce
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIK 67 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK 67 (233)
|++.++.|+.+|.+.+. +.+++|.+++ |++..++++.|+.|+++|+|+
T Consensus 1 l~~~~~~Il~~l~~~~~--~t~~ela~~~--~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 1 LDETQRKILNYLRENPR--ITQKELAEKL--GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp --HHHHHHHHHHHHCTT--S-HHHHHHHH--TS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHHcCC--CCHHHHHHHh--CCCHHHHHHHHHHHHHCcCcC
Confidence 67889999999999655 9999999999 999999999999999999996
No 11
>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=98.12 E-value=1.5e-05 Score=54.99 Aligned_cols=57 Identities=23% Similarity=0.330 Sum_probs=51.9
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCC
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG 76 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~ 76 (233)
||..|..++..|.+.|. +...+|.+.+ +++...++++++.|+++|+|.+..+-++.+
T Consensus 1 lt~~q~~iL~~l~~~~~--~~~~~la~~~--~~~~~~~t~~i~~L~~~g~I~r~~~~~D~R 57 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG--ITQSELAEKL--GISRSTVTRIIKRLEKKGLIERERDPDDRR 57 (59)
T ss_dssp STHHHHHHHHHHHHHSS--EEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEEETTETT
T ss_pred CCHHHHHHHHHHHHcCC--CCHHHHHHHH--CCChhHHHHHHHHHHHCCCEEeccCCCCCC
Confidence 67889999999999888 9999999999 999999999999999999999999887644
No 12
>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=97.96 E-value=4.2e-05 Score=60.01 Aligned_cols=66 Identities=9% Similarity=0.164 Sum_probs=58.4
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV 83 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~ 83 (233)
.+|+..+..|+..|...| |+.+++|.+.+ ++...++++.|+.||++|||.+.++-.+++++.|-|.
T Consensus 24 ~~lt~~q~~iL~~l~~~~--~~t~~ela~~~--~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT 89 (118)
T TIGR02337 24 HGLTEQQWRILRILAEQG--SMEFTQLANQA--CILRPSLTGILARLERDGLVTRLKASNDQRRVYISLT 89 (118)
T ss_pred cCCCHHHHHHHHHHHHcC--CcCHHHHHHHh--CCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEEC
Confidence 478999999999998755 69999999999 9999999999999999999999999988777766543
No 13
>PRK10870 transcriptional repressor MprA; Provisional
Probab=97.92 E-value=4.7e-05 Score=64.49 Aligned_cols=66 Identities=12% Similarity=0.176 Sum_probs=59.4
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL 80 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y 80 (233)
--+|+..+..|+..|...++.++.+++|...+ +++..+++++++.||++|||.+.++-.+++.+..
T Consensus 50 ~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l--~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v 115 (176)
T PRK10870 50 AQGINETLFMALITLESQENHSIQPSELSCAL--GSSRTNATRIADELEKRGWIERRESDNDRRCLHL 115 (176)
T ss_pred HCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEE
Confidence 34789999999999998888999999999999 9999999999999999999999999887555444
No 14
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=97.91 E-value=5.2e-05 Score=57.70 Aligned_cols=63 Identities=17% Similarity=0.283 Sum_probs=56.7
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
|+..|..|+..|...+..+. ++|.+.+ +++...+++.|+.||++|||++.++-.+++++++.|
T Consensus 20 lt~~q~~~L~~l~~~~~~~~--~~la~~l--~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~l 82 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITV--KELAERL--GLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRL 82 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcH--HHHHHHH--CCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEE
Confidence 89999999999999998776 9999999 999999999999999999999999998855555544
No 15
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.86 E-value=5.3e-05 Score=54.85 Aligned_cols=50 Identities=20% Similarity=0.300 Sum_probs=46.5
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
++.+..|+.++..+|.+|+..++|.+++ +|+.+.|+|+|..|+++|+|..
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~l--gl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNL--GLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEe
Confidence 3467799999999999999999999999 9999999999999999999955
No 16
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=97.85 E-value=8.1e-05 Score=60.43 Aligned_cols=63 Identities=17% Similarity=0.164 Sum_probs=55.8
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL 80 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y 80 (233)
-+|+..|..|+..|.. +.|+.+++|...+ +++..+++++|+.||++|||.+.++-.+++.+..
T Consensus 36 ~glt~~q~~vL~~l~~--~~~~t~~eLa~~l--~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l 98 (144)
T PRK11512 36 LDITAAQFKVLCSIRC--AACITPVELKKVL--SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLV 98 (144)
T ss_pred cCCCHHHHHHHHHHHH--cCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEe
Confidence 4799999999999965 4579999999999 9999999999999999999999999887555444
No 17
>PF13730 HTH_36: Helix-turn-helix domain
Probab=97.83 E-value=8.4e-05 Score=50.74 Aligned_cols=51 Identities=25% Similarity=0.493 Sum_probs=44.6
Q ss_pred CCCChHHHHHHHHHHhhC--CCccc--HHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026766 14 DSLTDHERLIYDVIRSKQ--DMGIW--TRDMKRELRVNLPDNIVTKSIKSLQNKSLI 66 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG--~~GIw--~~dik~~t~~~l~~~~v~k~LK~Le~k~lI 66 (233)
++|++.+++||-.|...- +.|.| +++|.+.+ ++..++|.|+|+.||++|+|
T Consensus 1 ~~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~--g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 1 KNLSPTAKLVYLYLASYANKNGGCFPSQETLAKDL--GVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCcCC
Confidence 479999999999998653 44444 79999999 99999999999999999997
No 18
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=97.79 E-value=0.00014 Score=53.76 Aligned_cols=64 Identities=16% Similarity=0.290 Sum_probs=53.7
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL 80 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y 80 (233)
--+|+..+..|+.+|...| ++..++|...+ +++...++++|+.|+++|+|...+.-..+..+.|
T Consensus 5 ~~~l~~~~~~il~~l~~~~--~~~~~~la~~~--~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~ 68 (101)
T smart00347 5 PLGLTPTQFLVLRILYEEG--PLSVSELAKRL--GVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLV 68 (101)
T ss_pred ccCCCHHHHHHHHHHHHcC--CcCHHHHHHHH--CCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEE
Confidence 3478999999999999877 59999999999 9999999999999999999988766443333333
No 19
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=97.77 E-value=0.00013 Score=58.84 Aligned_cols=66 Identities=12% Similarity=0.167 Sum_probs=57.0
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
-+|+..+..|+..|...+ .|+.+++|...+ ++...+|+++++.||++|||.+.++-.+++.+..-|
T Consensus 27 ~glt~~q~~vL~~l~~~~-~~~t~~eLa~~l--~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~L 92 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLP-PEQSQIQLAKAI--GIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKL 92 (144)
T ss_pred cCCCHHHHHHHHHHHHcC-CCCCHHHHHHHh--CCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEE
Confidence 479999999999997653 468999999999 999999999999999999999999988765555543
No 20
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=97.73 E-value=0.00014 Score=62.64 Aligned_cols=60 Identities=12% Similarity=0.022 Sum_probs=53.7
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK 77 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r 77 (233)
-+|+..|..|+.+|...+ |+.+++|.+.+ +++.++++++|+.||++|||.+.++-.+++.
T Consensus 41 ~gLt~~q~~iL~~L~~~~--~itq~eLa~~l--~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~ 100 (185)
T PRK13777 41 YDLNINEHHILWIAYHLK--GASISEIAKFG--VMHVSTAFNFSKKLEERGYLTFSKKEDDKRN 100 (185)
T ss_pred CCCCHHHHHHHHHHHhCC--CcCHHHHHHHH--CCCHhhHHHHHHHHHHCCCEEecCCCCCCCe
Confidence 479999999999997754 79999999999 9999999999999999999999988876433
No 21
>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=97.56 E-value=0.0023 Score=50.32 Aligned_cols=111 Identities=14% Similarity=0.195 Sum_probs=73.4
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCccc
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRV--NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISG 93 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~--~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTG 93 (233)
|++-|..|.++|=+.|. +..+||...++. +++.++|...|+.|++||+|...+. .+..+|- |..+
T Consensus 1 Ls~~E~~IM~~lW~~~~--~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~---gr~~~Y~-----p~is--- 67 (115)
T PF03965_consen 1 LSDLELEIMEILWESGE--ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKI---GRAYVYS-----PLIS--- 67 (115)
T ss_dssp --HHHHHHHHHHHHHSS--EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE---TTCEEEE-----ESSS---
T ss_pred CCHHHHHHHHHHHhCCC--CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeec---CCceEEE-----eCCc---
Confidence 68899999999999999 999999999833 6889999999999999999988654 2333441 1111
Q ss_pred CCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026766 94 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL 155 (233)
Q Consensus 94 G~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L 155 (233)
-. +.+...+.+++.+.-.-+...+..++-+.. .||.+|++.|-+.|
T Consensus 68 ---------~~---e~~~~~~~~~l~~~~~gs~~~l~~~l~~~~----~ls~~el~~L~~li 113 (115)
T PF03965_consen 68 ---------RE---EYLAQELRQFLDRLFDGSIPQLVAALVESE----ELSPEELEELRKLI 113 (115)
T ss_dssp ---------HH---HHHHHHHHHHHHHHSTTHHHHHHHHHHHCT-----S-HHHHHHHHHHH
T ss_pred ---------HH---HHHHHHHHHHHHHHhCCCHHHHHHHHHhcC----CCCHHHHHHHHHHH
Confidence 11 233444444444432335666666665554 69999999987765
No 22
>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=97.51 E-value=0.00033 Score=50.59 Aligned_cols=57 Identities=23% Similarity=0.387 Sum_probs=43.1
Q ss_pred CCCCChHHHHHHHHHHhhCC-Cc--ccHHHHHHHhhcCCC-hHHHHHHHHHHHhCCCceeeec
Q 026766 13 SDSLTDHERLIYDVIRSKQD-MG--IWTRDMKRELRVNLP-DNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~-~G--Iw~~dik~~t~~~l~-~~~v~k~LK~Le~k~lIK~vks 71 (233)
|+.||+-|+.||.+|.+--. .| =..+||.+.+ |+. .+.|.+.|+.||+||+|+..+.
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~--g~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEAL--GLKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHSS---HHHHHHHH--TSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHCcCccCCCC
Confidence 57899999999999986322 23 4679999999 998 8999999999999999988654
No 23
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=97.41 E-value=0.0008 Score=54.84 Aligned_cols=70 Identities=13% Similarity=0.140 Sum_probs=56.9
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccC
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPS 88 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs 88 (233)
+|++.+..||..+-+ .|.+...-+|...+ |+..++++|+|++|.+.|||.+.+---..|+..| +|.--|.
T Consensus 24 GLs~~Dv~v~~~LL~-~~~~~tvdelae~l--nr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~y-iY~~i~~ 93 (126)
T COG3355 24 GLSELDVEVYKALLE-ENGPLTVDELAEIL--NRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYY-LYKPIDP 93 (126)
T ss_pred CCcHHHHHHHHHHHh-hcCCcCHHHHHHHH--CccHHHHHHHHHHHHHcCCeeeeeeccCCCceeE-EEecCCH
Confidence 799999999999996 45569999999999 9999999999999999999999885444455444 4443333
No 24
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=97.22 E-value=0.0016 Score=52.65 Aligned_cols=71 Identities=21% Similarity=0.353 Sum_probs=61.2
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC---Cee--eEEeecccc
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK---GKK--HLMAVEFEP 87 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~---~rK--~Yml~~leP 87 (233)
+..|++-++.+++++...+. +..++|.+++ |++..++.+.+|+|++.|+|+....+-++ +.. +++....+|
T Consensus 3 ~~~lD~~D~~IL~~L~~d~r--~~~~eia~~l--glS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~a~v~v~~~~ 78 (154)
T COG1522 3 MMKLDDIDRRILRLLQEDAR--ISNAELAERV--GLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLER 78 (154)
T ss_pred cccccHHHHHHHHHHHHhCC--CCHHHHHHHH--CCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEEEEEEEEecC
Confidence 45789999999999999999 9999999999 99999999999999999999999987665 433 555555555
No 25
>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=97.22 E-value=0.0098 Score=48.19 Aligned_cols=112 Identities=19% Similarity=0.224 Sum_probs=71.6
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhh--cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR--VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS 92 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~--~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT 92 (233)
.|++.|..|.++|=..|. +..++|...++ .++..++|...|+.|++||+|...+. .+..+|- |-.+
T Consensus 1 ~Lt~~E~~VM~vlW~~~~--~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~---gr~~~Y~-----p~vs-- 68 (130)
T TIGR02698 1 SISDAEWEVMRVVWTLGE--TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKE---GRKFIYT-----ALVS-- 68 (130)
T ss_pred CCCHHHHHHHHHHHcCCC--CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecC---CCcEEEE-----ecCC--
Confidence 478999999999987764 78999777762 27899999999999999999977532 2233331 2111
Q ss_pred cCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026766 93 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL 155 (233)
Q Consensus 93 GG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L 155 (233)
-.++.....+.+.+.+. +.....-+..|+.. ..||.+|++.|-+.|
T Consensus 69 ----------~ee~~~~~~~~~~~~~f--~gs~~~ll~~l~~~-----~~ls~eele~L~~li 114 (130)
T TIGR02698 69 ----------EDEAVENAAQELFSRIC--SRKVGAVIADLIEE-----SPLSQTDIEKLEKLL 114 (130)
T ss_pred ----------HHHHHHHHHHHHHHHHH--CCCHHHHHHHHHhc-----CCCCHHHHHHHHHHH
Confidence 12333333333332222 22223445555553 369999999998754
No 26
>PHA02943 hypothetical protein; Provisional
Probab=97.18 E-value=0.0072 Score=50.93 Aligned_cols=112 Identities=13% Similarity=0.217 Sum_probs=82.0
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCC
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEG 100 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~ 100 (233)
..|+.+| ..|- ..+++|.+.+ +++..++..+|+.||..|.|++|+ .|+..| |+-+.
T Consensus 14 ~eILE~L-k~G~--~TtseIAkaL--GlS~~qa~~~LyvLErEG~VkrV~----~G~~ty---------------w~l~~ 69 (165)
T PHA02943 14 IKTLRLL-ADGC--KTTSRIANKL--GVSHSMARNALYQLAKEGMVLKVE----IGRAAI---------------WCLDE 69 (165)
T ss_pred HHHHHHH-hcCC--ccHHHHHHHH--CCCHHHHHHHHHHHHHcCceEEEe----ecceEE---------------EEECh
Confidence 4577788 4443 6799999999 999999999999999999999866 355555 34322
Q ss_pred CCCHHHHHHHHHHHHHHhhh--CCCCCHHHHHHHHHHh--------CCcccccCHHHHHHHHHHHh
Q 026766 101 SLDTEFIKVVKSQCLKQIIK--LKVATLEGISDSIKRS--------GAFKVDLTKQQIEEIVRALV 156 (233)
Q Consensus 101 e~D~efI~~l~~~~~~~i~~--~~~~T~~~I~~~I~~~--------~i~~~~Ls~~di~~il~~Lv 156 (233)
+==...|+.+.+-+..+|.+ ..++|+..+++.|.+- .+..|.-+-..|-+.|+-+.
T Consensus 70 day~~~v~~~~Relwrlv~s~~~kfi~p~~l~~li~kd~~a~~~~ak~v~v~~r~a~il~fln~~l 135 (165)
T PHA02943 70 DAYTNLVFEIKRELWRLVCNSRLKFITPSRLLRLIAKDTEAHNIFAKYVPVNSRHAHILSFLNSAL 135 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccChHHHHHHHHhCHHHHHHHHHhcCcccchHHHHHHHHHHH
Confidence 11122377777788888864 5799999999999864 24456777788877777543
No 27
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=97.13 E-value=0.0016 Score=48.58 Aligned_cols=54 Identities=17% Similarity=0.292 Sum_probs=40.9
Q ss_pred HHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026766 23 IYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL 80 (233)
Q Consensus 23 Vy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y 80 (233)
|+.++.. +..++-++|++.+ ++++..+++.|+.||+.|+|+.-|....++.++|
T Consensus 5 Il~~L~~--~~~~~f~~L~~~l--~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~ 58 (80)
T PF13601_consen 5 ILALLYA--NEEATFSELKEEL--GLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTW 58 (80)
T ss_dssp HHHHHHH--HSEEEHHHHHHHT--T--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEE
T ss_pred HHHHHhh--cCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEE
Confidence 4555555 4459999999999 9999999999999999999999998876544433
No 28
>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=97.11 E-value=0.0015 Score=55.73 Aligned_cols=56 Identities=21% Similarity=0.335 Sum_probs=49.9
Q ss_pred CCCCChHHHHHHHHHHhh---CCCcccHHHHHHHhhcCCC-hHHHHHHHHHHHhCCCceeee
Q 026766 13 SDSLTDHERLIYDVIRSK---QDMGIWTRDMKRELRVNLP-DNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~a---G~~GIw~~dik~~t~~~l~-~~~v~k~LK~Le~k~lIK~vk 70 (233)
|++||+.|..||..|.+. +..+...++|.+.+ +++ .+++.+.|++||++|+|+...
T Consensus 1 ~~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~--~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 1 MKPLTARQQEVLDLIRAHIESTGYPPSIREIARAV--GLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred CCccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHh--CCCChHHHHHHHHHHHHCCCEecCC
Confidence 457999999999999954 55668899999999 999 999999999999999998764
No 29
>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=97.02 E-value=0.0031 Score=54.26 Aligned_cols=55 Identities=13% Similarity=0.309 Sum_probs=49.8
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
..+|++.+..|+.+|...| ++..++|.+.+ ++++.++++.|+.|+++|+|...+.
T Consensus 138 ~~~ls~~~~~IL~~l~~~g--~~s~~eia~~l--~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 138 LAGLSREELKVLEVLKAEG--EKSVKNIAKKL--GKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred hcCCCHHHHHHHHHHHHcC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 4578999999999998765 49999999999 9999999999999999999998863
No 30
>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=97.02 E-value=0.0025 Score=54.81 Aligned_cols=129 Identities=11% Similarity=0.159 Sum_probs=76.9
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccC
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSE 99 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d 99 (233)
...|+.+|...|. +..++|...+ +++..+|++.|+.|+++|||...+.....+|.. .+|.|+|.-. .-|.+
T Consensus 3 r~~IL~~L~~~~~--~t~~eLA~~l--gis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~-~~y~LT~~G~----~~~~~ 73 (203)
T TIGR02702 3 KEDILSYLLKQGQ--ATAAALAEAL--AISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQ-YHYQLSRQGR----EQFPQ 73 (203)
T ss_pred HHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEeecccCCCCCc-eEEEECcchh----hhccc
Confidence 3578888887765 9999999999 999999999999999999999876544344443 3445555422 11111
Q ss_pred CCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcc-----cc---cC-HHHHHHHHHHHhcCCeEEEEe
Q 026766 100 GSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFK-----VD---LT-KQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 100 ~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~-----~~---Ls-~~di~~il~~Lv~Dg~ie~v~ 165 (233)
.+ ..+...+.+.+..- .+.+++.+++....-.. .. .+ .+-++.|.+.|--+|-.-++.
T Consensus 74 -~~-~~~~~~ll~~l~~~------l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Gy~~~~~ 140 (203)
T TIGR02702 74 -RH-GRFAVSLLDSLAET------LGPEQFEAVLQKQWQRKAEAYRRQLGQGSLAERLAQLVALRQQEGFMAEVH 140 (203)
T ss_pred -cH-HHHHHHHHHHHHHH------cCHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence 11 12222222222211 34555555554432000 01 11 456788888888777765554
No 31
>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=96.95 E-value=0.0035 Score=43.89 Aligned_cols=49 Identities=16% Similarity=0.244 Sum_probs=42.3
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
+.-..||.+| +.+.++...+|...+ +++++++++.|+.|++.|||+..+
T Consensus 10 p~R~~Il~~L--~~~~~~t~~ela~~l--~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 10 PTRLRILRLL--ASNGPMTVSELAEEL--GISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHHHH--HHCSTBEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHH--hcCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEec
Confidence 4556788888 566779999999999 999999999999999999998865
No 32
>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=96.91 E-value=0.0076 Score=41.49 Aligned_cols=58 Identities=12% Similarity=0.181 Sum_probs=47.3
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV 83 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~ 83 (233)
..+..|+..|...+ +..++|.+.+ +++.+++++.|+.|+++|+|....+- +++.|.+.
T Consensus 7 ~~~~~il~~l~~~~---~~~~ei~~~~--~i~~~~i~~~l~~L~~~g~i~~~~~~---~~~~~~~~ 64 (78)
T cd00090 7 PTRLRILRLLLEGP---LTVSELAERL--GLSQSTVSRHLKKLEEAGLVESRREG---RRVYYSLT 64 (78)
T ss_pred hHHHHHHHHHHHCC---cCHHHHHHHH--CcCHhHHHHHHHHHHHCCCeEEEEec---cEEEEEeC
Confidence 46778888887754 9999999999 99999999999999999999876543 45556443
No 33
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=96.86 E-value=0.0024 Score=48.91 Aligned_cols=54 Identities=19% Similarity=0.364 Sum_probs=47.9
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
|++.++.|+.++...|. +..++|.+++ |++..++++.|+.|+++|+|+.+..+-
T Consensus 1 ld~~D~~il~~L~~~~~--~~~~~la~~l--~~s~~tv~~~l~~L~~~g~i~~~~~~~ 54 (108)
T smart00344 1 LDEIDRKILEELQKDAR--ISLAELAKKV--GLSPSTVHNRVKRLEEEGVIKGYTAVI 54 (108)
T ss_pred CCHHHHHHHHHHHHhCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeceEEEe
Confidence 57788999999998765 9999999999 999999999999999999998655443
No 34
>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=96.75 E-value=0.0057 Score=46.88 Aligned_cols=56 Identities=20% Similarity=0.210 Sum_probs=46.8
Q ss_pred CCCCCChHHHHHHHHHHh-h-----CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 12 PSDSLTDHERLIYDVIRS-K-----QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~-a-----G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
...+++..+..++-.|.. . ...++.+++|...+ +++..+|+|+|+.||++|+|+..
T Consensus 19 ~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~--g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 19 PGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELT--GLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred HhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeee
Confidence 355778877777776643 1 47889999999999 99999999999999999999854
No 35
>PRK00215 LexA repressor; Validated
Probab=96.74 E-value=0.0043 Score=53.09 Aligned_cols=53 Identities=26% Similarity=0.391 Sum_probs=48.0
Q ss_pred CChHHHHHHHHHHh---hCCCcccHHHHHHHhhcCC-ChHHHHHHHHHHHhCCCceeee
Q 026766 16 LTDHERLIYDVIRS---KQDMGIWTRDMKRELRVNL-PDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 16 L~~~e~lVy~~I~~---aG~~GIw~~dik~~t~~~l-~~~~v~k~LK~Le~k~lIK~vk 70 (233)
||+.|..||..|.+ .++.++..+||.+.+ ++ +.+++++.|+.|+++|+|....
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~--~~~~~~tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADAL--GLRSPSAVHEHLKALERKGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHCCCEEeCC
Confidence 78899999999984 467788999999999 99 9999999999999999997755
No 36
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=96.62 E-value=0.01 Score=38.95 Aligned_cols=47 Identities=11% Similarity=0.326 Sum_probs=40.5
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
+..|+.+|.+. .++...+|...+ +++.+++++.|+.|+++|+|....
T Consensus 2 ~~~il~~l~~~--~~~s~~~l~~~l--~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 2 QQQILELLAQQ--GKVSVEELAELL--GVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHHHc--CCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEee
Confidence 34678888764 469999999999 999999999999999999997644
No 37
>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=96.62 E-value=0.012 Score=43.68 Aligned_cols=63 Identities=16% Similarity=0.245 Sum_probs=46.4
Q ss_pred HHHHHHHhhCCCc-ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026766 22 LIYDVIRSKQDMG-IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS 92 (233)
Q Consensus 22 lVy~~I~~aG~~G-Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT 92 (233)
.++-++...++.+ +..++|.+++ +++.+.+.++|+.|++.|+|++.+-.+ -=|.|.. |.++||
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~--~i~~~~l~kil~~L~~~Gli~s~~G~~----GGy~L~~--~~~~It 75 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERL--GISPSYLRKILQKLKKAGLIESSRGRG----GGYRLAR--PPEEIT 75 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEETSTT----SEEEESS---CCGSB
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHH--CcCHHHHHHHHHHHhhCCeeEecCCCC----CceeecC--CHHHCC
Confidence 3444555666666 9999999999 999999999999999999997765332 4566654 555554
No 38
>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=96.52 E-value=0.0063 Score=46.72 Aligned_cols=51 Identities=20% Similarity=0.408 Sum_probs=44.1
Q ss_pred CCChHHHHHHHHHHh--hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCce
Q 026766 15 SLTDHERLIYDVIRS--KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIK 67 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~--aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK 67 (233)
+|++-++.||++|++ ..+.||-..+|.+++ +|+...|+++|..|...|+|=
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--GMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHS--TS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--CcCHHHHHHHHHHHHhCCeEe
Confidence 799999999999997 568899999999999 999999999999999999983
No 39
>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=96.46 E-value=0.013 Score=41.52 Aligned_cols=45 Identities=24% Similarity=0.411 Sum_probs=38.5
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
+.||.+-+ ++..+..++|.+.+ ++.+.+++..||+|+++|||...
T Consensus 11 ~~Iy~l~~--~~~~v~~~~iA~~L--~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 11 KAIYELSE--EGGPVRTKDIAERL--GVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHHHHHHH--CTSSBBHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHc--CCCCccHHHHHHHH--CCChHHHHHHHHHHHHCCCEEec
Confidence 45676665 67779999999999 99999999999999999999754
No 40
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=96.40 E-value=0.0092 Score=54.46 Aligned_cols=58 Identities=16% Similarity=0.340 Sum_probs=51.7
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
.+...++.||..||.|-+|-+=+ ||...+|+-+|+.||.+|.||+ +-|..+.+++|+.
T Consensus 8 klir~Lk~a~~~GI~Q~eIeel~--GlSKStvSEaLs~LE~~giv~R-rkvsGKs~rVwLa 65 (321)
T COG3888 8 KLIRELKRAGPEGIDQTEIEELM--GLSKSTVSEALSELEKQGIVKR-RKVSGKSKRVWLA 65 (321)
T ss_pred HHHHHHHhcCCCCccHHHHHHHh--CcchhHHHHHHHHHHhcCeeee-eeecCcceEEeec
Confidence 56678999999999999999999 9999999999999999999999 5566678888853
No 41
>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=96.36 E-value=0.0065 Score=38.24 Aligned_cols=30 Identities=27% Similarity=0.450 Sum_probs=26.2
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI 66 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI 66 (233)
+.+.||..-+ |+...+|+|+|+.|+++|+|
T Consensus 3 mtr~diA~~l--G~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYL--GLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHH--TS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHh--CCcHHHHHHHHHHHHHcCCC
Confidence 6788999999 99999999999999999997
No 42
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=96.36 E-value=0.0065 Score=50.66 Aligned_cols=59 Identities=12% Similarity=0.265 Sum_probs=52.8
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK 75 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~ 75 (233)
...|++-++.|+.++...|. +..++|.+++ |++.+++.+-+++|++.|.|+....+-++
T Consensus 9 ~~~lD~~D~~IL~~Lq~d~R--~s~~eiA~~l--glS~~tv~~Ri~rL~~~GvI~~~~~~v~p 67 (164)
T PRK11169 9 GKDLDRIDRNILNELQKDGR--ISNVELSKRV--GLSPTPCLERVRRLERQGFIQGYTALLNP 67 (164)
T ss_pred hhhHHHHHHHHHHHhccCCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEEEEECH
Confidence 55689999999999999999 8889999999 99999999999999999999976654443
No 43
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=96.33 E-value=0.023 Score=38.07 Aligned_cols=43 Identities=16% Similarity=0.324 Sum_probs=36.2
Q ss_pred HHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 23 IYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 23 Vy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
|+.+|. +..+...+|...+ +++.++++++|+.|+++|+|....
T Consensus 2 il~~l~---~~~~~~~~i~~~l--~is~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 2 ILKLLA---EGELCVCELAEIL--GLSQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred HHHHhh---cCCccHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeeee
Confidence 345554 4568999999999 999999999999999999997543
No 44
>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=96.27 E-value=0.062 Score=50.11 Aligned_cols=127 Identities=22% Similarity=0.243 Sum_probs=82.3
Q ss_pred CCChHHHHHHHHHHhh-CCCcccHHHHHHH-hhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026766 15 SLTDHERLIYDVIRSK-QDMGIWTRDMKRE-LRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS 92 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~a-G~~GIw~~dik~~-t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT 92 (233)
+|.+-+..||+++.++ +.+|+.++||... . +++..++-.+|..|.++|+|+-++ ..+.-.|-+.+-+=...+.
T Consensus 6 ~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~--~~~~~~~~~~in~Ll~~~~~~~~~---~~~~l~~~~~~~~~a~k~~ 80 (327)
T PF05158_consen 6 KLSELEKKLLELCRENPSPKGFSQEDLQQLIP--GLDLQELVKAINELLSSGLLKLLK---KGGGLSYKAVSEEEAKKLK 80 (327)
T ss_dssp -HHHHHHHHHHHHHH---SS-EEHHHHHHH-T--TS-HHHHHHHHHHHHHHTSEEEEE----SSSEEEEE--SSS-----
T ss_pred hHHHHHHHHHHHHHHhcCCCCcCHHHHHhhcC--CCCHHHHHHHHHHHHhCCCEEEEE---cCCEEEEEEeCHHHHhhhc
Confidence 5777899999999999 9999999999999 5 899999999999999999999888 3455566554433333333
Q ss_pred cCCcccCCCCCHHHHHHHHHHHHHHhhhCC--CCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026766 93 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLK--VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN 167 (233)
Q Consensus 93 GG~wy~d~e~D~efI~~l~~~~~~~i~~~~--~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~ 167 (233)
|=+ .-.+.+|..|+..+ .....+|. .+..|....|..+|++|+=.+.|-+|++.
T Consensus 81 ~l~-------------~~e~lvy~~I~~ag~~GIw~~~i~--------~~t~l~~~~~~k~lk~Le~k~lIK~vksv 136 (327)
T PF05158_consen 81 GLS-------------DEERLVYQLIEEAGNKGIWTKDIK--------KKTNLHQTQLTKILKSLESKKLIKSVKSV 136 (327)
T ss_dssp SSS-------------CCHHHHHHHHHHHTTT-EEHHHHH--------HHCT--HHHHHHHHHHHHHTTSEEEE--S
T ss_pred CCC-------------HHHHHHHHHHHHhCCCCCcHHHHH--------HHcCCCHHHHHHHHHHHHhCCCEEEecCc
Confidence 321 11235666666432 23222222 23468899999999999999999999864
No 45
>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=96.21 E-value=0.011 Score=40.22 Aligned_cols=44 Identities=16% Similarity=0.364 Sum_probs=36.7
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.|++++.+++. |+..+||.+++ ++|..++.|.|+.|++.|+|.+
T Consensus 7 ~iL~~l~~~~~-~~t~~eia~~~--gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 7 RILEALAESGG-PLTLSEIARAL--GLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHCHHCTBS-CEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcCCC-CCCHHHHHHHH--CcCHHHHHHHHHHHHHCcCeec
Confidence 45566666544 58999999999 9999999999999999999976
No 46
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=96.18 E-value=0.018 Score=56.10 Aligned_cols=52 Identities=19% Similarity=0.328 Sum_probs=47.7
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
.+|++.|..|+..|...| ++.+.+|..++ +++..+|+++++.|+++|||...
T Consensus 2 ~~Lt~~e~~vL~~L~~~~--~~s~~eLA~~l--~l~~~tVt~~i~~Le~kGlV~~~ 53 (489)
T PRK04172 2 MELHPNEKKVLKALKELK--EATLEELAEKL--GLPPEAVMRAAEWLEEKGLVKVE 53 (489)
T ss_pred CCCCHHHHHHHHHHHhCC--CCCHHHHHHHh--CcCHHHHHHHHHHHHhCCCEEEE
Confidence 379999999999997665 69999999999 99999999999999999999875
No 47
>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=96.11 E-value=0.023 Score=37.85 Aligned_cols=43 Identities=19% Similarity=0.377 Sum_probs=36.1
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
..|+.+|.+ |. ....+|.+.+ ++++.++++.|+.|++.|+|++
T Consensus 5 ~~Il~~L~~-~~--~~~~el~~~l--~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 5 LRILKLLSE-GP--LTVSELAEEL--GLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHTT-SS--EEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHh-CC--CchhhHHHhc--cccchHHHHHHHHHHHCcCeeC
Confidence 456666666 55 8899999999 9999999999999999999974
No 48
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=96.03 E-value=0.0087 Score=44.14 Aligned_cols=55 Identities=24% Similarity=0.360 Sum_probs=41.0
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE 84 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~ 84 (233)
.+|+++++.-.+.|.-..+|...+ ||+...+.+.|+.|+++|||+. ....|.+.+
T Consensus 6 ~Ii~~IL~~l~~~~~~~t~i~~~~--~L~~~~~~~yL~~L~~~gLI~~-------~~~~Y~lTe 60 (77)
T PF14947_consen 6 EIIFDILKILSKGGAKKTEIMYKA--NLNYSTLKKYLKELEEKGLIKK-------KDGKYRLTE 60 (77)
T ss_dssp HHHHHHHHHH-TT-B-HHHHHTTS--T--HHHHHHHHHHHHHTTSEEE-------ETTEEEE-H
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCcCeeC-------CCCEEEECc
Confidence 377888887778889999999999 9999999999999999999933 345666543
No 49
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=95.96 E-value=0.024 Score=50.85 Aligned_cols=63 Identities=21% Similarity=0.287 Sum_probs=55.2
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE 84 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~ 84 (233)
=+||+.|-.||-.+-..|. ...++|...+ |+|++.|-.+|++||.||+|... ..+.+.|-..+
T Consensus 12 lGlt~yEa~vY~aLl~~g~--~tA~eis~~s--gvP~~kvY~vl~sLe~kG~v~~~----~g~P~~y~av~ 74 (247)
T COG1378 12 LGLTEYEAKVYLALLCLGE--ATAKEISEAS--GVPRPKVYDVLRSLEKKGLVEVI----EGRPKKYRAVP 74 (247)
T ss_pred cCCCHHHHHHHHHHHHhCC--ccHHHHHHHc--CCCchhHHHHHHHHHHCCCEEee----CCCCceEEeCC
Confidence 3799999999999999999 9999999999 99999999999999999999764 34556775544
No 50
>PRK06474 hypothetical protein; Provisional
Probab=95.91 E-value=0.1 Score=44.49 Aligned_cols=130 Identities=14% Similarity=0.230 Sum_probs=80.9
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEeeccccCCCcccCC
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMAVEFEPSKEISGGA 95 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml~~lePs~eiTGG~ 95 (233)
+.=..|++++...+. ++...+|...++ ++++.+|.+.|+.|++.|||..++.= .....|+|-+..- ...+.+..
T Consensus 11 p~R~~Il~~L~~~~~-~~ta~el~~~l~-~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~--~~~~~~~~ 86 (178)
T PRK06474 11 PVRMKICQVLMRNKE-GLTPLELVKILK-DVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEE--DAKIEGSE 86 (178)
T ss_pred HHHHHHHHHHHhCCC-CCCHHHHHHHhc-CCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccc--eeeeCHHH
Confidence 345578888877654 499999998872 59999999999999999999987653 3334577754431 11223333
Q ss_pred cccC---C--CCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHHHh
Q 026766 96 WYSE---G--SLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRALV 156 (233)
Q Consensus 96 wy~d---~--e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~Lv 156 (233)
|..+ + .+-+.|...+.+...+|+.+.+-. -.+-...+.+ ...||+++.+++.+-|.
T Consensus 87 ~~~~~~e~~~~~~~~~~~~~~~~~~~yl~~~~~~-----~~~~d~~~~s~~~L~Lt~ee~~el~~el~ 149 (178)
T PRK06474 87 WTGLSDDEKLNYISYYQLSLLQQYQSYLKSLEEQ-----NSKEDKATFSVVELKLDEEEFEEFQSELN 149 (178)
T ss_pred HHHhCHHHHHHHHHHHHHHHHHHHHHHHHhCccc-----chhccccceeeeeEecCHHHHHHHHHHHH
Confidence 3321 1 122345555556666677653211 1122333433 36799999888877664
No 51
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=95.90 E-value=0.022 Score=46.94 Aligned_cols=55 Identities=5% Similarity=0.156 Sum_probs=50.3
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI 72 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV 72 (233)
..|++.++.|+.++...|. +..++|.+++ |++..+|.+-+++|++.|+|+....+
T Consensus 5 ~~lD~~D~~Il~~Lq~d~R--~s~~eiA~~l--glS~~tV~~Ri~rL~~~GvI~~~~~~ 59 (153)
T PRK11179 5 YQIDNLDRGILEALMENAR--TPYAELAKQF--GVSPGTIHVRVEKMKQAGIITGTRVD 59 (153)
T ss_pred cccCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeEEEE
Confidence 3488999999999999999 9999999999 99999999999999999999876543
No 52
>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=95.87 E-value=0.035 Score=38.68 Aligned_cols=46 Identities=15% Similarity=0.441 Sum_probs=42.4
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
..|+++|.+.|. +..++|...+ +.+..+++|=|..|+++|+|+++.
T Consensus 3 ~~Il~~l~~~~~--~s~~ela~~~--~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKEKGK--VSVKELAEEF--GVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHcCC--EEHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEc
Confidence 578999999888 9999999999 999999999999999999997753
No 53
>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=95.87 E-value=0.039 Score=39.96 Aligned_cols=51 Identities=16% Similarity=0.181 Sum_probs=45.1
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
.+.|..|++++.+.|..++....+...+ +.+...|+++|=.|+++|.|...
T Consensus 3 ~~~ee~Il~~L~~~g~~~a~~ia~~~~L--~~~kk~VN~~LY~L~k~g~v~k~ 53 (66)
T PF02295_consen 3 QDLEEKILDFLKELGGSTATAIAKALGL--SVPKKEVNRVLYRLEKQGKVCKE 53 (66)
T ss_dssp HHHHHHHHHHHHHHTSSEEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred hhHHHHHHHHHHhcCCccHHHHHHHhCc--chhHHHHHHHHHHHHHCCCEeeC
Confidence 3568899999999998899999988888 99999999999999999999653
No 54
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=95.87 E-value=0.029 Score=40.31 Aligned_cols=49 Identities=14% Similarity=0.176 Sum_probs=40.5
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
.|+++|.+. +.++.++||...+ +|+..++++.|..||+.|.|+.++.=+
T Consensus 4 ~Il~~i~~~-~~p~~T~eiA~~~--gls~~~aR~yL~~Le~eG~V~~~~~~r 52 (62)
T PF04703_consen 4 KILEYIKEQ-NGPLKTREIADAL--GLSIYQARYYLEKLEKEGKVERSPVRR 52 (62)
T ss_dssp CHHHHHHHH-TS-EEHHHHHHHH--TS-HHHHHHHHHHHHHCTSEEEES-SS
T ss_pred HHHHHHHHc-CCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEecCCC
Confidence 477888886 5679999999999 999999999999999999998865433
No 55
>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=95.82 E-value=0.04 Score=41.51 Aligned_cols=58 Identities=14% Similarity=0.253 Sum_probs=44.3
Q ss_pred HHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026766 23 IYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE 84 (233)
Q Consensus 23 Vy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~ 84 (233)
|+..|.. | -.-..||++.+ ++++++++++.||.|++.|||.+...-..+.+..|.|.+
T Consensus 10 IL~~l~~-g--~~rf~el~~~l-~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~ 67 (90)
T PF01638_consen 10 ILRALFQ-G--PMRFSELQRRL-PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTE 67 (90)
T ss_dssp HHHHHTT-S--SEEHHHHHHHS-TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-H
T ss_pred HHHHHHh-C--CCcHHHHHHhc-chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCc
Confidence 4444444 4 47889999887 479999999999999999999888766667777787764
No 56
>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=95.80 E-value=0.028 Score=43.28 Aligned_cols=66 Identities=9% Similarity=0.123 Sum_probs=47.2
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHh-h--cCCChHHHHHHHHHHHhCCCceee--ecccCCCeeeEEeec
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKREL-R--VNLPDNIVTKSIKSLQNKSLIKEV--VNIHSKGKKHLMAVE 84 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t-~--~~l~~~~v~k~LK~Le~k~lIK~v--ksV~~~~rK~Yml~~ 84 (233)
-+..|+.++......|-...+.-.+. + ..+++.+|..+|+.||++|+|.+. .+-..+.||+|-+.+
T Consensus 5 l~~~iL~~L~~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~ 75 (100)
T TIGR03433 5 LDLLILKTLSLGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTA 75 (100)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECH
Confidence 46688888876666665544433332 1 168999999999999999999994 555667788886543
No 57
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=95.76 E-value=0.036 Score=49.03 Aligned_cols=129 Identities=12% Similarity=0.188 Sum_probs=75.7
Q ss_pred hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHH
Q 026766 30 KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKV 109 (233)
Q Consensus 30 aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~ 109 (233)
.++.+|.+++|.+.+ ++++.++++.|+.||++|||.+..+= .++.+++ ++. | .++++.
T Consensus 17 ~~~~~IS~~eLA~~L--~iS~~Tvsr~Lk~LEe~GlI~R~~~~--r~~~v~L----Tek-----------G---~~ll~~ 74 (217)
T PRK14165 17 NNTVKISSSEFANHT--GTSSKTAARILKQLEDEGYITRTIVP--RGQLITI----TEK-----------G---LDVLYN 74 (217)
T ss_pred CCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEEcC--CceEEEE----CHH-----------H---HHHHHH
Confidence 344479999999999 99999999999999999999886552 2222221 111 1 111111
Q ss_pred HHHHHHHHhh-----------------hCCCCCHHHHH-HHHHHhCCc------ccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 110 VKSQCLKQII-----------------KLKVATLEGIS-DSIKRSGAF------KVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 110 l~~~~~~~i~-----------------~~~~~T~~~I~-~~I~~~~i~------~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
+-....+.+. -+.|+|.+--. +|-+..|+. ++.|..+.++...+..-+++...+=-
T Consensus 75 ~~~d~~~if~~~~ei~l~G~v~sGlGeG~~y~~~~~Y~~~f~~~lGf~PypGTLNv~l~~~~~~~~~~~~~~~~i~i~g~ 154 (217)
T PRK14165 75 EYADYSRIFSIKDNLELEGNVVKGLGEGKYYINIKGYKIQFEEKLGFIPYPGTLNVKLDNSSSPLLRKLRESPGIRIEGF 154 (217)
T ss_pred HHHHHHHHhcccccceehhhhhhccCCccEEEeCHHHHHHHHHHhCCcCCCCcEEEEecchhHHHHHHHhcCCCEecCCC
Confidence 1111111111 12466665443 455566764 47787777666666667777543211
Q ss_pred eCCCCCcccccCcceeeec
Q 026766 166 SNGSGEFTNIPVGKVCYKN 184 (233)
Q Consensus 166 ~~~~g~f~~~~~g~~~Yr~ 184 (233)
.++...|.++ .||++
T Consensus 155 ~~~~r~~g~~----~~~~~ 169 (217)
T PRK14165 155 TDGERTFGGV----KCYPV 169 (217)
T ss_pred cCCCceeEEE----EEEEE
Confidence 1344456554 67875
No 58
>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=95.59 E-value=0.041 Score=38.11 Aligned_cols=36 Identities=19% Similarity=0.399 Sum_probs=33.0
Q ss_pred CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 32 DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 32 ~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
+..+..++|...+ +++..+++++|+.|+++|+|...
T Consensus 23 ~~~~s~~ela~~~--g~s~~tv~r~l~~L~~~g~i~~~ 58 (67)
T cd00092 23 QLPLTRQEIADYL--GLTRETVSRTLKELEEEGLISRR 58 (67)
T ss_pred cCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEec
Confidence 3458999999999 99999999999999999999764
No 59
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=95.56 E-value=0.031 Score=42.78 Aligned_cols=57 Identities=5% Similarity=0.136 Sum_probs=45.9
Q ss_pred HHHHHHH--hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 22 LIYDVIR--SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 22 lVy~~I~--~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
-.|+-|. -..-+=|+...|..++ ++.-+.-+++|+.|+++|+||.| +++.+..+|..
T Consensus 27 ~t~dkl~kEV~~~K~ITps~lserl--kI~~SlAr~~Lr~L~~kG~Ik~V--~~~~~q~IYt~ 85 (86)
T PRK09334 27 ELLKRVAKEVKKEKIVTPYTLASKY--GIKISVAKKVLRELEKRGVLVLY--SKNRRTPIYVP 85 (86)
T ss_pred HHHHHHHHHhccCcEEcHHHHHHHh--cchHHHHHHHHHHHHHCCCEEEE--ecCCCeEEecc
Confidence 3444443 2335568999999999 99999999999999999999998 56678889853
No 60
>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=95.50 E-value=0.036 Score=39.78 Aligned_cols=47 Identities=11% Similarity=0.214 Sum_probs=37.1
Q ss_pred HHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 112 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 112 ~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
..+.+||+.++.+|++||++.+ .++.+.|+.+|+.|+--|+|+++..
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~--------~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREF--------GISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHT--------T--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHHcCCcCHHHHHHHH--------CcCHHHHHHHHHHHHHCCcEEEecC
Confidence 4567788888888888888765 4889999999999999999998763
No 61
>PRK12423 LexA repressor; Provisional
Probab=95.43 E-value=0.057 Score=46.52 Aligned_cols=56 Identities=23% Similarity=0.399 Sum_probs=47.0
Q ss_pred CCCChHHHHHHHHHHhh-CCCcc--cHHHHHHHhhcCC-ChHHHHHHHHHHHhCCCceeeec
Q 026766 14 DSLTDHERLIYDVIRSK-QDMGI--WTRDMKRELRVNL-PDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~a-G~~GI--w~~dik~~t~~~l-~~~~v~k~LK~Le~k~lIK~vks 71 (233)
+.||+-++.||+.|.+. ...|+ ..++|.+.+ ++ ..+.++++|+.|+++|+|...+.
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~--g~~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAF--GFASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHCCCEEecCC
Confidence 45899999999999975 22334 899999999 96 78899999999999999987554
No 62
>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=95.39 E-value=0.047 Score=43.47 Aligned_cols=51 Identities=16% Similarity=0.233 Sum_probs=43.4
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
++.--.++.++..+++..+..++|..++ +++.+.|.++|+.|++.|+|.+.
T Consensus 8 ~~yal~~l~~la~~~~~~~s~~eia~~l--~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 8 TDYATLVLTTLAQNDSQPYSAAEIAEQT--GLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HhHHHHHHHHHHhCCCCCccHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEec
Confidence 3445566677777777789999999999 99999999999999999999764
No 63
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=95.36 E-value=0.069 Score=41.32 Aligned_cols=72 Identities=21% Similarity=0.433 Sum_probs=55.0
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec--ccCCCeeeEEeeccccCCCccc
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN--IHSKGKKHLMAVEFEPSKEISG 93 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks--V~~~~rK~Yml~~lePs~eiTG 93 (233)
+++.+..|+.++..+|.+ .-+-|.+.+ +++...|..+|+.||+.|||.++.+ ++...+ .+.|+.|+-.
T Consensus 5 ~~~l~~~IL~hl~~~~~D--y~k~ia~~l--~~~~~~v~~~l~~Le~~GLler~~g~~iK~~~~------k~K~~~e~~~ 74 (92)
T PF10007_consen 5 LDPLDLKILQHLKKAGPD--YAKSIARRL--KIPLEEVREALEKLEEMGLLERVEGKTIKRSEA------KFKPKKEVHK 74 (92)
T ss_pred cChhHHHHHHHHHHHCCC--cHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEecCcccchhhh------hcccchhhhc
Confidence 577889999999999995 455688889 9999999999999999999999874 333222 3456666543
Q ss_pred -CCcc
Q 026766 94 -GAWY 97 (233)
Q Consensus 94 -G~wy 97 (233)
+++|
T Consensus 75 hHtYY 79 (92)
T PF10007_consen 75 HHTYY 79 (92)
T ss_pred CCcee
Confidence 3444
No 64
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=95.33 E-value=0.069 Score=42.91 Aligned_cols=49 Identities=14% Similarity=0.306 Sum_probs=43.0
Q ss_pred ccHHHHHHHhhcC-CChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc
Q 026766 35 IWTRDMKRELRVN-LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF 85 (233)
Q Consensus 35 Iw~~dik~~t~~~-l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l 85 (233)
.-..+|++.+ + +++++|++.||.||+.|+|.+..-=..|-|.-|-|.++
T Consensus 37 ~RF~eL~r~i--~~Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~ 86 (120)
T COG1733 37 KRFNELRRSI--GGISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEK 86 (120)
T ss_pred CcHHHHHHHc--cccCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhh
Confidence 4788999999 7 99999999999999999999887766788888877665
No 65
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=95.23 E-value=0.61 Score=42.33 Aligned_cols=124 Identities=16% Similarity=0.142 Sum_probs=95.3
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcC------CChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccc-cCCCcc
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVN------LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFE-PSKEIS 92 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~------l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~le-Ps~eiT 92 (233)
...|+..|...|- +..+||...++.. .+.+....+|..|...|.|-....-. ..+++|-+.+-- |...
T Consensus 87 ~~~v~~~L~~~gp--lt~~eL~~~l~~~~~~~~~~~~~~~~~~l~~l~~~G~l~~~~~~~-g~~~~y~l~~~~lP~~~-- 161 (327)
T PF06224_consen 87 AEAVLDALRADGP--LTRAELREALAEAGWWGWGGPSSPWKHLLEYLWYRGLLCVGPRPR-GRWRTYDLTERWLPAPD-- 161 (327)
T ss_pred HHHHHHHHHhcCC--CCHHHHHHHhhhccccCCCCCCchHHHHHHHHHhCCeEEEeccCC-CceEEEechHHhCCCCc--
Confidence 4567777766665 9999999987333 45679999999999999997665332 345888776643 3222
Q ss_pred cCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026766 93 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN 167 (233)
Q Consensus 93 GG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~ 167 (233)
.| -=+.+.+.+.+|+..++.+|++|+..|. | |+..+++..++.|+-.|.|+++...
T Consensus 162 ---------~~--~~ea~~~Lv~Ryl~~~GPat~~d~a~w~---g-----l~~~~~r~~l~~l~~~~~L~~v~~~ 217 (327)
T PF06224_consen 162 ---------DD--REEALAELVRRYLRAYGPATLADFAWWS---G-----LPKTQARRALAQLVEEGELVEVEVE 217 (327)
T ss_pred ---------CC--HHHHHHHHHHHHHHHcCCccHHHHHHHh---c-----cCHHHHHHHHHhhccCCcEEEEEEc
Confidence 11 3356788899999999999999999994 3 8889999999999999999988754
No 66
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=95.18 E-value=0.23 Score=44.29 Aligned_cols=122 Identities=15% Similarity=0.184 Sum_probs=88.0
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcc
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWY 97 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy 97 (233)
.--..+|+.|..++. ....++++.. +++..+++..|+.||+.++|++ ....++-.|..+++. |
T Consensus 101 s~R~~Iy~~i~~nPG--~~lsEl~~nl--~i~R~TlRyhlriLe~~~li~a---~~~~g~~~yfpa~~t----------~ 163 (240)
T COG3398 101 SKRDGIYNYIKPNPG--FSLSELRANL--YINRSTLRYHLRILESNPLIEA---GRVGGALRYFPADMT----------Y 163 (240)
T ss_pred hhHHHHHHHhccCCC--ccHHHHHHhc--CCChHHHHHHHHHHHhCcchhh---hccCCceEEccCCCC----------c
Confidence 344578999987765 9999999999 9999999999999999999966 334466667555442 1
Q ss_pred cCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 98 SEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 98 ~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
.+.| =.++=+..++.+..+|++.+-.|.-+|+.-+. ||.+-|.==+..|.-=|.|.+-+
T Consensus 164 ~~~e-~~~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l~--------ls~aTV~~~lk~l~~~Gii~~~~ 222 (240)
T COG3398 164 GEAE-VLSLKNETSKAIIYEIQENKCNTNLLIAYELN--------LSVATVAYHLKKLEELGIIPEDR 222 (240)
T ss_pred ccch-HHHhhchhHHHHHHHHhcCCcchHHHHHHHcC--------ccHHHHHHHHHHHHHcCCCcccc
Confidence 1222 13445566777888888887777777776543 66666666677777777776643
No 67
>PRK09954 putative kinase; Provisional
Probab=95.16 E-value=0.069 Score=49.27 Aligned_cols=52 Identities=21% Similarity=0.264 Sum_probs=46.5
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
|++-++.|+.+|.+.+. |.+++|.+++ +++.+++.+.|++|+++|+|+...-
T Consensus 1 ~~~~~~~il~~l~~~~~--~s~~~la~~l--~~s~~~v~~~i~~L~~~g~i~~~~~ 52 (362)
T PRK09954 1 MNNREKEILAILRRNPL--IQQNEIADIL--QISRSRVAAHIMDLMRKGRIKGKGY 52 (362)
T ss_pred CChHHHHHHHHHHHCCC--CCHHHHHHHH--CCCHHHHHHHHHHHHHCCCcCCcEE
Confidence 56778889999999887 9999999999 9999999999999999999965443
No 68
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=95.09 E-value=0.076 Score=39.05 Aligned_cols=45 Identities=11% Similarity=0.271 Sum_probs=38.7
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
..|+.+|...+ .++...+|.+.+ +++.+++++.|+.|++.|+|..
T Consensus 8 ~~Il~~l~~~~-~~~t~~~ia~~l--~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 8 LAVLRALAEEP-GGLTLAELAERL--GLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHh--CCCHHHHHHHHHHHHHCCCeee
Confidence 35667776552 379999999999 9999999999999999999976
No 69
>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=95.09 E-value=0.074 Score=38.18 Aligned_cols=48 Identities=21% Similarity=0.309 Sum_probs=40.3
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
.|.++|++.|. +...+|..++ ++++.+|.-.|..|+.+|.|+++..-.
T Consensus 4 ~i~~~l~~~~~--~S~~eLa~~~--~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 4 EIRDYLRERGR--VSLAELAREF--GISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHHHHS-S--EEHHHHHHHT--T--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHHHHcCC--cCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 57888999998 9999999999 999999999999999999999876543
No 70
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=95.04 E-value=0.38 Score=35.77 Aligned_cols=33 Identities=24% Similarity=0.362 Sum_probs=29.7
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 37 TRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 37 ~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
.++|.+.+ ++++++++++|+.|+++|||...++
T Consensus 2 ~~ela~~l--~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 2 TSEIAERL--NVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHHHh--CCChHHHHHHHHHHHHCCCEEEcCC
Confidence 46889999 9999999999999999999988553
No 71
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=95.04 E-value=0.17 Score=41.20 Aligned_cols=83 Identities=19% Similarity=0.249 Sum_probs=56.3
Q ss_pred hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCC---CCCHHH
Q 026766 30 KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEG---SLDTEF 106 (233)
Q Consensus 30 aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~---e~D~ef 106 (233)
-|.+==..|+|...+ ++++++++|+.+.||+.|+|.... ++-+|+ +++ .+|...
T Consensus 31 pGdkLPSvRelA~~~--~VNpnTv~raY~eLE~eG~i~t~r-----g~G~fV----------------~~~~~~~~~~~~ 87 (125)
T COG1725 31 PGDKLPSVRELAKDL--GVNPNTVQRAYQELEREGIVETKR-----GKGTFV----------------TEDAKEILDQLK 87 (125)
T ss_pred CCCCCCcHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEec-----CeeEEE----------------cCCchhhHHHHH
Confidence 455555789999999 999999999999999999997642 444443 333 444444
Q ss_pred HHHHHHHHHHHhhh--CCCCCHHHHHHHHHH
Q 026766 107 IKVVKSQCLKQIIK--LKVATLEGISDSIKR 135 (233)
Q Consensus 107 I~~l~~~~~~~i~~--~~~~T~~~I~~~I~~ 135 (233)
-..+.+.+-.||.. .-..|.++|++++++
T Consensus 88 ~~~~~~~l~~~I~~~~~~G~s~eei~~~~~~ 118 (125)
T COG1725 88 RELAEEELEEFIEEAKALGLSLEEILELLKE 118 (125)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 45555555555542 234567777777663
No 72
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=94.89 E-value=0.19 Score=51.10 Aligned_cols=144 Identities=14% Similarity=0.201 Sum_probs=96.0
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCc-cc
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEI-SG 93 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~ei-TG 93 (233)
..|+++-.|..+-.+... -...++...+ |+|...++|.|+-..++|+|.+.+.+.++ -+|-+-+-+-+..- -|
T Consensus 599 tVsp~qA~iI~~Fqek~t--wt~eelse~l--~ip~~~lrrrL~fWi~~GvL~e~~~~s~t--gt~T~iEse~d~~q~~~ 672 (765)
T KOG2165|consen 599 TVSPEQAAIINLFQEKNT--WTLEELSESL--GIPVPALRRRLSFWIQKGVLREEPIISDT--GTLTVIESEMDFDQAEG 672 (765)
T ss_pred eeCHHHHHHHHHhcCccc--ccHHHHHHHh--CCCHHHHHHHHHHHHHcCeeecCCCCCCC--ceeeeccccccccccCC
Confidence 346777777766666555 6678999999 99999999999999999999998866433 33433332222211 11
Q ss_pred CCccc-CCCC----CHHHHHHHHH-------HHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHHHhcCC
Q 026766 94 GAWYS-EGSL----DTEFIKVVKS-------QCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRALVLDN 159 (233)
Q Consensus 94 G~wy~-d~e~----D~efI~~l~~-------~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~Lv~Dg 159 (233)
-+--. |.+- ...-++.++. .|...+.+.+...++-||++++=-+.. ....|.++++.-|+.+|-+|
T Consensus 673 ~~~~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~kV~e~ 752 (765)
T KOG2165|consen 673 TVLLEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQRKVREG 752 (765)
T ss_pred CcccccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHHHhhcc
Confidence 11111 1111 1123344333 233334467889999999999855543 36899999999999999999
Q ss_pred eEEEE
Q 026766 160 QIMEV 164 (233)
Q Consensus 160 ~ie~v 164 (233)
+++-+
T Consensus 753 kL~f~ 757 (765)
T KOG2165|consen 753 KLEFI 757 (765)
T ss_pred ceEEe
Confidence 99875
No 73
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=94.86 E-value=0.11 Score=34.73 Aligned_cols=34 Identities=15% Similarity=0.370 Sum_probs=31.3
Q ss_pred cc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 34 GI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 34 GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
-+ ..++|.... +++..+|+++|+.|++.|+|..+
T Consensus 19 ~l~s~~~la~~~--~vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 19 KLPSERELAAQL--GVSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred cCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe
Confidence 46 799999999 99999999999999999999764
No 74
>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=94.86 E-value=0.069 Score=42.26 Aligned_cols=57 Identities=19% Similarity=0.278 Sum_probs=46.2
Q ss_pred HHHHHHHH--hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026766 21 RLIYDVIR--SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM 81 (233)
Q Consensus 21 ~lVy~~I~--~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym 81 (233)
.-.|+-|. --+-+=|+...|..++ ++.-+.-+++|+.|+++|+|+.| +++.+..+|-
T Consensus 44 ~~~~~kl~kEV~~~K~ITp~~lserl--kI~~SlAr~~Lr~L~~kG~Ik~V--~k~~~~~IYt 102 (105)
T PF03297_consen 44 KETYDKLLKEVPKMKLITPSVLSERL--KINGSLARKALRELESKGLIKPV--SKHHRQRIYT 102 (105)
T ss_dssp CHHHHHHHHHCTTSSCECHHHHHHHH--CCSCHHHHHHHHHHHHCCSSEEE--ECCTTCEEEE
T ss_pred HHHHHHHHHHhccCcEeeHHHHHHhH--hhHHHHHHHHHHHHHHCCCEEEE--eccCCeEEEe
Confidence 34555554 2344569999999999 99999999999999999999998 5666888884
No 75
>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=94.83 E-value=0.17 Score=39.08 Aligned_cols=59 Identities=19% Similarity=0.263 Sum_probs=47.2
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
+.|++++.++ +.-+...+|..+++ ++++..+|.|+|+.|++.|+|+++..-. +...|.+
T Consensus 4 ~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~--~~~~y~~ 65 (116)
T cd07153 4 LAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGD--GKARYEL 65 (116)
T ss_pred HHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCC--CceEEEe
Confidence 5789999887 56799999998883 3689999999999999999999976554 3455543
No 76
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=94.72 E-value=0.086 Score=42.71 Aligned_cols=47 Identities=21% Similarity=0.222 Sum_probs=39.6
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
--..||.++...|. +..++|...+ ++++.+|++.|+.|+++|||...
T Consensus 9 yL~~I~~l~~~~~~--~~~~ela~~l--~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 9 YIEQIYLLIEEKGY--ARVSDIAEAL--SVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred HHHHHHHHHhcCCC--cCHHHHHHHh--CCChhHHHHHHHHHHHCCCEEEe
Confidence 34567777766654 7899999999 99999999999999999999754
No 77
>smart00351 PAX Paired Box domain.
Probab=94.62 E-value=0.62 Score=37.32 Aligned_cols=93 Identities=19% Similarity=0.171 Sum_probs=64.5
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccC
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGG 94 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG 94 (233)
.++.+++. .+|.... .|...++|.+++ +++..+|.|.++...+.|.++..+. ||
T Consensus 17 ~~s~~~R~--riv~~~~-~G~s~~~iA~~~--gvs~~tV~kwi~r~~~~G~~~pk~~---------------------gg 70 (125)
T smart00351 17 PLPDEERQ--RIVELAQ-NGVRPCDISRQL--CVSHGCVSKILGRYYETGSIRPGAI---------------------GG 70 (125)
T ss_pred CCCHHHHH--HHHHHHH-cCCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCcCCcCC---------------------CC
Confidence 36776654 2333332 578999999999 9999999999999999997654221 22
Q ss_pred CcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc
Q 026766 95 AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF 139 (233)
Q Consensus 95 ~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~ 139 (233)
..- ... .+.....+..++..++..|+.||.+.+.+.||.
T Consensus 71 ~rp--~~~----~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~ 109 (125)
T smart00351 71 SKP--KVA----TPKVVKKIADYKQENPGIFAWEIRDRLLSEGVC 109 (125)
T ss_pred CCC--Ccc----CHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCC
Confidence 111 011 123344566678889999999999999987753
No 78
>cd00131 PAX Paired Box domain
Probab=94.60 E-value=1.2 Score=35.90 Aligned_cols=109 Identities=18% Similarity=0.166 Sum_probs=73.7
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCccc
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISG 93 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTG 93 (233)
+-|+.+.+. .+|... ..|+..++|.+++ +++.++|.+.++...+.|-++..+. |
T Consensus 16 ~~lS~d~R~--rIv~~~-~~G~s~~~iA~~~--~Vs~~tV~r~i~r~~e~G~v~pk~~---------------------g 69 (128)
T cd00131 16 RPLPDSIRQ--RIVELA-QSGIRPCDISRQL--RVSHGCVSKILNRYYETGSIRPGAI---------------------G 69 (128)
T ss_pred CcCCHHHHH--HHHHHH-HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCcCCCCC---------------------C
Confidence 456665543 233333 3689999999999 9999999999999999996644221 1
Q ss_pred CCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHH
Q 026766 94 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRA 154 (233)
Q Consensus 94 G~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~ 154 (233)
| ..-...- +.....+..++..++..|+.|+.+.+...|+. .+..|..-|-.+|+.
T Consensus 70 g--~rpr~~~----~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 70 G--SKPRVAT----PEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred C--CCCCcCC----HHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 1 0000011 12223445567889999999999998777764 356788888777654
No 79
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=94.59 E-value=0.24 Score=40.81 Aligned_cols=58 Identities=14% Similarity=0.210 Sum_probs=51.2
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
.+|+.-..|++++.++++. ....+|=.++ ++++...+|-|+|+.|++.|+|.++..-.
T Consensus 18 r~T~qR~~vl~~L~~~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 18 RLTPQRLAVLELLLEADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred CcCHHHHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 5799999999999999887 9999998887 35799999999999999999998876655
No 80
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=94.51 E-value=0.085 Score=34.06 Aligned_cols=33 Identities=21% Similarity=0.419 Sum_probs=30.4
Q ss_pred cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 34 GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 34 GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.+..++|...+ +++..+++++|+.|+++|+|..
T Consensus 8 ~~s~~~la~~l--~~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELL--GLTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred ccCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence 36789999999 9999999999999999999964
No 81
>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=94.47 E-value=0.19 Score=39.37 Aligned_cols=92 Identities=13% Similarity=0.194 Sum_probs=63.3
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS 92 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT 92 (233)
+|..-..|+++|.++.. -+...+|.+.++ +++...+|-|+|+.|++.|+|.++..- .+...|-+.. .-.
T Consensus 6 ~T~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~--~~~~~Y~~~~-----~~~ 77 (120)
T PF01475_consen 6 LTPQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG--DGESRYELST-----CHH 77 (120)
T ss_dssp HHHHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET--TSEEEEEESS-----SSS
T ss_pred CCHHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC--CCcceEeecC-----CCc
Confidence 46777899999999988 899999999883 478889999999999999999998655 3556664444 111
Q ss_pred cCCcccCC-----CCCHHHHHHHHHHHH
Q 026766 93 GGAWYSEG-----SLDTEFIKVVKSQCL 115 (233)
Q Consensus 93 GG~wy~d~-----e~D~efI~~l~~~~~ 115 (233)
..-++-.. +|+.+.++.+.+.+.
T Consensus 78 h~h~iC~~Cg~v~~~~~~~~~~~~~~~~ 105 (120)
T PF01475_consen 78 HHHFICTQCGKVIDLDDPELEEILREIA 105 (120)
T ss_dssp CEEEEETTTS-EEEE-GHHHHHHHHHHH
T ss_pred ceEEEECCCCCEEEecchhHHHHHHHHH
Confidence 22233321 566666665555443
No 82
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=94.45 E-value=0.16 Score=43.73 Aligned_cols=60 Identities=10% Similarity=0.075 Sum_probs=46.2
Q ss_pred CCChHHHHHHHHHHhhCCC--cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 15 SLTDHERLIYDVIRSKQDM--GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~--GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
.++.++++..-++..+... ...+.+|...+ |++..+|+|+|++|+++|+|+. .+++++++
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~l--G~sretvsR~L~~L~~~G~I~~------~~~~i~I~ 209 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYL--GVSYRHLLYVLAQFIQDGYLKK------SKRGYLIK 209 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHH--CCcHHHHHHHHHHHHHCCCEEe------eCCEEEEe
Confidence 3466888877776544322 25789999999 9999999999999999999976 34566654
No 83
>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=94.42 E-value=0.15 Score=42.01 Aligned_cols=51 Identities=16% Similarity=0.182 Sum_probs=39.5
Q ss_pred CChHHHHHHHHHH---hhC---CCc------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 16 LTDHERLIYDVIR---SKQ---DMG------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 16 L~~~e~lVy~~I~---~aG---~~G------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.+.++++..-++. ..| +.| +.+.+|..-+ |++..+|+|+|++|+++|+|+.
T Consensus 113 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~l--G~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 113 RDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAI--GSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEe
Confidence 4556666654443 222 233 6899999999 9999999999999999999976
No 84
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=94.41 E-value=0.2 Score=40.21 Aligned_cols=57 Identities=16% Similarity=0.236 Sum_probs=45.8
Q ss_pred CCCCCCChHHH-HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 11 APSDSLTDHER-LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 11 ~~~~~L~~~e~-lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
..++-|.++-+ .|+.+|...|. ....+|...+ ++++.+|++.|+.|++.|||...+.
T Consensus 8 ~~fkaLadptRl~IL~~L~~~~~--~~v~ela~~l--~lsqstvS~HL~~L~~AGLV~~~r~ 65 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLRESGE--LCVCDLCTAL--DQSQPKISRHLALLRESGLLLDRKQ 65 (117)
T ss_pred HHHHHhCCHHHHHHHHHHHHcCC--cCHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEEE
Confidence 34556666544 78888876554 8889999999 9999999999999999999976554
No 85
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=94.40 E-value=0.42 Score=42.55 Aligned_cols=112 Identities=6% Similarity=-0.022 Sum_probs=78.6
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccC--CCcccCCc
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPS--KEISGGAW 96 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs--~eiTGG~w 96 (233)
-...|+.+|.+.|. +..++|.+.+ +.+..+++|=|+.||++|+|+++..-- ..+ +++ .+. ++
T Consensus 6 R~~~Il~~l~~~~~--~~~~ela~~l--~vS~~TirRdL~~Le~~g~i~r~~gga---~~~------~~~~~~~~---~~ 69 (251)
T PRK13509 6 RHQILLELLAQLGF--VTVEKVIERL--GISPATARRDINKLDESGKLKKVRNGA---EAI------TQQRPRWT---PM 69 (251)
T ss_pred HHHHHHHHHHHcCC--cCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEecCCc---ccc------CCCcccCC---CH
Confidence 45678999998777 9999999999 999999999999999999997733211 110 111 011 12
Q ss_pred ccCCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHhCCcccccCHH
Q 026766 97 YSEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSGAFKVDLTKQ 146 (233)
Q Consensus 97 y~d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~~i~~~~Ls~~ 146 (233)
..-...+.+.-..|-+.+..+|... +..|+-.++++|...+++=+.=+..
T Consensus 70 ~~r~~~~~~~K~~IA~~Aa~~I~~g~~Ifld~GsT~~~la~~L~~~~ltVvTnsl~ 125 (251)
T PRK13509 70 NIHQAQNHDEKVRIAKAASQLCNPGESVVINCGSTAFLLGRELCGKPVQIITNYLP 125 (251)
T ss_pred HHHHHhCHHHHHHHHHHHHHhCCCCCEEEECCcHHHHHHHHHhCCCCeEEEeCCHH
Confidence 2233456667777888888888753 5688889999997656544444443
No 86
>PRK11050 manganese transport regulator MntR; Provisional
Probab=94.24 E-value=1 Score=37.22 Aligned_cols=43 Identities=26% Similarity=0.319 Sum_probs=37.1
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.|+.+|... .++..++|...+ +++++.|++.|+.||++|+|..
T Consensus 41 ~I~~~l~~~--~~~t~~eLA~~l--~is~stVsr~l~~Le~~GlI~r 83 (152)
T PRK11050 41 LIADLIAEV--GEARQVDIAARL--GVSQPTVAKMLKRLARDGLVEM 83 (152)
T ss_pred HHHHHHHhc--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence 555666553 469999999999 9999999999999999999975
No 87
>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=94.21 E-value=0.2 Score=33.82 Aligned_cols=41 Identities=17% Similarity=0.374 Sum_probs=34.6
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCC
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKS 64 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~ 64 (233)
..|+.++.+++.. +...+|..++ +++.++|.+-|+.|++.+
T Consensus 3 ~~il~~L~~~~~~-it~~eLa~~l--~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEP-ITAKELAEEL--GVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTS-BEHHHHHHHC--TS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCC-cCHHHHHHHh--CCCHHHHHHHHHHHHHCC
Confidence 4567777666555 9999999999 999999999999999988
No 88
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=94.18 E-value=0.2 Score=42.91 Aligned_cols=50 Identities=12% Similarity=0.131 Sum_probs=43.9
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
++....|+.++...|. +.-.+|...+ +++.+.|+|+|..|++.|||...+
T Consensus 21 ~~~~~~Vl~~L~~~g~--~tdeeLA~~L--gi~~~~VRk~L~~L~e~gLv~~~r 70 (178)
T PRK06266 21 DEEGFEVLKALIKKGE--VTDEEIAEQT--GIKLNTVRKILYKLYDARLADYKR 70 (178)
T ss_pred CccHhHHHHHHHHcCC--cCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEee
Confidence 4456778888888886 9999999999 999999999999999999998533
No 89
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=94.07 E-value=0.035 Score=43.24 Aligned_cols=60 Identities=23% Similarity=0.258 Sum_probs=48.5
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF 85 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l 85 (233)
.+|++++...-+.|+-...|-... ||+-....+.++.|+++|+|+. -++++|+.|++.+.
T Consensus 18 eIi~dIL~~~~~~~~~~Tri~y~a--Nlny~~~~~yi~~L~~~Gli~~---~~~~~~~~y~lT~K 77 (95)
T COG3432 18 EIIFDILKAISEGGIGITRIIYGA--NLNYKRAQKYIEMLVEKGLIIK---QDNGRRKVYELTEK 77 (95)
T ss_pred HHHHHHHHHhcCCCCCceeeeeec--CcCHHHHHHHHHHHHhCCCEEe---ccCCccceEEEChh
Confidence 388999986666677777788888 9999999999999999998754 34566779988753
No 90
>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=93.95 E-value=0.12 Score=37.39 Aligned_cols=38 Identities=16% Similarity=0.237 Sum_probs=33.1
Q ss_pred CCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEeec
Q 026766 47 NLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMAVE 84 (233)
Q Consensus 47 ~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml~~ 84 (233)
+++..+|-.+|++||++|+|...... ..+.||+|-+.+
T Consensus 28 ~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~ 67 (75)
T PF03551_consen 28 KISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITE 67 (75)
T ss_dssp ETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESH
T ss_pred ccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECH
Confidence 68899999999999999999998876 677899997754
No 91
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=93.95 E-value=0.68 Score=41.05 Aligned_cols=121 Identities=12% Similarity=0.146 Sum_probs=81.5
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcc
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWY 97 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy 97 (233)
+-+..|+++|.+.+ .+..+||.+.+ ++...+++|-|+.|+++++|++. + +.-+|.... .+..+ -+|.
T Consensus 4 ~R~~~Il~~l~~~~--~~~~~eLa~~l--~VS~~TiRRdL~~L~~~~~l~r~---~--Gga~~~~~~-~~~~~---~~~~ 70 (240)
T PRK10411 4 ARQQAIVDLLLNHT--SLTTEALAEQL--NVSKETIRRDLNELQTQGKILRN---H--GRAKYIHRQ-NQDSG---DPFH 70 (240)
T ss_pred HHHHHHHHHHHHcC--CCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe---c--CeEEEecCC-CcccC---CCHH
Confidence 34667899999766 49999999999 99999999999999999999762 2 343443211 11111 1222
Q ss_pred cCCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHhCCcccccCHHHHHHH
Q 026766 98 SEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSGAFKVDLTKQQIEEI 151 (233)
Q Consensus 98 ~d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~~i~~~~Ls~~di~~i 151 (233)
.-...+.+.=..|-+.+..+|+.. +..|+.++.++|...+++-+.=+..-.+.+
T Consensus 71 ~r~~~~~~~K~~IA~~Aa~lI~~gd~Ifld~GtT~~~l~~~L~~~~ltVvTNs~~ia~~l 130 (240)
T PRK10411 71 IRLKSHYAHKADIAREALAWIEEGMVIALDASSTCWYLARQLPDINIQVFTNSHPICQEL 130 (240)
T ss_pred HHHHhHHHHHHHHHHHHHHhCCCCCEEEEcCcHHHHHHHHhhCCCCeEEEeCCHHHHHHH
Confidence 223345566677777788888753 568899999999765555444444444333
No 92
>PRK09462 fur ferric uptake regulator; Provisional
Probab=93.90 E-value=0.44 Score=38.93 Aligned_cols=64 Identities=13% Similarity=0.181 Sum_probs=53.0
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL 80 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y 80 (233)
.+|+.-..||++|.++.+.-+...+|-.++ ++++...+|-|.|+.|++.|+|.++..-. ++..|
T Consensus 14 r~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~--~~~~y 80 (148)
T PRK09462 14 KVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEG--GKSVF 80 (148)
T ss_pred CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCC--CcEEE
Confidence 478899999999998877789999998887 33688999999999999999998876333 44455
No 93
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=93.87 E-value=0.14 Score=42.78 Aligned_cols=110 Identities=16% Similarity=0.192 Sum_probs=72.9
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCccc-
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYS- 98 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~- 98 (233)
=..||.+++..|- +-++||...+ +..+.+|++.|++|+++|||.-++. ||.+-|
T Consensus 12 L~~Iy~l~~~~~~--~~~~diA~~L--~Vsp~sVt~ml~rL~~~GlV~~~~y---------------------~gi~LT~ 66 (154)
T COG1321 12 LETIYELLEEKGF--ARTKDIAERL--KVSPPSVTEMLKRLERLGLVEYEPY---------------------GGVTLTE 66 (154)
T ss_pred HHHHHHHHhccCc--ccHHHHHHHh--CCCcHHHHHHHHHHHHCCCeEEecC---------------------CCeEECh
Confidence 3467777774443 9999999999 9999999999999999999966432 233333
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhc
Q 026766 99 EGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVL 157 (233)
Q Consensus 99 d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~ 157 (233)
.|+==...+=...+.+..|+.+.-....+++++--.... -.+|.+-++.|-+.|-+
T Consensus 67 ~G~~~a~~~~r~hrlle~fL~~~lg~~~~~~~~ea~~le---h~~s~~~~~rl~~~l~~ 122 (154)
T COG1321 67 KGREKAKELLRKHRLLERFLVDVLGLDWEEAHEEAEGLE---HALSDETAERLDELLGF 122 (154)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHh---hcCCHHHHHHHHHHhCC
Confidence 222112222223334566776544556777775544333 34888888888888765
No 94
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=93.85 E-value=0.22 Score=41.45 Aligned_cols=52 Identities=13% Similarity=0.161 Sum_probs=40.5
Q ss_pred CCChHHHHHHHHHHhhCC------------CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 15 SLTDHERLIYDVIRSKQD------------MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~------------~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
..+..+++..-+++-+.. -=+.+.+|..-+ |++..+|+|+|+.|+++|+|+.
T Consensus 118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~l--G~tretvsR~l~~l~~~g~I~~ 181 (202)
T PRK13918 118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAV--GSVRETVTKVIGELSREGYIRS 181 (202)
T ss_pred hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHh--CccHHHHHHHHHHHHHCCCEEc
Confidence 345677777766543321 125799999999 9999999999999999999963
No 95
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=93.84 E-value=0.17 Score=43.29 Aligned_cols=52 Identities=13% Similarity=0.167 Sum_probs=40.5
Q ss_pred CCChHHHHHHHHHHhh---CC---C------cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 15 SLTDHERLIYDVIRSK---QD---M------GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~a---G~---~------GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
..+.++|+..-+.+.+ |. . -+.+++|..-+ |++..+|+|+|++|+++|+|+-
T Consensus 153 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~l--G~sr~tvsR~l~~l~~~g~I~~ 216 (235)
T PRK11161 153 KKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYL--GLTVETISRLLGRFQKSGMLAV 216 (235)
T ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEe
Confidence 3466777666555432 21 1 27899999999 9999999999999999999975
No 96
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=93.77 E-value=0.16 Score=44.01 Aligned_cols=53 Identities=23% Similarity=0.270 Sum_probs=41.7
Q ss_pred CCCChHHHHHHHHHHhh---CCC-----cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 14 DSLTDHERLIYDVIRSK---QDM-----GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~a---G~~-----GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
...+.++|++.-+++.+ |.. -+.+++|..-+ |++..+|+|+||+|+++|+|+.
T Consensus 151 ~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~l--GisretlsR~L~~L~~~GlI~~ 211 (230)
T PRK09391 151 GRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYL--GLTIETVSRALSQLQDRGLIGL 211 (230)
T ss_pred cCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEe
Confidence 34577888876666543 322 25789999999 9999999999999999999964
No 97
>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=93.75 E-value=0.12 Score=43.69 Aligned_cols=46 Identities=17% Similarity=0.426 Sum_probs=36.1
Q ss_pred HHHHHHHhhCCCc---ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 22 LIYDVIRSKQDMG---IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 22 lVy~~I~~aG~~G---Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
+++-+|+.....+ +.+++|..++ +++.++|+|++|.|+++++|+++
T Consensus 60 Vl~~il~~~d~~N~v~~t~~~ia~~l--~iS~~Tv~r~ik~L~e~~iI~k~ 108 (165)
T PF05732_consen 60 VLMYILENMDKDNAVVATQKEIAEKL--GISKPTVSRAIKELEEKNIIKKI 108 (165)
T ss_pred HHHHHHHhcCCCCeEEeeHHHHHHHh--CCCHHHHHHHHHHHHhCCcEEEc
Confidence 3333444444444 3688999999 99999999999999999999875
No 98
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=93.69 E-value=0.27 Score=39.85 Aligned_cols=53 Identities=11% Similarity=0.058 Sum_probs=41.7
Q ss_pred HHHHHHHHHHhhCC---CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 19 HERLIYDVIRSKQD---MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 19 ~e~lVy~~I~~aG~---~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
.+.-+..+|..+.. .=+..++|..+. +++.+.|.|+|+.|++.|||++.+...
T Consensus 7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~--~is~~~vrk~l~~L~~~Glv~s~~G~~ 62 (141)
T PRK11014 7 TDYGLRALIYMASLPEGRMTSISEVTEVY--GVSRNHMVKIINQLSRAGYVTAVRGKN 62 (141)
T ss_pred HhHHHHHHHHHhcCCCCCccCHHHHHHHH--CcCHHHHHHHHHHHHhCCEEEEecCCC
Confidence 45556666665532 236779999999 999999999999999999998876553
No 99
>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=93.61 E-value=0.2 Score=41.41 Aligned_cols=66 Identities=11% Similarity=0.143 Sum_probs=44.8
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhc-CCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEeec
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRV-NLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMAVE 84 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~-~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml~~ 84 (233)
-+..|+.+|....-.|=.....-...+. .+.+.+|..+|++||+.|+|.+.... ..+.||+|-|.+
T Consensus 25 l~~~IL~~L~~~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe 93 (138)
T TIGR02719 25 LVPFLLLCLKDWNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTD 93 (138)
T ss_pred HHHHHHHHHccCCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECH
Confidence 3567777776655555444333333322 68899999999999999999875433 346689997654
No 100
>PHA00738 putative HTH transcription regulator
Probab=93.58 E-value=0.3 Score=38.92 Aligned_cols=50 Identities=18% Similarity=0.151 Sum_probs=41.0
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
+-=+.|+.+|.+.+ +....+|...+ +|.+..|++.||.|++.|||.+-+.
T Consensus 12 ptRr~IL~lL~~~e--~~~V~eLae~l--~lSQptVS~HLKvLreAGLV~srK~ 61 (108)
T PHA00738 12 ILRRKILELIAENY--ILSASLISHTL--LLSYTTVLRHLKILNEQGYIELYKE 61 (108)
T ss_pred HHHHHHHHHHHHcC--CccHHHHHHhh--CCCHHHHHHHHHHHHHCCceEEEEE
Confidence 34456777776533 38899999999 9999999999999999999977553
No 101
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=93.43 E-value=0.12 Score=36.79 Aligned_cols=51 Identities=16% Similarity=0.210 Sum_probs=37.5
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHh--CCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 114 CLKQIIKLKVATLEGISDSIKRS--GAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 114 ~~~~i~~~~~~T~~~I~~~I~~~--~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
|...|.+.+..+++.||..++=. +-...+.|.+++++.|+.||-||+++..
T Consensus 2 I~gMLtN~gsl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~ 54 (60)
T PF08672_consen 2 IVGMLTNLGSLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECS 54 (60)
T ss_dssp HHHHHHHH-SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--
T ss_pred HhHHhhcCCCCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEec
Confidence 34556677888999999999977 3234689999999999999999999875
No 102
>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=93.35 E-value=0.15 Score=39.26 Aligned_cols=50 Identities=20% Similarity=0.254 Sum_probs=38.6
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
.++...|+.+|-..|. +.-.||.+.+ +|+.+.++++|-.|.+.|||+..+
T Consensus 12 g~~~~~Il~~L~~~~~--l~de~la~~~--~l~~~~vRkiL~~L~~~~lv~~~~ 61 (105)
T PF02002_consen 12 GEEAVRILDALLRKGE--LTDEDLAKKL--GLKPKEVRKILYKLYEDGLVSYRR 61 (105)
T ss_dssp -STTHHHHHHHHHH----B-HHHHHHTT---S-HHHHHHHHHHHHHHSS-EEEE
T ss_pred CchHHHHHHHHHHcCC--cCHHHHHHHh--CCCHHHHHHHHHHHHHCCCeEEEE
Confidence 3567788999988775 9999999999 999999999999999999996654
No 103
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=93.17 E-value=0.85 Score=40.74 Aligned_cols=111 Identities=8% Similarity=0.088 Sum_probs=78.3
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCccc
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYS 98 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~ 98 (233)
-...|+++|.+.|. +..+||.+.+ +.+..+++|=|+.||++|+|+++.- +- ++ . .++.+. ++..
T Consensus 6 R~~~Il~~L~~~~~--v~v~eLa~~l--~VS~~TIRRDL~~Le~~g~l~r~~G----ga-~~--~--~~~~~~---~~~~ 69 (256)
T PRK10434 6 RQAAILEYLQKQGK--TSVEELAQYF--DTTGTTIRKDLVILEHAGTVIRTYG----GV-VL--N--KEESDP---PIDH 69 (256)
T ss_pred HHHHHHHHHHHcCC--EEHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEEEC----CE-Ec--C--CCCCCC---CHHH
Confidence 45689999999888 9999999999 9999999999999999999987641 11 11 0 011111 2222
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHh-CCcccccCH
Q 026766 99 EGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTK 145 (233)
Q Consensus 99 d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~-~i~~~~Ls~ 145 (233)
-...+.+.=+.|-+....+|... +..|+-.++++|... +++=+.=|.
T Consensus 70 r~~~~~~~K~~IA~~Aa~~I~~g~tIfld~GtT~~~la~~L~~~~~ltVvTnsl 123 (256)
T PRK10434 70 KTLINTHKKELIAEAAVSLIHDGDSIILDAGSTVLQMVPLLSRFNNITVMTNSL 123 (256)
T ss_pred HHHhhHHHHHHHHHHHHhhCCCCCEEEEcCcHHHHHHHHHhccCCCeEEEECCH
Confidence 33456666677777788888753 568889999999764 444344333
No 104
>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=93.05 E-value=0.55 Score=35.36 Aligned_cols=55 Identities=15% Similarity=0.246 Sum_probs=43.9
Q ss_pred CChHHHHHHHHHH---hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026766 16 LTDHERLIYDVIR---SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI 72 (233)
Q Consensus 16 L~~~e~lVy~~I~---~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV 72 (233)
||+-++.|+..|- ...+.=|-.++|.+++ +.++.+|+..+..||+.|||.+++.-
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l--~~s~aTIRN~M~~Le~lGlve~~p~~ 59 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGSKTIAEEL--GRSPATIRNEMADLEELGLVESQPHP 59 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHH--CCChHHHHHHHHHHHHCCCccCCCCC
Confidence 6776776666554 2334559999999999 99999999999999999999766543
No 105
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=93.04 E-value=0.43 Score=39.93 Aligned_cols=32 Identities=22% Similarity=0.403 Sum_probs=30.1
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
+.+++|...+ |++..+|+|+|++|++.|+|+.
T Consensus 169 ~t~~~lA~~l--G~tr~tvsR~l~~l~~~gii~~ 200 (211)
T PRK11753 169 ITRQEIGRIV--GCSREMVGRVLKMLEDQGLISA 200 (211)
T ss_pred CCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe
Confidence 5689999999 9999999999999999999975
No 106
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=93.04 E-value=0.44 Score=31.10 Aligned_cols=43 Identities=19% Similarity=0.413 Sum_probs=36.3
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
..|++.|+.++.++. .|...++|...+ +++..+|.+.++.+.+
T Consensus 2 ~~l~~~e~~i~~~~~----~g~s~~eia~~l--~is~~tv~~~~~~~~~ 44 (58)
T smart00421 2 ASLTPREREVLRLLA----EGLTNKEIAERL--GISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence 468898888887753 578999999999 9999999999988754
No 107
>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=93.01 E-value=0.32 Score=34.58 Aligned_cols=33 Identities=15% Similarity=0.347 Sum_probs=30.9
Q ss_pred cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 34 GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 34 GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.+.+.+|..-+ |++..+++|+|+.|+++|+|..
T Consensus 28 ~lt~~~iA~~~--g~sr~tv~r~l~~l~~~g~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADML--GVSRETVSRILKRLKDEGIIEV 60 (76)
T ss_dssp ESSHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred cCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence 56799999999 9999999999999999999973
No 108
>PRK05638 threonine synthase; Validated
Probab=93.01 E-value=0.32 Score=46.70 Aligned_cols=61 Identities=16% Similarity=0.246 Sum_probs=47.5
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcC--CChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVN--LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV 83 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~--l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~ 83 (233)
+.+....|+.+|.+. -+.-.+|.+.+ + +++.+|+++||.||+.|||.+.. +..++++|-|.
T Consensus 369 ~~~~r~~IL~~L~~~---~~~~~el~~~l--~~~~s~~~v~~hL~~Le~~GLV~~~~--~~g~~~~Y~Lt 431 (442)
T PRK05638 369 IGGTKLEILKILSER---EMYGYEIWKAL--GKPLKYQAVYQHIKELEELGLIEEAY--RKGRRVYYKLT 431 (442)
T ss_pred ccchHHHHHHHHhhC---CccHHHHHHHH--cccCCcchHHHHHHHHHHCCCEEEee--cCCCcEEEEEC
Confidence 455678888888743 38899999999 7 89999999999999999997642 22456666554
No 109
>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=92.86 E-value=0.19 Score=34.24 Aligned_cols=32 Identities=19% Similarity=0.433 Sum_probs=29.5
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
..++|...+ +++..+|+++|+.|+++|+|...
T Consensus 27 ~~~~la~~~--~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 27 SERELAEEL--GVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEec
Confidence 489999999 99999999999999999999653
No 110
>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=92.74 E-value=0.32 Score=38.41 Aligned_cols=38 Identities=11% Similarity=0.302 Sum_probs=34.0
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 31 QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 31 G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
+...+..++|...+ ++|.+.|.++|..|++.|+|.+..
T Consensus 22 ~~~~~s~~eia~~~--~i~~~~v~~il~~L~~~gli~~~~ 59 (132)
T TIGR00738 22 DEGPVSVKEIAERQ--GISRSYLEKILRTLRRAGLVESVR 59 (132)
T ss_pred CCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEecc
Confidence 34479999999999 999999999999999999997643
No 111
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=92.62 E-value=0.22 Score=32.94 Aligned_cols=42 Identities=21% Similarity=0.369 Sum_probs=22.8
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
.+.||++|+....... +.|+..++|.+.+ |.+.++|.+-||.
T Consensus 2 ~~~Lt~~eR~~I~~l~---~~G~s~~~IA~~l--g~s~sTV~relkR 43 (44)
T PF13936_consen 2 YKHLTPEERNQIEALL---EQGMSIREIAKRL--GRSRSTVSRELKR 43 (44)
T ss_dssp ----------HHHHHH---CS---HHHHHHHT--T--HHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHH---HcCCCHHHHHHHH--CcCcHHHHHHHhc
Confidence 3568999988765554 5789999999999 9999999999984
No 112
>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=92.58 E-value=0.52 Score=31.03 Aligned_cols=42 Identities=21% Similarity=0.397 Sum_probs=34.9
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQ 61 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le 61 (233)
|++-++.|++.+...|. +..++|..++ |++..+|.+-++.||
T Consensus 1 lD~~D~~Il~~Lq~d~r--~s~~~la~~l--glS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 1 LDELDRKILRLLQEDGR--RSYAELAEEL--GLSESTVRRRIRRLE 42 (42)
T ss_dssp --HHHHHHHHHHHH-TT--S-HHHHHHHH--TS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC--ccHHHHHHHH--CcCHHHHHHHHHHhC
Confidence 56778999999999988 9999999999 999999999999996
No 113
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=92.57 E-value=0.51 Score=40.56 Aligned_cols=64 Identities=17% Similarity=0.187 Sum_probs=52.1
Q ss_pred CCCChHHH-HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc-eeeecccCCCeeeE
Q 026766 14 DSLTDHER-LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI-KEVVNIHSKGKKHL 80 (233)
Q Consensus 14 ~~L~~~e~-lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI-K~vksV~~~~rK~Y 80 (233)
..|++.|. .+..+|...-+.|...++|..++ ++..++|++.+..|.+.|+. ++++..+. +|..|
T Consensus 157 ~~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l--~iS~~Tv~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 222 (239)
T PRK10430 157 KGLTPQTLRTLCQWIDAHQDYEFSTDELANAV--NISRVSCRKYLIWLVNCHILFTSIHYGVT-GRPVY 222 (239)
T ss_pred CCCCHHHHHHHHHHHHhCCCCCcCHHHHHHHh--CchHHHHHHHHHHHHhCCEEEEEeeccCC-CCCCe
Confidence 35888774 56688888888999999999999 99999999999999999999 56666543 44433
No 114
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=92.53 E-value=0.37 Score=38.80 Aligned_cols=41 Identities=12% Similarity=0.140 Sum_probs=35.5
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 31 QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 31 G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
++.-+..++|..++ ++|.+.+.|+|..|.+.|||.+.+...
T Consensus 22 ~~~~~s~~~ia~~~--~ip~~~l~kil~~L~~~glv~s~~G~~ 62 (135)
T TIGR02010 22 ETGPVTLADISERQ--GISLSYLEQLFAKLRKAGLVKSVRGPG 62 (135)
T ss_pred CCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEeCCC
Confidence 33458999999999 999999999999999999998765543
No 115
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=92.34 E-value=0.49 Score=35.59 Aligned_cols=71 Identities=14% Similarity=0.211 Sum_probs=55.9
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCccc
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISG 93 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTG 93 (233)
....++.+...+++.=+.-.+|..++ ++....|.|++++|++.|+ .|.++++++.++=.+-++=|...+..
T Consensus 4 ~~~~~~~ll~~~~~~~~SGe~La~~L--giSRtaVwK~Iq~Lr~~G~--~I~s~~~kGY~L~~~~~ll~~~~i~~ 74 (79)
T COG1654 4 TSQMLLLLLLLLTGNFVSGEKLAEEL--GISRTAVWKHIQQLREEGV--DIESVRGKGYLLPQLPDLLPQEIIQA 74 (79)
T ss_pred hHHHHHHHHHHcCCCcccHHHHHHHH--CccHHHHHHHHHHHHHhCC--ceEecCCCceeccCccccCcHHHHHh
Confidence 34567777788888889999999999 9999999999999999998 46778877776666555555444443
No 116
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=92.06 E-value=3.6 Score=36.53 Aligned_cols=87 Identities=14% Similarity=0.252 Sum_probs=58.3
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe--eeEEeeccccCCCcccCCc
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK--KHLMAVEFEPSKEISGGAW 96 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r--K~Yml~~lePs~eiTGG~w 96 (233)
-...|+.++...|. +...||.+++ +++...+++.|..||.+|||...-.=...+| ++|-|. +++.+.-+
T Consensus 12 tr~~il~lL~~~g~--~sa~elA~~L--gis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt--~~g~~~f~--- 82 (218)
T COG2345 12 TRERILELLKKSGP--VSADELAEEL--GISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLT--EKGREQFP--- 82 (218)
T ss_pred HHHHHHHHHhccCC--ccHHHHHHHh--CCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeec--ccchhhcc---
Confidence 34566667777776 9999999999 9999999999999999999987622221233 455444 33333111
Q ss_pred ccCCCCCHHHHHHHHHHH
Q 026766 97 YSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 97 y~d~e~D~efI~~l~~~~ 114 (233)
+..++|=..+++.|.+..
T Consensus 83 ~~y~~l~~~~l~~l~~~~ 100 (218)
T COG2345 83 KRYGELALALLDALEETG 100 (218)
T ss_pred hhhHHHHHHHHHHHHHhc
Confidence 123455566666666554
No 117
>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=91.97 E-value=0.55 Score=31.21 Aligned_cols=43 Identities=19% Similarity=0.253 Sum_probs=35.1
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSL 60 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~L 60 (233)
+..||+.|+.|+.+.. -.|...++|...+ |++..+|++.++.-
T Consensus 2 l~~L~~~er~vi~~~y---~~~~t~~eIa~~l--g~s~~~V~~~~~~a 44 (50)
T PF04545_consen 2 LDQLPPREREVIRLRY---FEGLTLEEIAERL--GISRSTVRRILKRA 44 (50)
T ss_dssp HCTS-HHHHHHHHHHH---TST-SHHHHHHHH--TSCHHHHHHHHHHH
T ss_pred hhhCCHHHHHHHHHHh---cCCCCHHHHHHHH--CCcHHHHHHHHHHH
Confidence 4689999999988888 7789999999999 99999888776653
No 118
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=91.79 E-value=0.19 Score=46.38 Aligned_cols=55 Identities=16% Similarity=0.283 Sum_probs=43.5
Q ss_pred CCChHHHHHHHHHHhhC---CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 15 SLTDHERLIYDVIRSKQ---DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG---~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
+|+.-+..|+.++.+++ ..++-..+|+++ |-|+..+.|++.||.|+++||++++-
T Consensus 3 ~~~rk~ieIl~il~esd~plgak~Ia~el~kR-Gy~igeRavRYhlk~lderglt~kvg 60 (325)
T COG1693 3 NLNRKLIEILRILAESDEPLGAKIIALELRKR-GYNIGERAVRYHLKKLDERGLTRKVG 60 (325)
T ss_pred hHHHHHHHHHHHHHhcCCccchHHHHHHHHhc-ccchhHHHHHHHHHHHhhccchhhcc
Confidence 45666778999999998 334445555555 55999999999999999999998876
No 119
>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=91.30 E-value=0.72 Score=38.64 Aligned_cols=49 Identities=18% Similarity=0.180 Sum_probs=42.1
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
++...|+..+-..|. +.-.||...+ +|+.+.|+|+|..|.++|||...+
T Consensus 14 ~~~v~Vl~aL~~~~~--~tdEeLa~~L--gi~~~~VRk~L~~L~e~~Lv~~~r 62 (158)
T TIGR00373 14 EEVGLVLFSLGIKGE--FTDEEISLEL--GIKLNEVRKALYALYDAGLADYKR 62 (158)
T ss_pred hhHHHHHHHHhccCC--CCHHHHHHHH--CCCHHHHHHHHHHHHHCCCceeee
Confidence 355678888777775 9999999999 999999999999999999996443
No 120
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=91.25 E-value=0.38 Score=34.56 Aligned_cols=48 Identities=17% Similarity=0.151 Sum_probs=37.7
Q ss_pred HHHHHHHhhh-CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 111 KSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 111 ~~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
++.++.||.. ++.+|..||++-+ .+|.-.++.+|+.|+-+|+|+.+..
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~--------gls~~~aR~yL~~Le~eG~V~~~~~ 50 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADAL--------GLSIYQARYYLEKLEKEGKVERSPV 50 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHH--------TS-HHHHHHHHHHHHHCTSEEEES-
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCEEEecC
Confidence 5677888877 7778888888754 4888999999999999999998753
No 121
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=91.25 E-value=0.69 Score=38.36 Aligned_cols=46 Identities=11% Similarity=0.148 Sum_probs=38.3
Q ss_pred HHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 26 VIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 26 ~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
++......-+..++|..+. ++|.+-|.|+|..|...|||++++-.+
T Consensus 16 ~LA~~~~~~~s~~eIA~~~--~is~~~L~kIl~~L~~aGlv~S~rG~~ 61 (153)
T PRK11920 16 YCAANDGKLSRIPEIARAY--GVSELFLFKILQPLVEAGLVETVRGRN 61 (153)
T ss_pred HHHhCCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeecCCC
Confidence 3433344457899999999 999999999999999999998887654
No 122
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=91.01 E-value=0.6 Score=41.70 Aligned_cols=115 Identities=13% Similarity=0.176 Sum_probs=77.7
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcc
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWY 97 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy 97 (233)
+-...|+.++.+.|. +...||...+ +++..+++|=|+.||++|+|+++ + .+- + +. .+..+ -++.
T Consensus 5 ~R~~~Il~~l~~~~~--~~~~ela~~l--~vS~~TiRRdL~~Le~~g~l~r~---~-GGa-~--~~--~~~~~---~~~~ 68 (252)
T PRK10906 5 QRHDAIIELVKQQGY--VSTEELVEHF--SVSPQTIRRDLNDLAEQNKILRH---H-GGA-A--LP--SSSVN---TPWH 68 (252)
T ss_pred HHHHHHHHHHHHcCC--EeHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEe---c-CCE-E--ec--CCCCC---CCHH
Confidence 345678999988887 9999999999 99999999999999999999763 2 121 1 11 11111 1232
Q ss_pred cCCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHh-CCcccccCHHHH
Q 026766 98 SEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTKQQI 148 (233)
Q Consensus 98 ~d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~-~i~~~~Ls~~di 148 (233)
.-...+.+.=..|-+....+|... +..|+.+++++|... +++=+.=|..=+
T Consensus 69 ~r~~~~~~~K~~IA~~Aa~~I~~g~tIflD~GtT~~~la~~L~~~~~ltVvTNsl~ia 126 (252)
T PRK10906 69 DRKATQTEEKERIARKVASQIPNGATLFIDIGTTPEAVAHALLNHSNLRIVTNNLNVA 126 (252)
T ss_pred HHhhhcHHHHHHHHHHHHhhCCCCCEEEEcCcHHHHHHHHHhcCCCCcEEEECcHHHH
Confidence 223445555566777777788753 568899999999653 454444444333
No 123
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=90.93 E-value=1.6 Score=37.27 Aligned_cols=57 Identities=11% Similarity=0.174 Sum_probs=46.7
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK 77 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r 77 (233)
||. +.|+++|. .|..|...++|.+++ ++..++|++.+..|+..|++...-.-...+|
T Consensus 162 Lt~--r~Vl~~~~-~g~~g~s~~eIa~~l--~iS~~Tv~~~~~~~~~~~~~~~~~~~~~~gr 218 (225)
T PRK10046 162 LTL--NAVRKLFK-EPGVQHTAETVAQAL--TISRTTARRYLEYCASRHLIIAEIVHGKVGR 218 (225)
T ss_pred HHH--HHHHHHHH-cCCCCcCHHHHHHHh--CccHHHHHHHHHHHHhCCeEEEEeecCCCCC
Confidence 444 57888886 566789999999999 9999999999999999999987655443344
No 124
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=90.92 E-value=0.57 Score=41.65 Aligned_cols=44 Identities=18% Similarity=0.385 Sum_probs=40.0
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.|++++.+ +..|+...+|.+++ |||.+++.|.|..|++.|++..
T Consensus 8 ~iL~~l~~-~~~~l~l~ela~~~--glpksT~~RlL~tL~~~G~v~~ 51 (246)
T COG1414 8 AILDLLAE-GPGGLSLAELAERL--GLPKSTVHRLLQTLVELGYVEQ 51 (246)
T ss_pred HHHHHHHh-CCCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCEEE
Confidence 57778887 77778899999999 9999999999999999999976
No 125
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=90.73 E-value=0.64 Score=39.16 Aligned_cols=42 Identities=10% Similarity=0.110 Sum_probs=36.6
Q ss_pred hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 30 KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 30 aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
.+...+..++|..++ ++|.+.|.|+|..|.+.|||.+.+..+
T Consensus 21 ~~~~~vs~~eIA~~~--~ip~~~l~kIl~~L~~aGLv~s~rG~~ 62 (164)
T PRK10857 21 SEAGPVPLADISERQ--GISLSYLEQLFSRLRKNGLVSSVRGPG 62 (164)
T ss_pred CCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeCCCCC
Confidence 344568999999999 999999999999999999998865554
No 126
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=90.70 E-value=2.3 Score=36.10 Aligned_cols=124 Identities=15% Similarity=0.199 Sum_probs=77.0
Q ss_pred CCCCCCChHHHHHH---------HHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026766 11 APSDSLTDHERLIY---------DVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM 81 (233)
Q Consensus 11 ~~~~~L~~~e~lVy---------~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym 81 (233)
.+++.|+.++...| .++.-.+..+ .-..|.++++++++..+++++|..|++-||||.-.+ -.|.
T Consensus 8 ~~~~~l~~~~~~~~~~W~~~~ir~l~~l~~~~~-d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~------g~y~ 80 (171)
T PF14394_consen 8 NKVRVLDEDEFEYYSSWYHPAIRELLPLMPFAP-DPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD------GKYV 80 (171)
T ss_pred cceeeccHHHHHHHhhhHHHHHHHHhhcCCCCC-CHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC------CcEE
Confidence 34666777665543 4444444443 778999999999999999999999999999998554 2343
Q ss_pred eeccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHHHh
Q 026766 82 AVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRALV 156 (233)
Q Consensus 82 l~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~Lv 156 (233)
.. +..+|| ..+.-.+.|-.+..+++..-... ++.+- ..+..++ ...++.+++++|.+.|.
T Consensus 81 ~t----~~~l~~-----~~~~~~~avr~~h~q~~~lA~~a----l~~~p--~~~R~~s~~T~~vs~~~~~ki~~~i~ 142 (171)
T PF14394_consen 81 QT----DKSLTT-----SSEIPSEAVRSYHKQMLELAQEA----LDRVP--PEERDFSGLTMSVSREDYEKIKKEIR 142 (171)
T ss_pred Ee----cceeeC-----CCCCcHHHHHHHHHHHHHHHHHH----HHhCC--ccccceeeeEEEeCHHHHHHHHHHHH
Confidence 22 223333 34666777777777766554321 00000 0111233 35678888888877653
No 127
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=90.67 E-value=0.81 Score=37.81 Aligned_cols=68 Identities=10% Similarity=0.129 Sum_probs=48.2
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHH-HHHh-hc-CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDM-KREL-RV-NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE 84 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~di-k~~t-~~-~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~ 84 (233)
..+++-...|+.++... .-|-..... ...+ +. .++..+|-.+|+.||++|+|.+... .++||+|-+.+
T Consensus 39 ~~~~~~~l~IL~lL~~~-~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~--~~~RK~Y~ITe 109 (135)
T PRK09416 39 EKEEDILLAILQLLMNE-KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWD--HEGAKYYQLTD 109 (135)
T ss_pred cccccHHHHHHHHHhCC-CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeec--CCCceEEEECH
Confidence 35667778888888766 666655443 3333 11 4678999999999999999987543 46789986543
No 128
>PF13551 HTH_29: Winged helix-turn helix
Probab=90.63 E-value=4 Score=30.57 Aligned_cols=99 Identities=16% Similarity=0.214 Sum_probs=65.3
Q ss_pred Ccc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHH
Q 026766 33 MGI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVK 111 (233)
Q Consensus 33 ~GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~ 111 (233)
+|. ..+++.+.+ +++.++|.+.++..++.|+-. +.+-.. .||....- ++.+-.+.|.
T Consensus 10 ~g~~~~~~ia~~l--g~s~~Tv~r~~~~~~~~G~~~-l~~~~~-----------------~~g~~~~~--l~~~~~~~l~ 67 (112)
T PF13551_consen 10 EGVSTIAEIARRL--GISRRTVYRWLKRYREGGIEG-LLPRKP-----------------RGGRPRKR--LSEEQRAQLI 67 (112)
T ss_pred cCCCcHHHHHHHH--CcCHHHHHHHHHHHHcccHHH-HHhccc-----------------cCCCCCCC--CCHHHHHHHH
Confidence 466 499999999 999999999999999999322 121110 12222211 6666666555
Q ss_pred HHHHHHhhh-CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHH
Q 026766 112 SQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRA 154 (233)
Q Consensus 112 ~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~ 154 (233)
+.+...-.. ....|+++|.+++.+.. ..+.+|..-|..+|.-
T Consensus 68 ~~~~~~p~~g~~~~t~~~l~~~l~~~~-~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 68 ELLRENPPEGRSRWTLEELAEWLIEEE-FGIDVSPSTIRRILKR 110 (112)
T ss_pred HHHHHCCCCCCCcccHHHHHHHHHHhc-cCccCCHHHHHHHHHH
Confidence 555432222 12689999999983333 3468999999998864
No 129
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=90.60 E-value=1.5 Score=33.08 Aligned_cols=58 Identities=16% Similarity=0.101 Sum_probs=42.3
Q ss_pred CCCCChHHHHHHHHHHhhC--CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 13 SDSLTDHERLIYDVIRSKQ--DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG--~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
++.|++++-.|+..||..- -+=+....|.+.+ +|+...+.++|+.|-..+||.. ....
T Consensus 1 ~r~L~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s--~l~~~~~~~~L~~L~~~kLv~~-~~~~ 60 (82)
T PF09202_consen 1 LRYLSKEDFRVLRAIEMGMKNHEWVPLELIEKIS--GLSEGEVEKRLKRLVKLKLVSR-RNKP 60 (82)
T ss_dssp --T--HHHHHHHHHHHTTTTT-SSEEHHHHHHHH--T--HHHHHHHHHHHHHTTSEEE-E-SS
T ss_pred CCcCCHHHHHHHHHHHHcccCCccCCHHHHHHHh--CcCHHHHHHHHHHHHhcCCccc-cCCC
Confidence 4679999999999999542 2235578899999 9999999999999999999988 4433
No 130
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=90.33 E-value=0.72 Score=39.93 Aligned_cols=49 Identities=16% Similarity=0.280 Sum_probs=44.8
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
+-+++|+.++...|.+ +...+|.+++ ||..+.|+|.|=+|...+.|..+
T Consensus 4 ~~~~~i~~~l~~~~~~-~~a~~i~k~l--~i~k~~vNr~LY~L~~~~~v~~~ 52 (183)
T PHA02701 4 DCASLILTLLSSSGDK-LPAKRIAKEL--GISKHEANRCLYRLLESDAVSCE 52 (183)
T ss_pred hHHHHHHHHHHhcCCC-CcHHHHHHHh--CccHHHHHHHHHHHhhcCcEecC
Confidence 3578999999999966 9999999999 99999999999999999999655
No 131
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=90.30 E-value=1.4 Score=38.16 Aligned_cols=52 Identities=25% Similarity=0.270 Sum_probs=46.0
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI 72 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV 72 (233)
..||.....++.+|...+. |.+.+|.+.. |... +.+|+.|.++|||++...-
T Consensus 86 ~~LS~aaLEtLaiIay~qP--iTr~eI~~ir--Gv~~---~~ii~~L~~~gLI~e~gr~ 137 (188)
T PRK00135 86 QSLSQAALEVLAIIAYKQP--ITRIEIDEIR--GVNS---DGALQTLLAKGLIKEVGRK 137 (188)
T ss_pred CCCCHHHHHHHHHHHHcCC--cCHHHHHHHH--CCCH---HHHHHHHHHCCCeEEcCcC
Confidence 4799999999999988875 9999999999 8886 8999999999999986433
No 132
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=90.20 E-value=0.64 Score=41.63 Aligned_cols=44 Identities=18% Similarity=0.247 Sum_probs=37.8
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.|++++... +.++..+||.+.+ +||.+++.|.|+.|++.|++..
T Consensus 29 ~IL~~~~~~-~~~~tl~eIa~~l--glpkStv~RlL~tL~~~G~l~~ 72 (271)
T PRK10163 29 AILQYLEKS-GGSSSVSDISLNL--DLPLSTTFRLLKVLQAADFVYQ 72 (271)
T ss_pred HHHHHHHhC-CCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence 466666554 3578899999999 9999999999999999999955
No 133
>PRK11569 transcriptional repressor IclR; Provisional
Probab=90.19 E-value=0.89 Score=40.74 Aligned_cols=44 Identities=9% Similarity=0.347 Sum_probs=37.5
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.|++++.+ .+.++..+||.+.+ +||..++.|.|..|++.|++..
T Consensus 32 ~IL~~l~~-~~~~~~lseia~~l--glpksTv~RlL~tL~~~G~l~~ 75 (274)
T PRK11569 32 KLLEWIAE-SNGSVALTELAQQA--GLPNSTTHRLLTTMQQQGFVRQ 75 (274)
T ss_pred HHHHHHHh-CCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence 34555544 46779999999999 9999999999999999999964
No 134
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=90.14 E-value=3.4 Score=36.88 Aligned_cols=118 Identities=9% Similarity=0.151 Sum_probs=80.4
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCccc
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYS 98 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~ 98 (233)
-.+.|++++.+.|. +...||...+ +.+..+++|=|..||++|+++++----.. .+ .+..+ ++-.
T Consensus 6 R~~~Il~~l~~~g~--v~v~eLa~~~--~VS~~TIRRDL~~Le~~g~l~R~hGGa~~-------~~-~~~~~----~~~~ 69 (253)
T COG1349 6 RHQKILELLKEKGK--VSVEELAELF--GVSEMTIRRDLNELEEQGLLLRVHGGAVL-------PD-SESEY----PFSE 69 (253)
T ss_pred HHHHHHHHHHHcCc--EEHHHHHHHh--CCCHHHHHHhHHHHHHCCcEEEEeCCEec-------CC-Ccccc----cHHH
Confidence 45689999999999 9999999999 99999999999999999999764311100 00 00000 3333
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHhC-CcccccCHHHHHHHH
Q 026766 99 EGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSG-AFKVDLTKQQIEEIV 152 (233)
Q Consensus 99 d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~~-i~~~~Ls~~di~~il 152 (233)
......+-=..+-+....+|... ...|..++.++|.... ++=+.-+..-+..+.
T Consensus 70 r~~~~~~eK~~IA~~Aa~lI~~g~~ifld~GTT~~~la~~L~~~~~ltviTNsl~ia~~l~ 130 (253)
T COG1349 70 RKALNTEEKRAIAKAAATLIEDGDTIFLDAGTTTLALARALPDDNNLTVITNSLNIAAALL 130 (253)
T ss_pred HHHhhHHHHHHHHHHHHhhCCCCCEEEECCCcHHHHHHHHhCcCCCeEEEeCCHHHHHHHH
Confidence 44555555555666666677642 5789999999999665 554555555444443
No 135
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=90.12 E-value=3.5 Score=37.13 Aligned_cols=119 Identities=12% Similarity=0.150 Sum_probs=79.8
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc-ccCCCcccCCcc
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF-EPSKEISGGAWY 97 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l-ePs~eiTGG~wy 97 (233)
-...|+++|.+.|. +...||.+.+ +.+..+++|=|..||+.|+++++. .+. + +.+. .|..+. ++.
T Consensus 18 R~~~Il~~L~~~~~--vtv~eLa~~l--~VS~~TIRRDL~~Le~~G~l~r~~----GGa-~--~~~~~~~~~~~---~~~ 83 (269)
T PRK09802 18 RREQIIQRLRQQGS--VQVNDLSALY--GVSTVTIRNDLAFLEKQGIAVRAY----GGA-L--ICDSTTPSVEP---SVE 83 (269)
T ss_pred HHHHHHHHHHHcCC--EeHHHHHHHH--CCCHHHHHHHHHHHHhCCCeEEEe----CCE-E--ecCcCCCccCC---CHH
Confidence 45678889999888 9999999999 999999999999999999998543 121 1 1110 011111 122
Q ss_pred cCCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHh-CCcccccCHHHHHHH
Q 026766 98 SEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTKQQIEEI 151 (233)
Q Consensus 98 ~d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~-~i~~~~Ls~~di~~i 151 (233)
.-...+.+.-..|-+.+..||... +..|+-+++++|... +++=+.=+..-+..+
T Consensus 84 ~r~~~~~~~K~~IA~~Aa~~I~dgd~Ifld~GtT~~~la~~L~~~~~ltVvTnsl~ia~~l 144 (269)
T PRK09802 84 DKSALNTAMKRSVAKAAVELIQPGHRVILDSGTTTFEIARLMRKHTDVIAMTNGMNVANAL 144 (269)
T ss_pred HHHHhCHHHHHHHHHHHHhhCCCCCEEEECCchHHHHHHHhcCcCCCeEEEeCCHHHHHHH
Confidence 122345566677777788888753 578899999999654 454445454444433
No 136
>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=90.12 E-value=1.2 Score=29.21 Aligned_cols=41 Identities=17% Similarity=0.368 Sum_probs=34.5
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
|++.|+.++.++. .|+..++|.+.+ +++.+++.+.++.+.+
T Consensus 1 l~~~e~~i~~~~~----~~~s~~eia~~l--~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 1 LTPREREVLRLLA----EGKTNKEIADIL--GISEKTVKTHLRNIMR 41 (57)
T ss_pred CCHHHHHHHHHHH----cCCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence 5777888887763 579999999999 9999999999988754
No 137
>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=89.97 E-value=1.2 Score=34.85 Aligned_cols=54 Identities=19% Similarity=0.193 Sum_probs=44.0
Q ss_pred CCCCChHHHHHHHHHHh------hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 13 SDSLTDHERLIYDVIRS------KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~------aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
..+|+.-|..||-.|-. ...+-|....|...| +++.+.|+++++.|+++|+|..
T Consensus 27 ~~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~t--g~~~~~V~~al~~Li~~~vI~~ 86 (100)
T PF04492_consen 27 RADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMT--GLSRDHVSKALNELIRRGVIIR 86 (100)
T ss_pred hccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEe
Confidence 35788877777666652 345569999999999 9999999999999999999954
No 138
>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=89.84 E-value=0.67 Score=40.67 Aligned_cols=44 Identities=7% Similarity=0.124 Sum_probs=37.4
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.|++++.+ .+.++..+||.+++ +||.+++.|.|+.|++.|++..
T Consensus 13 ~IL~~l~~-~~~~~~l~eia~~l--glpksT~~RlL~tL~~~G~l~~ 56 (248)
T TIGR02431 13 AVIEAFGA-ERPRLTLTDVAEAT--GLTRAAARRFLLTLVELGYVTS 56 (248)
T ss_pred HHHHHHhc-CCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEe
Confidence 35555544 35789999999999 9999999999999999999964
No 139
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=89.60 E-value=0.9 Score=40.34 Aligned_cols=54 Identities=11% Similarity=0.109 Sum_probs=44.8
Q ss_pred CCCCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 4 RKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 4 ~~~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
|+-+...+....||+-|+.|+.+|.+ |...++|.+++ ++..++|.+.++.+-+|
T Consensus 132 ~~~~~~~~~~~~LS~RE~eVL~Lia~----G~SnkEIA~~L--~IS~~TVk~hvs~I~~K 185 (217)
T PRK13719 132 RGLSTNLEAKNKVTKYQNDVFILYSF----GFSHEYIAQLL--NITVGSSKNKISEILKF 185 (217)
T ss_pred hcccchhhccCCCCHHHHHHHHHHHC----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 34444456667899999999999976 79999999999 99999999888877654
No 140
>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=89.47 E-value=2.7 Score=31.19 Aligned_cols=51 Identities=10% Similarity=0.233 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
.|+..|.++ ..+ |++ .+...+|-.+| +++.+++...|..|.++|+|.+--.
T Consensus 3 klt~~~~IL-~~l--s~~-c~TLeeL~ekT--gi~k~~LlV~LsrL~k~GiI~Rkw~ 53 (72)
T PF05584_consen 3 KLTVTQKIL-IIL--SKR-CCTLEELEEKT--GISKNTLLVYLSRLAKRGIIERKWR 53 (72)
T ss_pred hhhHHHHHH-HHH--Hhc-cCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeeeeE
Confidence 455555332 222 333 89999999999 9999999999999999999988543
No 141
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=89.40 E-value=1.5 Score=31.49 Aligned_cols=49 Identities=10% Similarity=0.211 Sum_probs=41.1
Q ss_pred HHHHHHHHHHhhhCCC--CCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 108 KVVKSQCLKQIIKLKV--ATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 108 ~~l~~~~~~~i~~~~~--~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
+...+.++.+|..++. .|+.||++-+ .++...|.++|.+|.-+|.|+..
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~l--------gl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNL--------GLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEec
Confidence 3567889999998877 8999988755 37778999999999999999874
No 142
>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=89.21 E-value=2.2 Score=32.75 Aligned_cols=54 Identities=13% Similarity=0.215 Sum_probs=46.1
Q ss_pred HHHHHHHhhh-CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026766 111 KSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN 167 (233)
Q Consensus 111 ~~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~ 167 (233)
|..++++|.. ...+|++||++.+++.+. .++..-|-..|+.|+=.|.|.++...
T Consensus 3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~---~i~~~TVYR~L~~L~~~Gli~~~~~~ 57 (116)
T cd07153 3 RLAILEVLLESDGHLTAEEIYERLRKKGP---SISLATVYRTLELLEEAGLVREIELG 57 (116)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhcCC---CCCHHHHHHHHHHHHhCCCEEEEEeC
Confidence 5678888876 457999999999998862 58889999999999999999998754
No 143
>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=89.11 E-value=1.4 Score=31.30 Aligned_cols=44 Identities=20% Similarity=0.288 Sum_probs=37.0
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
..|+..+-..|. ...++|.+.+ +|+.++|.++|-.|.+.+++.=
T Consensus 16 ~~V~~~Ll~~G~--ltl~~i~~~t--~l~~~~Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 16 AKVGEVLLSRGR--LTLREIVRRT--GLSPKQVKKALVVLIQHNLVQY 59 (62)
T ss_dssp HHHHHHHHHC-S--EEHHHHHHHH--T--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHcCC--cCHHHHHHHh--CCCHHHHHHHHHHHHHcCCeee
Confidence 468888888887 8999999999 9999999999999999999853
No 144
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=89.07 E-value=1.3 Score=36.75 Aligned_cols=52 Identities=12% Similarity=0.165 Sum_probs=40.3
Q ss_pred HHHHHHHHHhh--CCC-cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 20 ERLIYDVIRSK--QDM-GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 20 e~lVy~~I~~a--G~~-GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
+..|--++.=| +.. -+..++|..+. |+++.-|.|+|..|.+.|||++++-.+
T Consensus 8 ~yal~~L~~LA~~~~~~~~s~~~IA~~~--~is~~~L~kil~~L~kaGlV~S~rG~~ 62 (150)
T COG1959 8 EYALRALLYLALLPGGGPVSSAEIAERQ--GISPSYLEKILSKLRKAGLVKSVRGKG 62 (150)
T ss_pred hHHHHHHHHHHhCCCCCcccHHHHHHHh--CcCHHHHHHHHHHHHHcCCEEeecCCC
Confidence 33444444433 333 36799999999 999999999999999999999988755
No 145
>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=88.87 E-value=0.4 Score=35.63 Aligned_cols=53 Identities=11% Similarity=0.125 Sum_probs=45.3
Q ss_pred CCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026766 10 NAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI 66 (233)
Q Consensus 10 ~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI 66 (233)
++.+..|++..+.+|.+-+. .+|+..++|...+ +++.++|...++.+++.|..
T Consensus 10 ~~~l~~l~~~~r~af~L~R~--~eGlS~kEIAe~L--GIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 10 AERLTWVDSLAEAAAALARE--EAGKTASEIAEEL--GRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHHhcCCHHHHHHHHHHHH--HcCCCHHHHHHHH--CcCHHHHHHHHhcCcccchH
Confidence 45677899999999988743 4679999999999 99999999999999887754
No 146
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=88.81 E-value=1.1 Score=39.77 Aligned_cols=46 Identities=13% Similarity=0.222 Sum_probs=38.2
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
.|+.++.+. ..++..+||.+++ +++..++.|.|+.|++.|+|....
T Consensus 15 ~iL~~l~~~-~~~ls~~eia~~l--gl~kstv~RlL~tL~~~g~v~~~~ 60 (263)
T PRK09834 15 MVLRALNRL-DGGATVGLLAELT--GLHRTTVRRLLETLQEEGYVRRSA 60 (263)
T ss_pred HHHHHHHhc-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEec
Confidence 455566543 4469999999999 999999999999999999997643
No 147
>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=88.49 E-value=0.96 Score=34.53 Aligned_cols=49 Identities=12% Similarity=0.311 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHhhh----CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026766 107 IKVVKSQCLKQIIK----LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME 163 (233)
Q Consensus 107 I~~l~~~~~~~i~~----~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~ 163 (233)
...+++.|+.||+. ...+++++|++-+ + +++++|+..|+.|+-+|.|..
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l---~-----~~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL---G-----MSENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHS---T-----S-HHHHHHHHHHHHHTTSEEE
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHh---C-----cCHHHHHHHHHHHHhCCeEec
Confidence 57889999999987 3468899998766 3 789999999999999999975
No 148
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=88.33 E-value=2.9 Score=26.89 Aligned_cols=46 Identities=13% Similarity=0.219 Sum_probs=38.5
Q ss_pred HHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 112 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 112 ~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
..+++++.+.+.+|..+|++.+ .++..-+...|+.|+-+|.|+...
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l--------~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELL--------GVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEEee
Confidence 3466777777889999999987 478889999999999999998754
No 149
>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=88.19 E-value=2.7 Score=32.76 Aligned_cols=57 Identities=14% Similarity=0.160 Sum_probs=47.2
Q ss_pred HHHHHHHHHHhhhC-CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026766 108 KVVKSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN 167 (233)
Q Consensus 108 ~~l~~~~~~~i~~~-~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~ 167 (233)
..-|.+++++|.+. ..+|++||++.+++.+ ..++..=|-..|+.|+=.|.|.++...
T Consensus 7 T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~---~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 7 TPQRLAILELLKESPEHLTAEEIYDKLRKKG---PRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHHHHHHSSSEEHHHHHHHHHHTT---TT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred CHHHHHHHHHHHcCCCCCCHHHHHHHhhhcc---CCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 35678899999864 5899999999999877 357889999999999999999998754
No 150
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=88.04 E-value=1 Score=39.80 Aligned_cols=43 Identities=7% Similarity=0.217 Sum_probs=36.8
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.|++++.+ ..++..+||.+++ +||.+++.|.|+.|++.|++..
T Consensus 18 ~IL~~l~~--~~~l~l~eia~~l--gl~kstv~Rll~tL~~~G~l~~ 60 (257)
T PRK15090 18 GILQALGE--EREIGITELSQRV--MMSKSTVYRFLQTMKTLGYVAQ 60 (257)
T ss_pred HHHHHhhc--CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence 45666644 3478999999999 9999999999999999999966
No 151
>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=87.94 E-value=1.5 Score=27.74 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=36.9
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
+..|++.++.++.+... .|...++|..++ |++.++|.+.++....
T Consensus 8 ~~~l~~~~~~~~~~~~~---~~~~~~~ia~~~--~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 8 LDKLPEREREVILLRFG---EGLSYEEIAEIL--GISRSTVRQRLHRALK 52 (55)
T ss_pred HHhCCHHHHHHHHHHHh---cCCCHHHHHHHH--CcCHHHHHHHHHHHHH
Confidence 45688988888766643 678999999999 9999999999887643
No 152
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=87.33 E-value=2.4 Score=36.31 Aligned_cols=50 Identities=14% Similarity=0.207 Sum_probs=39.2
Q ss_pred CCChHHHHHHHHHHhhCCCc--------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026766 15 SLTDHERLIYDVIRSKQDMG--------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI 66 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~G--------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI 66 (233)
..+..+++..-+++.+...| +.+++|..-+ |++..+|+|+|+.|+++|++
T Consensus 146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~l--G~tretvsR~l~~L~~~gl~ 203 (236)
T PRK09392 146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYL--GMTPENLSRAFAALASHGVH 203 (236)
T ss_pred cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHh--CCChhHHHHHHHHHHhCCeE
Confidence 45677877776665544333 4478999999 99999999999999999963
No 153
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=87.32 E-value=14 Score=30.02 Aligned_cols=112 Identities=16% Similarity=0.221 Sum_probs=73.7
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhh--cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR--VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS 92 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~--~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT 92 (233)
.+++-|..|.++|=+.|. ...+||-..++ .....++|+-.|..|.+||+|.+.|. .++=.| .|
T Consensus 3 ~Is~aE~eVM~ilW~~~~--~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kd---gr~~~y-----~p----- 67 (123)
T COG3682 3 SISAAEWEVMEILWSRGP--ATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKD---GRAFRY-----SP----- 67 (123)
T ss_pred cccHHHHHHHHHHHHcCC--ccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhc---CCeeee-----ec-----
Confidence 578889999999999997 88888888872 26889999999999999999976553 222222 00
Q ss_pred cCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026766 93 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL 155 (233)
Q Consensus 93 GG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L 155 (233)
-++ -.+.++...+-+++-+...+. ..=|..|+.+.. |+.+||++|-+.|
T Consensus 68 ---L~~----~~~~~~~~~~~~l~k~~d~~~--~~lv~~F~~~~~-----l~~~eie~L~~il 116 (123)
T COG3682 68 ---LLT----RDQYVAGESQDLLDKICDGGL--ASLVAHFAEKEK-----LTADEIEALKAIL 116 (123)
T ss_pred ---ccC----HHHHHHHHHHHHHHHHHcccc--hHHHHHHHHhcc-----CCHHHHHHHHHHH
Confidence 111 123333344334433333333 455788888655 6777777665554
No 154
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=87.30 E-value=1.9 Score=39.14 Aligned_cols=55 Identities=20% Similarity=0.363 Sum_probs=43.2
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc--CCCeeeE
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH--SKGKKHL 80 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~--~~~rK~Y 80 (233)
..|++++..+|. +-..+|...+ +|||++++--+|.||+.|||.. +.++ ...+|+-
T Consensus 26 v~Il~lL~~k~p--lNvneiAe~l--gLpqst~s~~ik~Le~aGlirT-~t~karkG~QKiC 82 (308)
T COG4189 26 VAILQLLHRKGP--LNVNEIAEAL--GLPQSTMSANIKVLEKAGLIRT-ETVKARKGSQKIC 82 (308)
T ss_pred HHHHHHHHHhCC--CCHHHHHHHh--CCchhhhhhhHHHHHhcCceee-eeeccccCceeEe
Confidence 356777777775 7789999999 9999999999999999999975 3333 2345554
No 155
>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=87.19 E-value=1.3 Score=30.97 Aligned_cols=35 Identities=14% Similarity=0.333 Sum_probs=30.1
Q ss_pred cc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 34 GI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 34 GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
=+ ..++|.++. +.+.+++.++|+.|++.|+|...+
T Consensus 23 ~lps~~~la~~~--~vsr~tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 23 RLPSERELAERY--GVSRTTVREALRRLEAEGLIERRP 58 (64)
T ss_dssp BE--HHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEET
T ss_pred EeCCHHHHHHHh--ccCCcHHHHHHHHHHHCCcEEEEC
Confidence 46 789999999 999999999999999999997754
No 156
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=87.19 E-value=7.9 Score=30.50 Aligned_cols=70 Identities=14% Similarity=0.262 Sum_probs=49.7
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
++++++.+.+ |++.++| ..-|++||+.+... . .|.+.| |.+-|+.|+ .
T Consensus 1 m~IgevA~~~--gvs~~tl----RyYe~~GLl~p~~~-~-~gyR~Y----------------------~~~~l~~l~--~ 48 (120)
T cd04781 1 LDIAEVARQS--GLPASTL----RYYEEKGLIASIGR-R-GLRRQY----------------------DPQVLDRLA--L 48 (120)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCcC-C-CCceec----------------------CHHHHHHHH--H
Confidence 4678899999 9998876 45788999977553 2 244443 556666775 3
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhC
Q 026766 115 LKQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
..+++..++ |+++|.+++...+
T Consensus 49 I~~lr~~G~-~L~eI~~~l~~~~ 70 (120)
T cd04781 49 IALGRAAGF-SLDEIQAMLSHDG 70 (120)
T ss_pred HHHHHHcCC-CHHHHHHHHhccC
Confidence 466666654 6999999998764
No 157
>PRK09483 response regulator; Provisional
Probab=87.09 E-value=2.1 Score=34.98 Aligned_cols=46 Identities=26% Similarity=0.302 Sum_probs=40.7
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
....||+-|+.|+.++. +|...++|..++ ++..++|+..++++-.|
T Consensus 145 ~~~~Lt~rE~~vl~~~~----~G~~~~~Ia~~l--~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 145 PFASLSERELQIMLMIT----KGQKVNEISEQL--NLSPKTVNSYRYRMFSK 190 (217)
T ss_pred cccccCHHHHHHHHHHH----CCCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 45679999999999884 779999999999 99999999999888765
No 158
>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=87.09 E-value=11 Score=28.83 Aligned_cols=72 Identities=6% Similarity=0.096 Sum_probs=47.6
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+...++.+.+ |++.++| +..|++|||.+.. .-.+|-|+ ||.+-|+.|+.+
T Consensus 1 m~I~eva~~~--gvs~~tl----R~Ye~~GLl~p~~-------------------r~~~g~r~----Y~~~dv~~l~~I- 50 (95)
T cd04780 1 MRMSELSKRS--GVSVATI----KYYLREGLLPEGR-------------------RLAPNQAE----YSEAHVERLRLI- 50 (95)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCc-------------------CCCCCCee----cCHHHHHHHHHH-
Confidence 3578899999 9998765 5688899995422 22233232 666667766654
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhC
Q 026766 115 LKQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
.++++.-..++++|.+.+...|
T Consensus 51 -~~L~~~~G~~l~~I~~~l~~~~ 72 (95)
T cd04780 51 -RALQQEGGLPISQIKEVLDAIA 72 (95)
T ss_pred -HHHHHHcCCCHHHHHHHHHhcC
Confidence 4444433577999999998733
No 159
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=87.07 E-value=0.85 Score=36.14 Aligned_cols=70 Identities=23% Similarity=0.389 Sum_probs=57.4
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccC
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPS 88 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs 88 (233)
-+|-..|.+||+++-+.|. ||-.++|..++ ++..+++.-+++.|-.+||+++ .-|+ ++=-=|+++.-.|.
T Consensus 17 ~glk~~eI~IY~lLve~~~-~mri~ei~rEl--~is~rtvr~~v~~l~rrGll~r-elvq-kgWvGYiya~~~P~ 86 (113)
T COG5625 17 IGLKKNEIRIYSLLVEKGR-GMRIREIQREL--GISERTVRAAVAVLLRRGLLAR-ELVQ-KGWVGYIYATTPPP 86 (113)
T ss_pred cCCCcchhhhhhHHHHhcC-CchHHHHHHHH--hHHHHHHHHHHHHHHHhhHHHH-HHHh-ccceeeEecCCCCc
Confidence 3567788999999988765 89999999999 9999999999999999999985 3444 45556776665554
No 160
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=86.95 E-value=4.4 Score=30.55 Aligned_cols=45 Identities=11% Similarity=0.142 Sum_probs=34.8
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 113 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 113 ~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
++.+||..++.+++.+|...+ ..+..=|+..|+.|+-=|+||++.
T Consensus 6 qlRd~l~~~gr~s~~~Ls~~~--------~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 6 QVRDLLALRGRMEAAQISQTL--------NTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHHcCcccHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEeec
Confidence 455666666666666666554 467888999999999999999985
No 161
>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=86.67 E-value=3.4 Score=30.14 Aligned_cols=55 Identities=15% Similarity=0.268 Sum_probs=45.0
Q ss_pred ChHHHHHHHHHHhhCC-CcccHHHHHHHhhc----CCCh----HHHHHHHHHHHhCCCceeeec
Q 026766 17 TDHERLIYDVIRSKQD-MGIWTRDMKRELRV----NLPD----NIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~-~GIw~~dik~~t~~----~l~~----~~v~k~LK~Le~k~lIK~vks 71 (233)
++-..+|...|.+.+. +|.....|++-... +++. ..|.++||.+.++|.+..++.
T Consensus 3 P~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg 66 (77)
T PF00538_consen 3 PPYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKG 66 (77)
T ss_dssp SCHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSC
T ss_pred CCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeecc
Confidence 4567899999998666 89999999987622 3444 689999999999999998884
No 162
>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=86.63 E-value=8.9 Score=31.94 Aligned_cols=108 Identities=21% Similarity=0.182 Sum_probs=70.8
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccC
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSE 99 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d 99 (233)
+..|++++.. .|+--...||-..++..++.+.|.|+|..|.++|.|.. |. ....+||..-.-.. ...+.. ..
T Consensus 3 e~~Il~y~~~-qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~-K~--~GKqkiY~~~Q~~~-~~~s~e---el 74 (169)
T PF07106_consen 3 EDAILEYMKE-QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVE-KE--YGKQKIYFANQDEL-EVPSPE---EL 74 (169)
T ss_pred HHHHHHHHHH-cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeee-ee--ecceEEEeeCcccc-CCCCch---hH
Confidence 4578888765 47778889999888667999999999999999999977 33 34668885432221 112211 02
Q ss_pred CCCCHHHHHHHHHHHHHHhh-----------hCCCCCHHHHHHHHHHh
Q 026766 100 GSLDTEFIKVVKSQCLKQII-----------KLKVATLEGISDSIKRS 136 (233)
Q Consensus 100 ~e~D~efI~~l~~~~~~~i~-----------~~~~~T~~~I~~~I~~~ 136 (233)
.++|.+ |..|+..+-..=. -.+.||.+++..-|.+.
T Consensus 75 ~~ld~e-i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l 121 (169)
T PF07106_consen 75 AELDAE-IKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEEL 121 (169)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence 345555 6666665432111 13678888888777655
No 163
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=86.46 E-value=12 Score=29.97 Aligned_cols=70 Identities=9% Similarity=0.171 Sum_probs=46.0
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+...++.+.+ |++.++| +.-|+.|||++.+.-. .+.+. ||.+-|+.|+.
T Consensus 1 m~IgE~A~~~--gvs~~TL----RyYE~~GLl~p~r~~~-~gyR~----------------------Y~~~~~~~l~~-- 49 (133)
T cd04787 1 MKVKELANAA--GVTPDTV----RFYTRIGLLRPTRDPV-NGYRL----------------------YSEKDLSRLRF-- 49 (133)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCcCCC-CCeee----------------------CCHHHHHHHHH--
Confidence 4678899999 9999877 4569999997642211 23333 35555555533
Q ss_pred HHHhhhCCCCCHHHHHHHHHHh
Q 026766 115 LKQIIKLKVATLEGISDSIKRS 136 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~ 136 (233)
..++++. ..|++||.+++...
T Consensus 50 I~~lr~~-G~sL~eI~~~l~~~ 70 (133)
T cd04787 50 ILSARQL-GFSLKDIKEILSHA 70 (133)
T ss_pred HHHHHHc-CCCHHHHHHHHhhh
Confidence 3334455 46799999999854
No 164
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=86.35 E-value=1.6 Score=40.75 Aligned_cols=51 Identities=14% Similarity=0.353 Sum_probs=44.4
Q ss_pred CCCChHHHHHHH-----HHHhhCCCcccHHHHHHH--hhcCCChHHHHHHHHHHHhCCCcee
Q 026766 14 DSLTDHERLIYD-----VIRSKQDMGIWTRDMKRE--LRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 14 ~~L~~~e~lVy~-----~I~~aG~~GIw~~dik~~--t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
+.|++-++.|+. +|..++. +-.++|.++ . ++++.++++-++.||+.|+|+.
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~~~p--v~s~~l~~~~~l--~~S~aTIR~dm~~Le~~G~l~~ 59 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIATGEP--VGSKTLSKRYGL--GVSSATIRNDMADLEELGLLEK 59 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCC--cCHHHHHHHhCC--CCChHHHHHHHHHHHhCCCcCC
Confidence 467887777876 7888777 999999987 7 9999999999999999999975
No 165
>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=86.29 E-value=2.1 Score=30.74 Aligned_cols=46 Identities=13% Similarity=0.394 Sum_probs=36.6
Q ss_pred HHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCcee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.|+.++.+++. -+-.+.|.+.+ |.++...+|.+.|+.||..|+++.
T Consensus 2 ~IL~~L~~~~~-P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~ 50 (66)
T PF08461_consen 2 FILRILAESDK-PLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRK 50 (66)
T ss_pred HHHHHHHHcCC-CCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccc
Confidence 46778877653 58888888887 336677999999999999998874
No 166
>PRK09462 fur ferric uptake regulator; Provisional
Probab=86.20 E-value=3.8 Score=33.37 Aligned_cols=55 Identities=5% Similarity=0.088 Sum_probs=47.0
Q ss_pred HHHHHHHHHhhhC--CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 109 VVKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 109 ~l~~~~~~~i~~~--~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
.-|..++++|.+. ..+|++||++.+++.+. .++..-|-..|+.|+=.|.|.++..
T Consensus 17 ~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~---~i~~aTVYR~L~~L~e~Gli~~~~~ 73 (148)
T PRK09462 17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGE---EIGLATVYRVLNQFDDAGIVTRHNF 73 (148)
T ss_pred HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHCCCEEEEEc
Confidence 3467789999853 58999999999998883 5788999999999999999999864
No 167
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=86.03 E-value=2 Score=36.01 Aligned_cols=45 Identities=18% Similarity=0.258 Sum_probs=40.1
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
...||+-|+.|+.++. +|...++|.+++ +++.++|+..++.+-.|
T Consensus 148 ~~~Lt~rE~evl~~~~----~G~s~~eIA~~l--~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 148 DKRLSPKESEVLRLFA----EGFLVTEIAKKL--NRSIKTISSQKKSAMMK 192 (216)
T ss_pred cccCCHHHHHHHHHHH----CCCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence 3569999999999996 789999999999 99999999988887765
No 168
>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=85.56 E-value=3.9 Score=26.72 Aligned_cols=47 Identities=9% Similarity=0.180 Sum_probs=37.8
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEE
Q 026766 108 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIM 162 (233)
Q Consensus 108 ~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie 162 (233)
+..+..++.+|...+..|..||++-+ .+|..-|...|+-|+=+|.|+
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~--------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKL--------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHH--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCcCcC
Confidence 45677889999999999999998865 378889999999999999875
No 169
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=85.42 E-value=1.2 Score=39.38 Aligned_cols=48 Identities=21% Similarity=0.419 Sum_probs=38.5
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee-eeccc-CCCeeeEEeec
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE-VVNIH-SKGKKHLMAVE 84 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~-vksV~-~~~rK~Yml~~ 84 (233)
=...+|...+ |+.|..|-++|+.||..|||-+ +--+. .+.||+|+...
T Consensus 29 ~yvsEiS~~l--gvsqkAVl~HL~~LE~AGlveS~ie~~~Rg~~rKYY~Is~ 78 (217)
T COG1777 29 CYVSEISREL--GVSQKAVLKHLRILERAGLVESRIEKIPRGRPRKYYMISR 78 (217)
T ss_pred hHHHHHHhhc--CcCHHHHHHHHHHHHHcCCchhhccccccCCCcceeeccC
Confidence 4567788888 9999999999999999999987 33332 46789997754
No 170
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=85.24 E-value=2.1 Score=35.00 Aligned_cols=42 Identities=14% Similarity=0.247 Sum_probs=37.7
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCce
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIK 67 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK 67 (233)
.|..++++.|. ++.+++...| +++-+++.+.++.|++.|-|-
T Consensus 16 rIvElVRe~GR--iTi~ql~~~T--GasR~Tvk~~lreLVa~G~l~ 57 (127)
T PF06163_consen 16 RIVELVREHGR--ITIKQLVAKT--GASRNTVKRYLRELVARGDLY 57 (127)
T ss_pred HHHHHHHHcCC--ccHHHHHHHH--CCCHHHHHHHHHHHHHcCCeE
Confidence 46667778888 9999999999 999999999999999999873
No 171
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=84.48 E-value=3.7 Score=37.96 Aligned_cols=58 Identities=19% Similarity=0.165 Sum_probs=47.2
Q ss_pred CCCCCChHHHHHHHHHHhhCC---CcccHHHHHHH-------hhcCCCh---HHHHHHHHHHHhCCCceeeec
Q 026766 12 PSDSLTDHERLIYDVIRSKQD---MGIWTRDMKRE-------LRVNLPD---NIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~---~GIw~~dik~~-------t~~~l~~---~~v~k~LK~Le~k~lIK~vks 71 (233)
.+.+||..|++++..|...+. ..+...++-++ . ++.+ +.+...|..|+..|||....+
T Consensus 290 ~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~--~~~~~~~~~~~~~l~~L~~~glI~~~~~ 360 (394)
T PRK00411 290 VLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEEL--GYEPRTHTRFYEYINKLDMLGIINTRYS 360 (394)
T ss_pred HHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHc--CCCcCcHHHHHHHHHHHHhcCCeEEEEe
Confidence 467899999999998876653 56888888855 5 6654 999999999999999987654
No 172
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=84.26 E-value=0.74 Score=39.34 Aligned_cols=72 Identities=8% Similarity=0.106 Sum_probs=55.5
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC----------CeeeEEeeccccC
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK----------GKKHLMAVEFEPS 88 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~----------~rK~Yml~~lePs 88 (233)
-+..|+.++...|- +...+|...+ +.+..+++|=|..|++.|++.+..++..+ +-.+=-+-+++|.
T Consensus 8 R~~~Il~~l~~~~~--~~~~~La~~~--~vS~~TiRRDl~~L~~~g~~~r~~~~~~~~~~~~~~~~~~~~vD~i~eie~g 83 (185)
T PRK04424 8 RQKALQELIEENPF--ITDEELAEKF--GVSIQTIRLDRMELGIPELRERIKHVAEKNYDKVKSLPEEEVVGELIDLELG 83 (185)
T ss_pred HHHHHHHHHHHCCC--EEHHHHHHHH--CcCHHHHHHHHHHHhcchHHHHHHHHHHHhHHhhhcCCcccceeeEEEecCC
Confidence 56789999999888 9999999999 99999999999999999999887664321 1222245566666
Q ss_pred CCcccC
Q 026766 89 KEISGG 94 (233)
Q Consensus 89 ~eiTGG 94 (233)
..++|=
T Consensus 84 ~~a~~~ 89 (185)
T PRK04424 84 RSAISI 89 (185)
T ss_pred cEEEEE
Confidence 555543
No 173
>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=84.01 E-value=4.1 Score=28.58 Aligned_cols=50 Identities=12% Similarity=0.204 Sum_probs=41.7
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 109 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 109 ~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
.....++.+|-..+..|++||++.+ .++...|..+|+.|+-.|.|+....
T Consensus 8 ~~E~~vy~~Ll~~~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~ 57 (68)
T PF01978_consen 8 ENEAKVYLALLKNGPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEG 57 (68)
T ss_dssp HHHHHHHHHHHHHCHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 3445677888788899999998865 3888999999999999999998763
No 174
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=83.98 E-value=1.1 Score=40.41 Aligned_cols=55 Identities=18% Similarity=0.236 Sum_probs=47.9
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
.-.|...|+++...++.++- |.++|...-. ++.++++.+++..||+||++-+++.
T Consensus 11 ~~~m~~~e~l~~laae~hki--iTirdvae~~--ev~~n~lr~lasrLekkG~LeRi~r 65 (269)
T COG5340 11 GLSMRESELLSHLAAEGHKI--ITIRDVAETL--EVAPNTLRELASRLEKKGWLERILR 65 (269)
T ss_pred hhhHHHHHHHHHHHHHhCce--EEeHHhhhhc--cCCHHHHHHHHhhhhhcchhhhhcC
Confidence 34567778888888887777 9999999999 9999999999999999999988753
No 175
>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=83.73 E-value=5.2 Score=27.79 Aligned_cols=46 Identities=22% Similarity=0.316 Sum_probs=40.1
Q ss_pred CChHHHHHHHHHHhhC----CCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 16 LTDHERLIYDVIRSKQ----DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG----~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
||+.|+.++..--+.| .+++...||.+++ |++..+++..|+.-|+|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~l--gis~st~~~~LRrae~k 50 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEEL--GISKSTVSEHLRRAERK 50 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 6888888888887777 7889999999999 99999999999887754
No 176
>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=83.59 E-value=2.8 Score=28.59 Aligned_cols=44 Identities=20% Similarity=0.414 Sum_probs=36.8
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
..||+.|..|+.++.. |...++|.... +++.++|...++.+-.|
T Consensus 2 ~~LT~~E~~vl~~l~~----G~~~~eIA~~l--~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 2 PSLTERELEVLRLLAQ----GMSNKEIAEEL--GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp GSS-HHHHHHHHHHHT----TS-HHHHHHHH--TSHHHHHHHHHHHHHHH
T ss_pred CccCHHHHHHHHHHHh----cCCcchhHHhc--CcchhhHHHHHHHHHHH
Confidence 5799999999999875 47799999999 99999999999888754
No 177
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=83.32 E-value=4.5 Score=34.02 Aligned_cols=56 Identities=14% Similarity=0.158 Sum_probs=47.7
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
.+|+.=..|++++.+. ..-+...+|-.++ ++++...+|-|.|+.|++.|||.++..
T Consensus 23 R~T~qR~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~ 81 (169)
T PRK11639 23 RLTPQRLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVES 81 (169)
T ss_pred CCCHHHHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEec
Confidence 4688888999999987 4579999998887 337889999999999999999988753
No 178
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=83.05 E-value=3.8 Score=32.65 Aligned_cols=67 Identities=19% Similarity=0.155 Sum_probs=45.8
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhc---CCChHHHHHHHHHHHhCCCceeeecccC--CCeeeEEeec
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRV---NLPDNIVTKSIKSLQNKSLIKEVVNIHS--KGKKHLMAVE 84 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~---~l~~~~v~k~LK~Le~k~lIK~vksV~~--~~rK~Yml~~ 84 (233)
.-+..|+.++...-..|-....--..... ..+..+|-.+|+.||+.|||....-... +.||+|-+.+
T Consensus 9 ~l~~~iL~~L~~~~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe 80 (138)
T COG1695 9 SLELLILSLLSEKPSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTE 80 (138)
T ss_pred hHHHHHHHHHhcCCchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECH
Confidence 35677888887776666544333333211 3678899999999999999988654432 4589996654
No 179
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=82.91 E-value=4.7 Score=39.91 Aligned_cols=60 Identities=18% Similarity=0.185 Sum_probs=47.5
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV 83 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~ 83 (233)
...|..|+..+.+.+ ..+...+|.+++ +++...|..+++.|+++|+|+...... ..|.|.
T Consensus 5 ~~~e~~iL~~l~~~~-~~~~~~~la~~~--~~~~~~v~~~~~~L~~kg~v~~~~~~~----~~~~LT 64 (494)
T PTZ00326 5 ELEENTILSKLESEN-EIVNSLALAESL--NIDHQKVVGAIKSLESANYITTEMKKS----NTWTLT 64 (494)
T ss_pred hHHHHHHHHHHHhcC-CCCCHHHHHHHc--CCCHHHHHHHHHHHHhCCCEEEEEEEE----EEEEEC
Confidence 456888888888743 348889999999 999999999999999999997655443 455554
No 180
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=82.46 E-value=22 Score=30.71 Aligned_cols=126 Identities=17% Similarity=0.115 Sum_probs=76.3
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC----CCceeeecccCCCeeeEEeeccccCCCcccC
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK----SLIKEVVNIHSKGKKHLMAVEFEPSKEISGG 94 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k----~lIK~vksV~~~~rK~Yml~~lePs~eiTGG 94 (233)
-...|-.+|..+|.-|+..++|.+-+ ++....|..+|..|..+ +--=++..+.. +=+++.-.++.+-..--.+
T Consensus 5 ~~~~iEA~LF~sg~pgls~~~La~~l--~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~-~y~l~tk~e~~~~v~~~~~ 81 (188)
T PRK00135 5 YKSIIEALLFVSGEEGLSLEQLAEIL--ELEPTEVQQLLEELQEKYEGDDRGLKLIEFND-VYKLVTKEENADYLQKLVK 81 (188)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHHHhhCCCCEEEEEECC-EEEEEEcHHHHHHHHHHhc
Confidence 45678888899999999999999999 99999999999999643 22222333321 2222222222222111111
Q ss_pred CcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 95 AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 95 ~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
.. ...+|....+++|. .|..++.+|-.||.+-- |++. ..+|+.|+-.|.|++.
T Consensus 82 ~~-~~~~LS~aaLEtLa-----iIay~qPiTr~eI~~ir---Gv~~--------~~ii~~L~~~gLI~e~ 134 (188)
T PRK00135 82 TP-IKQSLSQAALEVLA-----IIAYKQPITRIEIDEIR---GVNS--------DGALQTLLAKGLIKEV 134 (188)
T ss_pred cc-ccCCCCHHHHHHHH-----HHHHcCCcCHHHHHHHH---CCCH--------HHHHHHHHHCCCeEEc
Confidence 00 01244555554443 33346778888776533 4332 6789999999999875
No 181
>PHA02943 hypothetical protein; Provisional
Probab=82.43 E-value=6.5 Score=33.42 Aligned_cols=51 Identities=10% Similarity=0.190 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 107 IKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 107 I~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
|-.=...++.|| +.|..|..||++.+ .+|..+++-+|.+|.=+|+|++|+-
T Consensus 9 v~~R~~eILE~L-k~G~~TtseIAkaL--------GlS~~qa~~~LyvLErEG~VkrV~~ 59 (165)
T PHA02943 9 VHTRMIKTLRLL-ADGCKTTSRIANKL--------GVSHSMARNALYQLAKEGMVLKVEI 59 (165)
T ss_pred HHHHHHHHHHHH-hcCCccHHHHHHHH--------CCCHHHHHHHHHHHHHcCceEEEee
Confidence 333345677788 77888898988765 3889999999999999999999873
No 182
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=82.38 E-value=17 Score=27.05 Aligned_cols=72 Identities=14% Similarity=0.163 Sum_probs=46.1
Q ss_pred cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHH
Q 026766 34 GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQ 113 (233)
Q Consensus 34 GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~ 113 (233)
+...+++.+.+ +++.++|. ..|++|+|.+...-. .+.+.| +.+=|..|+.+
T Consensus 1 ~~ti~evA~~~--gvs~~tLR----~ye~~Gll~p~r~~~-~g~R~Y----------------------s~~dv~~l~~I 51 (88)
T cd01105 1 VIGIGEVSKLT--GVSPRQLR----YWEEKGLIKSIRSDG-GGQRKY----------------------SLADVDRLLVI 51 (88)
T ss_pred CcCHHHHHHHH--CcCHHHHH----HHHHCCCCCCCccCC-CCceec----------------------CHHHHHHHHHH
Confidence 35678899999 99998876 469999996432222 144444 33334444433
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHhC
Q 026766 114 CLKQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 114 ~~~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
..+++. ..|+++|.+.+...+
T Consensus 52 --~~Lr~~-G~sl~~i~~~l~~~~ 72 (88)
T cd01105 52 --KELLDE-GFTLAAAVEKLRRRR 72 (88)
T ss_pred --HHHHHC-CCCHHHHHHHHHHcc
Confidence 334454 567999999998655
No 183
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=82.26 E-value=1.3 Score=36.43 Aligned_cols=79 Identities=20% Similarity=0.254 Sum_probs=53.6
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec-ccCCCeeeEEeeccccCCCcccCCcccC
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN-IHSKGKKHLMAVEFEPSKEISGGAWYSE 99 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks-V~~~~rK~Yml~~lePs~eiTGG~wy~d 99 (233)
..|+..+-..|- +.-.||...+ +|+.+.|+|+|-.|.+.++|+..-- ..+ | -+|+||+-
T Consensus 4 ~~v~d~L~~~~~--~~dedLa~~l--~i~~n~vRkiL~~L~ed~~~~~~~~~e~~------------~----~~~~~~~~ 63 (147)
T smart00531 4 FLVLDALMRNGC--VTEEDLAELL--GIKQKQLRKILYLLYDEKLIKIDYKREKD------------P----ETKTWYRY 63 (147)
T ss_pred EeehHHHHhcCC--cCHHHHHHHh--CCCHHHHHHHHHHHHhhhcchhheeeeeC------------C----CCceEEEE
Confidence 456666666664 8999999999 9999999999999999888754321 111 1 12445543
Q ss_pred C-CCC-HHHHHHHHHHHHHHhh
Q 026766 100 G-SLD-TEFIKVVKSQCLKQII 119 (233)
Q Consensus 100 ~-e~D-~efI~~l~~~~~~~i~ 119 (233)
- -+| ..+++.|+-.+....+
T Consensus 64 yw~i~y~~~~~vik~r~~~~~~ 85 (147)
T smart00531 64 YWYINYDTLLDVVKYKLDKMRK 85 (147)
T ss_pred EEEecHHHHHHHHHHHHHHHHH
Confidence 2 455 5677777777665543
No 184
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=82.25 E-value=3.7 Score=37.50 Aligned_cols=46 Identities=17% Similarity=0.161 Sum_probs=38.8
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCC-ceee
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL-IKEV 69 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l-IK~v 69 (233)
++.|+.+|.+ +..+...+|..++ +++.++|.++|+.|++.|+ |.+.
T Consensus 6 ~~~il~~L~~--~~~~s~~~LA~~l--gvsr~tV~~~l~~L~~~G~~i~~~ 52 (319)
T PRK11886 6 MLQLLSLLAD--GDFHSGEQLGEEL--GISRAAIWKHIQTLEEWGLDIFSV 52 (319)
T ss_pred HHHHHHHHHc--CCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCceEEe
Confidence 4567777765 4668888999999 9999999999999999999 7554
No 185
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=82.09 E-value=2.9 Score=36.38 Aligned_cols=54 Identities=13% Similarity=0.286 Sum_probs=43.6
Q ss_pred HHHHHHHHhhCCCcccH--------HHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026766 21 RLIYDVIRSKQDMGIWT--------RDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM 81 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~--------~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym 81 (233)
..|++.|.+.=..|.|. ++|..+. |....+|+++|+.|++.|||.+. .++=+|+
T Consensus 12 ~qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~--~VSR~TvR~Al~~L~~eGli~r~-----~G~GTfV 73 (241)
T PRK11402 12 ATVRQRLLDDIAQGVYQAGQQIPTENELCTQY--NVSRITIRKAISDLVADGVLIRW-----QGKGTFV 73 (241)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe-----cCceeEE
Confidence 35677777766666664 7999999 99999999999999999999875 3555565
No 186
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=81.82 E-value=8.4 Score=27.14 Aligned_cols=43 Identities=16% Similarity=0.285 Sum_probs=35.8
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.++..+... ......+|...+ +++++++++.|+.|++.|+|..
T Consensus 29 ~il~~l~~~--~~~~~~~l~~~~--~~~~~~v~~hL~~L~~~glv~~ 71 (110)
T COG0640 29 EILSLLAEG--GELTVGELAEAL--GLSQSTVSHHLKVLREAGLVEL 71 (110)
T ss_pred HHHHHHHhc--CCccHHHHHHHH--CCChhHHHHHHHHHHHCCCeEE
Confidence 445555544 456789999999 9999999999999999999988
No 187
>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=81.81 E-value=4.1 Score=28.74 Aligned_cols=43 Identities=12% Similarity=0.150 Sum_probs=34.8
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
..++.++.++ -+..++|..++ ++..++|.+.|+.|++.|+.-.
T Consensus 3 ~~il~~L~~~---~~~~~eLa~~l--~vS~~tv~~~l~~L~~~g~~i~ 45 (69)
T TIGR00122 3 LRLLALLADN---PFSGEKLGEAL--GMSRTAVNKHIQTLREWGVDVL 45 (69)
T ss_pred HHHHHHHHcC---CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEE
Confidence 3455665533 26699999999 9999999999999999999644
No 188
>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=81.48 E-value=6.2 Score=28.28 Aligned_cols=38 Identities=11% Similarity=0.373 Sum_probs=28.4
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCC
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG 76 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~ 76 (233)
....|..+. +++.+++-.+|++||+.|+|.+ .|.--++
T Consensus 6 vas~iAd~~--GiTRSvIVNALRKleSaGvIes-rSlGmKG 43 (61)
T PF08222_consen 6 VASKIADRV--GITRSVIVNALRKLESAGVIES-RSLGMKG 43 (61)
T ss_dssp -HHHHHHHH--T--HHHHHHHHHHHHHTTSEEE-EETTSS-
T ss_pred hHHHHHHHh--CccHHHHHHHHHHHHhcCceee-cccCCCc
Confidence 456788899 9999999999999999999986 4544333
No 189
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=81.48 E-value=4.7 Score=32.94 Aligned_cols=47 Identities=13% Similarity=0.018 Sum_probs=37.9
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCC-----hH----HHHHHHHHHHh
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLP-----DN----IVTKSIKSLQN 62 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~-----~~----~v~k~LK~Le~ 62 (233)
..||+-|..|+.++.+..++|...++|.+.+ ... .+ .++++.++|..
T Consensus 153 ~~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l--~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 153 LTLTRYEFLLLKTLLLSPGRVFSRQQLMDIV--WEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred eecCHHHHHHHHHHHhCCCceECHHHHHHHh--cCCCCCCCccCHHHHHHHHHHHhcc
Confidence 4699999999999999999999999999999 664 33 45556666653
No 190
>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=81.29 E-value=24 Score=27.60 Aligned_cols=71 Identities=10% Similarity=0.155 Sum_probs=45.2
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+.+.++.+.+ |++.++|+ .-|++|||.+... +-+|--+|++ +-|..|+.
T Consensus 1 ~~I~eva~~~--gvs~~tLR----yYe~~GLl~p~~r------------------~~~gyR~Y~~-----~~i~~l~~-- 49 (123)
T cd04770 1 MKIGELAKAA--GVSPDTIR----YYERIGLLPPPQR------------------SENGYRLYGE-----ADLARLRF-- 49 (123)
T ss_pred CCHHHHHHHH--CcCHHHHH----HHHHCCCCCCCCC------------------CCCCCccCCH-----HHHHHHHH--
Confidence 3578899999 99998874 4999999964221 1122234443 44445533
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhC
Q 026766 115 LKQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
..++++. ..|++||.+++....
T Consensus 50 I~~lr~~-G~sl~eI~~~l~~~~ 71 (123)
T cd04770 50 IRRAQAL-GFSLAEIRELLSLRD 71 (123)
T ss_pred HHHHHHC-CCCHHHHHHHHHhhh
Confidence 3334555 467999999997543
No 191
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=81.28 E-value=3.2 Score=36.46 Aligned_cols=56 Identities=23% Similarity=0.357 Sum_probs=45.9
Q ss_pred HHHHHHHhhCCCcccH--------HHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026766 22 LIYDVIRSKQDMGIWT--------RDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE 84 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~--------~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~ 84 (233)
.|++.|++.=..|.|. ++|.++. |...-+|+|+|+.|++.|+|.+.. |+=+|+...
T Consensus 11 qI~~~i~~~I~~G~~~~G~~LPsE~eLa~~f--~VSR~TvRkAL~~L~~eGli~r~~-----G~GtfV~~~ 74 (236)
T COG2188 11 QIAEDIRQRIESGELPPGDKLPSERELAEQF--GVSRMTVRKALDELVEEGLIVRRQ-----GKGTFVASP 74 (236)
T ss_pred HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHH--CCcHHHHHHHHHHHHHCCcEEEEe-----cCeeEEcCc
Confidence 6777788777777775 6899999 999999999999999999998753 555666554
No 192
>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=81.15 E-value=3.4 Score=37.45 Aligned_cols=57 Identities=7% Similarity=0.206 Sum_probs=41.0
Q ss_pred CCCCCChHHH-HHHHHHHhhCC--CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 12 PSDSLTDHER-LIYDVIRSKQD--MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 12 ~~~~L~~~e~-lVy~~I~~aG~--~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
+++.|+=.|. .|=.+++.-.. --+..++|..+. |+..+.+..++++||+.|+|+..+
T Consensus 173 Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerl--GVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 173 AINTLSYSELEAVEHIFEELDGNEGLLVASKIADRV--GITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHhccHhHHHHHHHHHHHhccccccccHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecc
Confidence 3456665433 23333333222 248899999999 999999999999999999998744
No 193
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=81.07 E-value=4.2 Score=33.08 Aligned_cols=55 Identities=16% Similarity=0.262 Sum_probs=44.3
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcC-----CChHHHHHHHHHHHhC---CCceeeec
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVN-----LPDNIVTKSIKSLQNK---SLIKEVVN 71 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~-----l~~~~v~k~LK~Le~k---~lIK~vks 71 (233)
.||+-|..|+.++....+++...++|..++ . ...++|...++.|-+| .+|+.+..
T Consensus 149 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l--~~~~~~~~~~tv~~~i~~lr~Kl~~~~i~t~~g 211 (219)
T PRK10336 149 TLKPKEFALLELLMRNAGRVLPRKLIEEKL--YTWDEEVTSNAVEVHVHHLRRKLGSDFIRTVHG 211 (219)
T ss_pred ecCHHHHHHHHHHHhCCCccCcHHHHHHHh--cCCCCCCCccCHHHHHHHHHHhcCCCcEEEecC
Confidence 499999999999999999999999999998 5 7877777777666654 34544443
No 194
>PRK10651 transcriptional regulator NarL; Provisional
Probab=81.04 E-value=4.8 Score=32.42 Aligned_cols=46 Identities=26% Similarity=0.408 Sum_probs=40.0
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCC
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKS 64 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~ 64 (233)
...||+.|+.|+.++. +|...++|..++ +++.++|...++.|-.|=
T Consensus 153 ~~~Lt~rE~~vl~~l~----~g~~~~~ia~~l--~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 153 VNQLTPRERDILKLIA----QGLPNKMIARRL--DITESTVKVHVKHMLKKM 198 (216)
T ss_pred cccCCHHHHHHHHHHH----cCCCHHHHHHHc--CCCHHHHHHHHHHHHHHc
Confidence 4469999999999986 568899999999 999999999999987653
No 195
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=81.04 E-value=2.8 Score=27.51 Aligned_cols=30 Identities=23% Similarity=0.401 Sum_probs=19.8
Q ss_pred cccHHHHHHHhhcCCChHHHHHHHHHHHhCCC
Q 026766 34 GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL 65 (233)
Q Consensus 34 GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l 65 (233)
|...++|.+.+ |++.++|.+.+|...+.|+
T Consensus 17 G~s~~~ia~~l--gvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 17 GWSIREIAKRL--GVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp T--HHHHHHHH--TS-HHHHHHHHT-------
T ss_pred CCCHHHHHHHH--CcCHHHHHHHHHHcccccc
Confidence 89999999999 9999999999999988774
No 196
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.74 E-value=13 Score=38.51 Aligned_cols=140 Identities=8% Similarity=0.101 Sum_probs=98.5
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec--ccCCCeeeEEeecc-----------
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN--IHSKGKKHLMAVEF----------- 85 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks--V~~~~rK~Yml~~l----------- 85 (233)
-+.+|+.+ -.+++++.-.+|.+.| +|+...++++|..|-.-+++.-++. .-+|+-|-|.=.++
T Consensus 609 ~q~~vfll--~n~~e~lt~eei~e~T--~l~~~dl~~~L~sl~~ak~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~~ 684 (773)
T COG5647 609 YQLLVFLL--FNDHEELTFEEILELT--KLSTDDLKRVLQSLSCAKLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINY 684 (773)
T ss_pred HHHHHHHH--hcCccceeHHHHHhhc--CCChhhHHHHHHHHHhhheeeeccccccCCCCceEEEccccccccceeeecc
Confidence 34444433 4567889999999999 9999999999999999999988876 12234444432222
Q ss_pred --ccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026766 86 --EPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME 163 (233)
Q Consensus 86 --ePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~ 163 (233)
+|-..- +| -=+-..+|.+=.-.|+..|.+-+..++...-.++.+.+-+.-=++...++.+|.+-+++|+=-|-||+
T Consensus 685 ~~~~~~~q-~~-~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR 762 (773)
T COG5647 685 IAESECMQ-DN-LDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLER 762 (773)
T ss_pred cccchhhc-cc-hhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHh
Confidence 111111 11 11113456666667777788888888888888888777665557789999999999999998888887
Q ss_pred E
Q 026766 164 V 164 (233)
Q Consensus 164 v 164 (233)
.
T Consensus 763 ~ 763 (773)
T COG5647 763 Q 763 (773)
T ss_pred c
Confidence 4
No 197
>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=80.40 E-value=2.6 Score=36.33 Aligned_cols=55 Identities=20% Similarity=0.339 Sum_probs=41.4
Q ss_pred HHHHHHHHhhCCCcc--------cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 21 RLIYDVIRSKQDMGI--------WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 21 ~lVy~~I~~aG~~GI--------w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
..|++.|.+.=..|. .-++|.++. |....+|+++|+.|++.|||.+.. ++=+|..
T Consensus 11 ~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~--~VSR~TvR~Al~~L~~eGli~r~~-----G~GtfV~ 73 (238)
T TIGR02325 11 RQIADKIEQEIAAGHLRAGDYLPAEMQLAERF--GVNRHTVRRAIAALVERGLLRAEQ-----GRGTFVA 73 (238)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec-----CCEEEEC
Confidence 355666665433343 457999999 999999999999999999998753 4555653
No 198
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=80.31 E-value=14 Score=25.46 Aligned_cols=67 Identities=15% Similarity=0.269 Sum_probs=42.6
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL 115 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~ 115 (233)
.++|+.+.+ |++.++|. ..+++|++...+ ...+++.| +.+=|+.|.. .
T Consensus 2 ti~eva~~~--gvs~~tlr----~y~~~gll~~~~--~~~g~r~y----------------------~~~dv~~l~~--i 49 (69)
T PF13411_consen 2 TIKEVAKLL--GVSPSTLR----YYEREGLLPPPR--DENGYRYY----------------------SEEDVERLRE--I 49 (69)
T ss_dssp EHHHHHHHT--TTTHHHHH----HHHHTTSSTTBE--STTSSEEE-----------------------HHHHHHHHH--H
T ss_pred cHHHHHHHH--CcCHHHHH----HHHHhcCccccc--ccCceeec----------------------cHHHHHHHHH--H
Confidence 578999999 99998875 578899986655 23344444 4455555543 3
Q ss_pred HHhhhCCCCCHHHHHHHHHH
Q 026766 116 KQIIKLKVATLEGISDSIKR 135 (233)
Q Consensus 116 ~~i~~~~~~T~~~I~~~I~~ 135 (233)
..+.+ ...|+++|.+.+++
T Consensus 50 ~~l~~-~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 50 KELRK-QGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHH-TTTHHHHHHHHH--
T ss_pred HHHHH-CcCCHHHHHHHHcc
Confidence 34445 45678888888764
No 199
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=80.28 E-value=3.4 Score=37.64 Aligned_cols=47 Identities=11% Similarity=0.227 Sum_probs=39.4
Q ss_pred cccHHHHHHHhhc-CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026766 34 GIWTRDMKRELRV-NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV 83 (233)
Q Consensus 34 GIw~~dik~~t~~-~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~ 83 (233)
-||.++|-.-... ++..+.|.-+|..|+++|+|.+.. ..+|+.|-|.
T Consensus 17 ~i~~~~Li~l~~~~gi~~~~vr~al~RL~~~G~l~~~~---~grr~~Y~LT 64 (280)
T TIGR02277 17 AIWLGSLIEFLAGLGINERLVRTAVSRLVAQGWLQSER---KGRRSFYSLT 64 (280)
T ss_pred ceeHHHHHHHHHhcCCCcchHHHHHHHHHHCCCEEeee---cCCCCEEEEC
Confidence 5999999888744 999999999999999999998853 3567888653
No 200
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=80.12 E-value=4.1 Score=33.65 Aligned_cols=43 Identities=14% Similarity=0.384 Sum_probs=35.7
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHH----HHHHHHHh
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVT----KSIKSLQN 62 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~----k~LK~Le~ 62 (233)
.-||+.|+.|+.+. .+|..+++|..++ +++..+|+ +++++|..
T Consensus 5 ~~Lte~qr~VL~Lr----~~GlTq~EIAe~L--giS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELR----EKGLSQKEIAKEL--KTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHH----HcCCCHHHHHHHH--CcCHHHHHHHHHhHHHHHHH
Confidence 46899999999994 3789999999999 99999888 55555653
No 201
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=80.08 E-value=5.9 Score=28.67 Aligned_cols=54 Identities=11% Similarity=0.179 Sum_probs=39.7
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM 81 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym 81 (233)
.+.+++.+.+. +.+.-|.+++ .+.-+.-.+++..||+.|+|.+-... +.|++++
T Consensus 10 ~a~~~V~~~~~--~S~S~lQR~~--rIGynrAariid~LE~~GiVs~~~~~--~~R~Vl~ 63 (65)
T PF09397_consen 10 EAVEFVIEEGK--ASISLLQRKF--RIGYNRAARIIDQLEEEGIVSPANGS--KPREVLV 63 (65)
T ss_dssp HHHHHHHHCTC--ECHHHHHHHH--T--HHHHHHHHHHHHHCTSBE---TT--SEEEB-S
T ss_pred HHHHHHHHcCC--ccHHHHHHHh--CCCHHHHHHHHHHHHHCCCCCCCCCC--CCCeecc
Confidence 35566777776 9999999999 99999999999999999999876544 4566654
No 202
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=79.93 E-value=4.1 Score=38.05 Aligned_cols=49 Identities=14% Similarity=0.257 Sum_probs=41.4
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
+++++...+----=..|+.|++|.+++ ||+..+|+|-|+...++|+||-
T Consensus 10 ~~~~l~~~~A~lYY~~gltQ~eIA~~L--giSR~~v~rlL~~Ar~~GiV~I 58 (321)
T COG2390 10 EEERLLARAAWLYYVEGLTQSEIAERL--GISRATVSRLLAKAREEGIVKI 58 (321)
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCeEEE
Confidence 345565555555667899999999999 9999999999999999999964
No 203
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=79.67 E-value=5.1 Score=34.62 Aligned_cols=45 Identities=18% Similarity=0.176 Sum_probs=40.1
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
...||+-|+.|+.+|.+ |...++|..++ +++.++|+..++++-+|
T Consensus 132 ~~~LT~RE~eVL~ll~~----G~snkeIA~~L--~iS~~TV~~h~~~I~~K 176 (207)
T PRK11475 132 SRMLSPTEREILRFMSR----GYSMPQIAEQL--ERNIKTIRAHKFNVMSK 176 (207)
T ss_pred cCCCCHHHHHHHHHHHC----CCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence 45699999999999984 79999999999 99999999998888765
No 204
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=79.64 E-value=9.9 Score=31.20 Aligned_cols=55 Identities=9% Similarity=0.222 Sum_probs=46.7
Q ss_pred HHHHHHHhhhC-CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeCC
Q 026766 111 KSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNG 168 (233)
Q Consensus 111 ~~~~~~~i~~~-~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~~ 168 (233)
|..++++|.+. ..+|+++|++-+++.+ ..+|..-|...|+.|+--|.|.++...+
T Consensus 23 R~~vl~~L~~~~~~~sAeei~~~l~~~~---p~islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 23 RLAVLELLLEADGHLSAEELYEELREEG---PGISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhC---CCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 45688888754 5699999999999977 3588999999999999999999987643
No 205
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=79.27 E-value=5.3 Score=34.62 Aligned_cols=49 Identities=20% Similarity=0.290 Sum_probs=41.2
Q ss_pred HHHHHHHHhhCC-CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 21 RLIYDVIRSKQD-MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 21 ~lVy~~I~~aG~-~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
.+|-++|+.-|. .++...+|.+++ ||+.+.|+|+|=+|...|.+..+.+
T Consensus 13 ~lv~~~~~~l~~~~~~~a~~i~~~l--~~~k~~vNr~LY~l~~~~~v~~~~~ 62 (183)
T PHA03103 13 ELVKKEVKNLGLGEGITAIEISRKL--NIEKSEVNKQLYKLQREGMVYMSDS 62 (183)
T ss_pred HHHHHHHHHhccCCCccHHHHHHHh--CCCHHHHHHHHHHHHhcCceecCCC
Confidence 356666666665 899999999999 9999999999999999999866543
No 206
>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=79.13 E-value=4.7 Score=34.80 Aligned_cols=33 Identities=12% Similarity=0.249 Sum_probs=30.3
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
.-++|..+. |....+|+++|..|++.|||.+..
T Consensus 26 sE~eLa~~~--gVSR~TVR~Al~~L~~eGli~r~~ 58 (233)
T TIGR02404 26 SEHELMDQY--GASRETVRKALNLLTEAGYIQKIQ 58 (233)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEeC
Confidence 468999999 999999999999999999998764
No 207
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=78.83 E-value=5.8 Score=32.91 Aligned_cols=41 Identities=15% Similarity=0.166 Sum_probs=34.5
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
...||+.|+.|+.+. .+|..+++|...+ +++..+|++..+.
T Consensus 4 ~~~Lt~rqreVL~lr----~~GlTq~EIAe~L--GiS~~tVs~ie~r 44 (141)
T PRK03975 4 ESFLTERQIEVLRLR----ERGLTQQEIADIL--GTSRANVSSIEKR 44 (141)
T ss_pred ccCCCHHHHHHHHHH----HcCCCHHHHHHHH--CCCHHHHHHHHHH
Confidence 457999999999884 3789999999999 9999887766654
No 208
>PF13034 DUF3895: Protein of unknown function (DUF3895)
Probab=78.73 E-value=14 Score=27.78 Aligned_cols=60 Identities=10% Similarity=0.102 Sum_probs=48.5
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc-ccccC------HHHHHHHHHHHhcCCeEEEEeeCC
Q 026766 109 VVKSQCLKQIIKLKVATLEGISDSIKRSGAF-KVDLT------KQQIEEIVRALVLDNQIMEVKSNG 168 (233)
Q Consensus 109 ~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~-~~~Ls------~~di~~il~~Lv~Dg~ie~v~~~~ 168 (233)
..++.+..||++..-.|+.|+++|+-+.+-+ +-.++ =-+|-..|+-|+..|+|.-+.+.+
T Consensus 4 ~e~~~i~~yi~n~~~Isa~elcE~LI~~~~~~~~rysTgKpkiY~~Vc~yLe~L~~eg~l~~i~~~~ 70 (78)
T PF13034_consen 4 LEKEFINWYIQNEEEISARELCEYLIENGGSPNKRYSTGKPKIYPYVCNYLEYLVKEGKLSFIENDG 70 (78)
T ss_pred HHHHHHHHHHhccccccHHHHHHHHHHcCCCccccccCCCceeHHHHHHHHHHHHHCCeEEEEecCc
Confidence 3467788899999999999999999988744 33333 358999999999999999887654
No 209
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=78.53 E-value=5.5 Score=34.76 Aligned_cols=45 Identities=20% Similarity=0.277 Sum_probs=38.6
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
...||+-|+.|+.+|.+ |...++|..++ +++.++|+..++.+-+|
T Consensus 131 ~~~LSpRErEVLrLLAq----GkTnKEIAe~L--~IS~rTVkth~srImkK 175 (198)
T PRK15201 131 TRHFSVTERHLLKLIAS----GYHLSETAALL--SLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCCCHHHHHHHHHHHC----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 34599999999999976 78899999999 99999998877776554
No 210
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=78.23 E-value=7.6 Score=38.47 Aligned_cols=59 Identities=15% Similarity=0.113 Sum_probs=45.6
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE 84 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~ 84 (233)
.|..|+..+.+.+. .+...+|..++ +++...|..+++.|+++|+|+-..... +.|-|.+
T Consensus 4 ~e~~iL~~l~~~~~-~~~~~~la~~~--g~~~~~v~~~~~~L~~kg~v~~~~~~~----~~~~LT~ 62 (492)
T PLN02853 4 AEEALLGALSNNEE-ISDSGQFAASH--GLDHNEVVGVIKSLHGFRYVDAQDIKR----ETWVLTE 62 (492)
T ss_pred HHHHHHHHHHhcCC-CCCHHHHHHHc--CCCHHHHHHHHHHHHhCCCEEEEEEEE----EEEEECH
Confidence 47788888876432 27899999999 999999999999999999987654433 4565543
No 211
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=77.80 E-value=9.8 Score=32.75 Aligned_cols=52 Identities=19% Similarity=0.263 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
++-..|+.++...|. +.-.+|...+ ++-.+.|+|+|-.|.+.|+|.-.+...
T Consensus 18 ~~~~~v~~~l~~kge--~tDeela~~l--~i~~~~vrriL~~L~e~~li~~~k~rd 69 (176)
T COG1675 18 DEAVLVVDALLEKGE--LTDEELAELL--GIKKNEVRRILYALYEDGLISYRKKRD 69 (176)
T ss_pred chhhHHHHHHHhcCC--cChHHHHHHh--CccHHHHHHHHHHHHhCCceEEEeecc
Confidence 346678888888774 9999999999 999999999999999999998766655
No 212
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=77.78 E-value=29 Score=26.79 Aligned_cols=71 Identities=15% Similarity=0.174 Sum_probs=46.0
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL 115 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~ 115 (233)
..+++.+.+ |++.++| +.-|++|||.+...-...+.+ .||.+-|+.|. ..
T Consensus 2 ~i~eva~~~--gis~~tl----R~ye~~GLi~p~~~~~~ngyR----------------------~Y~~~~i~~l~--~I 51 (108)
T cd01107 2 TIGEFAKLS--NLSIKAL----RYYDKIGLLKPAYVDPDTGYR----------------------YYSAEQLERLN--RI 51 (108)
T ss_pred CHHHHHHHH--CcCHHHH----HHHHHcCCCCCCcCCCCCCcc----------------------ccCHHHHHHHH--HH
Confidence 567888999 9998776 568999999553211112222 24555566664 34
Q ss_pred HHhhhCCCCCHHHHHHHHHHhC
Q 026766 116 KQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 116 ~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
..+++.+ .++++|.+.+....
T Consensus 52 ~~lr~~G-~sl~~i~~l~~~~~ 72 (108)
T cd01107 52 KYLRDLG-FPLEEIKEILDADN 72 (108)
T ss_pred HHHHHcC-CCHHHHHHHHhcCC
Confidence 4455555 56999999888654
No 213
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=77.76 E-value=5.8 Score=34.45 Aligned_cols=45 Identities=29% Similarity=0.404 Sum_probs=39.7
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
...||+-|+.|+.++.. |...++|.+++ +++.++|+..+..+-.|
T Consensus 153 ~~~Lt~rE~~Vl~l~~~----G~s~~eIA~~L--~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 153 SALLTHREKEILNKLRI----GASNNEIARSL--FISENTVKTHLYNLFKK 197 (216)
T ss_pred cCCCCHHHHHHHHHHHc----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 45699999999999987 78999999999 99999999888887654
No 214
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=77.76 E-value=4.8 Score=39.59 Aligned_cols=67 Identities=18% Similarity=0.340 Sum_probs=52.6
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecccc
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEP 87 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~leP 87 (233)
+++.-+..++.++.+.|. ++.++|+..+ ++...+++|.|..|.++|+++..-+.+ +-.-|+..+.++
T Consensus 399 ~~~~~~~~il~~~~en~~--~T~~~L~~~l--~is~~~i~r~i~~Lv~~g~~~~~g~~~--~g~~~v~~~~~~ 465 (467)
T COG2865 399 SLSERQEKILELIKENGK--VTARELREIL--GISSETIRRRIANLVKRGLLKQLGSSG--RGTWYVKGEPEE 465 (467)
T ss_pred ChhHHHHHHHHHHhhccc--cCHHHHHHHh--CcchhhHHHHHHHHhcccHHHHhCcCC--CCcEEecCCccc
Confidence 355555678888888877 9999999999 999999999999999999999877643 334455444443
No 215
>PRK14999 histidine utilization repressor; Provisional
Probab=77.76 E-value=5.6 Score=34.61 Aligned_cols=39 Identities=5% Similarity=0.256 Sum_probs=33.7
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM 81 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym 81 (233)
.-++|.++. |....+|+++|..|++.|+|.+.. |+=+|.
T Consensus 38 sE~eLa~~~--gVSR~TVR~Al~~L~~eGli~r~~-----GkGTfV 76 (241)
T PRK14999 38 SEAELVAQY--GFSRMTINRALRELTDEGWLVRLQ-----GVGTFV 76 (241)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec-----CcEEEE
Confidence 579999999 999999999999999999997753 555565
No 216
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=77.31 E-value=2.1 Score=33.45 Aligned_cols=43 Identities=23% Similarity=0.462 Sum_probs=37.1
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCce
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIK 67 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK 67 (233)
-.|++.+-+.+--||- -|...| |||.+-|+++|.-||+.|+|+
T Consensus 17 l~Vl~~v~eeqPiGI~--klS~~T--Gmp~HKVRYSLRVLEq~~iI~ 59 (101)
T COG3388 17 LSVLKVVLEEQPIGII--KLSDET--GMPEHKVRYSLRVLEQENIIS 59 (101)
T ss_pred HHHHHHHHHhCCceeE--eechhc--CCchhhhhhhhhhhhhcCccC
Confidence 4577888888887775 477889 999999999999999999994
No 217
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=77.25 E-value=8.6 Score=33.21 Aligned_cols=57 Identities=19% Similarity=0.270 Sum_probs=47.6
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK 77 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r 77 (233)
..||.-+..++.+|.-..- |.+.+|..-= |-.. .++++.|.++|||+++.--..++|
T Consensus 88 ~~LSraalEtLAiIAY~QP--iTR~eI~~iR--Gv~~---~~~i~~L~e~glI~~~g~~~~~Gr 144 (184)
T COG1386 88 RELSRAALETLAIIAYKQP--VTRSEIEEIR--GVAV---SQVISTLLERGLIREVGRRDTPGR 144 (184)
T ss_pred ccccHHHHHHHHHHHHcCC--ccHHHHHHHh--CccH---HHHHHHHHHCCCeEecCCCCCCCC
Confidence 4699999999999988877 9999999777 5544 448999999999999887666665
No 218
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=77.12 E-value=6.1 Score=34.42 Aligned_cols=53 Identities=17% Similarity=0.354 Sum_probs=39.7
Q ss_pred HHHHHHHhhCCCc-------c-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026766 22 LIYDVIRSKQDMG-------I-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM 81 (233)
Q Consensus 22 lVy~~I~~aG~~G-------I-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym 81 (233)
.|++.|.+.=..| + .-++|.++. |....+|++||..|++.|+|.+++ ++-+|+
T Consensus 9 qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~--~VSR~TvR~Al~~L~~eGli~r~~-----G~GtfV 69 (240)
T PRK09764 9 QIADRIREQIARGELKPGDALPTESALQTEF--GVSRVTVRQALRQLVEQQILESIQ-----GSGTYV 69 (240)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec-----CceeEE
Confidence 4555555432222 3 359999999 999999999999999999998753 455565
No 219
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=77.09 E-value=32 Score=28.70 Aligned_cols=95 Identities=14% Similarity=0.205 Sum_probs=54.7
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+.+.++.+.+ |++.++| ..-|++|||.+.++ -.|+-+|++ +-|..|+ .
T Consensus 12 ~~IgevAk~~--gvs~~Tl----RyYE~~GLi~~~r~-------------------~~g~R~Y~~-----~~i~~L~--~ 59 (154)
T PRK15002 12 LTPGEVAKRS--GVAVSAL----HFYESKGLITSIRN-------------------SGNQRRYKR-----DVLRYVA--I 59 (154)
T ss_pred ccHHHHHHHH--CcCHHHH----HHHHHCCCCCCccC-------------------CCCCEEECH-----HHHHHHH--H
Confidence 6778899999 9998776 55899999965332 123334433 3344443 2
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHH--HhcCCeEEE
Q 026766 115 LKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRA--LVLDNQIME 163 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~--Lv~Dg~ie~ 163 (233)
...++..+ .|++||.+++.... .....+.+++..+++. ..++.+|++
T Consensus 60 I~~lr~lG-~sL~eIk~ll~~~~-~~~~~~~~~~~~ll~~k~~~l~~~I~~ 108 (154)
T PRK15002 60 IKIAQRIG-IPLATIGEAFGVLP-EGHTLSAKEWKQLSSQWREELDRRIHT 108 (154)
T ss_pred HHHHHHcC-CCHHHHHHHHHHhh-cCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33344454 67999999997421 0112344555555433 344444444
No 220
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=77.06 E-value=34 Score=26.97 Aligned_cols=68 Identities=13% Similarity=0.111 Sum_probs=45.1
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL 115 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~ 115 (233)
...++.+.+ |++.++| ..-|+.|||.+... .|.++ ||.+-|+.|+.+..
T Consensus 2 ~Igeva~~~--gvs~~tl----RyYe~~GLl~p~r~---~gyR~----------------------Y~~~~l~~l~~I~~ 50 (118)
T cd04776 2 TISELAREF--DVTPRTL----RFYEDKGLLSPERR---GQTRV----------------------YSRRDRARLKLILR 50 (118)
T ss_pred CHHHHHHHH--CcCHHHH----HHHHHCCCCCCcCC---CCccc----------------------cCHHHHHHHHHHHH
Confidence 467888999 9998776 55899999965321 13333 35555566554433
Q ss_pred HHhhhCCCCCHHHHHHHHHHhC
Q 026766 116 KQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 116 ~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
++..| .|+++|.+++....
T Consensus 51 --lr~~G-~~L~~I~~~l~~~~ 69 (118)
T cd04776 51 --GKRLG-FSLEEIRELLDLYD 69 (118)
T ss_pred --HHHCC-CCHHHHHHHHHhhc
Confidence 55555 56999999998643
No 221
>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=77.00 E-value=30 Score=31.56 Aligned_cols=122 Identities=15% Similarity=0.174 Sum_probs=73.3
Q ss_pred CCCCCCChHHHHHH-----HHHHhhCC--Ccc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 11 APSDSLTDHERLIY-----DVIRSKQD--MGI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 11 ~~~~~L~~~e~lVy-----~~I~~aG~--~GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
.+.+-|+.++...| -+|++.-. .|- ....|.+++++.++..+|+.+|..|++-||||.-.+ -.|..
T Consensus 106 ~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~------g~y~~ 179 (271)
T TIGR02147 106 PRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNED------GFYKQ 179 (271)
T ss_pred chheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCC------CcEEe
Confidence 34556777776543 34444331 244 355699999555999999999999999999987432 13433
Q ss_pred eccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhhC--CCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHHH
Q 026766 83 VEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKL--KVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRAL 155 (233)
Q Consensus 83 ~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~~--~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~L 155 (233)
.+ ..+||| ++.-.+.|-.+..+++.+-... ..|. .+..++ ...++.++.++|.+.|
T Consensus 180 t~----~~l~~~-----~~~~~~avr~~h~q~l~lA~~al~~~p~--------~eR~~S~lT~~i~~~~~~~i~~~i 239 (271)
T TIGR02147 180 TD----KAVSTG-----DEVIPLAVRQYQKQMIDLAKEALDALPP--------SERDVSTVTFGISEEAYKEIVKKI 239 (271)
T ss_pred ec----ceeecC-----CccchHHHHHHHHHHHHHHHHHHHhCCc--------cccccceeeEecCHHHHHHHHHHH
Confidence 32 234433 3455666777777766655432 1110 111233 2467888888887765
No 222
>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=76.90 E-value=19 Score=27.61 Aligned_cols=68 Identities=10% Similarity=0.128 Sum_probs=44.5
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
++++++.+.+ |++.++|. .-|+.|||.+.+. . .+. -+| +.+=|+.|+ .
T Consensus 2 ~~i~eva~~~--gvs~~tlR----~ye~~Gll~~~r~-~-~g~-----------------R~Y-----~~~~l~~l~--~ 49 (102)
T cd04789 2 YTISELAEKA--GISRSTLL----YYEKLGLITGTRN-A-NGY-----------------RLY-----PDSDLQRLL--L 49 (102)
T ss_pred CCHHHHHHHH--CcCHHHHH----HHHHCCCCCCCcC-C-CCC-----------------eeC-----CHHHHHHHH--H
Confidence 4678999999 99998876 6888999965221 1 223 334 344455555 3
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 026766 115 LKQIIKLKVATLEGISDSIKR 135 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~ 135 (233)
..++++.+ .|+++|.+++..
T Consensus 50 I~~l~~~G-~~l~ei~~~l~~ 69 (102)
T cd04789 50 IQQLQAGG-LSLKECLACLQG 69 (102)
T ss_pred HHHHHHCC-CCHHHHHHHHcC
Confidence 34455554 668999888753
No 223
>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=76.71 E-value=8.6 Score=27.54 Aligned_cols=48 Identities=17% Similarity=0.257 Sum_probs=40.6
Q ss_pred HHHHHhhhC-CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026766 113 QCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME 163 (233)
Q Consensus 113 ~~~~~i~~~-~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~ 163 (233)
.|+++|..+ ..++..+|.+.+...| .++|++-|+.-|+.|.-||.++.
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~g---~~~se~avRrrLr~me~~Glt~~ 50 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLRG---EELSEEAVRRRLRAMERDGLTRK 50 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhcC---hhhhHHHHHHHHHHHHHCCCccc
Confidence 467777665 5689999999999887 47999999999999999996664
No 224
>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=76.37 E-value=5.6 Score=35.53 Aligned_cols=48 Identities=17% Similarity=0.230 Sum_probs=39.1
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHH----HHHHHHHh
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVT----KSIKSLQN 62 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~----k~LK~Le~ 62 (233)
.+..|++.|+.|+.+-.-. .+|+..++|...+ |++...|+ ++|++|..
T Consensus 215 al~~L~~rer~vl~l~y~~-~~~~t~~eIA~~l--gvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 215 ALGSLDARSRRIIEARWLD-DDKLTLQELAAEY--GVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred HHHcCCHHHHHHHHHHhcC-CCCcCHHHHHHHH--CCCHHHHHHHHHHHHHHHHH
Confidence 4568999999998876622 5699999999999 99999999 66666653
No 225
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=76.37 E-value=17 Score=31.38 Aligned_cols=91 Identities=18% Similarity=0.289 Sum_probs=57.8
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCC
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGS 101 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e 101 (233)
.||.++--+ ++-+...+|...| +|..+.|+-+||.|+.-||++.++-=- -||-| |+...+
T Consensus 30 ~iYgilyls-~~Pmtl~Ei~E~l--g~Sks~vS~~lkkL~~~~lV~~~~~~G--~Rk~~---------------F~a~~d 89 (177)
T COG1510 30 QIYGILYLS-RKPLTLDEIAEAL--GMSKSNVSMGLKKLQDWNLVKKVFEKG--DRKDY---------------FEAEKD 89 (177)
T ss_pred HHhhhheec-CCCccHHHHHHHH--CCCcchHHHHHHHHHhcchHHhhhccC--cchhh---------------hcccch
Confidence 466666543 3458999999999 999999999999999999997654322 24444 344555
Q ss_pred CCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHh
Q 026766 102 LDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRS 136 (233)
Q Consensus 102 ~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~ 136 (233)
|=.-|.........+=| -+|.+.+.+-..++
T Consensus 90 f~~~f~t~f~ek~~ReI----d~t~e~l~k~~~e~ 120 (177)
T COG1510 90 FSQIFRTLFEEKWKREI----DPTKEALKKLLEEL 120 (177)
T ss_pred HHHHHHHHHHHHHHHHh----hhHHHHHHHHHHHc
Confidence 55555544444433333 34444444444433
No 226
>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=76.30 E-value=8.7 Score=26.46 Aligned_cols=46 Identities=13% Similarity=0.220 Sum_probs=39.3
Q ss_pred HHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 112 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 112 ~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
+.++++|..++.+|.+|+++.+ | .|..-|+.=|+.|+-.|.|.++.
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~---~-----VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEF---G-----VSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHH---C-----cCHHHHHHHHHHHHHCCCEEEEc
Confidence 5688899999999999998876 3 57788899999999999998875
No 227
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=75.83 E-value=5.8 Score=33.98 Aligned_cols=43 Identities=19% Similarity=0.269 Sum_probs=38.4
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
.||+-|+.|++++.+ |...++|.+++ ++..++|+..++.+-.|
T Consensus 137 ~LT~RE~eVL~lla~----G~snkeIA~~L--~iS~~TVk~h~~~I~~K 179 (207)
T PRK15411 137 SLSRTESSMLRMWMA----GQGTIQISDQM--NIKAKTVSSHKGNIKRK 179 (207)
T ss_pred cCCHHHHHHHHHHHc----CCCHHHHHHHc--CCCHHHHHHHHHHHHHH
Confidence 499999999999975 68899999999 99999999998887654
No 228
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=75.68 E-value=19 Score=29.75 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 122 KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 122 ~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
..+|.++|++.+ .++..-+++|+..|+-.|.|+..+.
T Consensus 23 ~~~s~~eIA~~~--------~is~~~L~kIl~~L~~aGlv~S~rG 59 (153)
T PRK11920 23 KLSRIPEIARAY--------GVSELFLFKILQPLVEAGLVETVRG 59 (153)
T ss_pred CcCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEeecC
Confidence 456788887754 4788999999999999999999873
No 229
>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=75.62 E-value=5.9 Score=37.06 Aligned_cols=42 Identities=14% Similarity=0.337 Sum_probs=37.4
Q ss_pred HHHHhhCCCcccHHHHHHH--hhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 25 DVIRSKQDMGIWTRDMKRE--LRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 25 ~~I~~aG~~GIw~~dik~~--t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
.+|..++. +..++|.++ + +.++.++++-|..||+.|++.+.-
T Consensus 14 ~~l~~~~p--v~s~~l~~~~~~--~vS~aTiR~d~~~Le~~G~l~~~h 57 (337)
T TIGR00331 14 EYIKTGQP--VGSKTLLEKYNL--GLSSATIRNDMADLEDLGFIEKPH 57 (337)
T ss_pred HHHhcCCC--cCHHHHHhhcCC--CCChHHHHHHHHHHHHCCCccCCC
Confidence 57777777 999999999 7 999999999999999999997744
No 230
>PRK04217 hypothetical protein; Provisional
Probab=75.61 E-value=6.3 Score=31.34 Aligned_cols=45 Identities=13% Similarity=0.195 Sum_probs=36.2
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQ 61 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le 61 (233)
....|+++|+.++.+. .-+|+..++|.+.+ +++.++|.+.|+...
T Consensus 39 p~~~Lt~eereai~l~---~~eGlS~~EIAk~L--GIS~sTV~r~L~RAr 83 (110)
T PRK04217 39 PPIFMTYEEFEALRLV---DYEGLTQEEAGKRM--GVSRGTVWRALTSAR 83 (110)
T ss_pred CcccCCHHHHHHHHHH---HHcCCCHHHHHHHH--CcCHHHHHHHHHHHH
Confidence 3678999998666544 44678999999999 999999998887644
No 231
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=75.35 E-value=12 Score=28.87 Aligned_cols=74 Identities=15% Similarity=0.223 Sum_probs=43.5
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCC---eeeEEeeccccCCCcccCCcc
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG---KKHLMAVEFEPSKEISGGAWY 97 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~---rK~Yml~~lePs~eiTGG~wy 97 (233)
++-+..+-+.|.. ....|-+.| |||.+++..+|+.|.+-+..-.+.- ... -=.|++.+-
T Consensus 10 rlyla~li~~~~~--nvp~L~~~T--GmPrRT~Qd~i~aL~~~~I~~~Fvq--~G~R~~~GyY~i~~W------------ 71 (90)
T PF09904_consen 10 RLYLAYLIDSGER--NVPALMEAT--GMPRRTIQDTIKALPELGIECEFVQ--DGERNNAGYYRISDW------------ 71 (90)
T ss_dssp HHHHHHHHHHS-B---HHHHHHHH-----HHHHHHHHHGGGGGT-EEEEE----TTS-S--EEEEEE-------------
T ss_pred HHHHHHHHhcCCc--cHHHHHHHh--CCCHhHHHHHHHHhhcCCeEEEEEe--cCccCCCCcEEeeec------------
Confidence 3444555566666 889999999 9999999999999998887755442 211 125665442
Q ss_pred cCCCCCHHHHHHHHHHH
Q 026766 98 SEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 98 ~d~e~D~efI~~l~~~~ 114 (233)
|-||.+-|+.=.+.+
T Consensus 72 --G~id~~wi~~~~~~i 86 (90)
T PF09904_consen 72 --GPIDRKWIADHLQEI 86 (90)
T ss_dssp --TTB-HHHHHHHHHHH
T ss_pred --CCCCHHHHHHHHHHH
Confidence 667777776544443
No 232
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=75.17 E-value=12 Score=29.65 Aligned_cols=45 Identities=27% Similarity=0.333 Sum_probs=37.2
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
...||+.|+.|+.++. +|...++|..++ +++.++|...++.+-.|
T Consensus 147 ~~~lt~~e~~vl~l~~----~g~~~~~Ia~~l--~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 147 PPLLTPRERQILKLIT----EGYTNRDIAEQL--SISIKTVETHRLNMMRK 191 (211)
T ss_pred ccCCCHHHHHHHHHHH----CCCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 4569999999999974 456799999999 99999988877776654
No 233
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=75.16 E-value=6.1 Score=35.46 Aligned_cols=46 Identities=24% Similarity=0.171 Sum_probs=38.5
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
++.+...|.+. ++....+|+.+. |++-.+|+..+|+||+-|+|++-
T Consensus 176 ~k~I~~eiq~~--~~~t~~~ia~~l--~ls~aTV~~~lk~l~~~Gii~~~ 221 (240)
T COG3398 176 SKAIIYEIQEN--KCNTNLLIAYEL--NLSVATVAYHLKKLEELGIIPED 221 (240)
T ss_pred HHHHHHHHhcC--CcchHHHHHHHc--CccHHHHHHHHHHHHHcCCCccc
Confidence 35555566654 448999999999 99999999999999999999774
No 234
>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=74.84 E-value=40 Score=26.69 Aligned_cols=69 Identities=12% Similarity=0.237 Sum_probs=44.1
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+.+.++.+.+ |++.++| ..-|++|||.+...-. .+.+ +| +.+-|..|+.
T Consensus 1 m~I~e~a~~~--gvs~~tl----RyYe~~GLl~p~~r~~-~gyR-----------------~Y-----~~~~l~~l~~-- 49 (127)
T TIGR02044 1 MNIGQVAKLT--GLSSKMI----RYYEEKGLIPPPLRSE-GGYR-----------------TY-----TQQHLDELRL-- 49 (127)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCCcCC-CCCe-----------------ec-----CHHHHHHHHH--
Confidence 4578899999 9998776 4689999996543212 2333 33 3444455542
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 026766 115 LKQIIKLKVATLEGISDSIKR 135 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~ 135 (233)
...+++.+ .|++||.+++..
T Consensus 50 I~~lr~~G-~sL~eI~~~l~~ 69 (127)
T TIGR02044 50 ISRARQVG-FSLEECKELLNL 69 (127)
T ss_pred HHHHHHCC-CCHHHHHHHHHh
Confidence 23345555 579999999873
No 235
>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=74.77 E-value=9 Score=25.40 Aligned_cols=42 Identities=14% Similarity=0.302 Sum_probs=31.0
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
+..||+.++.|+.+..-. |...++|...+ |++.++|.+.|..
T Consensus 8 l~~L~~~~r~i~~l~~~~---g~s~~eIa~~l--~~s~~~v~~~l~r 49 (54)
T PF08281_consen 8 LAQLPERQREIFLLRYFQ---GMSYAEIAEIL--GISESTVKRRLRR 49 (54)
T ss_dssp HHCS-HHHHHHHHHHHTS------HHHHHHHC--TS-HHHHHHHHHH
T ss_pred HHCCCHHHHHHHHHHHHH---CcCHHHHHHHH--CcCHHHHHHHHHH
Confidence 467999999998877664 68999999999 9999998877754
No 236
>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=74.69 E-value=4.7 Score=34.82 Aligned_cols=39 Identities=10% Similarity=0.257 Sum_probs=33.5
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM 81 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym 81 (233)
.-++|.++. |....+|+++|..|++.|||.+++ ++=+|.
T Consensus 27 sE~eLa~~~--~VSR~TVR~Al~~L~~eGli~r~~-----G~GtfV 65 (230)
T TIGR02018 27 SEHELVAQY--GCSRMTVNRALRELTDAGLLERRQ-----GVGTFV 65 (230)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec-----CCEEEE
Confidence 568999999 999999999999999999997753 555565
No 237
>PRK10736 hypothetical protein; Provisional
Probab=74.64 E-value=7.3 Score=37.21 Aligned_cols=50 Identities=10% Similarity=-0.044 Sum_probs=43.1
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
.++.++..||+.+.. .++..-+|-.++ +|+...+.-+|-.||-+|+|.+.
T Consensus 305 ~~~~~~~~v~~~l~~---~~~~iD~L~~~~--~l~~~~v~~~L~~LEl~G~v~~~ 354 (374)
T PRK10736 305 EVALPFPELLANVGD---EVTPVDVVAERA--GQPVPEVVTQLLELELAGWIAAV 354 (374)
T ss_pred cccchHHHHHHhcCC---CCCCHHHHHHHH--CcCHHHHHHHHHHHHhCCcEEEc
Confidence 466677888888753 457899999999 99999999999999999999875
No 238
>KOG3095 consensus Transcription initiation factor IIE, beta subunit [Transcription]
Probab=74.19 E-value=21 Score=33.02 Aligned_cols=100 Identities=18% Similarity=0.318 Sum_probs=69.7
Q ss_pred HHHHHHHhhCC-CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCC
Q 026766 22 LIYDVIRSKQD-MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEG 100 (233)
Q Consensus 22 lVy~~I~~aG~-~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~ 100 (233)
-++.+++..+. .||...||+.-. ..+...||+||+-+=|=-+..-.+.+.++ .||.|.
T Consensus 143 ~Ll~llr~~~~~~GI~v~DL~d~~------pNv~~~lk~L~~s~eIl~l~t~~d~k~ki---------------vf~ND~ 201 (284)
T KOG3095|consen 143 QLLKLLRKHDTLGGILVSDLKDAW------PNVDEDLKELEKSGEILVLRTPKDDKPKI---------------VFYNDK 201 (284)
T ss_pred HHHHHHHhcCccCceehHHhhhcc------cchHHHHHHHhcCCcEEEEeccCCCCCce---------------EEecCC
Confidence 45667776655 699999999876 46788999999888776665554434433 489886
Q ss_pred ----CCCHHHHHHHHHHHHHHhhhCCCCC-HHHHHHHHHHhCCcccc-cCHHHHHH
Q 026766 101 ----SLDTEFIKVVKSQCLKQIIKLKVAT-LEGISDSIKRSGAFKVD-LTKQQIEE 150 (233)
Q Consensus 101 ----e~D~efI~~l~~~~~~~i~~~~~~T-~~~I~~~I~~~~i~~~~-Ls~~di~~ 150 (233)
..|.||....+++ ..++ ..+|-+++.+.|+.... +.+.-+..
T Consensus 202 ~~~~~VDdEFk~LWr~V--------~Ip~~~~dle~eL~k~GLkp~~~v~p~~~~~ 249 (284)
T KOG3095|consen 202 SCSFSVDDEFKKLWRSV--------TIPSMELDLEEELQKQGLKPMKDVDPKKAAP 249 (284)
T ss_pred CCCcccCHHHHHHHHhC--------CCChHHHHHHHHHHHhCCCcccccchHHhhh
Confidence 4578998777654 2455 67888888888876654 55554444
No 239
>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=74.17 E-value=41 Score=26.53 Aligned_cols=71 Identities=14% Similarity=0.229 Sum_probs=45.4
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+..+++.+.+ |++.++| ..-|+.|||.+...-. .+.+ + |+.+-|..|+.
T Consensus 1 m~I~e~a~~~--gvs~~tl----R~Ye~~GLl~~~~r~~-~gyR-----------------~-----Y~~~~l~~l~~-- 49 (126)
T cd04783 1 LTIGELAKAA--GVNVETI----RYYQRRGLLPEPPRPE-GGYR-----------------R-----YPEETVTRLRF-- 49 (126)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCCcCC-CCCe-----------------e-----cCHHHHHHHHH--
Confidence 3578899999 9999887 6689999996321111 1222 2 34444555542
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhC
Q 026766 115 LKQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
...+++.+ .|+++|.+++....
T Consensus 50 I~~lr~~G-~sL~eI~~~l~~~~ 71 (126)
T cd04783 50 IKRAQELG-FTLDEIAELLELDD 71 (126)
T ss_pred HHHHHHcC-CCHHHHHHHHhccc
Confidence 33445554 67999999997543
No 240
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=73.96 E-value=11 Score=25.44 Aligned_cols=44 Identities=9% Similarity=0.243 Sum_probs=39.3
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
+|+.+|++++-+..-.-| ....+|...- |+++++++|+.+..+.
T Consensus 2 kLs~~d~lll~L~~LR~~--~~~~~La~~F--gIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLN--LTFQDLAYRF--GISQSTVSRIFHEWIP 45 (53)
T ss_pred CCCHHHHHHHHHHHHHcC--CcHhHHhhhe--eecHHHHHHHHHHHHH
Confidence 588999999998888866 9999999999 9999999999988764
No 241
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=73.87 E-value=5.6 Score=29.15 Aligned_cols=36 Identities=11% Similarity=0.279 Sum_probs=28.4
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
.++..+.+.-..+|+.++++.+.+ ++++..|++.++
T Consensus 18 ~l~~~i~~~~~~~~ltQ~e~A~~l--gisq~~vS~l~~ 53 (80)
T PF13744_consen 18 QLMAAIRELREERGLTQAELAERL--GISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHCCT--HHHHHHHH--TS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH--CCChhHHHHHHc
Confidence 456667777788999999999999 999999999875
No 242
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=73.86 E-value=17 Score=33.65 Aligned_cols=127 Identities=17% Similarity=0.153 Sum_probs=83.2
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccC
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGG 94 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG 94 (233)
.|+.+-+-++..|..+--.||.+.+|.+.+| .++.+++..+|..|-++|+|+-++ .++.-+|-.-+.+ +..++
T Consensus 7 ~~~~e~~~~~~~~~~~~p~git~q~L~~~~p-~~~~~~~~salN~lLs~~~l~llr---~~~~l~yr~~d~~---~a~~~ 79 (297)
T KOG3233|consen 7 ALPVEIENILIQIVKQIPEGITQQELQSEMP-QISATDRASALNILLSRGLLDLLR---QNTGLVYRAKDPK---SASKG 79 (297)
T ss_pred cChHHHHHHHHHHHHhccccccHHHHHHHcC-CCcHHHHHHHHHHHHhcCcchhhc---cCCcceEeccCch---hhccc
Confidence 4566666667777777788999999999993 599999999999999999996654 3434455433322 22222
Q ss_pred CcccCCCCCHHHHHHHHHHHHHHhhhCC--CCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 95 AWYSEGSLDTEFIKVVKSQCLKQIIKLK--VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 95 ~wy~d~e~D~efI~~l~~~~~~~i~~~~--~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
. ..| .=.+.++.+|+..+ .+...+|.. +..|-...|..+|..|.--..|-.|++
T Consensus 80 ~-----~~e-----~eEk~vy~lIe~sg~~GIW~k~ik~--------ksnLp~~~v~K~LkSLEsKkLIKsVKs 135 (297)
T KOG3233|consen 80 K-----GME-----NEEKLVYSLIEESGNEGIWSKEIKR--------KSNLPQTVVNKILKSLESKKLIKSVKS 135 (297)
T ss_pred c-----cCC-----hHHHHHHHHHHHcCCCceeeehhhh--------ccCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 1 111 11245667776543 343332221 235778888899999988888777765
No 243
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=73.73 E-value=13 Score=31.19 Aligned_cols=54 Identities=9% Similarity=0.111 Sum_probs=44.3
Q ss_pred HHHHHHHHhhh-CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 110 VKSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 110 l~~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
-|..|+++|.. .+.+|++||.+.+++.+. .++..-|-..|+.|+=.|.|.++..
T Consensus 27 qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~---~is~aTVYRtL~~L~e~Glv~~~~~ 81 (169)
T PRK11639 27 QRLEVLRLMSLQPGAISAYDLLDLLREAEP---QAKPPTVYRALDFLLEQGFVHKVES 81 (169)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHhhCC---CCCcchHHHHHHHHHHCCCEEEEec
Confidence 34557777764 468999999999999883 4677889999999999999999864
No 244
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=73.55 E-value=40 Score=26.06 Aligned_cols=70 Identities=11% Similarity=0.172 Sum_probs=46.1
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
++++++.+.+ |++.++|.. -|+.|||.+...-. .+.+.| +.+=|..|+.+
T Consensus 1 ~~i~eva~~~--gvs~~tlR~----ye~~Gll~p~~~~~-~g~R~Y----------------------~~~dl~~l~~I- 50 (108)
T cd04773 1 MTIGELAHLL--GVPPSTLRH----WEKEGLLSPDREPE-TGYRVY----------------------DPSDVRDARLI- 50 (108)
T ss_pred CCHHHHHHHH--CcCHHHHHH----HHHCCCCCCCcCCC-CCceee----------------------CHHHHHHHHHH-
Confidence 3578899999 999988765 58899996543222 233333 44445555443
Q ss_pred HHHhhhCCCCCHHHHHHHHHHh
Q 026766 115 LKQIIKLKVATLEGISDSIKRS 136 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~ 136 (233)
..+++.++ ++++|.+++...
T Consensus 51 -~~lr~~G~-~l~~I~~~l~~~ 70 (108)
T cd04773 51 -HLLRRGGY-LLEQIATVVEQL 70 (108)
T ss_pred -HHHHHCCC-CHHHHHHHHHHh
Confidence 45556654 699999999854
No 245
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=73.40 E-value=8 Score=33.35 Aligned_cols=46 Identities=7% Similarity=0.102 Sum_probs=37.1
Q ss_pred HHHHHHHhhCCCc-------c-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 22 LIYDVIRSKQDMG-------I-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 22 lVy~~I~~aG~~G-------I-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
.||+.|.+.=-.| + .-++|..+. |+..+.|+.+|+.|+..|||...
T Consensus 11 ~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~--gVSRt~VReAL~~L~~eGlv~~~ 64 (239)
T PRK04984 11 FAEEYIIESIWNNRFPPGSILPAERELSELI--GVTRTTLREVLQRLARDGWLTIQ 64 (239)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe
Confidence 4666666432223 5 688999999 99999999999999999999764
No 246
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=73.31 E-value=49 Score=33.49 Aligned_cols=103 Identities=11% Similarity=0.059 Sum_probs=73.1
Q ss_pred CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHH
Q 026766 33 MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKS 112 (233)
Q Consensus 33 ~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~ 112 (233)
.|+...+|+.+....++.......|..|.++|.|+.... .+-+.+..| .++.+- ..+.+
T Consensus 438 ~g~~~~~l~~~~~~~~~~~~~~~~l~~l~~~~~i~~~~~-------~~~~~~~~~-------------~~~~~~-~~~~~ 496 (614)
T PRK10512 438 PGPGRERLRRMALPMEDEALVLLLIEKMRESGDIHSHHG-------WLHLPDHKA-------------GFSEEQ-QALWQ 496 (614)
T ss_pred cCCCHHHHHhhcccCCCHHHHHHHHHHHHhCCCEEEeCC-------EEECCCCCC-------------CCCHHH-HHHHH
Confidence 799999999887556999999999999999999976332 222222222 233332 34445
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 113 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 113 ~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
.+...+. ...|++.|+.+.+ | +..++.+++|..|+-.|+|.++.
T Consensus 497 ~l~~~~~-~~p~~~~~~~~~l---~-----~~~~~~~~~l~~l~~~g~lv~l~ 540 (614)
T PRK10512 497 KAEPLFG-DEPWWVRDLAKET---G-----TDEQAMRLTLRQAAQQGIITAIV 540 (614)
T ss_pred HHHHHHh-cCCCCHHHHHHHh---C-----CCHHHHHHHHHHHHHCCCEEEec
Confidence 5555554 5678888877644 3 67888999999999999998875
No 247
>PF14502 HTH_41: Helix-turn-helix domain
Probab=73.22 E-value=7.8 Score=26.61 Aligned_cols=39 Identities=13% Similarity=0.135 Sum_probs=32.1
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 31 QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 31 G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
|++=-...++..+. ++...+|.++||.||+.+-|+=.+.
T Consensus 3 GdRi~tI~e~~~~~--~vs~GtiQ~Alk~Le~~gaI~Le~r 41 (48)
T PF14502_consen 3 GDRIPTISEYSEKF--GVSRGTIQNALKFLEENGAIKLESR 41 (48)
T ss_pred CcccCCHHHHHHHh--CcchhHHHHHHHHHHHCCcEEeeec
Confidence 33334577899999 9999999999999999999976543
No 248
>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=73.16 E-value=11 Score=25.85 Aligned_cols=41 Identities=32% Similarity=0.505 Sum_probs=26.3
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
..||-+|++ ++|+.. ..|...++|.++. |++.++|+.++|.
T Consensus 5 ~~LTl~eK~--~iI~~~-e~g~s~~~ia~~f--gv~~sTv~~I~K~ 45 (53)
T PF04218_consen 5 KSLTLEEKL--EIIKRL-EEGESKRDIAREF--GVSRSTVSTILKN 45 (53)
T ss_dssp SS--HHHHH--HHHHHH-HCTT-HHHHHHHH--T--CCHHHHHHHC
T ss_pred ccCCHHHHH--HHHHHH-HcCCCHHHHHHHh--CCCHHHHHHHHHh
Confidence 347777653 444443 2345899999999 9999999999986
No 249
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=72.93 E-value=8.5 Score=34.69 Aligned_cols=57 Identities=14% Similarity=0.155 Sum_probs=43.8
Q ss_pred CCCCCCCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCcee
Q 026766 1 MSKRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIKE 68 (233)
Q Consensus 1 ~~~~~~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK~ 68 (233)
||-|.|+- .+|+-.+..++..|.+.|+ +..+ .+++ +++|..|++.||+||+ -.|+.+
T Consensus 1 ~~~~~~~~-----~~m~l~~L~~F~~v~e~gs--~s~A--A~~L--~iSQpavS~~I~~LE~~lG~~LF~R 60 (310)
T PRK15092 1 MINANRPI-----INLDLDLLRTFVAVADLNT--FAAA--AAAV--CRTQSAVSQQMQRLEQLVGKELFAR 60 (310)
T ss_pred Ccchhhhh-----hcCCHHHHHHHHHHHHcCC--HHHH--HHHh--CCChHHHHHHHHHHHHHhCcceEEE
Confidence 66666664 2578888899999999998 4333 4668 9999999999999997 445544
No 250
>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=72.75 E-value=13 Score=25.51 Aligned_cols=43 Identities=16% Similarity=0.293 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCcee
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIKE 68 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK~ 68 (233)
+..++..|.+.|+ ...-.+.+ ++++..|++.|+.||+ ..|+.+
T Consensus 3 ~l~~f~~v~~~gs----~~~AA~~l--~is~~~vs~~i~~LE~~lg~~Lf~r 48 (60)
T PF00126_consen 3 QLRYFLAVAETGS----ISAAAEEL--GISQSAVSRQIKQLEEELGVPLFER 48 (60)
T ss_dssp HHHHHHHHHHHSS----HHHHHHHC--TSSHHHHHHHHHHHHHHHTS-SEEE
T ss_pred HHHHHHHHHHhCC----HHHHHHHh--hccchHHHHHHHHHHHHhCCeEEEE
Confidence 3456667777776 33445667 9999999999999996 455543
No 251
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=72.66 E-value=7 Score=32.37 Aligned_cols=47 Identities=13% Similarity=0.131 Sum_probs=38.1
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcC-----CChH----HHHHHHHHHHh
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVN-----LPDN----IVTKSIKSLQN 62 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~-----l~~~----~v~k~LK~Le~ 62 (233)
-.||+.|+.|+.++....++|+...+|..+. . ...+ .++++.++|+.
T Consensus 159 ~~Lt~~e~~il~~l~~~~~~~~s~~~i~~~~--~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 159 LDLTPAEFRLLKTLSHEPGKVFSREQLLNHL--YDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred eecCHHHHHHHHHHHhCCCceEcHHHHHHHh--cCcCcCCCccCHHHHHHHHHHHhhc
Confidence 3699999999999999999999999999998 5 5544 45566666764
No 252
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=72.37 E-value=32 Score=26.13 Aligned_cols=70 Identities=13% Similarity=0.148 Sum_probs=43.9
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL 115 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~ 115 (233)
+.+++.+.+ |++.++|..= |+.|||.+..+- .+.+. |+ .+=|..|+.+
T Consensus 2 ~I~e~a~~~--gvs~~tLR~y----e~~Gll~p~r~~--~g~R~-----------------Y~-----~~dv~~l~~I-- 49 (96)
T cd04774 2 KVDEVAKRL--GLTKRTLKYY----EEIGLVSPERSE--GRYRL-----------------YS-----EEDLKRLERI-- 49 (96)
T ss_pred CHHHHHHHH--CcCHHHHHHH----HHCCCCCCCcCC--CCCEE-----------------EC-----HHHHHHHHHH--
Confidence 578899999 9999988654 778999643321 23333 33 3333444333
Q ss_pred HHhhhCCCCCHHHHHHHHHHhC
Q 026766 116 KQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 116 ~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
..+.+....|+++|..+++...
T Consensus 50 ~~L~~~~G~~l~ei~~~l~~~~ 71 (96)
T cd04774 50 LRLREVLGFSLQEVTHFLERPL 71 (96)
T ss_pred HHHHHHcCCCHHHHHHHHhccc
Confidence 3344523577999999998644
No 253
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=72.26 E-value=11 Score=30.18 Aligned_cols=44 Identities=27% Similarity=0.413 Sum_probs=38.8
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
..||+.|..|+.++.+ |...++|..++ +++.++|...+++|.+|
T Consensus 136 ~~Lt~~E~~il~~l~~----g~~~~~Ia~~l--~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ----GMAVKEIAAEL--GLSPKTVHVHRANLMEK 179 (196)
T ss_pred cCCCHHHHHHHHHHHC----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 4699999999999874 58999999999 99999999998888765
No 254
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=72.12 E-value=15 Score=33.34 Aligned_cols=51 Identities=20% Similarity=0.348 Sum_probs=41.1
Q ss_pred HHHHHHHHhh-CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026766 21 RLIYDVIRSK-QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM 81 (233)
Q Consensus 21 ~lVy~~I~~a-G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym 81 (233)
.+|+..|... ++ +-++||.+++ +++...|+..+|.|.+.|||.+ .+|--|-
T Consensus 13 fqIL~ei~~~qp~--v~q~eIA~~l--giT~QaVsehiK~Lv~eG~i~~------~gR~~Y~ 64 (260)
T COG1497 13 FQILSEIAVRQPR--VKQKEIAKKL--GITLQAVSEHIKELVKEGLIEK------EGRGEYE 64 (260)
T ss_pred HHHHHHHHHhCCC--CCHHHHHHHc--CCCHHHHHHHHHHHHhccceee------cCCeeEE
Confidence 3455555444 66 8999999999 9999999999999999999977 3565664
No 255
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=71.85 E-value=45 Score=25.91 Aligned_cols=69 Identities=12% Similarity=0.158 Sum_probs=42.9
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+.+.++.+.+ |++.++|. .-|+.|||++.++ . .|--+|+ .+=|..|+.+
T Consensus 1 m~i~eva~~~--gvs~~tlR----~Ye~~GLl~p~r~--~-----------------~g~R~Y~-----~~~~~~l~~I- 49 (112)
T cd01282 1 MRIGELAART--GVSVRSLR----YYEEQGLLVPERS--A-----------------NGYRDYD-----EAAVDRVRQI- 49 (112)
T ss_pred CCHHHHHHHH--CCCHHHHH----HHHHCCCCCCCcC--C-----------------CCCeecC-----HHHHHHHHHH-
Confidence 3578899999 99988765 5788999965322 1 2223344 3334444433
Q ss_pred HHHhhhCCCCCHHHHHHHHHHh
Q 026766 115 LKQIIKLKVATLEGISDSIKRS 136 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~ 136 (233)
..++.. ..++++|.+++...
T Consensus 50 -~~lr~~-G~sl~eI~~~l~~~ 69 (112)
T cd01282 50 -RRLLAA-GLTLEEIREFLPCL 69 (112)
T ss_pred -HHHHHc-CCCHHHHHHHHHHh
Confidence 234444 46699999998753
No 256
>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=71.71 E-value=49 Score=26.26 Aligned_cols=69 Identities=14% Similarity=0.187 Sum_probs=43.4
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+.+.++.+.+ |++.++|+ .-|+.|||.+...-. .|.+ +|+ .+=|+.|+.+
T Consensus 1 m~I~e~a~~~--gvs~~tlR----yYe~~GLl~~~~r~~-~g~R-----------------~Y~-----~~~~~~l~~I- 50 (127)
T cd01108 1 MNIGEAAKLT--GLSAKMIR----YYEEIGLIPPPSRSD-NGYR-----------------VYN-----QRDIEELRFI- 50 (127)
T ss_pred CCHHHHHHHH--CcCHHHHH----HHHHCCCCCCCCcCC-CCce-----------------ecC-----HHHHHHHHHH-
Confidence 3578899999 99988764 689999996422211 1222 333 3444444433
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 026766 115 LKQIIKLKVATLEGISDSIKR 135 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~ 135 (233)
.++++.+ .|+++|.+++..
T Consensus 51 -~~lr~~G-~sL~eI~~~l~~ 69 (127)
T cd01108 51 -RRARDLG-FSLEEIRELLAL 69 (127)
T ss_pred -HHHHHcC-CCHHHHHHHHHH
Confidence 4445555 579999999874
No 257
>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=71.60 E-value=15 Score=26.25 Aligned_cols=46 Identities=15% Similarity=0.140 Sum_probs=31.7
Q ss_pred HHHHHHhhhCC-CCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 112 SQCLKQIIKLK-VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 112 ~~~~~~i~~~~-~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
+.+..|+..++ .||+.||++.+ |+. |..-|+.-|+.|+-.|.|...
T Consensus 13 ~~I~~~~~~~G~~Pt~rEIa~~~---g~~----S~~tv~~~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 13 EFIREYIEENGYPPTVREIAEAL---GLK----STSTVQRHLKALERKGYIRRD 59 (65)
T ss_dssp HHHHHHHHHHSS---HHHHHHHH---TSS----SHHHHHHHHHHHHHTTSEEEG
T ss_pred HHHHHHHHHcCCCCCHHHHHHHh---CCC----ChHHHHHHHHHHHHCcCccCC
Confidence 34444444444 58999999887 432 578899999999999999874
No 258
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=71.39 E-value=9.2 Score=35.95 Aligned_cols=48 Identities=27% Similarity=0.344 Sum_probs=37.6
Q ss_pred HHHHHHHHHhhCCCcc--------cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 20 ERLIYDVIRSKQDMGI--------WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 20 e~lVy~~I~~aG~~GI--------w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
...||+.|.+.=-.|. ..++|.++. +++.++|.+++..|++.|+|...
T Consensus 7 ~~~~~~~i~~~i~~g~l~~g~~lps~r~la~~~--~vsr~tv~~a~~~L~~~g~i~~~ 62 (431)
T PRK15481 7 ANEIFDSIRQLIQAGRLRPGDSLPPVRELASEL--GVNRNTVAAAYKRLVTAGLAQSQ 62 (431)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe
Confidence 3456666664433333 479999999 99999999999999999999754
No 259
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=71.17 E-value=11 Score=33.32 Aligned_cols=70 Identities=13% Similarity=0.065 Sum_probs=54.5
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee-ccccCCCcccCCcccCCCCCHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV-EFEPSKEISGGAWYSEGSLDTEFIKVVKSQ 113 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~-~lePs~eiTGG~wy~d~e~D~efI~~l~~~ 113 (233)
.-++|..+. |...++|+=+|+.|+.+|||-.- ++.-+|..- +..+ .+.---+|..+..+|..++..|.+.
T Consensus 36 ~EreLae~f--gVSR~~vREAl~~L~a~Glve~r-----~G~Gt~V~~~~~~~-~~~~~~~~~~~~~~~~~~~~~lle~ 106 (241)
T COG2186 36 SERELAERF--GVSRTVVREALKRLEAKGLVEIR-----QGSGTFVRPRSEWN-LDPLVLPLRLLLEDDPDSIFDLLEA 106 (241)
T ss_pred CHHHHHHHH--CCCcHHHHHHHHHHHHCCCeeec-----CCCceEecCCccCc-cchhhhHHHHHcccChhhHHHHHHH
Confidence 368999999 99999999999999999999652 466677652 2223 4555567888888888888888766
No 260
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=70.78 E-value=12 Score=32.31 Aligned_cols=63 Identities=24% Similarity=0.232 Sum_probs=50.5
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChH-HHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDN-IVTKSIKSLQNKSLIKEVVNIHSKGKKHL 80 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~-~v~k~LK~Le~k~lIK~vksV~~~~rK~Y 80 (233)
-..+|+..|.+|+.+|+-.+. --.-+||..-+ |..+. .++++|++|++-|||-.-++-+. ++|
T Consensus 77 g~~~ls~~e~l~lH~irhrdR-~K~laDic~~l--n~eDth~itYslrKL~k~gLit~t~~gke---vTy 140 (199)
T COG5631 77 GEFSLSGPENLLLHIIRHRDR-PKSLADICQML--NREDTHNITYSLRKLLKGGLITRTGSGKE---VTY 140 (199)
T ss_pred cCCCCcchHHHHHHHHhhcCc-hhhHHHHHHHh--ccccchhHHHHHHHHHhccceecCCCCce---EEE
Confidence 356899999999999987655 34678888888 88754 89999999999999977666553 666
No 261
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=70.75 E-value=6.4 Score=34.25 Aligned_cols=40 Identities=13% Similarity=0.228 Sum_probs=33.3
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
.-++|..+. +....+|+|+|..|++.|||.+.. ++=+|..
T Consensus 37 sE~eLa~~~--~VSR~TVR~Al~~L~~eGli~r~~-----G~GtfV~ 76 (241)
T PRK10079 37 AEQQLAARY--EVNRHTLRRAIDQLVEKGWVQRRQ-----GVGVLVL 76 (241)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec-----CCEEEEe
Confidence 358999999 999999999999999999997643 5555653
No 262
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=70.66 E-value=15 Score=29.63 Aligned_cols=48 Identities=21% Similarity=0.215 Sum_probs=40.7
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI 66 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI 66 (233)
...||+-|..|+.++.+ |...++|..+. ++..++|...++.|-+|=-+
T Consensus 141 ~~~lt~~E~~vl~~l~~----g~~~~~I~~~l--~~s~~tv~~~~~~l~~Kl~~ 188 (204)
T PRK09958 141 LDSLSKQEISVMRYILD----GKDNNDIAEKM--FISNKTVSTYKSRLMEKLEC 188 (204)
T ss_pred cccCCHHHHHHHHHHHc----CCCHHHHHHHh--CCCHHHHHHHHHHHHHHcCC
Confidence 45699999999999984 56799999999 99999999999888876444
No 263
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=70.55 E-value=13 Score=26.82 Aligned_cols=53 Identities=19% Similarity=0.242 Sum_probs=43.2
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL 80 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y 80 (233)
.+.+++-+.+. +.+.-|.++. .+--+.-.+++-.||+.|+|-+... ++.|+++
T Consensus 9 ~a~~~V~~~~~--~S~S~lQR~~--~IGynrAariid~lE~~GiV~p~~g--~~~R~Vl 61 (63)
T smart00843 9 EAVELVIETQK--ASTSLLQRRL--RIGYNRAARLIDQLEEEGIVGPANG--SKPREVL 61 (63)
T ss_pred HHHHHHHHhCC--CChHHHHHHH--hcchhHHHHHHHHHHHCcCCCCCCC--CCCCeec
Confidence 45567777777 7999999999 8888999999999999999987655 3466665
No 264
>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=70.52 E-value=44 Score=25.27 Aligned_cols=69 Identities=14% Similarity=0.230 Sum_probs=43.8
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL 115 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~ 115 (233)
.++++.+.+ |++.++|+ .-|+.|||.+...-. .+. -+|+ .+=|..|+. .
T Consensus 2 ~i~eva~~~--gvs~~tlR----~ye~~Gll~p~~~~~-~gy-----------------R~Y~-----~~~~~~l~~--I 50 (97)
T cd04782 2 TTGEFAKLC--GISKQTLF----HYDKIGLFKPEIVKE-NGY-----------------RYYT-----LEQFEQLDI--I 50 (97)
T ss_pred CHHHHHHHH--CcCHHHHH----HHHHCCCCCCCccCC-CCC-----------------ccCC-----HHHHHHHHH--H
Confidence 467889999 99988765 468899996533111 122 2333 344444444 3
Q ss_pred HHhhhCCCCCHHHHHHHHHHh
Q 026766 116 KQIIKLKVATLEGISDSIKRS 136 (233)
Q Consensus 116 ~~i~~~~~~T~~~I~~~I~~~ 136 (233)
.+++..+ .++++|.+++...
T Consensus 51 ~~lr~~G-~~l~eI~~~l~~~ 70 (97)
T cd04782 51 LLLKELG-ISLKEIKDYLDNR 70 (97)
T ss_pred HHHHHcC-CCHHHHHHHHhcC
Confidence 3455665 6699999999754
No 265
>PF07574 SMC_Nse1: Nse1 non-SMC component of SMC5-6 complex; InterPro: IPR011513 Saccharomyces cerevisiae Nse1 (Q07913 from SWISSPROT) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism [, ]. It is conserved in eukaryotes from yeast to human.; PDB: 3NW0_A.
Probab=70.44 E-value=69 Score=27.48 Aligned_cols=106 Identities=11% Similarity=0.104 Sum_probs=56.5
Q ss_pred HHHHHHHHhCCC-ceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhhCCCC-CH--HHH
Q 026766 54 TKSIKSLQNKSL-IKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVA-TL--EGI 129 (233)
Q Consensus 54 ~k~LK~Le~k~l-IK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~-T~--~~I 129 (233)
+.+=++|..-++ |+.+++=+..++.+|.+.++.+++..--++ .|..+-|+-++..+-..+...+.. +. .+
T Consensus 51 ~~IN~~L~~l~~~Ir~~~~~q~~g~~~y~lVN~~~D~~sklaT-----~ys~~Ei~ffK~lle~I~~~~~~~~~~~~~~- 124 (200)
T PF07574_consen 51 NEINSKLSPLDFEIRRIRDGQPDGERYYALVNTSSDEISKLAT-----TYSPNEIAFFKKLLEEIVESENTSRSESASS- 124 (200)
T ss_dssp HHHHHHHGGGTEEEEEEE--TTT--EEEEEEESSS-TTHHHHT-----TS-HHHHHHHHHHHHHHHHSSSS-EEH-----
T ss_pred HHHHHhhhhcCcEEEEEeccCCCCCEEEEEEeCCCCHHHHhcC-----CCCHHHHHHHHHHHHHHHhCCCCceehhhHH-
Confidence 333334444333 555555123799999999999999877665 455555677777776666654332 11 01
Q ss_pred HHHHHHhC---Cc-----------------------ccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 130 SDSIKRSG---AF-----------------------KVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 130 ~~~I~~~~---i~-----------------------~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
...++... .. ...|+..+++++|+.||=||=++.-+
T Consensus 125 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~eae~lL~~lv~~gWl~~s~ 186 (200)
T PF07574_consen 125 IMALNEVQAIKLKRPGDPSQWTQGVSYAGGSTQLAQDKGLSKSEAESLLDRLVEDGWLYRSR 186 (200)
T ss_dssp HHHHGGGTT-SSS---H-------------------------HHHHHHHHHHHHTTSE-EEE
T ss_pred HHHHHHHHHHHHhccCcccccccccccccccccccccccchHHHHHHHHHHHHHCCCceeCC
Confidence 22222211 00 12588999999999999999997753
No 266
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=70.28 E-value=14 Score=30.73 Aligned_cols=60 Identities=12% Similarity=0.100 Sum_probs=50.3
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCee
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKK 78 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK 78 (233)
-|++.-+.++.+|...+- -...++...+ +=.-..|.+-|..|+.-|+|---+..+.+.-+
T Consensus 61 vLsp~nleLl~~Ia~~~P--~Si~ElAe~v--gRdv~nvhr~Ls~l~~~GlI~fe~~gq~k~P~ 120 (144)
T COG4190 61 VLSPRNLELLELIAQEEP--ASINELAELV--GRDVKNVHRTLSTLADLGLIFFEEDGQRKQPV 120 (144)
T ss_pred HhChhHHHHHHHHHhcCc--ccHHHHHHHh--CcchHHHHHHHHHHHhcCeEEEecCCcccCce
Confidence 467777788899988877 7789999999 88899999999999999999888877654433
No 267
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=70.15 E-value=17 Score=33.22 Aligned_cols=57 Identities=16% Similarity=0.297 Sum_probs=44.3
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF 85 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l 85 (233)
++-=+.++-++.+ |- -...+|+..+ +.++..+...||+|++.|||-. ..+.|.|..+
T Consensus 12 SekRk~lLllL~e-gP--kti~EI~~~l--~vs~~ai~pqiKkL~~~~LV~~-------~~~~Y~LS~~ 68 (260)
T COG4742 12 SEKRKDLLLLLKE-GP--KTIEEIKNEL--NVSSSAILPQIKKLKDKGLVVQ-------EGDRYSLSSL 68 (260)
T ss_pred cHHHHHHHHHHHh-CC--CCHHHHHHHh--CCCcHHHHHHHHHHhhCCCEEe-------cCCEEEecch
Confidence 3444556666666 44 6789999999 9999999999999999999955 3567877653
No 268
>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=70.00 E-value=45 Score=25.17 Aligned_cols=71 Identities=13% Similarity=0.171 Sum_probs=44.9
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+...++.+.+ |++.++|. .-|+.|||.+...-. .+.+.| +.+=|..|..+
T Consensus 1 m~i~eva~~~--gvs~~tlR----~ye~~Gll~p~~r~~-~gyR~Y----------------------~~~~l~~l~~I- 50 (96)
T cd04788 1 WKIGELARRT--GLSVRTLH----HYDHIGLLSPSQRTE-GGHRLY----------------------DRADIRRLHQI- 50 (96)
T ss_pred CCHHHHHHHH--CcCHHHHH----HHHHCCCCCCCccCC-CCceee----------------------CHHHHHHHHHH-
Confidence 3567889999 99987764 578899996532222 233333 44444444433
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhC
Q 026766 115 LKQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
..+++.+ .++++|.+++....
T Consensus 51 -~~lr~~G-~~l~eI~~~l~~~~ 71 (96)
T cd04788 51 -IALRRLG-FSLREIGRALDGPD 71 (96)
T ss_pred -HHHHHcC-CCHHHHHHHHhCCC
Confidence 3345555 66999999997543
No 269
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=69.49 E-value=13 Score=30.36 Aligned_cols=55 Identities=11% Similarity=0.184 Sum_probs=47.2
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026766 109 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN 167 (233)
Q Consensus 109 ~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~ 167 (233)
.+-..+.+.|=.++.+|++||+++|.+.. +++..-|..+|+-|+=-|.|-..+.+
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~~----ews~sTV~TLl~RL~KKg~l~~~kdg 60 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPADR----EWSYSTVKTLLNRLVKKGLLTRKKDG 60 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhcc----cccHHHHHHHHHHHHhccchhhhhcC
Confidence 45567778888899999999999999774 89999999999999999998877643
No 270
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=69.43 E-value=4 Score=32.45 Aligned_cols=44 Identities=18% Similarity=0.247 Sum_probs=36.1
Q ss_pred CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026766 33 MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL 80 (233)
Q Consensus 33 ~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y 80 (233)
+=|...-|-.++ ++.-..-.++|+.|.++|+|+.| .+|.++-||
T Consensus 59 k~it~svl~dRl--kIngsLAr~alr~L~~kG~Ik~V--s~h~~q~IY 102 (110)
T KOG1767|consen 59 KLITPSVLSDRL--KINGSLARAALRELSNKGVIKQV--SKHSKQVIY 102 (110)
T ss_pred eeecHHHhhhhh--hhchHHHHHHHHHHHhcchHHHH--hhcchheee
Confidence 346777788888 99999999999999999999875 345677777
No 271
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=69.29 E-value=15 Score=32.90 Aligned_cols=45 Identities=18% Similarity=0.232 Sum_probs=39.8
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
...||+.|+.|+.++. +|...++|...+ +++.++|+..++.+-.|
T Consensus 188 ~~~LT~RE~evl~l~a----~G~s~~eIA~~L--~IS~~TVk~hl~~i~~K 232 (247)
T TIGR03020 188 AGLITAREAEILAWVR----DGKTNEEIAAIL--GISSLTVKNHLQHIFKK 232 (247)
T ss_pred ccCCCHHHHHHHHHHH----CCCCHHHHHHHH--CcCHHHHHHHHHHHHHH
Confidence 6689999999999863 789999999999 99999999999887654
No 272
>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=69.25 E-value=8.1 Score=32.65 Aligned_cols=46 Identities=17% Similarity=0.289 Sum_probs=37.7
Q ss_pred HHHHHHHhhCC-------CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 22 LIYDVIRSKQD-------MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 22 lVy~~I~~aG~-------~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
.||+.|++.=- .=|...+|.++. |+..+.|+.+|+.|+..|||...
T Consensus 15 ~v~~~l~~~I~~g~l~pG~~L~e~~La~~l--gVSRtpVReAL~~L~~eGlv~~~ 67 (212)
T TIGR03338 15 LVQDEIERAILSGELPPGAKLNESDIAARL--GVSRGPVREAFRALEEAGLVRNE 67 (212)
T ss_pred HHHHHHHHHHHcCCCCCCCEecHHHHHHHh--CCChHHHHHHHHHHHHCCCEEEe
Confidence 67888875422 235678999999 99999999999999999999753
No 273
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=69.16 E-value=9.3 Score=32.13 Aligned_cols=61 Identities=21% Similarity=0.237 Sum_probs=46.5
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe-eeE
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK-KHL 80 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r-K~Y 80 (233)
...||.....++.+|.-.+- |.+.+|-.-= |.. -..+|++|.++|||+.+..-..+|| .+|
T Consensus 77 ~~~LS~aalEtLAiIAY~QP--iTr~eIe~IR--Gv~---s~~~i~~L~e~glI~~~gr~~~~Grp~ly 138 (159)
T PF04079_consen 77 PPKLSQAALETLAIIAYKQP--ITRAEIEEIR--GVN---SDSVIKTLLERGLIEEVGRKDTPGRPILY 138 (159)
T ss_dssp CHHHHHHHHHHHHHHHHH-S--EEHHHHHHHH--TS-----HCHHHHHHHTTSEEEEEE-TTTT--EEE
T ss_pred cCCCCHHHHHHHHHHHhcCC--cCHHHHHHHc--CCC---hHHHHHHHHHCCCEEecCcCCCCCCCeEe
Confidence 44688888999999988876 9999999887 554 4667899999999999997776664 444
No 274
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=69.13 E-value=21 Score=26.90 Aligned_cols=45 Identities=11% Similarity=0.274 Sum_probs=41.4
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
.|=++|+..|. +..++|..+. ++|...|.--|..|+.+|-|.+|.
T Consensus 6 qlRd~l~~~gr--~s~~~Ls~~~--~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 6 QVRDLLALRGR--MEAAQISQTL--NTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHHcCc--ccHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeec
Confidence 46678899998 8899999999 999999999999999999999886
No 275
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=69.06 E-value=4.8 Score=32.74 Aligned_cols=47 Identities=13% Similarity=0.123 Sum_probs=35.6
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHh-hc--CCChHHHHHHHHHHH
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKREL-RV--NLPDNIVTKSIKSLQ 61 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t-~~--~l~~~~v~k~LK~Le 61 (233)
.||+-|..|+.++.++-++|+...+|..+. +. ++..++|...++.|-
T Consensus 154 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~ 203 (226)
T TIGR02154 154 SLGPTEFRLLHFFMTHPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLR 203 (226)
T ss_pred EcCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHH
Confidence 599999999999999999999999985543 11 667666655554444
No 276
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=68.84 E-value=18 Score=27.99 Aligned_cols=48 Identities=13% Similarity=0.185 Sum_probs=36.6
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 110 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 110 l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
+.-.|+.++...+.-.+.-|+..+ .++.++|+.+++.|+--|.||++.
T Consensus 8 l~~~IL~hl~~~~~Dy~k~ia~~l--------~~~~~~v~~~l~~Le~~GLler~~ 55 (92)
T PF10007_consen 8 LDLKILQHLKKAGPDYAKSIARRL--------KIPLEEVREALEKLEEMGLLERVE 55 (92)
T ss_pred hHHHHHHHHHHHCCCcHHHHHHHH--------CCCHHHHHHHHHHHHHCCCeEEec
Confidence 344566666666655566565543 789999999999999999999986
No 277
>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=68.80 E-value=12 Score=32.25 Aligned_cols=47 Identities=6% Similarity=0.097 Sum_probs=37.6
Q ss_pred HHHHHHHhhC-------CCcc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 22 LIYDVIRSKQ-------DMGI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 22 lVy~~I~~aG-------~~GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
.||+.|.+.= ++=+ ..++|.++. |+..+.|+-+|+.|+..|||...+
T Consensus 10 ~v~~~l~~~I~~g~l~pG~~LpsE~~La~~l--gVSRtpVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 10 FAEEYIVESIWNNRFPPGSILPAERELSELI--GVTRTTLREVLQRLARDGWLTIQH 64 (235)
T ss_pred HHHHHHHHHHHcCCCCCCCcCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEeC
Confidence 4666666432 2226 688999999 999999999999999999998654
No 278
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=68.76 E-value=62 Score=26.27 Aligned_cols=69 Identities=13% Similarity=0.226 Sum_probs=43.8
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
..+.++.+.+ |++.++|+ .-|++|||.+...-. .+.+ +|+ .+=|..|+.+
T Consensus 2 ~~I~e~a~~~--gvs~~tlR----~Ye~~GLl~p~~r~~-~gyR-----------------~Y~-----~~~l~~l~~I- 51 (140)
T PRK09514 2 YRIGELAKLA--EVTPDTLR----FYEKQGLMDPEVRTE-GGYR-----------------LYT-----EQDLQRLRFI- 51 (140)
T ss_pred CcHHHHHHHH--CcCHHHHH----HHHHCCCCCCcccCC-CCCe-----------------eeC-----HHHHHHHHHH-
Confidence 3578899999 99988765 469999996532111 2333 333 3334444433
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 026766 115 LKQIIKLKVATLEGISDSIKR 135 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~ 135 (233)
..++..+ .|+++|.+++..
T Consensus 52 -~~lr~~G-~sL~eI~~~l~~ 70 (140)
T PRK09514 52 -RRAKQLG-FTLEEIRELLSI 70 (140)
T ss_pred -HHHHHcC-CCHHHHHHHHHh
Confidence 3345554 579999999974
No 279
>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=68.74 E-value=18 Score=27.82 Aligned_cols=41 Identities=10% Similarity=0.152 Sum_probs=32.9
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
|+..+..++..|.+.|+ | ..=.+.+ |++++.+++.|+.||+
T Consensus 2 ~~~~~l~~~~av~~~gS--i--s~AA~~L--~iS~stvs~~I~~LE~ 42 (99)
T TIGR00637 2 ADPRRVALLKAIARMGS--I--SQAAKDA--GISYKSAWDYIRAMNN 42 (99)
T ss_pred CCHHHHHHHHHHHHhCC--H--HHHHHHH--CCCHHHHHHHHHHHHH
Confidence 45667788889999888 3 3334567 9999999999999996
No 280
>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=68.64 E-value=34 Score=24.94 Aligned_cols=35 Identities=11% Similarity=0.237 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 123 ~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
.+|.++|++.+ .++...+++|++.|+-.|.|+..+
T Consensus 25 ~~s~~eiA~~~--------~i~~~~l~kil~~L~~~Gli~s~~ 59 (83)
T PF02082_consen 25 PVSSKEIAERL--------GISPSYLRKILQKLKKAGLIESSR 59 (83)
T ss_dssp -BEHHHHHHHH--------TS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CCCHHHHHHHH--------CcCHHHHHHHHHHHhhCCeeEecC
Confidence 38999999854 378899999999999999998765
No 281
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=68.60 E-value=6.5 Score=34.72 Aligned_cols=52 Identities=19% Similarity=0.268 Sum_probs=45.8
Q ss_pred CCCCCChHHHHHHHHHHhhCCC--cccHHHHHHHhhcCCChHHHHHHHHHHHhCCC
Q 026766 12 PSDSLTDHERLIYDVIRSKQDM--GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL 65 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~--GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l 65 (233)
...+||+.|+.|.++|.+..+. -+..++|.+++ +..+.+|.|-.|+|==+|+
T Consensus 10 ~~~~Lt~~e~~Ia~yil~n~~~v~~~si~~lA~~~--~vS~aTv~Rf~kklG~~gf 63 (284)
T PRK11302 10 RLEHLSKSERKVAEVILASPQTAIHSSIATLAKMA--NVSEPTVNRFCRSLDTKGF 63 (284)
T ss_pred HHhhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHh--CCCHHHHHHHHHHcCCCCH
Confidence 3567999999999999987765 47899999999 9999999999999977776
No 282
>PRK10403 transcriptional regulator NarP; Provisional
Probab=68.51 E-value=18 Score=28.89 Aligned_cols=45 Identities=22% Similarity=0.341 Sum_probs=38.5
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
...||+.|..|+.++. +|...++|..++ +++.++|...++.|-+|
T Consensus 151 ~~~Lt~~e~~vl~~~~----~g~s~~~ia~~l--~~s~~tv~~~~~~i~~k 195 (215)
T PRK10403 151 FSVLTERELDVLHELA----QGLSNKQIASVL--NISEQTVKVHIRNLLRK 195 (215)
T ss_pred cccCCHHHHHHHHHHH----CCCCHHHHHHHc--CCCHHHHHHHHHHHHHH
Confidence 4579999999999885 469999999999 99999988888887654
No 283
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=68.50 E-value=12 Score=31.40 Aligned_cols=45 Identities=11% Similarity=0.256 Sum_probs=33.8
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCC-------ChHH-------HHHHHHHHHhCCCceeee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNL-------PDNI-------VTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l-------~~~~-------v~k~LK~Le~k~lIK~vk 70 (233)
.|+..|-..|. |=...|++.. |. |.+. ++++|++||+.|||+..+
T Consensus 57 sIlR~vY~~gp--vGV~~L~~~y--Gg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 57 SILRKVYIDGP--VGVERLRTAY--GGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred HHHHHHHHcCC--ccHHHHHHHH--CCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 45555656665 6667889988 66 5444 999999999999997643
No 284
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=68.24 E-value=12 Score=35.77 Aligned_cols=44 Identities=9% Similarity=0.157 Sum_probs=37.1
Q ss_pred HHHHHH--hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 23 IYDVIR--SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 23 Vy~~I~--~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
|+.++. ..+.++....+|.+++ +++...++++|..|++.|||.+
T Consensus 297 iL~~l~~~~~~g~~~t~~~La~~l--~~~~~~v~~iL~~L~~agLI~~ 342 (412)
T PRK04214 297 LLGRLDQARKHGKALDVDEIRRLE--PMGYDELGELLCELARIGLLRR 342 (412)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHh--CCCHHHHHHHHHHHHhCCCeEe
Confidence 444553 3455799999999999 9999999999999999999963
No 285
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=68.11 E-value=16 Score=32.32 Aligned_cols=52 Identities=17% Similarity=0.209 Sum_probs=41.2
Q ss_pred CCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCcee
Q 026766 11 APSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIKE 68 (233)
Q Consensus 11 ~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK~ 68 (233)
..+++++-.+..++..|.+.|+ +. .=.+++ +++|..|++.|+.||+ -.|..+
T Consensus 3 ~~~~~~~l~~L~~F~~va~~gs--~s--~AA~~L--~isQpavS~~I~~LE~~lg~~Lf~R 57 (302)
T TIGR02036 3 RRLNSFQLSKMHTFEVAARHQS--FS--LAAEEL--SLTPSAISHRINQLEEELGIQLFVR 57 (302)
T ss_pred ccccCcCHHHHHHHHHHHHhCC--HH--HHHHHH--CCCHHHHHHHHHHHHHHhCCceEEE
Confidence 4577888899999999999988 33 335667 9999999999999997 455544
No 286
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=67.96 E-value=22 Score=32.38 Aligned_cols=60 Identities=15% Similarity=0.212 Sum_probs=45.7
Q ss_pred CCCCCChHHHHHHHHHH---hhCCCcccHHHHHHH-------hhc-CCChHHHHHHHHHHHhCCCceeeec
Q 026766 12 PSDSLTDHERLIYDVIR---SKQDMGIWTRDMKRE-------LRV-NLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~---~aG~~GIw~~dik~~-------t~~-~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
.+++|+..+++++..|. ..++..+..+++-.+ .+. -+..+++...|..||..|||....+
T Consensus 282 ~i~~l~~~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~~ 352 (365)
T TIGR02928 282 LIRGLPTHSKLVLLAIANLAANDEDPFRTGEVYEVYKEVCEDIGVDPLTQRRISDLLNELDMLGLVEAEER 352 (365)
T ss_pred HHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEEE
Confidence 45789999998888776 336667888866653 211 2778999999999999999998653
No 287
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=67.67 E-value=11 Score=37.17 Aligned_cols=104 Identities=10% Similarity=0.110 Sum_probs=73.6
Q ss_pred HHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHH
Q 026766 53 VTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDS 132 (233)
Q Consensus 53 v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~ 132 (233)
|+|+.+.++..||-+..-... ..-..+.+.--.+.++.|...==..++- -.+..+..|+.|+...++.|..++.+-
T Consensus 350 i~rm~~~~~~~gl~~p~f~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~il~~~~en~~~T~~~L~~~ 425 (467)
T COG2865 350 IRRMFDLMEENGLPKPEFEED-NDYVTVILHGKGENEDETEEKVTRQEET---SLSERQEKILELIKENGKVTARELREI 425 (467)
T ss_pred HHHHHHHHHHcCCCCceeecc-CCeEEEEEeccchHHHhhcccccccccc---ChhHHHHHHHHHHhhccccCHHHHHHH
Confidence 567778888888887755544 4666666666555555555421112222 234555789999999999999998876
Q ss_pred HHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeCC
Q 026766 133 IKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNG 168 (233)
Q Consensus 133 I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~~ 168 (233)
+. +|.+.+...|.-|+-.|++..+-+++
T Consensus 426 l~--------is~~~i~r~i~~Lv~~g~~~~~g~~~ 453 (467)
T COG2865 426 LG--------ISSETIRRRIANLVKRGLLKQLGSSG 453 (467)
T ss_pred hC--------cchhhHHHHHHHHhcccHHHHhCcCC
Confidence 54 77888999999999999998875443
No 288
>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=67.65 E-value=24 Score=23.64 Aligned_cols=48 Identities=13% Similarity=0.222 Sum_probs=39.0
Q ss_pred HHHHHHHhhhCCC--CCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 111 KSQCLKQIIKLKV--ATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 111 ~~~~~~~i~~~~~--~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
.-.++.+|...+. .|..||++.+. ++..-|-.+|+.|+-.|.|+...+
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l~--------~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERLG--------ISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHHT--------S-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHC--------cCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4467888888877 79999998764 778889999999999999998764
No 289
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=67.53 E-value=28 Score=28.10 Aligned_cols=28 Identities=18% Similarity=0.127 Sum_probs=23.5
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
++.+++.+.+ |++.++|+ ..|++|||..
T Consensus 2 ysI~eVA~~~--GVs~~TLR----~wE~~GLl~p 29 (120)
T cd04767 2 YPIGVVAELL--NIHPETLR----IWERHGLIKP 29 (120)
T ss_pred CCHHHHHHHH--CcCHHHHH----HHHHCCCCCC
Confidence 4678899999 99998876 7888999965
No 290
>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=67.48 E-value=10 Score=28.08 Aligned_cols=38 Identities=29% Similarity=0.335 Sum_probs=26.6
Q ss_pred HhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCC
Q 026766 117 QIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDN 159 (233)
Q Consensus 117 ~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg 159 (233)
.=+++|++|.++|.+++... .++.++|..|+.+|.=-|
T Consensus 15 ~gK~~G~lT~~eI~~~L~~~-----~~~~e~id~i~~~L~~~g 52 (82)
T PF03979_consen 15 KGKKKGYLTYDEINDALPED-----DLDPEQIDEIYDTLEDEG 52 (82)
T ss_dssp HHHHHSS-BHHHHHHH-S-S--------HHHHHHHHHHHHTT-
T ss_pred HHhhcCcCCHHHHHHHcCcc-----CCCHHHHHHHHHHHHHCC
Confidence 33568999999999999744 489999999999998666
No 291
>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=67.30 E-value=12 Score=29.13 Aligned_cols=44 Identities=18% Similarity=0.263 Sum_probs=32.6
Q ss_pred CChHHHHH----HHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 026766 16 LTDHERLI----YDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQ 61 (233)
Q Consensus 16 L~~~e~lV----y~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le 61 (233)
||++|+.+ |.++.+-=+.|+.+++|.+++ |...++|+|.=+.|.
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~l--GiS~atIsR~sn~lk 80 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKL--GVSIATITRGSNNLK 80 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHh--CCChhhhhHHHhhcc
Confidence 67777655 334443335789999999999 999999988766654
No 292
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=66.98 E-value=16 Score=32.23 Aligned_cols=44 Identities=20% Similarity=0.252 Sum_probs=39.2
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
..||+-|+.|+..+. +|...++|...+ ++..++|+..|+.+-+|
T Consensus 178 ~~LT~rE~evl~~~a----~G~t~~eIa~~l--~is~~TV~~h~~~~~~K 221 (240)
T PRK10188 178 MNFSKREKEILKWTA----EGKTSAEIAMIL--SISENTVNFHQKNMQKK 221 (240)
T ss_pred CCCCHHHHHHHHHHH----cCCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 479999999999994 678999999999 99999999999887654
No 293
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=66.81 E-value=67 Score=26.18 Aligned_cols=106 Identities=17% Similarity=0.189 Sum_probs=61.5
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCC
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGA 95 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~ 95 (233)
|+.+.+ ..+|+-|. .|+--.||.+++ .++..-|+|+|+...+-|-|..= .+...+.|+
T Consensus 18 Lp~~~R--~rIvela~-~G~rp~~Isr~l--~Vs~gcVsKIl~Ry~eTGsi~Pg-~iGGskprv---------------- 75 (125)
T PF00292_consen 18 LPNELR--QRIVELAK-EGVRPCDISRQL--RVSHGCVSKILSRYRETGSIRPG-PIGGSKPRV---------------- 75 (125)
T ss_dssp S-HHHH--HHHHHHHH-TT--HHHHHHHH--T--HHHHHHHHHHHHHHS-SS-----S----SS----------------
T ss_pred CcHHHH--HHHHHHhh-hcCCHHHHHHHH--ccchhHHHHHHHHHHHhcccCcc-cccCCCCCC----------------
Confidence 444433 35666664 599999999999 99999999999999999988552 222111111
Q ss_pred cccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcc--cccCHHHHHHHHH
Q 026766 96 WYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFK--VDLTKQQIEEIVR 153 (233)
Q Consensus 96 wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~--~~Ls~~di~~il~ 153 (233)
...+ +-..+..|...++...+.||.+-+.+.||.. ..=|+..|-.||+
T Consensus 76 ------~tp~----v~~~I~~~k~enP~ifawEiR~~L~~~gvc~~~~~PsvssInRilr 125 (125)
T PF00292_consen 76 ------ATPE----VVEKIEQYKRENPTIFAWEIRDRLIADGVCDRSNVPSVSSINRILR 125 (125)
T ss_dssp ------S-HC----HHHHHHHHHHH-TTS-HHHHHHHHHHTTSS-TTTS--HHHHHHHHH
T ss_pred ------CChH----HHHHHHHHHhcCCCcchHHHHHHHHHcCCCCCCCCCCHHHHHHhhC
Confidence 1111 3334445666788888999999999999875 2346666666653
No 294
>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=66.77 E-value=59 Score=25.30 Aligned_cols=70 Identities=9% Similarity=0.207 Sum_probs=44.1
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
++..++.+.+ |++.++| ..-|+.|||++++. .. +.++| + .+=+..|+ .
T Consensus 1 ~~ige~a~~~--gvs~~tL----ryYe~~GLi~p~~~-~~-~yR~Y-----------------~-----~~d~~~l~--~ 48 (116)
T cd04769 1 MYIGELAQQT--GVTIKAI----RLYEEKGLLPSPKR-SG-NYRVY-----------------D-----AQHVECLR--F 48 (116)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCCC-CC-Cceee-----------------C-----HHHHHHHH--H
Confidence 4578889999 9998776 45889999976442 21 44444 2 22233332 2
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhC
Q 026766 115 LKQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
..+++.. ..++++|.+++....
T Consensus 49 I~~lr~~-G~sl~eI~~~l~~~~ 70 (116)
T cd04769 49 IKEARQL-GFTLAELKAIFAGHE 70 (116)
T ss_pred HHHHHHc-CCCHHHHHHHHhccc
Confidence 3334455 466999999998654
No 295
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=66.66 E-value=13 Score=32.02 Aligned_cols=48 Identities=17% Similarity=0.282 Sum_probs=35.8
Q ss_pred CCCCChHHHHHHHHHHh-hCCCcccHHHHHHHhhcCCChHHHHH----HHHHHHh
Q 026766 13 SDSLTDHERLIYDVIRS-KQDMGIWTRDMKRELRVNLPDNIVTK----SIKSLQN 62 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~-aG~~GIw~~dik~~t~~~l~~~~v~k----~LK~Le~ 62 (233)
+..||+.++.|+.+..- ..-.|...++|...+ |++.++|.+ ++++|.+
T Consensus 176 l~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~l--gis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 176 LKKLSDREKQIMELRFGLNGGEEKTQKEVADML--GISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred HHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHHHHH
Confidence 55688888888877542 336789999999999 999998854 4555543
No 296
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=66.52 E-value=16 Score=32.61 Aligned_cols=45 Identities=16% Similarity=0.252 Sum_probs=38.3
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
.+++|+-.+-.++..|.+.|+ +... .+++ +++|..|++.|+.||+
T Consensus 4 ~~~~mdl~~L~~f~av~e~gs--~t~A--A~~L--~iSQpavS~~I~~LE~ 48 (319)
T PRK10216 4 SLTTLDLNLLLCLQLLMQERS--VTKA--AKRM--NVTPSAVSKSLAKLRA 48 (319)
T ss_pred chhhcCHHHHHHHHHHHHhCC--HHHH--HHHh--CCCHHHHHHHHHHHHH
Confidence 357788899999999999998 4444 4778 9999999999999997
No 297
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=66.15 E-value=70 Score=25.91 Aligned_cols=69 Identities=12% Similarity=0.193 Sum_probs=45.4
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+.+.++.+.+ |++.++| ..-|+.|||.+...-. .|.++| |.+-|..|+.+
T Consensus 1 m~Ige~a~~~--gvs~~tl----RyYE~~GLl~p~~r~~-~gyR~Y----------------------~~~~l~~l~~I- 50 (135)
T PRK10227 1 MNISDVAKIT--GLTSKAI----RFYEEKGLVTPPMRSE-NGYRTY----------------------TQQHLNELTLL- 50 (135)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCcccCC-CCcccC----------------------CHHHHHHHHHH-
Confidence 3568899999 9998765 5689999997654322 244443 44555555432
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 026766 115 LKQIIKLKVATLEGISDSIKR 135 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~ 135 (233)
..+++. ..++++|.+++.-
T Consensus 51 -~~lr~~-G~sl~eI~~~l~~ 69 (135)
T PRK10227 51 -RQARQV-GFNLEESGELVNL 69 (135)
T ss_pred -HHHHHC-CCCHHHHHHHHHh
Confidence 334455 4679999999974
No 298
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=66.07 E-value=17 Score=33.59 Aligned_cols=86 Identities=17% Similarity=0.201 Sum_probs=61.7
Q ss_pred CCCCChHHHHHHHHHH---hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc---CCCeeeEEeeccc
Q 026766 13 SDSLTDHERLIYDVIR---SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH---SKGKKHLMAVEFE 86 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~---~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~---~~~rK~Yml~~le 86 (233)
+..||+.|+-|++.+- ...+.-|-.++|...+ |-++.+|+..+..|...||+..++--+ -|+-|-|=.-+++
T Consensus 1 ~~~LT~~QkeIL~aLi~LY~~~~r~IKgeeIA~~l--~rnpGTVRNqmq~LkaLgLVegvpGPkGGY~PT~kAYe~L~iq 78 (294)
T COG2524 1 MKELTSSQKEILQALINLYRRKKRPIKGEEIAEVL--NRNPGTVRNQMQSLKALGLVEGVPGPKGGYKPTSKAYEALSIQ 78 (294)
T ss_pred CccccHHHHHHHHHHHHHHHhcCCCcchHHHHHHH--ccCcchHHHHHHHHHhcCccccccCCCCCccccHHHHHHhccC
Confidence 4579999998887654 3444479999999999 999999999999999999999988665 3455556433333
Q ss_pred cCCCcccCCcccCC
Q 026766 87 PSKEISGGAWYSEG 100 (233)
Q Consensus 87 Ps~eiTGG~wy~d~ 100 (233)
--+..+-=+-|.||
T Consensus 79 t~~~~~~Vpi~~~G 92 (294)
T COG2524 79 TLETEFVVPIYKDG 92 (294)
T ss_pred CCCcceEEEEEEcC
Confidence 32333333445554
No 299
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=66.06 E-value=32 Score=26.04 Aligned_cols=57 Identities=11% Similarity=0.025 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026766 107 IKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME 163 (233)
Q Consensus 107 I~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~ 163 (233)
=|.|+.++.+.=.....+|.+.|.+++.+.==.=..=|.+-|..-|.+|+-++||..
T Consensus 13 ~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY~ 69 (80)
T PF10264_consen 13 PEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKIYH 69 (80)
T ss_pred HHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCceee
Confidence 356666666666677899999999999987311124689999999999999999976
No 300
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=65.80 E-value=77 Score=32.10 Aligned_cols=111 Identities=10% Similarity=0.189 Sum_probs=83.1
Q ss_pred CCChHHHHHHHHHHhh-CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCccc
Q 026766 15 SLTDHERLIYDVIRSK-QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISG 93 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~a-G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTG 93 (233)
.+++++..+.+.|++. .-.=-|.+||-+.+ +++...+...|+.|...|.+-++.. .+|
T Consensus 486 ~~~~~~~~~~~~l~~~~~~~p~~~~~~~~~l--~~~~~~~~~~l~~l~~~g~lv~l~~------~~~------------- 544 (614)
T PRK10512 486 GFSEEQQALWQKAEPLFGDEPWWVRDLAKET--GTDEQAMRLTLRQAAQQGIITAIVK------DRY------------- 544 (614)
T ss_pred CCCHHHHHHHHHHHHHHhcCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEecC------CEE-------------
Confidence 4677766666666541 23457889999999 9999999999999999997755432 233
Q ss_pred CCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEE
Q 026766 94 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIM 162 (233)
Q Consensus 94 G~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie 162 (233)
|+.+.++.+.+.+..+++..+..|+.+..+.+ | +|-.-.-.+|+-|=-.|...
T Consensus 545 --------~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~---g-----~sRK~~i~lLE~~D~~~~T~ 597 (614)
T PRK10512 545 --------YRNDRIVQFANMIRELDQECGSTCAADFRDRL---G-----VGRKLAIQILEYFDRIGFTR 597 (614)
T ss_pred --------ECHHHHHHHHHHHHHHHhhCCcEeHHHHHHHh---C-----ccHHHHHHHHHHhccCCCEE
Confidence 46788899999999999999999999988876 3 44555666677666555443
No 301
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=65.12 E-value=1e+02 Score=27.47 Aligned_cols=58 Identities=19% Similarity=0.283 Sum_probs=42.5
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC-CcccccCHHHHHHHHHHHh
Q 026766 99 EGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSG-AFKVDLTKQQIEEIVRALV 156 (233)
Q Consensus 99 d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~-i~~~~Ls~~di~~il~~Lv 156 (233)
..+++.+-++.+-..+-.-|.+...-|.+||.+.|++.- --.+.||.+|+++|++.|.
T Consensus 147 ~~~~~~~k~~~~i~~iK~~va~~~~~t~~eI~~IV~~~~~~~~i~ls~~q~~~i~~l~~ 205 (225)
T PF06207_consen 147 GDGIGDEKANAAIAEIKEEVAKQKPKTDEEIRNIVNNVLNNYNINLSDEQIQQIVNLMK 205 (225)
T ss_pred ccCCCHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 445677766666666777776777679999999887541 1124599999999999885
No 302
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=65.06 E-value=20 Score=31.25 Aligned_cols=46 Identities=20% Similarity=0.340 Sum_probs=39.5
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
....||+.|+.|+..+. .|...++|...+ +++.++|...|++..+|
T Consensus 168 ~~~~Lt~re~evl~~~a----~G~t~~eIa~~l--~is~~Tv~~~l~~~~~k 213 (232)
T TIGR03541 168 EAGVLSEREREVLAWTA----LGRRQADIAAIL--GISERTVENHLRSARRK 213 (232)
T ss_pred hhccCCHHHHHHHHHHH----CCCCHHHHHHHH--CcCHHHHHHHHHHHHHH
Confidence 35579999999999963 779999999999 99999999888887654
No 303
>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=64.97 E-value=6.8 Score=27.09 Aligned_cols=39 Identities=15% Similarity=0.240 Sum_probs=32.6
Q ss_pred CCcccHHHHHHHhhc-CCChHHHHHHHHHHHhCCCceeee
Q 026766 32 DMGIWTRDMKRELRV-NLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 32 ~~GIw~~dik~~t~~-~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
..||-..+|+.++.. +++++.....|..|+++|.|+.-.
T Consensus 15 r~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~~g 54 (59)
T PF09106_consen 15 RPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKVEG 54 (59)
T ss_dssp SS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEEES
T ss_pred ccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeeeEC
Confidence 579999999988855 889999999999999999998743
No 304
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=64.93 E-value=17 Score=32.19 Aligned_cols=36 Identities=11% Similarity=0.391 Sum_probs=33.0
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 31 QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 31 G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
++.++..+++.+++ +.++.+..|.|+.||..++|-+
T Consensus 16 ~~~~~t~~ela~~l--~~S~qta~R~l~~le~~~~I~R 51 (214)
T COG1339 16 RGVKVTSSELAKRL--GVSSQTAARKLKELEDEGYITR 51 (214)
T ss_pred cCccccHHHHHHHh--CcCcHHHHHHHHhhccCCcEEE
Confidence 34669999999999 9999999999999999999965
No 305
>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=64.85 E-value=39 Score=24.48 Aligned_cols=49 Identities=27% Similarity=0.391 Sum_probs=38.4
Q ss_pred hhhCCCCCHHHHHHHHHHhCCcccccCH----HHHHHHHHHHhcCCeEEEEeeCC
Q 026766 118 IIKLKVATLEGISDSIKRSGAFKVDLTK----QQIEEIVRALVLDNQIMEVKSNG 168 (233)
Q Consensus 118 i~~~~~~T~~~I~~~I~~~~i~~~~Ls~----~di~~il~~Lv~Dg~ie~v~~~~ 168 (233)
+.....+|...|..||...- .+.+.. .-+..-|..+|-.|.+++++..|
T Consensus 16 l~er~GsS~~aI~kyI~~~y--~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~G 68 (77)
T PF00538_consen 16 LKERKGSSLQAIKKYIKAKY--KVDLNPANFKSRLKRALKRGVEKGKLVQVKGKG 68 (77)
T ss_dssp CCSSSSEEHHHHHHHHHHHS--SCCCCHTTHHHHHHHHHHHHHHCTSEEECSCST
T ss_pred cCCCCCCCHHHHHHHHHHhc--CcCCChHHHHHHHHHHHHHHHHCCcEEeecccC
Confidence 34567899999999999865 334554 56888999999999999987443
No 306
>PF10576 EndIII_4Fe-2S: Iron-sulfur binding domain of endonuclease III; InterPro: IPR003651 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs. The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The iron-sulphur cluster loop (FCL) is also found in DNA-(apurinic or apyrimidinic site) lyase, a subfamily of endonuclease III. The enzyme has both apurinic and apyrimidinic endonuclease activity and a DNA N-glycosylase activity. It cuts damaged DNA at cytosines, thymines and guanines, and acts on the damaged strand 5' of the damaged site. The enzyme binds a 4Fe-4S cluster which is not important for the catalytic activity, but is probably involved in the alignment of the enzyme along the DNA strand.; GO: 0004519 endonuclease activity, 0051539 4 iron, 4 sulfur cluster binding; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A 2ABK_A 1KG7_A 1KG2_A 1MUN_A ....
Probab=64.84 E-value=2.3 Score=23.03 Aligned_cols=11 Identities=36% Similarity=1.147 Sum_probs=7.4
Q ss_pred CCCCCCccccC
Q 026766 203 PCGVCPQINIC 213 (233)
Q Consensus 203 PCg~CPv~~~C 213 (233)
-|+.||+.+.|
T Consensus 7 ~C~~Cpl~~~C 17 (17)
T PF10576_consen 7 KCEECPLADYC 17 (17)
T ss_dssp -GGG-TTGGG-
T ss_pred ccccCCCcccC
Confidence 49999999887
No 307
>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=64.74 E-value=56 Score=24.33 Aligned_cols=70 Identities=10% Similarity=0.087 Sum_probs=45.2
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
++.+++.+.+ |+++++|.+ .+++|+|...+ +-.|.-. |+.+-|..++...
T Consensus 1 ~~~~eva~~~--gi~~~tlr~----~~~~Gll~~~~-------------------~~~g~r~-----y~~~dv~~l~~i~ 50 (100)
T cd00592 1 YTIGEVAKLL--GVSVRTLRY----YEEKGLLPPER-------------------SENGYRL-----YSEEDLERLRLIR 50 (100)
T ss_pred CCHHHHHHHH--CcCHHHHHH----HHHCCCcCCCc-------------------CCCCCcc-----cCHHHHHHHHHHH
Confidence 3578899999 999998865 57789985321 1112222 4555555555544
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhC
Q 026766 115 LKQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
.+++ ...++++|..++....
T Consensus 51 --~l~~-~g~~~~~i~~~l~~~~ 70 (100)
T cd00592 51 --RLRE-LGLSLKEIRELLDARD 70 (100)
T ss_pred --HHHH-cCCCHHHHHHHHhccc
Confidence 4445 5677999999998554
No 308
>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=64.70 E-value=13 Score=28.13 Aligned_cols=45 Identities=16% Similarity=0.254 Sum_probs=35.7
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
+..|++.|+.|+.+.-- .|...++|.+.+ |++..+|++.++...+
T Consensus 108 l~~L~~~~~~ii~~~~~---~g~s~~eIA~~l--~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 108 LEKLPEREREVLVLRYL---EGLSYKEIAEIL--GISVGTVKRRLKRARK 152 (158)
T ss_pred HHhCCHHHHHHHhhHHh---cCCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence 45788888887654432 378999999999 9999999998887654
No 309
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=64.68 E-value=10 Score=33.18 Aligned_cols=47 Identities=17% Similarity=0.219 Sum_probs=37.2
Q ss_pred HHHHHHHhhC-------CCcc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 22 LIYDVIRSKQ-------DMGI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 22 lVy~~I~~aG-------~~GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
.||..|.+.= +.=+ ..++|.++. |+..+.|+-+|+.|+..|||...+
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~--gVSRtpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEML--DVTRTVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEec
Confidence 5666666432 2235 488999999 999999999999999999997654
No 310
>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=64.40 E-value=35 Score=29.06 Aligned_cols=47 Identities=17% Similarity=0.257 Sum_probs=40.4
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 111 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 111 ~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
++.++.+|...+.+|..+|++.+ .++..-|...|+.|+-+|.|+...
T Consensus 3 r~~IL~~L~~~~~~t~~eLA~~l--------gis~~tV~~~L~~Le~~GlV~r~~ 49 (203)
T TIGR02702 3 KEDILSYLLKQGQATAAALAEAL--------AISPQAVRRHLKDLETEGLIEYEA 49 (203)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEEee
Confidence 56788888888889999999887 367888999999999999999763
No 311
>PRK03837 transcriptional regulator NanR; Provisional
Probab=64.30 E-value=11 Score=32.46 Aligned_cols=46 Identities=11% Similarity=0.184 Sum_probs=36.8
Q ss_pred HHHHHHHhhCCC-------cc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 22 LIYDVIRSKQDM-------GI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 22 lVy~~I~~aG~~-------GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
.||+.|.+.=-. =+ .-++|..+. +...+.|+.+|+.|+..|||...
T Consensus 17 ~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~--gVSRt~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 17 EVEERLEQMIRSGEFGPGDQLPSERELMAFF--GVGRPAVREALQALKRKGLVQIS 70 (241)
T ss_pred HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEe
Confidence 566666643221 24 689999999 99999999999999999999774
No 312
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=64.25 E-value=9.8 Score=35.21 Aligned_cols=50 Identities=14% Similarity=0.230 Sum_probs=40.5
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
+++++ ++.++-.--=.+|+.|.+|.+++ +++...|+|.|+.=.+.|+|+=
T Consensus 12 ~~~~~-l~~~vA~lYY~~g~tQ~eIA~~l--giSR~~VsRlL~~Ar~~GiV~I 61 (318)
T PRK15418 12 MCEEE-LVARIAWFYYHDGLTQSEIGERL--GLTRLKVSRLLEKGRQSGIIRV 61 (318)
T ss_pred cChHH-HHHHHHHHHHhcCCCHHHHHHHh--CCCHHHHHHHHHHHHHcCcEEE
Confidence 44444 44455555556889999999999 9999999999999999999964
No 313
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=64.22 E-value=47 Score=29.74 Aligned_cols=65 Identities=8% Similarity=0.253 Sum_probs=53.1
Q ss_pred CCCCCh-HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026766 13 SDSLTD-HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL 80 (233)
Q Consensus 13 ~~~L~~-~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y 80 (233)
.++|++ -.+.|.+.|+ ..+.+.+.-++.+.+ +++..+++|=|+.|++.+.++.--+--.-||..|
T Consensus 152 PkGi~~~Tl~~i~~~~~-~~~~~~Taeela~~~--giSRvTaRRYLeyl~~~~~l~a~i~yG~vGRP~r 217 (224)
T COG4565 152 PKGLDELTLQKVREALK-EPDQELTAEELAQAL--GISRVTARRYLEYLVSNGILEAEIHYGKVGRPER 217 (224)
T ss_pred CCCcCHHHHHHHHHHHh-CcCCccCHHHHHHHh--CccHHHHHHHHHHHHhcCeeeEEeeccccCCcce
Confidence 467777 5778888998 889999999999999 9999999999999999999987544333344433
No 314
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=64.18 E-value=21 Score=30.43 Aligned_cols=44 Identities=20% Similarity=0.164 Sum_probs=33.4
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 113 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 113 ~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
.++..|..++..|.++++.-+ .++..+|+++|..|.-||.|...
T Consensus 26 ~Vl~~L~~~g~~tdeeLA~~L--------gi~~~~VRk~L~~L~e~gLv~~~ 69 (178)
T PRK06266 26 EVLKALIKKGEVTDEEIAEQT--------GIKLNTVRKILYKLYDARLADYK 69 (178)
T ss_pred HHHHHHHHcCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCeEEe
Confidence 344455566677777777655 37899999999999999999943
No 315
>PF13518 HTH_28: Helix-turn-helix domain
Probab=64.01 E-value=18 Score=23.43 Aligned_cols=30 Identities=23% Similarity=0.406 Sum_probs=27.8
Q ss_pred cccHHHHHHHhhcCCChHHHHHHHHHHHhCCC
Q 026766 34 GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL 65 (233)
Q Consensus 34 GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l 65 (233)
|...+++..+. +++.++|.+-++..++.|+
T Consensus 12 g~s~~~~a~~~--gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 12 GESVREIAREF--GISRSTVYRWIKRYREGGI 41 (52)
T ss_pred CCCHHHHHHHH--CCCHhHHHHHHHHHHhcCH
Confidence 56999999999 9999999999999999883
No 316
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=63.81 E-value=38 Score=31.04 Aligned_cols=51 Identities=14% Similarity=0.246 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026766 105 EFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME 163 (233)
Q Consensus 105 efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~ 163 (233)
.+-..+|-++++.|.+++...+.||++.+ | |...-+-.=+++|+--|.|+.
T Consensus 19 alaS~vRv~Il~lL~~k~plNvneiAe~l---g-----Lpqst~s~~ik~Le~aGlirT 69 (308)
T COG4189 19 ALASKVRVAILQLLHRKGPLNVNEIAEAL---G-----LPQSTMSANIKVLEKAGLIRT 69 (308)
T ss_pred HHHHHHHHHHHHHHHHhCCCCHHHHHHHh---C-----CchhhhhhhHHHHHhcCceee
Confidence 34455677789999999999999999876 3 444445555788888898874
No 317
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=63.73 E-value=19 Score=31.83 Aligned_cols=43 Identities=14% Similarity=0.200 Sum_probs=34.9
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
..|+-.+..++..|.+.|+ +..+ .+++ ++++..|++.|+.||+
T Consensus 2 ~~m~l~~L~~F~~v~e~gs--~s~A--A~~L--~isqpavS~~I~~LE~ 44 (296)
T PRK11062 2 SHINYNHLYYFWMVCKEGS--VVGA--AEAL--FLTPQTITGQIKALEE 44 (296)
T ss_pred CccCHHHHHHHHHHHhcCC--HHHH--HHHh--CCChHHHHHHHHHHHH
Confidence 4577778888888888888 4333 4668 9999999999999997
No 318
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=63.71 E-value=14 Score=32.04 Aligned_cols=43 Identities=14% Similarity=0.210 Sum_probs=35.0
Q ss_pred CCCCChHHHHHHHHHHhhC-CCcccHHHHHHHhhcCCChHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQ-DMGIWTRDMKRELRVNLPDNIVTKSI 57 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG-~~GIw~~dik~~t~~~l~~~~v~k~L 57 (233)
+..||+.++.|+.+..-.. -.|...++|...+ |++.++|.+.+
T Consensus 173 l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~l--gis~~tV~~~~ 216 (233)
T PRK05803 173 IDILDEREKEVIEMRYGLGNGKEKTQREIAKAL--GISRSYVSRIE 216 (233)
T ss_pred HHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHH--CcCHHHHHHHH
Confidence 4578889999998866434 4889999999999 99998886664
No 319
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=63.70 E-value=19 Score=32.05 Aligned_cols=44 Identities=18% Similarity=0.225 Sum_probs=36.7
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
+++|+-.+..++..|.+.|+ + ..=.+++ +++|..|++.||+||+
T Consensus 11 ~~~~~l~~L~~f~~va~~gs--~--s~AA~~L--~iSQpavS~~I~~LE~ 54 (311)
T PRK10086 11 LNGWQLSKLHTFEVAARHQS--F--ALAADEL--SLTPSAVSHRINQLEE 54 (311)
T ss_pred hcCCcHHHHHHHHHHHHcCC--H--HHHHHHH--CCCHHHHHHHHHHHHH
Confidence 56788888899999999988 3 3335667 9999999999999997
No 320
>PF06648 DUF1160: Protein of unknown function (DUF1160); InterPro: IPR010594 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf75; it is a family of uncharacterised viral proteins.
Probab=63.65 E-value=13 Score=30.15 Aligned_cols=65 Identities=14% Similarity=0.176 Sum_probs=54.9
Q ss_pred cccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 96 WYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 96 wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
|..|.+=|.-|-+.+.+++..||.+. .+.+.+.+-+.... ...||..++.=+.+....|+.|..+
T Consensus 25 ylkel~~d~tf~~Kl~~Il~mFl~~e--id~e~~y~l~~~~d--~~~LT~~Qi~Yl~~~~~~n~~I~~I 89 (122)
T PF06648_consen 25 YLKELERDETFLDKLIKILKMFLNDE--IDVEDMYNLFGAVD--GLKLTRSQIDYLYNRVYNNRYIINI 89 (122)
T ss_pred HHHHhccCchHHHHHHHHHHHHHhCC--CCHHHHHHHHhccc--HhhcCHHHHHHHHHHHHccHHHHHH
Confidence 56677778999999999999999766 88999999998653 2389999999999999999887765
No 321
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=63.50 E-value=24 Score=22.85 Aligned_cols=43 Identities=9% Similarity=0.126 Sum_probs=34.1
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 114 CLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 114 ~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
++.+|. .+..|..+|.+++. ++...+..+|+.|+-+|.|+...
T Consensus 2 il~~l~-~~~~~~~~i~~~l~--------is~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILG--------LSQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHC--------CCHHHHHHHHHHHHHCCCeeeee
Confidence 345565 66788999998873 67788999999999999998654
No 322
>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=63.49 E-value=15 Score=26.70 Aligned_cols=50 Identities=18% Similarity=0.200 Sum_probs=36.6
Q ss_pred CCCCChHHHHHHHHHHhhCC--CcccHHHHHHHhhcCCChHHHHHHHHHHHhCC
Q 026766 13 SDSLTDHERLIYDVIRSKQD--MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKS 64 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~--~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~ 64 (233)
..+|++.|+.|.++|.+.-. .-+..++|.+++ +..+.+|.|-.|+|-=.|
T Consensus 11 ~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~--~vS~sti~Rf~kkLG~~g 62 (77)
T PF01418_consen 11 YNSLSPTEKKIADYILENPDEIAFMSISELAEKA--GVSPSTIVRFCKKLGFSG 62 (77)
T ss_dssp GGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHC--TS-HHHHHHHHHHCTTTC
T ss_pred HhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHc--CCCHHHHHHHHHHhCCCC
Confidence 35789999999998875432 248899999999 999999999999885444
No 323
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=63.47 E-value=8.8 Score=33.95 Aligned_cols=52 Identities=17% Similarity=0.240 Sum_probs=45.3
Q ss_pred CCCCCChHHHHHHHHHHhhCCC--cccHHHHHHHhhcCCChHHHHHHHHHHHhCCC
Q 026766 12 PSDSLTDHERLIYDVIRSKQDM--GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL 65 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~--GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l 65 (233)
...+||+.|+.|.++|-+..++ .+..++|.+++ +.++.+|.|-.|+|==+|+
T Consensus 6 ~~~~Lt~~e~~ia~yil~n~~~v~~~si~elA~~~--~vS~aTv~Rf~kklG~~Gf 59 (278)
T PRK11557 6 RYPGLAQSDRKLADYLLLQPDTARHLSSQQLANEA--GVSQSSVVKFAQKLGYKGF 59 (278)
T ss_pred hhhhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHh--CCCHHHHHHHHHHcCCCCH
Confidence 3567999999999999877655 48999999999 9999999999999976665
No 324
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=63.27 E-value=17 Score=29.41 Aligned_cols=45 Identities=18% Similarity=0.253 Sum_probs=33.9
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHH----HHHHHHHHh
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIV----TKSIKSLQN 62 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v----~k~LK~Le~ 62 (233)
+..|++.++.|+.+-. -.|...++|...+ |++..+| .|++++|.+
T Consensus 116 l~~L~~~~r~vl~L~~---~~g~s~~EIA~~l--gis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 116 LAQLSPEHRAVLVRSY---YRGWSTAQIAADL--GIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred HHhCCHHHHHHHHHHH---HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHHHHH
Confidence 4567777777766543 2378999999999 9999888 667777664
No 325
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=63.21 E-value=7.6 Score=26.46 Aligned_cols=26 Identities=15% Similarity=0.433 Sum_probs=19.4
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 31 QDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 31 G~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
..+||.+++|.+++ |++.+++++.++
T Consensus 7 ~~~~it~~~La~~~--gis~~tl~~~~~ 32 (63)
T PF13443_consen 7 AERGITQKDLARKT--GISRSTLSRILN 32 (63)
T ss_dssp HHTT--HHHHHHHH--T--HHHHHHHHT
T ss_pred HHcCCCHHHHHHHH--CcCHHHHHHHHh
Confidence 34689999999999 999999999876
No 326
>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=63.07 E-value=16 Score=25.04 Aligned_cols=34 Identities=9% Similarity=0.205 Sum_probs=26.4
Q ss_pred HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHH
Q 026766 22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSI 57 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~L 57 (233)
.++..+.+.|-+-|...+|...+ |+++.+|+|=|
T Consensus 16 r~L~~l~~~G~~~vSS~~La~~~--gi~~~qVRKDl 49 (50)
T PF06971_consen 16 RYLEQLKEEGVERVSSQELAEAL--GITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHTT-SEE-HHHHHHHH--TS-HHHHHHHH
T ss_pred HHHHHHHHcCCeeECHHHHHHHH--CCCHHHhcccC
Confidence 35667778899999999999999 99999999844
No 327
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=63.00 E-value=36 Score=29.39 Aligned_cols=59 Identities=17% Similarity=0.188 Sum_probs=46.0
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe-eeE
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK-KHL 80 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r-K~Y 80 (233)
.||.....++.+|.-.+. |.+.+|-.-= |... ..+|++|.++|||+..---..++| .+|
T Consensus 84 ~LS~aaLEtLAIIAY~QP--ITr~eIe~IR--Gv~s---~~~l~~L~ergLI~~~Gr~~~~Grp~ly 143 (186)
T TIGR00281 84 NLNSASLEVLAIIAYKQP--ITRARINEIR--GVKS---YQIVDDLVEKGLVVELGRKDTPGRSFIY 143 (186)
T ss_pred cCCHHHHHHHHHHHHcCC--cCHHHHHHHc--CCCH---HHHHHHHHHCCCeEecCcCCCCCCCeee
Confidence 399999999999988775 9999999888 6653 678999999999999733323343 345
No 328
>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=62.82 E-value=19 Score=30.77 Aligned_cols=33 Identities=18% Similarity=0.286 Sum_probs=30.1
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
.-++|.++. +++..++.++|..|+..|+|.+..
T Consensus 27 sE~eLa~~~--~Vsr~Tvr~Al~~L~~eGli~~~~ 59 (231)
T TIGR03337 27 SERDLGERF--NTTRVTIREALQQLEAEGLIYRED 59 (231)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCeEEEeC
Confidence 478999999 999999999999999999997743
No 329
>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=62.75 E-value=20 Score=31.85 Aligned_cols=53 Identities=11% Similarity=0.152 Sum_probs=45.0
Q ss_pred CCCCChHHHHHHH-HHHhhCCCcccHHHHHHHhhcCCChHHHHHHHH-HHHhCCCce
Q 026766 13 SDSLTDHERLIYD-VIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIK-SLQNKSLIK 67 (233)
Q Consensus 13 ~~~L~~~e~lVy~-~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK-~Le~k~lIK 67 (233)
...|+..++..+. ++...++.....+++...+ |.+..++...+. .|..++||.
T Consensus 233 ~~~l~~~~~~~L~al~~~~~~~~~~~~~ia~~l--g~~~~~~~~~~e~~Li~~~li~ 287 (305)
T TIGR00635 233 ELGLDEIDRKLLSVLIEQFQGGPVGLKTLAAAL--GEDADTIEDVYEPYLLQIGFLQ 287 (305)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccHHHHHHHh--CCCcchHHHhhhHHHHHcCCcc
Confidence 4678888888777 5565555568899999999 999999999999 699999994
No 330
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=62.74 E-value=20 Score=29.13 Aligned_cols=35 Identities=17% Similarity=0.265 Sum_probs=31.9
Q ss_pred CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 32 DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 32 ~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.+-+..++|-..+ ||-|..|+=+.+-|.++|.|..
T Consensus 39 ~~E~sS~~IE~~s--gLRQPEVSiAMr~Lre~gWV~~ 73 (124)
T COG4738 39 GDEASSREIERVS--GLRQPEVSIAMRYLRENGWVDE 73 (124)
T ss_pred CcchhhhhhHHhh--cCCCchhHHHHHHHHHccccch
Confidence 3458999999999 9999999999999999999975
No 331
>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=62.60 E-value=66 Score=24.39 Aligned_cols=70 Identities=11% Similarity=0.125 Sum_probs=46.6
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL 115 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~ 115 (233)
+++++.+.+ |++.++|+ ..|++|+|.....-. .+.+. |+.+=|+.|+..+
T Consensus 2 ti~eva~~~--gvs~~tlR----~ye~~Gll~~~~~~~-~g~R~----------------------y~~~di~~l~~i~- 51 (103)
T cd01106 2 TVGEVAKLT--GVSVRTLH----YYDEIGLLKPSRRTE-NGYRL----------------------YTEEDLERLQQIL- 51 (103)
T ss_pred CHHHHHHHH--CcCHHHHH----HHHHCCCCCCCccCC-CCcee----------------------eCHHHHHHHHHHH-
Confidence 578899999 99999887 457789985432111 12222 5666667776664
Q ss_pred HHhhhCCCCCHHHHHHHHHHhC
Q 026766 116 KQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 116 ~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
++++. ..|+++|.+++....
T Consensus 52 -~lr~~-g~~l~~i~~~~~~~~ 71 (103)
T cd01106 52 -FLKEL-GFSLKEIKELLKDPS 71 (103)
T ss_pred -HHHHc-CCCHHHHHHHHHcCc
Confidence 35555 466999999997543
No 332
>PF13814 Replic_Relax: Replication-relaxation
Probab=62.59 E-value=22 Score=29.41 Aligned_cols=35 Identities=17% Similarity=0.244 Sum_probs=29.5
Q ss_pred ccHHHHHHHhhcCCChH---HHHHHHHHHHhCCCceeeec
Q 026766 35 IWTRDMKRELRVNLPDN---IVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~---~v~k~LK~Le~k~lIK~vks 71 (233)
+.+.+|..-. +.... .+++.|+.|++.|||+.++.
T Consensus 10 lt~~Qi~~l~--~~~~~~~~~~~rrL~~L~~~glv~~~~~ 47 (191)
T PF13814_consen 10 LTTDQIARLL--FPSSKSERTARRRLKRLRELGLVDRFRR 47 (191)
T ss_pred cCHHHHHHHH--cCCCcchHHHHHHHHHHhhCCcEEeecc
Confidence 6777888877 66655 89999999999999999876
No 333
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=62.50 E-value=67 Score=24.47 Aligned_cols=69 Identities=10% Similarity=0.110 Sum_probs=45.7
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
.+++++.+.+ |++.++| ...|++|||.+..+ ..+.+.| |.+=|+.|+.+.
T Consensus 2 ~~i~eva~~~--gvs~~tL----R~ye~~Gll~~~r~--~~g~R~Y----------------------~~~dl~~l~~I~ 51 (102)
T cd04775 2 YTIGQMSRKF--GVSRSTL----LYYESIGLIPSARS--EANYRLY----------------------SEADLSRLEKIV 51 (102)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCCC--CCCCeee----------------------CHHHHHHHHHHH
Confidence 4688999999 9999887 67899999933221 1233333 445555555544
Q ss_pred HHHhhhCCCCCHHHHHHHHHHh
Q 026766 115 LKQIIKLKVATLEGISDSIKRS 136 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~ 136 (233)
. +++. ..|+++|.+++...
T Consensus 52 ~--l~~~-G~~l~ei~~~~~~~ 70 (102)
T cd04775 52 F--LQAG-GLPLEEIAGCLAQP 70 (102)
T ss_pred H--HHHC-CCCHHHHHHHHcCC
Confidence 3 3455 57799999988753
No 334
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=62.38 E-value=13 Score=31.69 Aligned_cols=46 Identities=13% Similarity=0.135 Sum_probs=37.1
Q ss_pred HHHHHHHhhC-------CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 22 LIYDVIRSKQ-------DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 22 lVy~~I~~aG-------~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
.||+.|.+.= +.=+...+|.++. |+..+.|+-+|+.|+..|||..+
T Consensus 11 ~vy~~i~~~I~~g~l~pG~~L~e~eLae~l--gVSRtpVREAL~~L~~eGlv~~~ 63 (224)
T PRK11534 11 DGYRWLKNDIIRGNFQPDEKLRMSLLTSRY--ALGVGPLREALSQLVAERLVTVV 63 (224)
T ss_pred HHHHHHHHHHHhCCCCCCCcCCHHHHHHHH--CCChHHHHHHHHHHHHCCCEEEe
Confidence 4677776431 2236788999999 99999999999999999999764
No 335
>PRK00118 putative DNA-binding protein; Validated
Probab=62.25 E-value=25 Score=27.71 Aligned_cols=42 Identities=19% Similarity=0.210 Sum_probs=33.6
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
+..|++.++.|+.+-. -.|...++|...+ |++.++|.+.|+.
T Consensus 15 ~~~L~ekqRevl~L~y---~eg~S~~EIAe~l--GIS~~TV~r~L~R 56 (104)
T PRK00118 15 GSLLTEKQRNYMELYY---LDDYSLGEIAEEF--NVSRQAVYDNIKR 56 (104)
T ss_pred hccCCHHHHHHHHHHH---HcCCCHHHHHHHH--CcCHHHHHHHHHH
Confidence 4578898888875443 3479999999999 9999999888764
No 336
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=62.11 E-value=37 Score=24.11 Aligned_cols=60 Identities=7% Similarity=0.060 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 105 EFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 105 efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
+-...+..++.+.+.+..-.+.+++...+.+.=-.....+..+|+.-|+.|+-.+-|++-
T Consensus 4 ~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd 63 (68)
T PF10557_consen 4 DRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERD 63 (68)
T ss_dssp HHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEE
T ss_pred hhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcC
Confidence 344678888999999999999999999998775446789999999999999999999874
No 337
>PRK11642 exoribonuclease R; Provisional
Probab=62.11 E-value=25 Score=36.85 Aligned_cols=50 Identities=10% Similarity=0.294 Sum_probs=40.8
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCCh----HHHHHHHHHHHhCCCcee
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPD----NIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~----~~v~k~LK~Le~k~lIK~ 68 (233)
.|+..+ .|++++.+.+ +++..++|.+++ +++. ..+.++|+.|+..|.|..
T Consensus 17 ~~~~~~-~Il~~l~~~~-~~~~~~~L~~~l--~l~~~~~~~~l~~~L~~L~~~g~l~~ 70 (813)
T PRK11642 17 PIPSRE-FILEHLTKRE-KPASREELAVEL--NIEGEEQLEALRRRLRAMERDGQLVF 70 (813)
T ss_pred CCCCHH-HHHHHHHhcC-CCCCHHHHHHHh--CCCChHHHHHHHHHHHHHHHCCCEEE
Confidence 354433 6889998755 899999999999 9974 459999999999999964
No 338
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=61.98 E-value=54 Score=25.16 Aligned_cols=70 Identities=10% Similarity=0.122 Sum_probs=45.1
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL 115 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~ 115 (233)
.++++.+.+ |++.++| ..-|++|||.+...-. .+.++| ++. =++.|.. .
T Consensus 2 ~I~eva~~~--gvs~~tL----RyYE~~GLl~p~~~~~-~gyR~Y-----------------s~~-----dl~~l~~--I 50 (124)
T COG0789 2 TIGEVAKLT--GVSVRTL----RFYERKGLLSPERRDE-GGYRYY-----------------TPE-----DLELLQI--I 50 (124)
T ss_pred cHHHHHHHh--CCCHHHH----HHHHHcCCCCCcccCC-CCceec-----------------CHH-----HHHHHHH--H
Confidence 467888889 9998776 5689999997755554 355555 222 1222222 2
Q ss_pred HHhhhCCCCCHHHHHHHHHHhC
Q 026766 116 KQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 116 ~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
..++.. ..++++|.+++....
T Consensus 51 ~~~r~~-G~~L~~I~~~l~~~~ 71 (124)
T COG0789 51 KTLREL-GFSLAEIKELLDLLS 71 (124)
T ss_pred HHHHHc-CCCHHHHHHHHhccc
Confidence 233344 567999999998765
No 339
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=61.97 E-value=14 Score=32.04 Aligned_cols=51 Identities=12% Similarity=0.090 Sum_probs=39.3
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCcee
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIKE 68 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK~ 68 (233)
++.+|+-.+..++..|.+.|+ +..+ .+++ ++++..|++.||.||+ -.|+.+
T Consensus 3 ~~~~~~l~~l~~f~~v~~~gs--~t~A--A~~L--~itq~avS~~i~~LE~~lg~~Lf~R 56 (294)
T PRK09986 3 RLYRIDLKLLRYFLAVAEELH--FGRA--AARL--NISQPPLSIHIKELEDQLGTPLFIR 56 (294)
T ss_pred hhhhhhHHHHHHHHHHHHhcC--HHHH--HHHh--CCCCCHHHHHHHHHHHHhCCeeEee
Confidence 345677788888888988887 4443 4567 9999999999999997 455544
No 340
>PRK14137 recX recombination regulator RecX; Provisional
Probab=61.79 E-value=31 Score=29.98 Aligned_cols=54 Identities=7% Similarity=0.057 Sum_probs=47.1
Q ss_pred CHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEE
Q 026766 103 DTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIM 162 (233)
Q Consensus 103 D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie 162 (233)
++++-+.+...++.||..+. =|..|+.+.+.+.| ++.+.|+.+|+-|.=.|.|.
T Consensus 35 ~~e~~~~~~~~Al~~Ls~R~-rS~~ELr~KL~~kg-----~~~e~Ie~vI~rL~e~gyLD 88 (195)
T PRK14137 35 PDEAREALLAYAFRALAARA-MTAAELRAKLERRS-----EDEALVTEVLERVQELGYQD 88 (195)
T ss_pred HHHHHHHHHHHHHHHHhcch-hhHHHHHHHHHhcC-----CCHHHHHHHHHHHHHcCCCC
Confidence 45899999999999998775 45899999999887 67899999999999988874
No 341
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=61.62 E-value=22 Score=31.70 Aligned_cols=44 Identities=14% Similarity=0.226 Sum_probs=36.7
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
+.+|+-.+..++..|.+.|+ +. .-.+++ ++++..|++.|++||+
T Consensus 19 ~~~~~l~~L~~f~avae~gs--~s--~AA~~L--~isQpavS~~I~~LE~ 62 (314)
T PRK09508 19 LRMVDLNLLTVFDAVMQEQN--IT--RAAHNL--GMSQPAVSNAVARLKV 62 (314)
T ss_pred ccccChHHHHHHHHHHhcCC--HH--HHHHHh--CCCHHHHHHHHHHHHH
Confidence 56777788888999999998 33 335678 9999999999999996
No 342
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=61.53 E-value=16 Score=32.03 Aligned_cols=46 Identities=15% Similarity=0.257 Sum_probs=38.5
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
.+..|++.|+.|+.+.. -.|...++|...+ |++...|+++.+.+..
T Consensus 180 ~l~~L~~~er~vi~l~~---~~~~t~~EIA~~l--gis~~~V~q~~~~~~~ 225 (231)
T PRK12427 180 ALSQLDEREQLILHLYY---QHEMSLKEIALVL--DLTEARICQLNKKIAQ 225 (231)
T ss_pred HHHcCCHHHHHHHHHHH---HcCCCHHHHHHHH--CcCHHHHHHHHHHHHH
Confidence 45678998888888776 3578999999999 9999999988887754
No 343
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=61.50 E-value=18 Score=31.28 Aligned_cols=48 Identities=17% Similarity=0.218 Sum_probs=36.3
Q ss_pred CCCCChHHHHHHHHHHhhCC-CcccHHHHHHHhhcCCChHHHHHH----HHHHHh
Q 026766 13 SDSLTDHERLIYDVIRSKQD-MGIWTRDMKRELRVNLPDNIVTKS----IKSLQN 62 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~-~GIw~~dik~~t~~~l~~~~v~k~----LK~Le~ 62 (233)
+..|++.++.|+.+..-.+. +|...++|...+ |++..+|.+. +++|..
T Consensus 172 i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~l--gis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 172 LSVLDGREREVIEMRYGLGDGRRKTQREIAKIL--GISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred HHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHHHHH
Confidence 46778888888877665443 789999999999 9998877554 555544
No 344
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=61.29 E-value=13 Score=32.54 Aligned_cols=34 Identities=12% Similarity=0.252 Sum_probs=30.7
Q ss_pred c-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 35 I-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 35 I-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
+ ..++|..+. |+..+.|+-+|+.|+..|||...+
T Consensus 26 LpsE~eLae~~--gVSRtpVREAL~~Le~~GlV~~~~ 60 (253)
T PRK10421 26 LPAERQLAMQL--GVSRNSLREALAKLVSEGVLLSRR 60 (253)
T ss_pred CCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEeC
Confidence 5 478999999 999999999999999999997643
No 345
>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=61.28 E-value=33 Score=26.27 Aligned_cols=67 Identities=12% Similarity=0.164 Sum_probs=42.9
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+...++.+.+ |++.++| .-=|++|||.+. ...|+-.| +.+-++.|+ .
T Consensus 1 m~Ige~a~~~--gvs~~tl----RyYe~~GLl~p~--------------------~~~g~r~Y-----~~~~~~~l~--~ 47 (107)
T cd04777 1 MKIGKFAKKN--NITIDTV----RHYIDLGLLIPE--------------------KKGGQYFF-----DEKCQDDLE--F 47 (107)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCcCCc--------------------cCCCcccc-----CHHHHHHHH--H
Confidence 4578899999 9998765 568999999541 11233334 444444443 2
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 026766 115 LKQIIKLKVATLEGISDSIKR 135 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~ 135 (233)
..++++.+ .|++||.+++..
T Consensus 48 I~~lr~~G-~sL~eI~~~l~~ 67 (107)
T cd04777 48 ILELKGLG-FSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHCC-CCHHHHHHHHHh
Confidence 24445554 679999999975
No 346
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=61.24 E-value=17 Score=27.94 Aligned_cols=64 Identities=16% Similarity=0.060 Sum_probs=41.4
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecccc
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEP 87 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~leP 87 (233)
|-|+-.||+...-..+. ....-. +.+..++..+++.|.+.|||.....-...+.-.|...+|++
T Consensus 8 R~iLl~iE~~~~~~~~~-~~~~~~--~y~~~~i~YHl~lL~eagli~~~~~~~~~~~~~~~i~~LT~ 71 (102)
T PF10711_consen 8 RDILLEIEENPDPPNPI-EEDEID--GYSKEEIAYHLKLLDEAGLIEGSVSGTMNGPYSFIIKRLTW 71 (102)
T ss_pred HHHHHHHHcCCCcCccc-chhccc--CCCHHHHHHHHHHHHHCCCeeeccccccCCccchhhcccCh
Confidence 55666777776554443 222223 78899999999999999999886554433333344444443
No 347
>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=61.01 E-value=29 Score=24.16 Aligned_cols=27 Identities=7% Similarity=0.172 Sum_probs=20.2
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhC-CCcee
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNK-SLIKE 68 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k-~lIK~ 68 (233)
+.+++.+.+ +++.++|. ..|.+ |++..
T Consensus 2 ~i~e~A~~~--gVs~~tlr----~ye~~~gl~~~ 29 (68)
T cd04763 2 TIGEVALLT--GIKPHVLR----AWEREFGLLKP 29 (68)
T ss_pred CHHHHHHHH--CcCHHHHH----HHHHhcCCCCC
Confidence 567888999 99998886 45665 77744
No 348
>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=60.94 E-value=30 Score=26.77 Aligned_cols=53 Identities=11% Similarity=0.184 Sum_probs=43.4
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 110 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 110 l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
+...+.++|=+++.+|+.||++.+.+.. .++..-|..+|+.|+=-|.|..-+.
T Consensus 4 ~E~~IM~~lW~~~~~t~~eI~~~l~~~~----~~~~sTv~t~L~rL~~Kg~l~~~~~ 56 (115)
T PF03965_consen 4 LELEIMEILWESGEATVREIHEALPEER----SWAYSTVQTLLNRLVEKGFLTREKI 56 (115)
T ss_dssp HHHHHHHHHHHHSSEEHHHHHHHHCTTS----S--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHhcc----ccchhHHHHHHHHHHhCCceeEeec
Confidence 4556777887777899999999998773 5788999999999999999998764
No 349
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=60.74 E-value=13 Score=32.43 Aligned_cols=47 Identities=13% Similarity=0.183 Sum_probs=36.9
Q ss_pred HHHHHHHhhCCC-------cc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 22 LIYDVIRSKQDM-------GI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 22 lVy~~I~~aG~~-------GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
.||+.|.+.=-. =+ ..++|..+. |+..+.|+-+|+.|+..|||...+
T Consensus 12 ~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~--gVSRtpVREAL~~L~~eGlV~~~~ 66 (253)
T PRK11523 12 QLAAELKERIEQGVYLVGDKLPAERFIADEK--NVSRTVVREAIIMLEVEGYVEVRK 66 (253)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec
Confidence 566666643222 24 368999999 999999999999999999997654
No 350
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=60.74 E-value=22 Score=31.45 Aligned_cols=45 Identities=7% Similarity=0.092 Sum_probs=37.3
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
-+.+|+-.+..++..|.+.|+ +..+ .+++ +++|..|++.||.||+
T Consensus 7 ~~~~m~~~~l~~F~av~e~gS--~t~A--A~~L--~iSQpavS~~I~~LE~ 51 (303)
T PRK10082 7 GLHNIETKWLYDFLTLEKCRN--FSQA--AVSR--NVSQPAFSRRIRALEQ 51 (303)
T ss_pred cccccchHHHHHHHHHHhcCC--HHHH--HHHh--CCChHHHHHHHHHHHH
Confidence 457788888888889999888 4433 5678 9999999999999997
No 351
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=60.73 E-value=42 Score=27.65 Aligned_cols=54 Identities=13% Similarity=0.174 Sum_probs=36.8
Q ss_pred HHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026766 22 LIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV 83 (233)
Q Consensus 22 lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~ 83 (233)
.+..+|++..- ..+.||..++ |.++++.+|+| -|++.|+||.. + ..++..|-+.
T Consensus 6 ~i~~Li~~~~i--~tqeeL~~~L~~~G~~vsqaTIsR---dL~elglvk~~-~--~~g~~~Y~~~ 62 (146)
T TIGR01529 6 RIKEIITEEKI--STQEELVALLKAEGIEVTQATVSR---DLRELGAVKVR-D--EDGSYVYSLP 62 (146)
T ss_pred HHHHHHHcCCC--CCHHHHHHHHHHhCCCcCHHHHHH---HHHHcCCEEEE-C--CCCcEEEeec
Confidence 45556654443 6788887776 34788999999 67778999753 3 4566677543
No 352
>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=60.53 E-value=23 Score=25.13 Aligned_cols=42 Identities=14% Similarity=0.264 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhhhC-CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026766 106 FIKVVKSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL 155 (233)
Q Consensus 106 fI~~l~~~~~~~i~~~-~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L 155 (233)
-+..|.++...+-++. ..||.+||++++ .++.++|+.++...
T Consensus 2 ~l~~i~~a~~~L~~~lgr~Pt~eEiA~~l--------gis~~~v~~~l~~~ 44 (78)
T PF04539_consen 2 KLRKIERARRELEQELGREPTDEEIAEEL--------GISVEEVRELLQAS 44 (78)
T ss_dssp HHHHHHHHHHHHHHHHSS--BHHHHHHHH--------TS-HHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHhCCCCCHHHHHHHH--------cccHHHHHHHHHhC
Confidence 4556666666666654 689999999998 38999999999864
No 353
>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=60.38 E-value=21 Score=36.46 Aligned_cols=48 Identities=21% Similarity=0.468 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCCh----HHHHHHHHHHHhCCCcee
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPD----NIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~----~~v~k~LK~Le~k~lIK~ 68 (233)
.+..|+++++++..+++..++|.+++ +++. ..+.++|+.|+..|.|..
T Consensus 3 ~~~~il~~l~~~~~~~~~~~~l~~~l--~~~~~~~~~~l~~~l~~l~~~g~l~~ 54 (709)
T TIGR02063 3 LRELILEFLKSKKGKPISLKELAKAF--HLKGADEKKALRKRLRALEDDGLVKK 54 (709)
T ss_pred cHHHHHHHHHhCCCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHHHHCCCEEE
Confidence 34579999999999999999999999 9874 469999999999999964
No 354
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=59.89 E-value=19 Score=28.84 Aligned_cols=41 Identities=17% Similarity=0.161 Sum_probs=31.6
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
+..|++.++.|+.+.. -.|...++|...+ |++.++|...++
T Consensus 126 l~~L~~~~r~vl~l~~---~~~~s~~eIA~~l--gis~~tV~~~l~ 166 (182)
T PRK09652 126 IESLPEELRTAITLRE---IEGLSYEEIAEIM--GCPIGTVRSRIF 166 (182)
T ss_pred HHhCCHHHHHHHHHHH---HcCCCHHHHHHHH--CCCHHHHHHHHH
Confidence 4568888887776543 2689999999999 999988865544
No 355
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=59.89 E-value=25 Score=31.16 Aligned_cols=49 Identities=10% Similarity=0.222 Sum_probs=37.6
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCcee
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIKE 68 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK~ 68 (233)
..|+-.+-.++-.+.+.|+ ...=.+++ ++++..|++.||+||+ -.|+.+
T Consensus 2 ~~~~l~~L~~f~av~~~gS----~s~AAe~L--~isqsavS~~Ik~LE~~lg~~Lf~R 53 (309)
T PRK11013 2 AAVSLRHIEIFHAVMTAGS----LTEAARLL--HTSQPTVSRELARFEKVIGLKLFER 53 (309)
T ss_pred CCccHHHHHHHHHHHHhCc----HHHHHHHH--CCCcHHHHHHHHHHHHHhCceeeee
Confidence 3467777888888888887 33335667 9999999999999997 456544
No 356
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=59.58 E-value=5.2 Score=35.93 Aligned_cols=59 Identities=10% Similarity=0.245 Sum_probs=46.1
Q ss_pred CCCCCChHHHHHHHHHH--hhCCCcccHH-HHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 12 PSDSLTDHERLIYDVIR--SKQDMGIWTR-DMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~--~aG~~GIw~~-dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
+++.|+=.|..-..+|. -.||+|...+ -|..+. |++.+++-.+|++||+.|.|.+ .|.-
T Consensus 179 Ai~tLSYSEleAve~I~eELdG~EG~lvASkiADrv--GITRSVIVNALRKlESAGvIeS-RSLG 240 (261)
T COG4465 179 AISTLSYSELEAVEHIFEELDGNEGLLVASKIADRV--GITRSVIVNALRKLESAGVIES-RSLG 240 (261)
T ss_pred HHhhccHHHHHHHHHHHHhcCCccceeeehhhhhhh--CchHHHHHHHHHHhhhcCceee-cccC
Confidence 45678877766666654 3689997764 577778 9999999999999999999977 5554
No 357
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=59.36 E-value=15 Score=32.09 Aligned_cols=53 Identities=13% Similarity=0.219 Sum_probs=40.1
Q ss_pred HHHHHHHhhCCC-------cc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026766 22 LIYDVIRSKQDM-------GI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM 81 (233)
Q Consensus 22 lVy~~I~~aG~~-------GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym 81 (233)
.||+.|++.=-. =+ .-++|..+. |+..+.|+-+|+.|+..|||...+ ++-+|+
T Consensus 14 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~l--gVSRtpVREAL~~L~~eGlv~~~~-----~~G~~V 74 (254)
T PRK09464 14 VIEQQLEFLILEGTLRPGEKLPPERELAKQF--DVSRPSLREAIQRLEAKGLLLRRQ-----GGGTFV 74 (254)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEec-----CceeEE
Confidence 466666643211 24 688999999 999999999999999999998653 445554
No 358
>smart00753 PAM PCI/PINT associated module.
Probab=59.18 E-value=25 Score=25.47 Aligned_cols=51 Identities=14% Similarity=0.246 Sum_probs=36.8
Q ss_pred HHHHHHHHH-HHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 106 FIKVVKSQC-LKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 106 fI~~l~~~~-~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
+.+.++..+ ..+.+..+.++.++|.+.+ .++.++++.+|-.|+.+|.|..-
T Consensus 6 l~~~~~~~~l~~l~~~y~~i~~~~i~~~~--------~l~~~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00753 6 LQRKIRLTNLLQLSEPYSSISLSDLAKLL--------GLSVPEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHHHHHHhHHhceeeHHHHHHHh--------CcCHHHHHHHHHHHHHCCCeEEE
Confidence 444444444 4455556778888888543 47788999999999999998754
No 359
>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=59.18 E-value=25 Score=25.47 Aligned_cols=51 Identities=14% Similarity=0.246 Sum_probs=36.8
Q ss_pred HHHHHHHHH-HHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 106 FIKVVKSQC-LKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 106 fI~~l~~~~-~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
+.+.++..+ ..+.+..+.++.++|.+.+ .++.++++.+|-.|+.+|.|..-
T Consensus 6 l~~~~~~~~l~~l~~~y~~i~~~~i~~~~--------~l~~~~vE~~i~~~i~~~~l~~~ 57 (88)
T smart00088 6 LQRKIRLTNLLQLSEPYSSISLSDLAKLL--------GLSVPEVEKLVSKAIRDGEISAK 57 (88)
T ss_pred HHHHHHHHHHHHHhHHhceeeHHHHHHHh--------CcCHHHHHHHHHHHHHCCCeEEE
Confidence 444444444 4455556778888888543 47788999999999999998754
No 360
>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=59.08 E-value=17 Score=26.30 Aligned_cols=44 Identities=16% Similarity=0.233 Sum_probs=37.8
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
-.||+++.+.|. +..++|++.+ ++++..+..+|==|-..+-|.-
T Consensus 11 G~Vw~~L~~~~~--~s~~el~k~~--~l~~~~~~~AiGWLarE~KI~~ 54 (65)
T PF10771_consen 11 GKVWQLLNENGE--WSVSELKKAT--GLSDKEVYLAIGWLARENKIEF 54 (65)
T ss_dssp HHHHHHHCCSSS--EEHHHHHHHC--T-SCHHHHHHHHHHHCTTSEEE
T ss_pred HHHHHHHhhCCC--cCHHHHHHHh--CcCHHHHHHHHHHHhccCceeE
Confidence 479999999665 9999999999 9999999999999998887743
No 361
>CHL00148 orf27 Ycf27; Reviewed
Probab=58.95 E-value=18 Score=29.91 Aligned_cols=47 Identities=17% Similarity=0.195 Sum_probs=36.6
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHh-hc----CCChHHHH----HHHHHHH
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKREL-RV----NLPDNIVT----KSIKSLQ 61 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t-~~----~l~~~~v~----k~LK~Le 61 (233)
.|++-|..|+.++-+..++|+..++|...+ +. +...++|. ++.++|.
T Consensus 161 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~ 216 (240)
T CHL00148 161 RLTGMEFSLLELLISKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLE 216 (240)
T ss_pred EcCHHHHHHHHHHHHCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhc
Confidence 599999999999999999999999999988 21 14555555 5555554
No 362
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=58.69 E-value=15 Score=31.88 Aligned_cols=47 Identities=11% Similarity=0.258 Sum_probs=37.6
Q ss_pred HHHHHHHhh-------CCCcc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 22 LIYDVIRSK-------QDMGI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 22 lVy~~I~~a-------G~~GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
.||+.|.+. -+.-+ .-++|..+. |+..+.|+-+|+.|+..|||...+
T Consensus 11 ~v~~~i~~~I~~g~l~pG~~LPsE~eLa~~~--gVSRtpVREAL~~L~~eGlV~~~~ 65 (251)
T PRK09990 11 VVAERIERLIVDGVLKVGQALPSERRLCEKL--GFSRSALREGLTVLRGRGIIETAQ 65 (251)
T ss_pred HHHHHHHHHHHcCCCCCCCcCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEeC
Confidence 466666632 22346 689999999 999999999999999999997754
No 363
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=58.64 E-value=89 Score=24.65 Aligned_cols=68 Identities=16% Similarity=0.235 Sum_probs=43.2
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHHH
Q 026766 37 TRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLK 116 (233)
Q Consensus 37 ~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~ 116 (233)
++++.+++ |++.++| ..-|+.|||.+...-. .+.+.| +.+-|+.|+ ...
T Consensus 2 I~e~a~~~--gvs~~tl----R~Ye~~GLl~~~~r~~-~g~R~Y----------------------~~~~l~~l~--~I~ 50 (124)
T TIGR02051 2 IGELAKAA--GVNVETI----RYYERKGLLPEPDRPE-GGYRRY----------------------PEETVKRLR--FIK 50 (124)
T ss_pred HHHHHHHH--CcCHHHH----HHHHHCCCCCCCccCC-CCCEeE----------------------CHHHHHHHH--HHH
Confidence 57888999 9999887 4459999996422111 233333 444555553 333
Q ss_pred HhhhCCCCCHHHHHHHHHHh
Q 026766 117 QIIKLKVATLEGISDSIKRS 136 (233)
Q Consensus 117 ~i~~~~~~T~~~I~~~I~~~ 136 (233)
.++..+ .|+++|.+++...
T Consensus 51 ~l~~~G-~sl~eI~~~l~~~ 69 (124)
T TIGR02051 51 RAQELG-FSLEEIGGLLGLV 69 (124)
T ss_pred HHHHCC-CCHHHHHHHHhcc
Confidence 455555 5799999999743
No 364
>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=58.62 E-value=50 Score=24.77 Aligned_cols=54 Identities=24% Similarity=0.353 Sum_probs=36.2
Q ss_pred HHHHHHhhh-CCCCCHHHHHHHHHHhCCcc---------------cccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 112 SQCLKQIIK-LKVATLEGISDSIKRSGAFK---------------VDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 112 ~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~---------------~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
+.+++.|.+ .+..|...|.+.++-+.-.. ..++..+++++++.|+.+|.|+...
T Consensus 7 ~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~ 76 (106)
T PF09382_consen 7 KKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDN 76 (106)
T ss_dssp HHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecC
Confidence 345555554 35688999998888654211 2589999999999999999996543
No 365
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=58.48 E-value=84 Score=27.84 Aligned_cols=115 Identities=10% Similarity=0.037 Sum_probs=74.6
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCccc
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYS 98 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~ 98 (233)
-+..|++++.+.|. +..++|.+.+ +.+..+++|=|+.||+++ + ++. +-.+ . .|. ....-+|..
T Consensus 8 R~~~I~~~l~~~~~--v~v~eLa~~~--~VS~~TIRRDL~~Le~~~--~----~~g-Ga~~-~----~~~-~~~~~~~~~ 70 (252)
T PRK10681 8 RIGQLLQALKRSDK--LHLKDAAALL--GVSEMTIRRDLNAHSAPV--V----LLG-GYIV-L----EPR-SASHYLLSD 70 (252)
T ss_pred HHHHHHHHHHHcCC--CcHHHHHHHh--CCCHHHHHHHHHHhhcCe--E----EEC-CEEE-e----ccc-cccCcCHHH
Confidence 45689999999988 9999999999 999999999999999543 1 332 2221 1 111 111112222
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHh-CCcccccCHHHHHH
Q 026766 99 EGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTKQQIEE 150 (233)
Q Consensus 99 d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~-~i~~~~Ls~~di~~ 150 (233)
-...+.+.=..|-+....+|... +..|+-+++++|.+. +++=+.-|..-+..
T Consensus 71 r~~~~~~~K~~IA~~Aa~lI~~g~tIflD~GtT~~~la~~L~~~~~ltvvTnsl~i~~~ 129 (252)
T PRK10681 71 QKSRLVEEKRRAAQLAATLVEPNQTLFFDCGTTTPWIIEAIDNELPFTAVCYSLNTFLA 129 (252)
T ss_pred HHHhCHHHHHHHHHHHHhhcCCCCEEEEECCccHHHHHHhcCCCCCeEEEECCHHHHHH
Confidence 23344455566777777788753 578999999999754 44444444444433
No 366
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=58.45 E-value=43 Score=25.00 Aligned_cols=54 Identities=11% Similarity=0.137 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHhhh---CCCCCHHHHHHHHHHh-CCcccccCHHHHHHHHHHHhcCC
Q 026766 105 EFIKVVKSQCLKQIIK---LKVATLEGISDSIKRS-GAFKVDLTKQQIEEIVRALVLDN 159 (233)
Q Consensus 105 efI~~l~~~~~~~i~~---~~~~T~~~I~~~I~~~-~i~~~~Ls~~di~~il~~Lv~Dg 159 (233)
+-|..|-....+|-.+ .++.|.+|+.+.+++. .. ...++.++|+++++.+=.|+
T Consensus 7 ~~~~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~l-g~k~t~~ev~~m~~~~D~d~ 64 (88)
T cd05029 7 QAIGLLVAIFHKYSGREGDKNTLSKKELKELIQKELTI-GSKLQDAEIAKLMEDLDRNK 64 (88)
T ss_pred HHHHHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhc-CCCCCHHHHHHHHHHhcCCC
Confidence 4566777777888875 4599999999999752 11 13589999999999885443
No 367
>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=58.30 E-value=9.9 Score=33.17 Aligned_cols=61 Identities=15% Similarity=0.137 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHHHHHHhhhC-CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCe
Q 026766 100 GSLDTEFIKVVKSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQ 160 (233)
Q Consensus 100 ~e~D~efI~~l~~~~~~~i~~~-~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ 160 (233)
++|-.|+--.|-++|......+ +..++.|+...+++.......+|++||.+-++.|.--|.
T Consensus 89 ~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~lg~ 150 (223)
T PF04157_consen 89 GDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGSELISPEDILRACKLLEVLGL 150 (223)
T ss_dssp HHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTSST--HHHHHHHHHHHCCCTS
T ss_pred hhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHcCC
Confidence 3444555555555666555554 479999999999998744558999999999999976554
No 368
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=58.27 E-value=1.1e+02 Score=25.37 Aligned_cols=92 Identities=16% Similarity=0.231 Sum_probs=69.8
Q ss_pred CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHH
Q 026766 33 MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKS 112 (233)
Q Consensus 33 ~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~ 112 (233)
.|+..+++.++. +.+..++.+=++..++.|+. .+....++| -..+|.+=++.|.+
T Consensus 20 ~G~S~re~Ak~~--gvs~sTvy~wv~r~~e~G~~--l~~~~~~Gr---------------------P~kl~~~q~~~l~e 74 (138)
T COG3415 20 EGLSCREAAKRF--GVSISTVYRWVRRYRETGLD--LPPKPRKGR---------------------PRKLSEEQLEILLE 74 (138)
T ss_pred cCccHHHHHHHh--CccHHHHHHHHHHhcccccc--ccCccCCCC---------------------CcccCHHHHHHHHH
Confidence 469999999999 99999999999999999998 344433333 34567776666665
Q ss_pred HHHHHhhhCCCCCHHHHHHHHH-HhCCcccccCHHHHHHHHHHHhc
Q 026766 113 QCLKQIIKLKVATLEGISDSIK-RSGAFKVDLTKQQIEEIVRALVL 157 (233)
Q Consensus 113 ~~~~~i~~~~~~T~~~I~~~I~-~~~i~~~~Ls~~di~~il~~Lv~ 157 (233)
.+- ....|+.++...|. +-| |.++...|-.+|+-|=+
T Consensus 75 ~~~-----~k~wTl~~~~~~l~~e~g---v~y~~~~v~~~l~~~Gl 112 (138)
T COG3415 75 RLR-----EKDWTLKELVEELGLEFG---VWYHASAVRRLLHELGL 112 (138)
T ss_pred HHh-----cccchHHHHHHHHhhhcC---eEEeHHHHHHHHHHcCC
Confidence 553 33499999999887 555 56888888888876644
No 369
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=58.25 E-value=57 Score=22.30 Aligned_cols=27 Identities=4% Similarity=0.032 Sum_probs=21.1
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
..+++.+.+ |+++++|.+ .+++|+|..
T Consensus 2 s~~eva~~~--gvs~~tlr~----~~~~gli~~ 28 (70)
T smart00422 2 TIGEVAKLA--GVSVRTLRY----YERIGLLPP 28 (70)
T ss_pred CHHHHHHHH--CcCHHHHHH----HHHCCCCCC
Confidence 467888999 999988865 467899844
No 370
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=58.25 E-value=1e+02 Score=25.19 Aligned_cols=68 Identities=13% Similarity=0.281 Sum_probs=43.6
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+.+.++.+.+ |++.++| ..-|+.|||.+.+.- .+.+ +| +.+-|..|+.
T Consensus 2 ~~IgevA~~~--Gvs~~tL----RyYE~~GLl~~~r~~--~g~R-----------------~Y-----~~~di~~l~~-- 49 (142)
T TIGR01950 2 LTVGELAKRS--GVAVSAL----HFYESKGLITSIRNS--GNQR-----------------RY-----KRDVLRRVAV-- 49 (142)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCccCC--CCCE-----------------EE-----CHHHHHHHHH--
Confidence 4578899999 9998776 568999999653221 1222 23 4444555544
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 026766 115 LKQIIKLKVATLEGISDSIKR 135 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~ 135 (233)
...+++.+ .|+++|.+++..
T Consensus 50 I~~lr~~G-~sL~eI~~~l~~ 69 (142)
T TIGR01950 50 IKAAQRVG-IPLATIGEALAV 69 (142)
T ss_pred HHHHHHcC-CCHHHHHHHHHh
Confidence 23334554 679999999974
No 371
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=58.23 E-value=26 Score=33.11 Aligned_cols=55 Identities=16% Similarity=0.352 Sum_probs=44.3
Q ss_pred CCCChHHHHHHHHHHh---hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 14 DSLTDHERLIYDVIRS---KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~---aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
..|++-++.|++.|-+ +..+=|=.|.|.++..-++.+.+++.-++.||+.|||..
T Consensus 2 ~~l~~Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~l~~SsATIRN~Ma~LE~~GlI~k 59 (346)
T COG1420 2 GKLDERQRLILRAIVEDYLATGEPVGSKTLSEKYNLDLSSATIRNEMADLEKLGLIEK 59 (346)
T ss_pred CCchHHHHHHHHHHHHHHHhcCCccchHHHHHHhCCCCCchhHHHHHHHHHHCCCccC
Confidence 4577877777776652 445558899999998556889999999999999999976
No 372
>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=58.06 E-value=25 Score=23.44 Aligned_cols=46 Identities=11% Similarity=0.232 Sum_probs=38.0
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 113 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 113 ~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
.++.+|.+++..|..+|.+++. ++..-+-.+++-|+-.|.|++..+
T Consensus 7 ~iL~~l~~~~~~~~~~la~~~~--------~~~~~~t~~i~~L~~~g~I~r~~~ 52 (59)
T PF01047_consen 7 RILRILYENGGITQSELAEKLG--------ISRSTVTRIIKRLEKKGLIERERD 52 (59)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHT--------S-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHcCCCCHHHHHHHHC--------CChhHHHHHHHHHHHCCCEEeccC
Confidence 4677788888899999988874 677888899999999999998764
No 373
>COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]
Probab=57.94 E-value=1.8e+02 Score=28.03 Aligned_cols=142 Identities=16% Similarity=0.192 Sum_probs=83.5
Q ss_pred HHHHHHHHhhCCCccc--------HHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc-----cCCCeeeEEee----
Q 026766 21 RLIYDVIRSKQDMGIW--------TRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI-----HSKGKKHLMAV---- 83 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw--------~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV-----~~~~rK~Yml~---- 83 (233)
+.+|+.|+++=..|.| +|++...+ ++..++|.++.+.|+.+|+|.+.+-- .......-...
T Consensus 7 ~ql~~~i~~~I~~g~l~~g~rLPs~R~la~~l--~vs~~Tv~~ay~~L~~~G~i~~~~gs~~~~~~~~~~~~~~~~~~~~ 84 (459)
T COG1167 7 QQLAEQLREAILSGRLKPGDRLPSIRQLAQDL--GVSRSTVSRAYEELEARGYIESRPGSAPPSGRPVRLELLKPSDPEL 84 (459)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCcHHHHHHHh--CCcHHHHHHHHHHHHhCcceeeccCCCcccccccccchhhhhhccc
Confidence 4567777765555554 78999999 99999999999999999999887621 00001111111
Q ss_pred -ccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhh---------hCCCCCH-HHHHHHHH-HhCCcc-------cccC
Q 026766 84 -EFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQII---------KLKVATL-EGISDSIK-RSGAFK-------VDLT 144 (233)
Q Consensus 84 -~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~---------~~~~~T~-~~I~~~I~-~~~i~~-------~~Ls 144 (233)
+-.|+.---++.|-...-|+.+-.........+... ..+++.+ +.|++++. ..|+.. +.=+
T Consensus 85 ~~~~~~~i~f~~g~p~~~~fp~~~~~~~~~~~~~~~~~~~~~~y~~~~G~~~LR~~ia~~l~~~~g~~~~~~~IiiT~G~ 164 (459)
T COG1167 85 LEDDPSVIDFAGGLPDPSLFPLEALRRALARVLRNYGASLALQYGPTAGLPELREAIAAYLLARRGISCEPEQIVITSGA 164 (459)
T ss_pred ccCCCceecCCCCCCCcccCCHHHHHHHHHHHHhhcchhhhhcCCCCCCcHHHHHHHHHHHHHhcCCccCcCeEEEeCCH
Confidence 112333333444555678888766655544432221 1344444 48889998 667542 1234
Q ss_pred HHHHHHHHHHHhcCCeEEEE
Q 026766 145 KQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 145 ~~di~~il~~Lv~Dg~ie~v 164 (233)
.+=+.-++++|.=-|...-+
T Consensus 165 q~al~l~~~~l~~pGd~v~v 184 (459)
T COG1167 165 QQALDLLLRLLLDPGDTVLV 184 (459)
T ss_pred HHHHHHHHHHhCCCCCEEEE
Confidence 45555555555554554444
No 374
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=57.75 E-value=25 Score=28.03 Aligned_cols=44 Identities=9% Similarity=-0.018 Sum_probs=30.4
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHH----HHHHHHHHh
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIV----TKSIKSLQN 62 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v----~k~LK~Le~ 62 (233)
..||+.++.|+.+- --.|...++|...+ |++.++| .|+++.|.+
T Consensus 105 ~~Lp~~~r~v~~l~---~~~g~s~~EIA~~l--gis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 105 RELPENYRDVVLAH---YLEEKSYQEIALQE--KIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HhCCHHHHHHHHHH---HHhCCCHHHHHHHH--CCCHHHHHHHHHHHHHHHHH
Confidence 44555555555443 34679999999999 9999988 555555543
No 375
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=57.68 E-value=39 Score=22.50 Aligned_cols=44 Identities=23% Similarity=0.429 Sum_probs=37.7
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
..||+-|..|+.++.+ |...++|.... +++..+|...++.+..|
T Consensus 3 ~~Lt~rE~~v~~l~~~----G~s~~eia~~l--~is~~tV~~h~~~i~~K 46 (65)
T COG2771 3 ADLTPREREILRLVAQ----GKSNKEIARIL--GISEETVKTHLRNIYRK 46 (65)
T ss_pred ccCCHHHHHHHHHHHC----CCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence 4689999888888765 48899999999 99999999999888654
No 376
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=57.61 E-value=16 Score=31.28 Aligned_cols=52 Identities=8% Similarity=0.151 Sum_probs=39.4
Q ss_pred CCChHHHHHHHHHHhh-------CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026766 15 SLTDHERLIYDVIRSK-------QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~a-------G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v 69 (233)
..+-.| .||+.|.+. -+.=|...+|.++. |+..+.|+-+|+.|+..|||...
T Consensus 9 ~~~~~e-~v~~~l~~~I~~g~l~pG~~L~e~~La~~l--gVSRtpVREAL~~L~~eGLV~~~ 67 (221)
T PRK11414 9 HISLTL-QVENDLKHQLSIGALKPGARLITKNLAEQL--GMSITPVREALLRLVSVNALSVA 67 (221)
T ss_pred CCCHHH-HHHHHHHHHHHhCCCCCCCccCHHHHHHHH--CCCchhHHHHHHHHHHCCCEEec
Confidence 334333 466666643 22446788999999 99999999999999999999753
No 377
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=57.47 E-value=26 Score=30.21 Aligned_cols=44 Identities=23% Similarity=0.424 Sum_probs=38.3
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
..||+.|..|+++|. +|...++|..++ ++..++|+..+..+-+|
T Consensus 147 ~~LT~RE~eVL~lla----~G~snkeIA~~L--~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLA----EGLSNKEIAEEL--NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHH----CCCCHHHHHHHH--CCCHhHHHHHHHHHHHH
Confidence 479999999999996 469999999999 99999998877776654
No 378
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=57.39 E-value=25 Score=30.54 Aligned_cols=40 Identities=8% Similarity=0.152 Sum_probs=31.0
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
+-.+..++..|.+.|+ +.. =.+++ ++++..|++.||+||+
T Consensus 2 ~l~~L~~f~~v~~~gs--~s~--AA~~L--~isqsavS~~i~~LE~ 41 (296)
T PRK11242 2 LLRHIRYFLAVAEHGN--FTR--AAEAL--HVSQPTLSQQIRQLEE 41 (296)
T ss_pred ChHHHHHHHHHHHhCC--HHH--HHHHc--CCCchHHHHHHHHHHH
Confidence 3455667777888877 433 35668 9999999999999997
No 379
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=57.39 E-value=23 Score=30.35 Aligned_cols=40 Identities=18% Similarity=0.282 Sum_probs=32.3
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSI 57 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~L 57 (233)
+..|++.++.|+.+.. -.|...++|...+ |++..+|.+.+
T Consensus 173 l~~L~~~~r~il~l~y---~~~~s~~eIA~~l--gis~~tV~~~~ 212 (224)
T TIGR02479 173 IESLSEREQLVLSLYY---YEELNLKEIGEVL--GLTESRVSQIH 212 (224)
T ss_pred HHhCCHHHHHHHHHHH---hCCCCHHHHHHHh--CCCHHHHHHHH
Confidence 4578888888777665 4678999999999 99999888643
No 380
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=57.32 E-value=21 Score=32.16 Aligned_cols=52 Identities=17% Similarity=0.255 Sum_probs=40.8
Q ss_pred CCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCcee
Q 026766 11 APSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIKE 68 (233)
Q Consensus 11 ~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK~ 68 (233)
..+++|+-.+..++..|.+.|+ +.. =.+++ ++++..|++.||+||+ -.|..+
T Consensus 24 ~~~~~m~l~~L~~f~av~e~gs--~s~--AA~~L--~isQpavS~~I~~LE~~lG~~LF~R 78 (317)
T PRK11482 24 RTLRNIDLNLLTIFEAVYVHKG--IVN--AAKIL--NLTPSAISQSIQKLRVIFPDPLFIR 78 (317)
T ss_pred hcccccchhHHHHHHHHHHcCC--HHH--HHHHh--CCChHHHHHHHHHHHHHhCCcceEe
Confidence 4567788888888889999887 333 35668 9999999999999997 455544
No 381
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=57.28 E-value=40 Score=28.27 Aligned_cols=38 Identities=16% Similarity=0.248 Sum_probs=31.9
Q ss_pred hCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 120 KLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 120 ~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
..+.+|.++|.+.+ .++..-+++||+.|.-.|.|+..+
T Consensus 22 ~~~~vs~~eIA~~~--------~ip~~~l~kIl~~L~~aGLv~s~r 59 (164)
T PRK10857 22 EAGPVPLADISERQ--------GISLSYLEQLFSRLRKNGLVSSVR 59 (164)
T ss_pred CCCcCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEeCC
Confidence 34578999998765 488899999999999999999854
No 382
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=57.05 E-value=29 Score=30.44 Aligned_cols=42 Identities=24% Similarity=0.340 Sum_probs=34.2
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
.|+-.+-.++..|.+.|+ ...-.+++ +++|..|++.||+||+
T Consensus 4 ~~~l~~L~~f~~v~~~gs----~s~AA~~L--~isQ~avS~~i~~LE~ 45 (302)
T PRK09791 4 QVKIHQIRAFVEVARQGS----IRGASRML--NMSQPALTKSIQELEE 45 (302)
T ss_pred cccHHHHHHHHHHHHcCC----HHHHHHHh--CCChHHHHHHHHHHHH
Confidence 466777788888888887 34445778 9999999999999997
No 383
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=56.89 E-value=20 Score=31.77 Aligned_cols=44 Identities=11% Similarity=0.262 Sum_probs=35.1
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHH----HHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVT----KSIKSLQ 61 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~----k~LK~Le 61 (233)
+..|++.++.|+.+.. -.|...++|...+ |++..+|. ++++.|.
T Consensus 210 l~~L~~~~r~vl~l~~---~~~~s~~eIA~~l--gis~~tV~~~~~ra~~~Lr 257 (268)
T PRK06288 210 IKTLPEREKKVLILYY---YEDLTLKEIGKVL--GVTESRISQLHTKAVLQLR 257 (268)
T ss_pred HHhCCHHHHHHHHHHH---HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHHHH
Confidence 4578998888877765 3579999999999 99999998 5555554
No 384
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=56.86 E-value=14 Score=32.99 Aligned_cols=51 Identities=18% Similarity=0.283 Sum_probs=43.9
Q ss_pred CCCCChHHHHHHHHHHhhCCC--cccHHHHHHHhhcCCChHHHHHHHHHHHhCCC
Q 026766 13 SDSLTDHERLIYDVIRSKQDM--GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL 65 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~--GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l 65 (233)
...||+.|+.|.++|-+.... .+..++|.+++ +..+.+|.|-.|+|==+|+
T Consensus 23 ~~~Lt~~e~~Ia~yil~~~~~v~~~si~~lA~~~--~vS~aTi~Rf~kkLGf~gf 75 (292)
T PRK11337 23 QEGLTPLESRVVEWLLKPGDLSEATALKDIAEAL--AVSEAMIVKVAKKLGFSGF 75 (292)
T ss_pred HhhcCHHHHHHHHHHHhCHHHHHhcCHHHHHHHh--CCChHHHHHHHHHcCCCCH
Confidence 457999999999999876543 46789999999 9999999999999976665
No 385
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=56.76 E-value=40 Score=24.26 Aligned_cols=43 Identities=14% Similarity=0.196 Sum_probs=35.9
Q ss_pred HHHHhhhC-CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 114 CLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 114 ~~~~i~~~-~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
++.+|.+. +..|+.||++.+ .++..-|..+|+.|+-.|.|+..
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l--------~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERL--------GLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCeeec
Confidence 56677665 689999999887 36888999999999999999874
No 386
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=56.48 E-value=34 Score=27.62 Aligned_cols=51 Identities=22% Similarity=0.298 Sum_probs=40.9
Q ss_pred CChHHHHHHHHHHhhCCC------------cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 16 LTDHERLIYDVIRSKQDM------------GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~------------GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.+..+++...++.-+... -+.+.+|..-+ +++...+++.++.|+..|+|..
T Consensus 141 ~~~~~r~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~ia~~~--g~~~~~vsr~l~~l~~~g~i~~ 203 (214)
T COG0664 141 KDVEERLARFLLNLGRRLGIATEDGILIPLPLTHKDLAEYL--GLSRETVSRILKELRKDGLISV 203 (214)
T ss_pred ccHHHHHHHHHHHHhhccCCCCCCCcEEeccCCHHHHHHHh--CCchhhHHHHHHHHHhCCcEee
Confidence 344666666666555443 48899999999 9999999999999999999966
No 387
>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=56.46 E-value=27 Score=26.24 Aligned_cols=33 Identities=15% Similarity=0.137 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHH
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSI 57 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~L 57 (233)
...|.++|.+ |. +..+||.+.+ |++..+|+++|
T Consensus 8 ~~~I~e~l~~-~~--~ti~dvA~~~--gvS~~TVsr~L 40 (80)
T TIGR02844 8 VLEIGKYIVE-TK--ATVRETAKVF--GVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHH-CC--CCHHHHHHHh--CCCHHHHHHHh
Confidence 4578899999 88 8999999999 99999999987
No 388
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=56.32 E-value=1.1e+02 Score=25.03 Aligned_cols=69 Identities=13% Similarity=0.155 Sum_probs=45.3
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+.+.++.+.+ |++.++| ..-|+.|||++...-. .+.++| |.+-|+.|+ .
T Consensus 8 ~~IgevAk~~--Gvs~~TL----RyYE~~GLl~p~~r~~-~gyR~Y----------------------~~~~l~rl~--~ 56 (144)
T PRK13752 8 LTIGVFAKAA--GVNVETI----RFYQRKGLLPEPDKPY-GSIRRY----------------------GEADVTRVR--F 56 (144)
T ss_pred ccHHHHHHHH--CcCHHHH----HHHHHCCCCCCCccCC-CCCeec----------------------CHHHHHHHH--H
Confidence 7889999999 9998776 5589999997533222 233333 444444443 2
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 026766 115 LKQIIKLKVATLEGISDSIKR 135 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~ 135 (233)
...++..+ .|+++|.+++..
T Consensus 57 I~~lr~~G-~sL~eI~~ll~~ 76 (144)
T PRK13752 57 VKSAQRLG-FSLDEIAELLRL 76 (144)
T ss_pred HHHHHHcC-CCHHHHHHHHhc
Confidence 34455565 479999999964
No 389
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=56.28 E-value=29 Score=30.91 Aligned_cols=41 Identities=10% Similarity=0.095 Sum_probs=32.7
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
|+-++..++..|.+.|+ -..-.+++ |++|..|++.||+||+
T Consensus 2 ~~~~~L~~f~~v~e~gs----~s~AA~~L--~iSQpavS~~I~~LE~ 42 (308)
T PRK10094 2 FDPETLRTFIAVAETGS----FSKAAERL--CKTTATISYRIKLLEE 42 (308)
T ss_pred CCHHHHHHHHHHHHhCC----HHHHHHHh--cCCHHHHHHHHHHHHH
Confidence 44566678888888887 34446778 9999999999999996
No 390
>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat
Probab=56.27 E-value=47 Score=26.73 Aligned_cols=47 Identities=21% Similarity=0.294 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHh
Q 026766 106 FIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALV 156 (233)
Q Consensus 106 fI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv 156 (233)
..+.++..+.. .+++..|.+++...|..+. ...+|.+|++..|+.|.
T Consensus 46 la~~v~~if~s--~~k~~l~~e~l~~kl~~S~--~~~~s~~E~E~~l~LL~ 92 (126)
T cd08767 46 LARILRNIFVS--EKKTVLPLEELVYKLQASY--PSILSRGEVEEHLRLLA 92 (126)
T ss_pred HHHHHHHHHHh--cccccccHHHHHHHHHHhC--CCCCCHHHHHHHHHHHH
Confidence 34444444443 4678999999999999987 45789999999999998
No 391
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=56.23 E-value=87 Score=23.75 Aligned_cols=70 Identities=11% Similarity=0.108 Sum_probs=43.8
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
.+.+++.+.+ |++.++|.+ .++.|+|.+.++ .||.|| |+.+-|+.|+.++
T Consensus 2 ~~i~eva~~~--gVs~~tLR~----ye~~Gli~p~r~--------------------~~g~R~----Ys~~dv~~l~~I~ 51 (98)
T cd01279 2 YPISVAAELL--GIHPQTLRV----YDRLGLVSPART--------------------NGGGRR----YSNNDLELLRQVQ 51 (98)
T ss_pred cCHHHHHHHH--CcCHHHHHH----HHHCCCCCCCcC--------------------CCCCee----ECHHHHHHHHHHH
Confidence 3567888899 999988765 478999944221 123232 4445555555443
Q ss_pred HHHhhhCCCCCHHHHHHHHHHh
Q 026766 115 LKQIIKLKVATLEGISDSIKRS 136 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~ 136 (233)
.+.+....++++|..++.-.
T Consensus 52 --~L~~~~G~~l~~i~~~l~l~ 71 (98)
T cd01279 52 --RLSQDEGFNLAGIKRIIELY 71 (98)
T ss_pred --HHHHHCCCCHHHHHHHHHhh
Confidence 34442457799999888754
No 392
>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=56.00 E-value=33 Score=23.67 Aligned_cols=39 Identities=13% Similarity=0.357 Sum_probs=32.4
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
+..++.++-+ ++.+..++|.+++ |++.++|.+-+..|..
T Consensus 7 q~~Ll~~L~~--~~~~~~~ela~~l--~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 7 QLKLLELLLK--NKWITLKELAKKL--NISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHHHH--HTSBBHHHHHHHC--TS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHHc--CCCCcHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence 5567777777 5669999999999 9999999999999974
No 393
>PF09279 EF-hand_like: Phosphoinositide-specific phospholipase C, efhand-like; InterPro: IPR015359 This domain is predominantly found in the enzyme phosphoinositol-specific phospholipase C. It adopts a structure consisting of a core of four alpha helices, in an EF like fold, and is required for functioning of the enzyme []. ; PDB: 3OHM_B 3QR0_A 2ZKM_X 2FJU_B 3QR1_D 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B ....
Probab=55.92 E-value=29 Score=25.01 Aligned_cols=46 Identities=15% Similarity=0.129 Sum_probs=34.4
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHh
Q 026766 110 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALV 156 (233)
Q Consensus 110 l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv 156 (233)
|..+..+|-....+.|+++..+|+++.. ....++.+++++|++.-.
T Consensus 2 i~~if~~ys~~~~~mt~~~f~~FL~~eQ-~~~~~~~~~~~~li~~~~ 47 (83)
T PF09279_consen 2 IEEIFRKYSSDKEYMTAEEFRRFLREEQ-GEPRLTDEQAKELIEKFE 47 (83)
T ss_dssp HHHHHHHHCTTSSSEEHHHHHHHHHHTS-S-TTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCCCcCCHHHHHHHHHHHh-ccccCcHHHHHHHHHHHc
Confidence 4455566655578999999999998665 123569999999998854
No 394
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=55.92 E-value=34 Score=27.81 Aligned_cols=47 Identities=19% Similarity=0.195 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhhhC--CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCC
Q 026766 108 KVVKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDN 159 (233)
Q Consensus 108 ~~l~~~~~~~i~~~--~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg 159 (233)
+.|-+...+||+.- ..++.+.=.+||++.| ||.+||++.|+..--+.
T Consensus 3 e~li~~A~~FL~~p~V~~sp~~~k~~FL~sKG-----Lt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 3 EDLIEQAVKFLQDPKVRNSPLEKKIAFLESKG-----LTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHHCTTTCCCS-HHHHHHHHHHCT-------HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHHhCCcccccCCHHHHHHHHHcCC-----CCHHHHHHHHHhcCCcc
Confidence 45667788899864 3466888999999998 99999999999876655
No 395
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=55.89 E-value=1.5e+02 Score=29.77 Aligned_cols=108 Identities=10% Similarity=0.105 Sum_probs=75.8
Q ss_pred HHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcc-cCCCC
Q 026766 24 YDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWY-SEGSL 102 (233)
Q Consensus 24 y~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy-~d~e~ 102 (233)
-..|-..|.--. ..-+.+++ +++-..|.++|=.|.+.++++-+....+.++++|--+..+---.+ --| .+--.
T Consensus 25 ~~~Llr~G~lss-~~~~~~~t--~i~~~kVk~aL~sLiQh~~V~y~~~~~~~g~vt~Y~~~~~ei~hi---lry~r~~~i 98 (551)
T KOG2587|consen 25 GEHLLRTGRLSS-LRVIAKDT--GISLDKVKKALVSLIQHNCVSYQVHTRNSGKVTTYEAQCSEILHI---LRYPRYIYI 98 (551)
T ss_pred HHHHHHcCCcch-hHHHHhhc--CCChHHHHHHHHHHHHhcceEEEEecCCCCceEEEEehhhHHHHH---Hhcccceee
Confidence 334444455222 56677888 999999999999999999999998888777777643322110000 001 23345
Q ss_pred CHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC
Q 026766 103 DTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 103 D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
+.+.-+...+.+..+|-.+|..|+.|+.+-+.+.+
T Consensus 99 ~~~~~~q~~~sIv~~Lls~GrLTv~e~i~rv~~~~ 133 (551)
T KOG2587|consen 99 TKTLYSQTAESIVEELLSNGRLTVSEVIKRVADRL 133 (551)
T ss_pred HHHHhhhHHHHHHHHHHhcCceeHHHHHHHHHhcc
Confidence 66667777788888888999999999998888776
No 396
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=55.84 E-value=64 Score=24.65 Aligned_cols=56 Identities=18% Similarity=0.212 Sum_probs=46.2
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHh----hc-CCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKREL----RV-NLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t----~~-~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
|++.+||+++....+.-....+|.... +. .++.+.+=.++=-||..|+|.+-.+-+
T Consensus 4 p~~~~I~~iL~~~~~~~~~i~~L~~e~~~~~~~~~~TKNelL~~vYWLE~ngyI~R~~~~~ 64 (85)
T PF11313_consen 4 PSEELIYQILNFVKDPNATINHLTFEFIDFPGAYDFTKNELLYTVYWLEENGYIFRDNNNN 64 (85)
T ss_pred ccHHHHHHHHHHhcCccccHHHHHHHHHhccccccccHHHHHHHHHHHhhcCeeEeecCCC
Confidence 467899999998888888888877663 33 688899999999999999999976654
No 397
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=55.67 E-value=31 Score=25.49 Aligned_cols=48 Identities=19% Similarity=0.389 Sum_probs=38.5
Q ss_pred CCCCCCChHHHHHHHHHHhh-----CC-----Cc-----ccHHHHHHHhhcCCChHHHHHHHHHH
Q 026766 11 APSDSLTDHERLIYDVIRSK-----QD-----MG-----IWTRDMKRELRVNLPDNIVTKSIKSL 60 (233)
Q Consensus 11 ~~~~~L~~~e~lVy~~I~~a-----G~-----~G-----Iw~~dik~~t~~~l~~~~v~k~LK~L 60 (233)
...++|+.+.+++|.++... .| +| -...+|.+.+ |....+|.+++|.|
T Consensus 14 ~~y~~Ls~~Ak~lY~ll~dR~~lS~kn~wiDe~G~vYi~~s~eel~~~L--~~s~~tv~~~~keL 76 (76)
T PF06970_consen 14 PKYKKLSNDAKILYSLLLDRLRLSLKNGWIDENGNVYIIFSIEELMELL--NCSKSTVIKAKKEL 76 (76)
T ss_pred cccccCCHHHHHHHHHHHHHHHhhhhcCcCCCCCCEEEEeeHHHHHHHH--CCCHHHHHHHHHcC
Confidence 45789999999999998732 22 23 2468999999 99999999999876
No 398
>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=55.66 E-value=38 Score=28.10 Aligned_cols=47 Identities=17% Similarity=0.325 Sum_probs=39.0
Q ss_pred HHHHHHHhhhC-CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026766 111 KSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME 163 (233)
Q Consensus 111 ~~~~~~~i~~~-~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~ 163 (233)
...|+.|+.++ ..-|+.+|..-+++ .++...|+.+|+.|+-+|+|..
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~------~~~K~~v~k~Ld~L~~~g~i~~ 50 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHN------KVGKTAVQKALDSLVEEGKIVE 50 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHh------hccHHHHHHHHHHHHhCCCeee
Confidence 46788999754 45679999998885 4778899999999999999976
No 399
>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=55.55 E-value=8.7 Score=32.41 Aligned_cols=87 Identities=18% Similarity=0.247 Sum_probs=18.8
Q ss_pred CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHH
Q 026766 32 DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVK 111 (233)
Q Consensus 32 ~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~ 111 (233)
-.-+..+||...+ |+|.++|+|+++. |-++.+. -+|-|-+|=++.--+|+ ++++.. +.++
T Consensus 47 l~PLt~~~iA~~l--gl~~STVSRav~~----------Ky~~t~~-Gi~plk~fF~~~~~~~~----~~~~S~---~~ik 106 (160)
T PF04552_consen 47 LKPLTMKDIADEL--GLHESTVSRAVKN----------KYIQTPR-GIFPLKDFFSRSVSSGS----GEEFSS---EAIK 106 (160)
T ss_dssp ---------------------------------------------------S-----SS--SS-----SS------TTH-
T ss_pred CcCCCHHHHHHHh--CCCHhHHHHHHcC----------ceeecCC-eeeeHHHhccccccCCC----CcccHH---HHHH
Confidence 3457889999999 9999999999874 3444333 36666666555433322 122222 2455
Q ss_pred HHHHHHhhh---CCCCCHHHHHHHHHHhCC
Q 026766 112 SQCLKQIIK---LKVATLEGISDSIKRSGA 138 (233)
Q Consensus 112 ~~~~~~i~~---~~~~T~~~I~~~I~~~~i 138 (233)
..+...|.. ....|=++|.+.+++.||
T Consensus 107 ~~i~~lI~~Ed~~~PlSD~~i~~~L~~~gi 136 (160)
T PF04552_consen 107 ARIKELIEEEDKKKPLSDQEIAELLKEEGI 136 (160)
T ss_dssp HHHHHHHTTS-TTS---HHHHHHHHTTTTS
T ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHHHcCC
Confidence 555556654 345667777777777774
No 400
>smart00526 H15 Domain in histone families 1 and 5.
Probab=55.42 E-value=58 Score=22.72 Aligned_cols=53 Identities=13% Similarity=0.226 Sum_probs=38.1
Q ss_pred hHHHHHHHHHHhhCC-CcccHHHHHHHhhc--CC----ChHHHHHHHHHHHhCCCceeee
Q 026766 18 DHERLIYDVIRSKQD-MGIWTRDMKRELRV--NL----PDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~-~GIw~~dik~~t~~--~l----~~~~v~k~LK~Le~k~lIK~vk 70 (233)
+-..+|...|.+..+ .|.....|++-..- ++ ....|+++||.+.++|.+..++
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~k 65 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQVK 65 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeecC
Confidence 445678888877666 77888888876522 22 1356899999999999987654
No 401
>smart00049 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
Probab=55.40 E-value=50 Score=23.41 Aligned_cols=56 Identities=14% Similarity=0.147 Sum_probs=42.8
Q ss_pred CCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeCCCCCcccccCcceeeec
Q 026766 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYKN 184 (233)
Q Consensus 123 ~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~~~g~f~~~~~g~~~Yr~ 184 (233)
--|-.|+.+||.+.+. ..+.++...|.+.|+--|.|+.|.......|.+- ...||.
T Consensus 20 ~F~G~e~v~wL~~~~~---~~~r~eA~~l~~~ll~~g~i~~v~~~~~~~F~d~---~~~Yrf 75 (77)
T smart00049 20 CFTGSELVDWLMDNLE---IIDREEAVHLGQLLLDEGLIHHVNGPNKHTFKDS---KALYRF 75 (77)
T ss_pred eeEcHHHHHHHHHcCC---cCCHHHHHHHHHHHHHCCCEEEeCCCCcCccccC---CEEEEe
Confidence 3567889999998884 3688999999999999999999874344456542 456775
No 402
>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=55.37 E-value=24 Score=27.93 Aligned_cols=44 Identities=18% Similarity=0.287 Sum_probs=34.7
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQ 61 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le 61 (233)
+..||+.++.|+.+-. -.|...++|...+ |++.++|...+...-
T Consensus 109 i~~L~~~~r~v~~l~~---~~g~~~~eIA~~l--~is~~tv~~~l~Rar 152 (159)
T TIGR02989 109 LEKLPERQRELLQLRY---QRGVSLTALAEQL--GRTVNAVYKALSRLR 152 (159)
T ss_pred HHHCCHHHHHHHHHHH---hcCCCHHHHHHHh--CCCHHHHHHHHHHHH
Confidence 4578888888887744 3579999999999 999998887765543
No 403
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=55.23 E-value=30 Score=28.67 Aligned_cols=49 Identities=20% Similarity=0.299 Sum_probs=36.7
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHH----HHHHHHHHhCCC
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIV----TKSIKSLQNKSL 65 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v----~k~LK~Le~k~l 65 (233)
.+..||+.++.|+.+..- .|...++|...+ |++.++| .|+++.|....|
T Consensus 128 ~l~~L~~~~r~i~~l~~~---~g~s~~EIAe~l--gis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 128 LINDLEKLDREIFIRRYL---LGEKIEEIAKKL--GLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred HHHhCCHHHHHHHHHHHH---ccCCHHHHHHHH--CCCHHHHHHHHHHHHHHHHHccc
Confidence 356789988888876542 469999999999 9997765 556666766555
No 404
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=55.10 E-value=46 Score=26.59 Aligned_cols=44 Identities=20% Similarity=0.338 Sum_probs=37.8
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
-.|++-|..|+.++.+ |...++|..++ +++.++|...++.+-+|
T Consensus 148 ~~lt~re~~vl~~l~~----g~s~~eIa~~l--~~s~~tv~~~~~~~~~k 191 (210)
T PRK09935 148 TVLSNREVTILRYLVS----GLSNKEIADQL--LLSNKTVSAHKSNIYGK 191 (210)
T ss_pred ccCCHHHHHHHHHHHc----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 3589999999988753 39999999999 99999999999988765
No 405
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=54.92 E-value=24 Score=30.58 Aligned_cols=45 Identities=20% Similarity=0.374 Sum_probs=34.7
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHH----HHHHHHHh
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVT----KSIKSLQN 62 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~----k~LK~Le~ 62 (233)
+..|++.++.|+.+.. -.|...++|...+ |++..+|. ++++.|.+
T Consensus 182 l~~L~~~~r~vl~l~~---~~g~s~~EIA~~l--gis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 182 IESLPEREQLVLSLYY---QEELNLKEIGAVL--GVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred HHhCCHHHHHHHHhHh---ccCCCHHHHHHHH--CCCHHHHHHHHHHHHHHHHH
Confidence 4578888888876655 4679999999999 99998887 55555543
No 406
>PF13565 HTH_32: Homeodomain-like domain
Probab=54.75 E-value=39 Score=23.77 Aligned_cols=44 Identities=11% Similarity=0.136 Sum_probs=30.7
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHH
Q 026766 109 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIV 152 (233)
Q Consensus 109 ~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il 152 (233)
.+.+.+.+.+..+..-|+.+|+++|.+..-.++.+|..-|..+|
T Consensus 34 e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 34 EQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 34455566666777899999999999873233456887777664
No 407
>PRK05572 sporulation sigma factor SigF; Validated
Probab=54.54 E-value=24 Score=30.93 Aligned_cols=43 Identities=19% Similarity=0.183 Sum_probs=35.5
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
.+..|++.++.|+.+..- .|...++|...+ |++..+|.++.+.
T Consensus 199 ~l~~L~~~~~~v~~l~~~---~~~s~~eIA~~l--gis~~~V~~~~~r 241 (252)
T PRK05572 199 AIRELDERERLIVYLRYF---KDKTQSEVAKRL--GISQVQVSRLEKK 241 (252)
T ss_pred HHHcCCHHHHHHHHHHHh---CCCCHHHHHHHH--CcCHHHHHHHHHH
Confidence 456899999999988663 579999999999 9999998875443
No 408
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=54.46 E-value=23 Score=23.23 Aligned_cols=37 Identities=16% Similarity=0.276 Sum_probs=29.6
Q ss_pred CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCC
Q 026766 121 LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDN 159 (233)
Q Consensus 121 ~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg 159 (233)
.+..|.+++..++...|+.. ++.++++.|++.+=.|+
T Consensus 2 ~G~i~~~~~~~~l~~~g~~~--~s~~e~~~l~~~~D~~~ 38 (54)
T PF13833_consen 2 DGKITREEFRRALSKLGIKD--LSEEEVDRLFREFDTDG 38 (54)
T ss_dssp SSEEEHHHHHHHHHHTTSSS--SCHHHHHHHHHHHTTSS
T ss_pred cCEECHHHHHHHHHHhCCCC--CCHHHHHHHHHhcccCC
Confidence 46788999999997777543 99999999999876554
No 409
>PRK01381 Trp operon repressor; Provisional
Probab=54.25 E-value=20 Score=28.15 Aligned_cols=44 Identities=25% Similarity=0.320 Sum_probs=32.2
Q ss_pred CChHHHHHH----HHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 026766 16 LTDHERLIY----DVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQ 61 (233)
Q Consensus 16 L~~~e~lVy----~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le 61 (233)
||++|+..+ +++..--..++.+++|..++ |....+|+|.=+.|.
T Consensus 33 lTp~Er~al~~R~~I~~~L~~g~~sQREIa~~l--GvSiaTITRgsn~Lk 80 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLRGELSQREIKQEL--GVGIATITRGSNSLK 80 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHh--CCceeeehhhHHHhc
Confidence 677777653 45554334459999999999 988888887766665
No 410
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=54.24 E-value=25 Score=28.79 Aligned_cols=44 Identities=23% Similarity=0.375 Sum_probs=31.5
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHH----HHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVT----KSIKSLQ 61 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~----k~LK~Le 61 (233)
+..|++.++.|+.+-. -.|...++|...+ |++..+|. |++++|.
T Consensus 133 l~~L~~~~r~vl~l~~---~~~~s~~eIA~~l--gis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 133 LKALSPEERRVIEVLY---YQGYTHREAAQLL--GLPLGTLKTRARRALSRLK 180 (186)
T ss_pred HHhCCHHHHHHHHHHH---HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHHHH
Confidence 3456666666665433 3579999999999 99999888 5555554
No 411
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=54.12 E-value=39 Score=29.62 Aligned_cols=110 Identities=15% Similarity=0.190 Sum_probs=0.0
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHH---------HHHHHhCCCceeeecccCCCeeeEEee
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKS---------IKSLQNKSLIKEVVNIHSKGKKHLMAV 83 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~---------LK~Le~k~lIK~vksV~~~~rK~Yml~ 83 (233)
|.+|+.+|..++......|+...+..=+..-. .+=-+.+.+. ..-|.+-++|+-.+++..
T Consensus 1 ~~~~~~~e~~l~~~~~~~~d~~a~~~L~~~y~--~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~--------- 69 (251)
T PRK07670 1 MQSLTYEEQKLWDRWKEERDPDAADELIRRYM--PLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEK--------- 69 (251)
T ss_pred CcchhHHHHHHHHHHHHcCCHHHHHHHHHHHH--HHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHH---------
Q ss_pred ccccCCCcccCCcccC---CCCCHHHHHHHHHHHHHHhhhCC--------------------------CCCHHHHHHHHH
Q 026766 84 EFEPSKEISGGAWYSE---GSLDTEFIKVVKSQCLKQIIKLK--------------------------VATLEGISDSIK 134 (233)
Q Consensus 84 ~lePs~eiTGG~wy~d---~e~D~efI~~l~~~~~~~i~~~~--------------------------~~T~~~I~~~I~ 134 (233)
|.. ..|-+-+.-.++..|.+|++++. .||.++|+..+.
T Consensus 70 -------------f~~~~~~~f~tyl~~~irn~~~d~lR~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~ 136 (251)
T PRK07670 70 -------------FDPSRDLKFDTYASFRIRGAIIDGLRKEDWLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELG 136 (251)
T ss_pred -------------cCcccCCCHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhC
Q ss_pred HhCCcccccCHHHHHHHHHH
Q 026766 135 RSGAFKVDLTKQQIEEIVRA 154 (233)
Q Consensus 135 ~~~i~~~~Ls~~di~~il~~ 154 (233)
+++++|+.++..
T Consensus 137 --------~~~~~v~~~~~~ 148 (251)
T PRK07670 137 --------MTEEEVEATMNE 148 (251)
T ss_pred --------cCHHHHHHHHHH
No 412
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=53.91 E-value=26 Score=31.46 Aligned_cols=45 Identities=11% Similarity=-0.047 Sum_probs=35.6
Q ss_pred CCCCCChHHHHHHHHHH-hhCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 12 PSDSLTDHERLIYDVIR-SKQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~-~aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
.+..|++.++.|+.+.. -..-+|...++|...+ |++..+|.+.++
T Consensus 219 al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~L--gis~~tVk~~l~ 264 (285)
T TIGR02394 219 WLAELNERQREVLARRFGLLGYEPATLEEVAAEV--GLTRERVRQIQV 264 (285)
T ss_pred HHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHH--CCCHHHHHHHHH
Confidence 46788999998887765 3457789999999999 999887765443
No 413
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=53.85 E-value=26 Score=30.42 Aligned_cols=45 Identities=13% Similarity=0.160 Sum_probs=35.7
Q ss_pred CCCCCChHHHHHHHHHHh-hCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 12 PSDSLTDHERLIYDVIRS-KQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~-aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
.+..|++.|+.|+.+..- .+.+|...++|...+ |++...|++..+
T Consensus 173 ~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~l--gis~~~V~q~~~ 218 (238)
T TIGR02393 173 VLETLTERERKVLRMRYGLLDGRPHTLEEVGKEF--NVTRERIRQIES 218 (238)
T ss_pred HHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHH--CCCHHHHHHHHH
Confidence 356899999999887762 225889999999999 999988876543
No 414
>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=53.56 E-value=1.2e+02 Score=24.46 Aligned_cols=70 Identities=11% Similarity=0.178 Sum_probs=43.0
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+.+.++.+.+ |++.++| ..-|+.|||.+...-. .+- -.| |.+-|+.|..+
T Consensus 1 m~Ige~a~~~--gvs~~tL----RyYE~~GLl~p~~r~~-~gy-----------------R~Y-----~~~~v~~l~~I- 50 (131)
T cd04786 1 MKIGELAKRS--GMAASRI----RFYEAEGLLSSVERSA-NGY-----------------RDY-----PPETVWVLEII- 50 (131)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCCcCC-CCC-----------------eec-----CHHHHHHHHHH-
Confidence 4578889999 9998776 4589999995422111 122 233 33434444332
Q ss_pred HHHhhhCCCCCHHHHHHHHHHh
Q 026766 115 LKQIIKLKVATLEGISDSIKRS 136 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~ 136 (233)
..+++.++ |+++|.+++...
T Consensus 51 -~~lr~~Gf-sL~eI~~ll~~~ 70 (131)
T cd04786 51 -SSAQQAGF-SLDEIRQLLPAD 70 (131)
T ss_pred -HHHHHcCC-CHHHHHHHHhcc
Confidence 22456665 799999999743
No 415
>PF01454 MAGE: MAGE family; InterPro: IPR002190 The first mammalian members of the MAGE (melanoma-associated antigen) gene family were originally described as completely silent in normal adult tissues, with the exception of male germ cells and, for some of them, placenta. By contrast, these genes were expressed in various kinds of tumors. However, other members of the family were recently found to be expressed in normal cells, indicating that the family is larger and more disparate than initially expected. MAGE-like genes have also been identified in non-mammalian species, including Drosophila melanogaster (Fruit fly) and Danio rerio (Zebrafish). Although no MAGE homologous sequences have been identified in Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast) or Schizosaccharomyces pombe (Fission yeast), MAGE sequences have been found in several vegetal species, including Arabidopsis thaliana (Mouse-ear cress) []. The only region of homology shared by all of the members of the family is a stretch of about 200 amino acids which has been named the MAGE conserved domain. The MAGE conserved domain is usually located close to the C-terminal, although it can also be found in a more central position in some proteins. The MAGE conserved domain is generally present as a single copy but it is duplicated in some proteins. It has been proposed that the MAGE conserved domain of MAGE-D proteins might interact with p75 neurotrophin or related receptors [].; PDB: 3NW0_B 2WA0_A 1I4F_C.
Probab=53.53 E-value=1.1e+02 Score=25.63 Aligned_cols=139 Identities=12% Similarity=0.129 Sum_probs=74.5
Q ss_pred HHHHhhCCCcccHHHHHHHhhc---CCChHHHHHHHHHHHh-CCC-ceeeeccc------------CCCeeeEEeecccc
Q 026766 25 DVIRSKQDMGIWTRDMKRELRV---NLPDNIVTKSIKSLQN-KSL-IKEVVNIH------------SKGKKHLMAVEFEP 87 (233)
Q Consensus 25 ~~I~~aG~~GIw~~dik~~t~~---~l~~~~v~k~LK~Le~-k~l-IK~vksV~------------~~~rK~Yml~~leP 87 (233)
-+..+....-|..+||.+..-. .--+..+.++=+.|+. =|+ +++++.-. ....+.|+|.+.-|
T Consensus 5 ~L~~~~~k~pI~r~~i~k~v~~~~~~~f~~v~~~a~~~L~~vFG~eL~ev~~~~~~~~~~~~~~~~~~~~~~yiL~n~L~ 84 (195)
T PF01454_consen 5 LLFKEQKKQPIRRSDILKKVLKEYRRKFPEVFERANEILEDVFGFELVEVPPKKKDKKRASKKSKKSSSSKSYILVNTLP 84 (195)
T ss_dssp HHHHHHCT--EEHHHHHHHTTCCGGGGHHHHHHHHHHHHHHHH-EEEEESSTT-----------------SEEEEEEGCG
T ss_pred HHHHHhCCCCccHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHhceEEEEeCCcccccccccccccccccCCEEEEEecCC
Confidence 3455666678999999998611 2235566666667775 243 23333321 12368999998888
Q ss_pred CCCcccCCcccCCCCCH-HHHHHHHHHHHHHhh-hCCCCCHHHHHHHHHHhCCc---ccccCHHHHHHHH-HHHhcCCeE
Q 026766 88 SKEISGGAWYSEGSLDT-EFIKVVKSQCLKQII-KLKVATLEGISDSIKRSGAF---KVDLTKQQIEEIV-RALVLDNQI 161 (233)
Q Consensus 88 s~eiTGG~wy~d~e~D~-efI~~l~~~~~~~i~-~~~~~T~~~I~~~I~~~~i~---~~~Ls~~di~~il-~~Lv~Dg~i 161 (233)
.+.... +=.+..... .--..|...++.+|. +.+.++-+++++++++.||. ....-..|++.++ +.||=.+-|
T Consensus 85 ~~~~~~--~~~~~~~~~~~~~~Gll~~IL~lI~~~g~~i~E~~L~~~L~~lgi~~~~~~~~~g~~~~~~i~~~~vkq~YL 162 (195)
T PF01454_consen 85 PEYRNE--LSDDSETPSNLAKTGLLMLILSLIFMSGNSISEDDLWKFLRRLGIDEDEKHPILGMDIKKLILKEFVKQGYL 162 (195)
T ss_dssp -S-----------SSH----HHHHHHHHHHHHHHCTT-EEHHHHHHHHHHTT--TTS-BTTTB--HHHHHHCHHHHCTSE
T ss_pred Ccccee--ecCCCCCchhHhHhhHHHHHHHHHHhcCCccCHHHHHHHHHhcCCCccccCccCCCCHHHHHHHHHHHhcCH
Confidence 776332 111222221 112234445555554 45678899999999999987 2333344888888 999999999
Q ss_pred EEEe
Q 026766 162 MEVK 165 (233)
Q Consensus 162 e~v~ 165 (233)
++.+
T Consensus 163 ~~~k 166 (195)
T PF01454_consen 163 VRYK 166 (195)
T ss_dssp -EEE
T ss_pred Hhee
Confidence 7765
No 416
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=53.30 E-value=31 Score=28.26 Aligned_cols=46 Identities=15% Similarity=0.169 Sum_probs=33.4
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHH--HHHhhcCCChHHHHHHHHHHH
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDM--KRELRVNLPDNIVTKSIKSLQ 61 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~di--k~~t~~~l~~~~v~k~LK~Le 61 (233)
-.||+-|..|+.++....+.=+...+| .... ++..++|...++.|-
T Consensus 155 ~~Lt~~E~~il~~l~~~~g~v~s~~~i~~~~~~--~~~~~tv~~~v~rlr 202 (227)
T TIGR03787 155 IDLTVTEFWMVHALAKHPGHVKSRQQLMDAAKI--VVDDSTITSHIKRIR 202 (227)
T ss_pred ecCCHHHHHHHHHHHhCCCccccHHHHHHHhhh--cCCccCHHHHHHHHH
Confidence 359999999999999876666788889 4445 666666665555444
No 417
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=53.16 E-value=24 Score=27.94 Aligned_cols=41 Identities=10% Similarity=0.076 Sum_probs=35.8
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
..|..+|++.=..-+...+|...+ +++.+.+.+.+|.-...
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~--g~S~~~l~r~Fk~~~G~ 52 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERS--GYSKWHLQRMFKKETGH 52 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHH--CcCHHHHHHHHHHHHCc
Confidence 467888888888889999999999 99999999999987653
No 418
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=53.14 E-value=36 Score=29.71 Aligned_cols=40 Identities=15% Similarity=0.156 Sum_probs=31.4
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
+-.+...+..|.+.|+ +..+ .+++ +++|..|++.||+||+
T Consensus 2 ~~~~l~~f~~v~~~gs--~s~A--A~~L--~isqpavS~~I~~LE~ 41 (275)
T PRK03601 2 DTELLKTFLEVSRTRH--FGRA--AESL--YLTQSAVSFRIRQLEN 41 (275)
T ss_pred CHHHHHHHHHHHHcCC--HHHH--HHHh--CCChHHHHHHHHHHHH
Confidence 3456677778888888 4433 4668 9999999999999997
No 419
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=53.13 E-value=25 Score=32.15 Aligned_cols=37 Identities=14% Similarity=0.330 Sum_probs=32.3
Q ss_pred CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 32 DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 32 ~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
+.=|-++.|.++.+.++++.+|+..++.||+.|+|..
T Consensus 20 ~~PVGSk~L~~~~~l~~SsATIRn~m~~LE~~G~L~q 56 (260)
T PRK03911 20 NEPIGSNELKSLMNLKISAATIRNYFKKLSDEGLLTQ 56 (260)
T ss_pred CCccCHHHHHHHcCCCCCcHHHHHHHHHHHHCcCccC
Confidence 3448899999998557889999999999999999965
No 420
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=53.13 E-value=30 Score=27.91 Aligned_cols=47 Identities=15% Similarity=0.239 Sum_probs=36.3
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcC-----CChHHHHHHHHHHHhC
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVN-----LPDNIVTKSIKSLQNK 63 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~-----l~~~~v~k~LK~Le~k 63 (233)
.||+-|..|+.++....++.....+|...+ . +..++|...+++|-.|
T Consensus 148 ~Lt~~E~~il~~l~~~~~~~~~~~~i~~~l--~~~~~~~~~~tv~~~i~~ir~k 199 (221)
T PRK15479 148 ALTPREQALLTVLMYRRTRPVSRQQLFEQV--FSLNDEVSPESIELYIHRLRKK 199 (221)
T ss_pred ecCHHHHHHHHHHHhCCCCcCcHHHHHHHh--cCCCCCCCcccHHHHHHHHHHh
Confidence 599999999999988878888999999887 4 6666666555555443
No 421
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=53.05 E-value=26 Score=28.91 Aligned_cols=46 Identities=11% Similarity=0.125 Sum_probs=34.6
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHh-hc--CCChHHHHHHHHHH
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKREL-RV--NLPDNIVTKSIKSL 60 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t-~~--~l~~~~v~k~LK~L 60 (233)
.||+-|..|+.++.++.++|+...+|-.+. +. ++..++|...++.|
T Consensus 154 ~Lt~~E~~ll~~l~~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rl 202 (229)
T PRK10161 154 EMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRL 202 (229)
T ss_pred EcCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHH
Confidence 599999999999999999999999987755 22 45555555444443
No 422
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=53.01 E-value=64 Score=21.29 Aligned_cols=47 Identities=9% Similarity=0.231 Sum_probs=37.3
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 110 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 110 l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
.+..++.++...+ .+..||.+.+ .++...+...|+.|+-.|.|....
T Consensus 8 ~~~~il~~l~~~~-~~~~ei~~~~--------~i~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 8 TRLRILRLLLEGP-LTVSELAERL--------GLSQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHHHHHHHHHHCC-cCHHHHHHHH--------CcCHhHHHHHHHHHHHCCCeEEEE
Confidence 3456677777776 8899988865 367788999999999999998764
No 423
>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=52.97 E-value=16 Score=24.02 Aligned_cols=26 Identities=8% Similarity=0.365 Sum_probs=21.0
Q ss_pred CCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 32 DMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 32 ~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
..|+.++++.+.+ |++.++|++.++.
T Consensus 7 ~~gls~~~la~~~--gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKL--GISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHH--TS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHh--CCCcchhHHHhcC
Confidence 4689999999999 9999999987754
No 424
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=52.86 E-value=34 Score=29.95 Aligned_cols=47 Identities=15% Similarity=0.205 Sum_probs=34.8
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCcee
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIKE 68 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK~ 68 (233)
|+-.+-.++..|.+.|+ +. .=.+++ +++|..|++.|+.||+ -.|..+
T Consensus 2 ~~l~~L~~f~~va~~gs--~s--~AA~~L--~isQpavS~~I~~LE~~lG~~LF~R 51 (301)
T PRK14997 2 TDLNDFAWFVHVVEEGG--FA--AAGRAL--DEPKSKLSRRIAQLEERLGVRLIQR 51 (301)
T ss_pred ccHHHHHHHHHHHHcCC--HH--HHHHHh--CCCHHHHHHHHHHHHHHhCCEeeee
Confidence 44456677888888887 33 335678 9999999999999997 345544
No 425
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=52.24 E-value=30 Score=28.42 Aligned_cols=42 Identities=19% Similarity=0.242 Sum_probs=32.7
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
.+..||+.++.|+.+-.- .|...++|...+ |++.++|...|.
T Consensus 124 ~l~~Lp~~~R~v~~L~~~---~g~s~~EIA~~l--gis~~tVk~~l~ 165 (178)
T PRK12529 124 LLDTLRPRVKQAFLMATL---DGMKQKDIAQAL--DIALPTVKKYIH 165 (178)
T ss_pred HHHhCCHHHHHHHHHHHH---cCCCHHHHHHHH--CCCHHHHHHHHH
Confidence 356788888888877554 579999999999 999887765443
No 426
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=52.18 E-value=39 Score=29.51 Aligned_cols=47 Identities=11% Similarity=0.258 Sum_probs=35.4
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCcee
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIKE 68 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK~ 68 (233)
|+-.+..++..+.+.|+ ...-.+++ ++++..|++.||+||+ -.|..+
T Consensus 3 m~l~~l~~f~~v~~~gS----~s~AA~~L--~isq~avS~~I~~LE~~lg~~LF~R 52 (300)
T TIGR02424 3 IKFRHLQCFVEVARQGS----VKRAAEAL--HITQPAVSKTLRELEEILGTPLFER 52 (300)
T ss_pred ccHHHHHHHHHHHHhCC----HHHHHHHh--CCChHHHHHHHHHHHHHhCCeEEEE
Confidence 55567778888888887 33345678 9999999999999996 345443
No 427
>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=52.02 E-value=1.1e+02 Score=24.00 Aligned_cols=36 Identities=14% Similarity=0.280 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 122 KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 122 ~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
+.+|..||++.+ .++..-+.++|+.|+-.|.|+..+
T Consensus 24 ~~~s~~eia~~l--------~is~~~v~~~l~~L~~~Gli~~~~ 59 (130)
T TIGR02944 24 QPYSAAEIAEQT--------GLNAPTVSKILKQLSLAGIVTSKR 59 (130)
T ss_pred CCccHHHHHHHH--------CcCHHHHHHHHHHHHHCCcEEecC
Confidence 467899988765 478889999999999999998754
No 428
>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=51.83 E-value=25 Score=24.12 Aligned_cols=40 Identities=15% Similarity=0.154 Sum_probs=29.8
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCC---hHHHHHHHHHH
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLP---DNIVTKSIKSL 60 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~---~~~v~k~LK~L 60 (233)
|--|.++|..+|+..++-.||-.+++. .+ ...|.|+++-|
T Consensus 8 eLgI~dii~~~g~~~ls~~eia~~l~~-~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 8 ELGIPDIIHNAGGGPLSLSEIAARLPT-SNPSAPPMLDRIMRLL 50 (51)
T ss_dssp HTTHHHHHHHHTTS-BEHHHHHHTSTC-T-TTHHHHHHHHHHHH
T ss_pred HcCcHHHHHHcCCCCCCHHHHHHHcCC-CCcchHHHHHHHHHHh
Confidence 445889999999889999999999831 33 44778888776
No 429
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=51.54 E-value=32 Score=30.58 Aligned_cols=25 Identities=12% Similarity=0.077 Sum_probs=17.9
Q ss_pred CcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 33 MGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 33 ~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
+-+..+||.++. |.+..+|+|+|..
T Consensus 5 ~~~Ti~dIA~~a--gVS~~TVSr~Ln~ 29 (342)
T PRK10014 5 KKITIHDVALAA--GVSVSTVSLVLSG 29 (342)
T ss_pred CCCcHHHHHHHh--CCCHHHHHHHHCC
Confidence 346777777777 7777777777754
No 430
>PF06479 Ribonuc_2-5A: Ribonuclease 2-5A; InterPro: IPR010513 The proteins listed below share a common architecture with a protein kinase homology domain (see PDOC00100 from PROSITEDOC) followed by an ~135-residue globular kinase-extension nuclease (KEN) domain made of eight helices []: - Mammalian 2-5A-dependent RNase or RNase L (EC 3.1.26.-), an interferon- induced enzyme implicated in both the molecular mechanisms of interferon action and the fundamental control of RNA stability. 2-5A-dependent RNase is a unique enzyme in that it requires 2-5A, unusual oligoadenylates with 2',5'-phosphodiester linkages. RNase L is catalytically active only after binding to an unusual activator molecule containing a 5'-phosphorylated 2', 5'-linked oligoadenylate (2-5A), in the N-terminal half. RNase L consists of three domains, namely the N-terminal ankyrin repeat domain (see PDOC50088 from PROSITEDOC), the protein kinase homology domain, and the C-terminal KEN domain [, , ]. - Eukaryotic Ire1/Ern1, an ancient transmembrane sensor of endoplasmic reticulum (ER) stress with dual protein kinase and ribonuclease activities. In response to ER stress Ire1/Ern1 catalyzes the splicing of target mRNAs in a spliceosome-independent manner. Ire1/Ern1 is a type 1 transmembrane receptor consisting of an N-terminal ER luminal domain, a transmembrane segment and a cytoplasmic region. The cytoplasmic region encompasses a protein kinase domain followed by a C-terminal KEN domain [, ]. The dimerisation of the kinase domain activates the ribonuclease function of the KEN domain [].; GO: 0016891 endoribonuclease activity, producing 5'-phosphomonoesters, 0006397 mRNA processing; PDB: 3SDJ_D 3FBV_L 3LJ2_A 3SDM_A 3LJ0_A 2RIO_A 3LJ1_A 3P23_A.
Probab=51.53 E-value=6.6 Score=31.96 Aligned_cols=57 Identities=19% Similarity=0.416 Sum_probs=39.0
Q ss_pred CCCcccCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHH
Q 026766 88 SKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIV 152 (233)
Q Consensus 88 s~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il 152 (233)
+..+.||.|. ..+|.++++.|... ++..+-++.|+.++|++..----+| .++++++|
T Consensus 32 ~~~v~~~~W~--~~ld~~l~~~l~~~-----R~Y~~~sv~DLLR~IRNk~~Hy~el-~~~~k~~l 88 (129)
T PF06479_consen 32 AEDVLGGDWD--KKLDPELLDDLGKY-----RKYDGDSVRDLLRAIRNKKHHYQEL-PEEVKEIL 88 (129)
T ss_dssp CCCCTTS-CG--GCSBHHHHHCCTTT-----SS--TT-HHHHHHHHHHHHHTCCCS--HHHHHHC
T ss_pred CCCCCCccHh--HHhCHHHHHHHHhc-----cCCCccCHHHHHHHHHcchHhHHHC-CHHHHHHh
Confidence 5567789995 57899999988753 4567788999999999876222455 67777765
No 431
>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=51.51 E-value=79 Score=24.28 Aligned_cols=61 Identities=16% Similarity=0.174 Sum_probs=48.6
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHH----------HHHhCCCceeeecccCCCeeeEEeec
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIK----------SLQNKSLIKEVVNIHSKGKKHLMAVE 84 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK----------~Le~k~lIK~vksV~~~~rK~Yml~~ 84 (233)
=+.|+.++.+.-.......+|.+.+ +...+.|.-+|+ +|...||+-... ...+.|+|-+.+
T Consensus 11 R~~vl~~L~~~yp~~~~~~eIar~v--~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~--~~~g~k~Y~lT~ 81 (90)
T PF07381_consen 11 RKKVLEYLCSIYPEPAYPSEIARSV--GSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEE--EKGGFKYYRLTE 81 (90)
T ss_pred HHHHHHHHHHcCCCcCCHHHHHHHH--CCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEee--ecCCeeEEEeCh
Confidence 4678889999988899999999999 999999999997 589999992222 223667876654
No 432
>PRK14135 recX recombination regulator RecX; Provisional
Probab=51.16 E-value=66 Score=28.42 Aligned_cols=36 Identities=14% Similarity=0.292 Sum_probs=30.8
Q ss_pred CCCcccHHHHHHHhhc-CCChHHHHHHHHHHHhCCCc
Q 026766 31 QDMGIWTRDMKRELRV-NLPDNIVTKSIKSLQNKSLI 66 (233)
Q Consensus 31 G~~GIw~~dik~~t~~-~l~~~~v~k~LK~Le~k~lI 66 (233)
....-..++|+.++.. ++++..+..+|..|++.|+|
T Consensus 68 ~~r~~s~~el~~kL~~kg~~~~~Ie~vl~~l~~~~~l 104 (263)
T PRK14135 68 SYQMRTEKEVRDYLKKHEISEEIISEVIDKLKEEKYI 104 (263)
T ss_pred hhccccHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCC
Confidence 3445677999999854 99999999999999999998
No 433
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=51.12 E-value=44 Score=28.72 Aligned_cols=47 Identities=15% Similarity=0.299 Sum_probs=41.2
Q ss_pred CCChHHHHHHHHHHhhC----CCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026766 15 SLTDHERLIYDVIRSKQ----DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK 63 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG----~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k 63 (233)
.||+-|+.|+..=-..| .+.+..+||.+++ |+...++...|++=|+|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~l--GISkst~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKEL--GISKSTLSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 59999999998888877 6789999999999 99999998888877654
No 434
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=51.04 E-value=38 Score=29.76 Aligned_cols=40 Identities=8% Similarity=0.134 Sum_probs=30.6
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
+-.+..++-.|.+.|+ ...=.+++ +++|..|++.||+||+
T Consensus 2 ~l~~L~~f~~v~~~gS----~s~AA~~L--~itQpavS~~i~~LE~ 41 (305)
T PRK11151 2 NIRDLEYLVALAEHRH----FRRAADSC--HVSQPTLSGQIRKLED 41 (305)
T ss_pred CHHHHHHHHHHHHhCC----HHHHHHHh--CCCchHHHHHHHHHHH
Confidence 4455667777777776 33335678 9999999999999996
No 435
>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=50.91 E-value=41 Score=18.44 Aligned_cols=22 Identities=14% Similarity=0.252 Sum_probs=19.2
Q ss_pred CcccHHHHHHHhhcCCChHHHHHH
Q 026766 33 MGIWTRDMKRELRVNLPDNIVTKS 56 (233)
Q Consensus 33 ~GIw~~dik~~t~~~l~~~~v~k~ 56 (233)
.|...+++.+.+ +++.+++.+.
T Consensus 20 ~~~s~~~ia~~~--~is~~tv~~~ 41 (42)
T cd00569 20 AGESVAEIARRL--GVSRSTLYRY 41 (42)
T ss_pred cCCCHHHHHHHH--CCCHHHHHHh
Confidence 567999999999 9999998875
No 436
>COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]
Probab=50.88 E-value=48 Score=30.97 Aligned_cols=61 Identities=11% Similarity=0.139 Sum_probs=49.2
Q ss_pred CCCCCCCChHHHHHHHHHHhhCCCc--ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 10 NAPSDSLTDHERLIYDVIRSKQDMG--IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 10 ~~~~~~L~~~e~lVy~~I~~aG~~G--Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
++.+..|++++-.|+..|+..-..= +....|.+.+ .|+...+.++||.|-..+||.. +.+.
T Consensus 5 ~~~~~~l~~~D~rlLraiE~~mR~~e~VP~~~i~~~a--r~~~~~~~~~L~~L~~l~lv~r-~~~~ 67 (304)
T COG0478 5 AEAYPKLSKEDFRLLRAIEGGMRSHEWVPLELIKKRA--RMDEEELLYRLKRLDKLKLVSR-RTIS 67 (304)
T ss_pred hhhhhhcCHHHHHHHHHHHhcccccccccHHHHHHHc--CCCHHHHHHHHHHHHhcCceec-cCCc
Confidence 4557789999999999999643322 3356789999 9999999999999999999987 4444
No 437
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=50.74 E-value=95 Score=25.55 Aligned_cols=44 Identities=16% Similarity=0.214 Sum_probs=34.2
Q ss_pred HHHhhhCC---CCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026766 115 LKQIIKLK---VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS 166 (233)
Q Consensus 115 ~~~i~~~~---~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~ 166 (233)
+-||..++ .+|.++|++.. .++..-+++|+..|.=.|.|+.++.
T Consensus 14 L~~LA~~~~~~~~s~~~IA~~~--------~is~~~L~kil~~L~kaGlV~S~rG 60 (150)
T COG1959 14 LLYLALLPGGGPVSSAEIAERQ--------GISPSYLEKILSKLRKAGLVKSVRG 60 (150)
T ss_pred HHHHHhCCCCCcccHHHHHHHh--------CcCHHHHHHHHHHHHHcCCEEeecC
Confidence 44554432 57789988754 4788899999999999999999874
No 438
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 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 [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=50.68 E-value=17 Score=30.20 Aligned_cols=46 Identities=11% Similarity=0.192 Sum_probs=30.4
Q ss_pred HHHHHHhhCCCcccHHHHHHHhhc------------CCChHHHHHHHHHHHhCCCceeee
Q 026766 23 IYDVIRSKQDMGIWTRDMKRELRV------------NLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 23 Vy~~I~~aG~~GIw~~dik~~t~~------------~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
|+..|--.|. +-...|++.-|- .=....++++|++||+.|||...+
T Consensus 57 ilRklY~~g~--~GV~~lr~~YGg~k~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~ 114 (139)
T PF01090_consen 57 ILRKLYIRGP--VGVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDP 114 (139)
T ss_dssp HHHHHHHCTS--B-HHHHHHHH--EEEETSSCCEE--CHHHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHHhcC--cchHHHHHHhCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecC
Confidence 4444445564 556777776410 123569999999999999998865
No 439
>PRK14135 recX recombination regulator RecX; Provisional
Probab=50.65 E-value=55 Score=28.90 Aligned_cols=74 Identities=15% Similarity=0.184 Sum_probs=53.2
Q ss_pred ccccCCCcccCCcc-----cCCCCCHHHHHHHHHH---------HHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHH
Q 026766 84 EFEPSKEISGGAWY-----SEGSLDTEFIKVVKSQ---------CLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIE 149 (233)
Q Consensus 84 ~lePs~eiTGG~wy-----~d~e~D~efI~~l~~~---------~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~ 149 (233)
|=++.-.|+-+.++ .+.++|.+.++.|... .+.||..+. -|-.+|.+.+.+.| ++.+.|+
T Consensus 19 d~~~~~~~~~~~~~~~~L~~g~~l~~~~~~~i~~~~~~~~a~~~Al~~L~~r~-~s~~el~~kL~~kg-----~~~~~Ie 92 (263)
T PRK14135 19 DEKYAFSVDEDTLVKFMLKKGKELDEEDLEEIQYADQVSKGKNLALYYLSYQM-RTEKEVRDYLKKHE-----ISEEIIS 92 (263)
T ss_pred cCCeEEEeeHHHHHHhcCcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHhhhcc-ccHHHHHHHHHHCC-----CCHHHHH
Confidence 33344444444443 2579999988888653 466676554 55799999999887 5689999
Q ss_pred HHHHHHhcCCeEEE
Q 026766 150 EIVRALVLDNQIME 163 (233)
Q Consensus 150 ~il~~Lv~Dg~ie~ 163 (233)
.+|+-|.-.|.|.-
T Consensus 93 ~vl~~l~~~~~ldD 106 (263)
T PRK14135 93 EVIDKLKEEKYIDD 106 (263)
T ss_pred HHHHHHHHcCCCCH
Confidence 99999999888754
No 440
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=50.60 E-value=81 Score=22.89 Aligned_cols=51 Identities=12% Similarity=0.208 Sum_probs=36.0
Q ss_pred hCCCcccHHHHHHHhhc-CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026766 30 KQDMGIWTRDMKRELRV-NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV 83 (233)
Q Consensus 30 aG~~GIw~~dik~~t~~-~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~ 83 (233)
....-||.++|-.-... +++.+.++-+|..|.++|++.+.+. .++-.|-|.
T Consensus 16 ~~g~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~---Gr~~~Y~Lt 67 (70)
T PF07848_consen 16 PRGGWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLESERR---GRRSYYRLT 67 (70)
T ss_dssp TTTS-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEEECC---CTEEEEEE-
T ss_pred cCCCceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCceeeeec---CccceEeeC
Confidence 33456899999888744 9999999999999999999976443 345566554
No 441
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=50.56 E-value=33 Score=27.36 Aligned_cols=41 Identities=24% Similarity=0.393 Sum_probs=30.1
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
+..|++.++.|+.+.. -.|...++|...+ |++.++|...|.
T Consensus 107 l~~L~~~~r~v~~l~~---~~~~s~~EIA~~l--gis~~tV~~~l~ 147 (163)
T PRK07037 107 LSELPARTRYAFEMYR---LHGETQKDIAREL--GVSPTLVNFMIR 147 (163)
T ss_pred HHhCCHHHHHHHHHHH---HcCCCHHHHHHHH--CCCHHHHHHHHH
Confidence 3466777777765543 3478999999999 999988876544
No 442
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=50.27 E-value=33 Score=29.70 Aligned_cols=44 Identities=14% Similarity=0.183 Sum_probs=34.0
Q ss_pred CCCCChHHHHHHHHHHh-hCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRS-KQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~-aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
+..|++.++.|+.+-.- ..-.|...++|.+.+ |++.++|.+.+.
T Consensus 176 i~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~L--gis~~tV~~~l~ 220 (234)
T TIGR02835 176 LAKLNDREKKIMELRFGLVGGTEKTQKEVADML--GISQSYISRLEK 220 (234)
T ss_pred HHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHH--CCCHHHHHHHHH
Confidence 45678878877776553 224789999999999 999999877753
No 443
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=50.12 E-value=49 Score=28.44 Aligned_cols=52 Identities=13% Similarity=0.289 Sum_probs=42.2
Q ss_pred ChHHHHHHHHHHhh-------CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026766 17 TDHERLIYDVIRSK-------QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV 70 (233)
Q Consensus 17 ~~~e~lVy~~I~~a-------G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk 70 (233)
......||+.|.++ -+.=+...+|..+. |++.+-|+.+|..|+..|||...+
T Consensus 15 ~~~~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~--gvSrtPVReAL~rL~~eGlv~~~p 73 (230)
T COG1802 15 DTLADQVYEELREAILSGELAPGERLSEEELAEEL--GVSRTPVREALRRLEAEGLVEIEP 73 (230)
T ss_pred ccHHHHHHHHHHHHHHhCCCCCCCCccHHHHHHHh--CCCCccHHHHHHHHHHCCCeEecC
Confidence 33455788888754 23448899999999 999999999999999999997653
No 444
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=49.91 E-value=43 Score=26.65 Aligned_cols=60 Identities=7% Similarity=0.160 Sum_probs=44.3
Q ss_pred HHHHHHHHHHhhCCCc-ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026766 19 HERLIYDVIRSKQDMG-IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA 82 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~G-Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml 82 (233)
+|.++=.+..+-++.- |+--.|-.+. |+.-+.-.++|+.||++|.|+-|. +|.+.-+|.-
T Consensus 43 dee~~~ki~KEV~~~r~VTpy~la~r~--gI~~SvAr~vLR~LeeeGvv~lvs--knrR~~IY~~ 103 (107)
T COG4901 43 DEELLDKIRKEVPRERVVTPYVLASRY--GINGSVARIVLRHLEEEGVVQLVS--KNRRQAIYTR 103 (107)
T ss_pred cHHHHHHHHHhcccceeecHHHHHHHh--ccchHHHHHHHHHHHhCCceeeec--cCccceeeec
Confidence 4445555555655544 5667889999 999999999999999999997653 3445667753
No 445
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=49.79 E-value=37 Score=29.59 Aligned_cols=38 Identities=13% Similarity=0.229 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
.+..++..+.+.|+ .+.-.+++ +++|..|+|.||+||+
T Consensus 4 ~~L~~f~~v~~~gs----~s~AA~~L--~isQ~avSr~i~~LE~ 41 (296)
T PRK09906 4 RHLRYFVAVAEELN----FTKAAEKL--HTAQPSLSQQIKDLEN 41 (296)
T ss_pred HHHHHHHHHHhhCC----HHHHHHHh--CCCCcHHHHHHHHHHH
Confidence 45556667777776 33445678 9999999999999997
No 446
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=49.74 E-value=35 Score=29.19 Aligned_cols=42 Identities=14% Similarity=0.148 Sum_probs=34.0
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
+..|++.|+.|+.+..- .|...++|...+ |++.++|.+.++.
T Consensus 176 l~~L~~~~r~vl~l~y~---~~~s~~eIA~~l--gis~~~v~~~~~r 217 (227)
T TIGR02980 176 LAALPERERRILLLRFF---EDKTQSEIAERL--GISQMHVSRLLRR 217 (227)
T ss_pred HHcCCHHHHHHHHHHHh---cCCCHHHHHHHH--CcCHHHHHHHHHH
Confidence 35789988888877653 579999999999 9999988776654
No 447
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=49.69 E-value=54 Score=24.54 Aligned_cols=49 Identities=14% Similarity=0.222 Sum_probs=40.9
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 109 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 109 ~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
.+-..++.+++..+..|..+|.+.+ .++...+...++.|.-+|.|....
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l--------~~s~~tv~~~l~~L~~~g~i~~~~ 51 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV--------GLSPSTVHNRVKRLEEEGVIKGYT 51 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeeceE
Confidence 3456788888888889999998876 488999999999999999998554
No 448
>COG0826 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]
Probab=49.63 E-value=67 Score=30.32 Aligned_cols=95 Identities=20% Similarity=0.216 Sum_probs=60.0
Q ss_pred CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCC--HHHHHHHHHH-----------
Q 026766 47 NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLD--TEFIKVVKSQ----------- 113 (233)
Q Consensus 47 ~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D--~efI~~l~~~----------- 113 (233)
|++...+..+++. .|..++|+|...+. .-++++.+ .++++.|.+.
T Consensus 45 nfs~~~l~e~i~~------------ah~~gkk~~V~~N~----------~~~~~~~~~~~~~l~~l~e~GvDaviv~Dpg 102 (347)
T COG0826 45 NFSVEDLAEAVEL------------AHSAGKKVYVAVNT----------LLHNDELETLERYLDRLVELGVDAVIVADPG 102 (347)
T ss_pred cCCHHHHHHHHHH------------HHHcCCeEEEEecc----------ccccchhhHHHHHHHHHHHcCCCEEEEcCHH
Confidence 4555555555444 45567889965554 45566666 4555555544
Q ss_pred HHHHhhh-----------CCCCCHHHHHHHHHHhCCcc----cccCHHHHHHHHHHHhcCCeEEEE
Q 026766 114 CLKQIIK-----------LKVATLEGISDSIKRSGAFK----VDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 114 ~~~~i~~-----------~~~~T~~~I~~~I~~~~i~~----~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
++.++.. +..+|-.+=.+|..+.|..+ -+||.++|.+|.+.+. |=.||-.
T Consensus 103 ~i~l~~e~~p~l~ih~S~q~~v~N~~~~~f~~~~G~~rvVl~rEls~~ei~~i~~~~~-~veiEvf 167 (347)
T COG0826 103 LIMLARERGPDLPIHVSTQANVTNAETAKFWKELGAKRVVLPRELSLEEIKEIKEQTP-DVEIEVF 167 (347)
T ss_pred HHHHHHHhCCCCcEEEeeeEecCCHHHHHHHHHcCCEEEEeCccCCHHHHHHHHHhCC-CceEEEE
Confidence 3334432 23456666678999999665 3899999999999997 5344443
No 449
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=49.48 E-value=41 Score=29.23 Aligned_cols=50 Identities=18% Similarity=0.378 Sum_probs=36.7
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhc----CCChHHHHHHHHHHHhCCCc
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRV----NLPDNIVTKSIKSLQNKSLI 66 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~----~l~~~~v~k~LK~Le~k~lI 66 (233)
+.+||++++.|+..+-+.|. | +.-..++|. +--++.+.|+...|.++|+|
T Consensus 135 l~~Ls~~~~~iL~~~~~~gs--l--RkaA~klgg~~kr~~ir~vLrKay~~L~~rGli 188 (188)
T COG2411 135 LDNLSERDKRILELFVEEGS--L--RKAAKKLGGLEKRGRIRRVLRKAYHELKKRGLI 188 (188)
T ss_pred cccCCHHHHHHHHHHHHcCc--H--HHHHHHhcCcchhhHHHHHHHHHHHHHHhccCC
Confidence 45699999999999999986 2 222333322 33467889999999999986
No 450
>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=49.30 E-value=54 Score=25.49 Aligned_cols=36 Identities=17% Similarity=0.329 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 122 KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 122 ~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
+.+|.++|++.+. ++..-++++++.|+-.|.|...+
T Consensus 24 ~~~s~~eia~~~~--------i~~~~v~~il~~L~~~gli~~~~ 59 (132)
T TIGR00738 24 GPVSVKEIAERQG--------ISRSYLEKILRTLRRAGLVESVR 59 (132)
T ss_pred CcCcHHHHHHHHC--------cCHHHHHHHHHHHHHCCcEEecc
Confidence 4789999988764 77889999999999999998754
No 451
>TIGR03303 OM_YaeT outer membrane protein assembly complex, YaeT protein. Members of this protein family are the YaeT protein of the YaeT/YfiO complex for assembling proteins into the outer membrane of Gram-negative bacteria. This protein is similar in sequence and function to a non-essential paralog, YtfM, that is also in the Omp85 family. Members of this family typically have five tandem copies of the surface antigen variable number repeat (pfam07244), followed by an outer membrane beta-barrel domain (pfam01103), while the YtfM family typically has a single pfam07244 repeat.
Probab=49.23 E-value=1e+02 Score=30.66 Aligned_cols=99 Identities=11% Similarity=0.168 Sum_probs=65.2
Q ss_pred HHHhhCCCcccHHHHHHHh-hc----CCChHHHHHHHHHH----HhCCCcee-eec-cc-CCCeeeEEeeccccCC----
Q 026766 26 VIRSKQDMGIWTRDMKREL-RV----NLPDNIVTKSIKSL----QNKSLIKE-VVN-IH-SKGKKHLMAVEFEPSK---- 89 (233)
Q Consensus 26 ~I~~aG~~GIw~~dik~~t-~~----~l~~~~v~k~LK~L----e~k~lIK~-vks-V~-~~~rK~Yml~~lePs~---- 89 (233)
-|+=.||+.+..++|+.++ +. -+.+..+....+.| .++|+..+ |.. +. ....++-+.+.+.|-.
T Consensus 73 ~i~~~G~~~~~~~~l~~~~~~~~~g~~~~~~~~~~~~~~l~~~y~~~Gy~~a~V~~~~~~~~~~~~~v~~~v~eg~~~~i 152 (741)
T TIGR03303 73 SIVFSGNKEIKKDQLKKALVGIKKGEIFNRAKLEKDEKALKEFYRSRGKYNAKVEAKVTPLPRNRVDLEFNIKEGKKAKI 152 (741)
T ss_pred EEEEECCccCCHHHHHHHHhhccCCCcCCHHHHHHHHHHHHHHHHHcCcceeEEEEEEEECCCCeEEEEEEEecCCEEEE
Confidence 3455688889999998887 32 47788888887777 67999854 332 11 1234455555555443
Q ss_pred ---CcccCC--------------------ccc-CCCCCHHHHHHHHHHHHHHhhhCCCC
Q 026766 90 ---EISGGA--------------------WYS-EGSLDTEFIKVVKSQCLKQIIKLKVA 124 (233)
Q Consensus 90 ---eiTGG~--------------------wy~-d~e~D~efI~~l~~~~~~~i~~~~~~ 124 (233)
+++|.. |.. ++.||.+.++..++.+.+|+.+++|.
T Consensus 153 ~~i~~~Gn~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~y~~~Gy~ 211 (741)
T TIGR03303 153 KKINFVGNKAFSDSELRDVFALKESNFWSWFTGDDKYSKQKLEADLELLRSFYLNRGYL 211 (741)
T ss_pred EEEEEECCCcCCHHHHHHHHhcCcchhHHhccCCCeECHHHHhhhHHHHHHHHHhCCcE
Confidence 223321 222 46799999999999999999887764
No 452
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=49.02 E-value=43 Score=30.06 Aligned_cols=41 Identities=7% Similarity=0.122 Sum_probs=32.8
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
|+-.+-.++..|.+.|+ ...-.+++ ++++..|++.||+||+
T Consensus 2 m~l~~L~~f~av~~~gs----~s~AA~~L--~iSqpaVS~~Ik~LE~ 42 (317)
T PRK15421 2 IEVKHLKTLQALRNCGS----LAAAAATL--HQTQSALSHQFSDLEQ 42 (317)
T ss_pred ccHHHHHHHHHHHHcCC----HHHHHHHh--CCCHHHHHHHHHHHHH
Confidence 45567778888888887 33445778 9999999999999997
No 453
>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=48.93 E-value=1.2e+02 Score=23.29 Aligned_cols=69 Identities=9% Similarity=0.081 Sum_probs=44.0
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL 115 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~ 115 (233)
.+.++.+.+ |++.++|. ..|++|||++...-. .|--+ |+.+-++.|+.+.
T Consensus 2 ~i~e~a~~~--gvs~~tlr----~ye~~gll~~~~r~~------------------~gyR~-----Y~~~~l~~l~~I~- 51 (113)
T cd01109 2 TIKEVAEKT--GLSADTLR----YYEKEGLLPPVKRDE------------------NGIRD-----FTEEDLEWLEFIK- 51 (113)
T ss_pred CHHHHHHHH--CcCHHHHH----HHHHCCCCCCCCcCC------------------CCCcc-----CCHHHHHHHHHHH-
Confidence 567899999 99988775 568899996432211 12222 4455556664333
Q ss_pred HHhhhCCCCCHHHHHHHHHHh
Q 026766 116 KQIIKLKVATLEGISDSIKRS 136 (233)
Q Consensus 116 ~~i~~~~~~T~~~I~~~I~~~ 136 (233)
++++.+ .|++||.+++...
T Consensus 52 -~lr~~G-~sL~eI~~~l~~~ 70 (113)
T cd01109 52 -CLRNTG-MSIKDIKEYAELR 70 (113)
T ss_pred -HHHHcC-CCHHHHHHHHHHH
Confidence 345554 6699999998753
No 454
>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=48.72 E-value=52 Score=23.94 Aligned_cols=60 Identities=13% Similarity=0.131 Sum_probs=34.9
Q ss_pred hCCCcccHHHHHHH-------hhc-CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCC
Q 026766 30 KQDMGIWTRDMKRE-------LRV-NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSK 89 (233)
Q Consensus 30 aG~~GIw~~dik~~-------t~~-~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~ 89 (233)
.+...+.+.++-+. .+. .+..+.+...|+.|+..|+|...+.=.-.++=.|..+.|.-+.
T Consensus 11 ~~~~~~~~~~vy~~Y~~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~~~~G~~~G~~~~~~l~~d~ 78 (85)
T PF09079_consen 11 GGKEEVTTGEVYEVYEELCESLGVDPLSYRRFSDYLSELEMLGLIESERKGRGRGRGRTREISLNVDP 78 (85)
T ss_dssp CTSSSEEHHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHTTSEEEEEEE-TT-CTEEEEEEECSSS
T ss_pred CCCCceeHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEeecCCCCCCeEEEEEecCCH
Confidence 33355555554433 222 5888999999999999999987664332234455555555443
No 455
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=48.63 E-value=81 Score=23.41 Aligned_cols=59 Identities=12% Similarity=0.158 Sum_probs=45.8
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCC-eeeEEe
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG-KKHLMA 82 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~-rK~Yml 82 (233)
+-.|..++... .|....+|.+.+ +-.+++++=+|.-|-.|++==.+.+.+..+ .++|.+
T Consensus 12 qa~li~mL~rp--~GATi~ei~~at--GWq~HTvRgalsg~~kKklGl~i~s~k~~g~~r~YrI 71 (72)
T PF11994_consen 12 QAQLIAMLRRP--EGATIAEICEAT--GWQPHTVRGALSGLLKKKLGLTITSEKVDGGGRRYRI 71 (72)
T ss_pred HHHHHHHHcCC--CCCCHHHHHHhh--CCchhhHHHHHHHHHHHhcCcEEEeeecCCCeeeEee
Confidence 34666677655 568999999999 999999999999997666655666665555 788865
No 456
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=48.63 E-value=1.2e+02 Score=23.14 Aligned_cols=70 Identities=16% Similarity=0.264 Sum_probs=42.9
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhC-CCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNK-SLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k-~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
..+++.+.+ |++.++|++ .|.+ ++|...++ ..+++.| +.+=|..|+.+.
T Consensus 2 ti~EvA~~~--gVs~~tLR~----ye~~~gli~p~r~--~~g~R~Y----------------------t~~di~~l~~I~ 51 (99)
T cd04765 2 SIGEVAEIL--GLPPHVLRY----WETEFPQLKPVKR--AGGRRYY----------------------RPKDVELLLLIK 51 (99)
T ss_pred CHHHHHHHH--CcCHHHHHH----HHHHcCCCCCcCC--CCCCeee----------------------CHHHHHHHHHHH
Confidence 467888889 999888764 5665 67644332 2233333 344445554432
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhC
Q 026766 115 LKQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
.+++.. ..|+++|.+++...+
T Consensus 52 -~llr~~-G~~l~~i~~~l~~~~ 72 (99)
T cd04765 52 -HLLYEK-GYTIEGAKQALKEDG 72 (99)
T ss_pred -HHHHHC-CCCHHHHHHHHHhcc
Confidence 233444 467999999998765
No 457
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=48.50 E-value=36 Score=27.15 Aligned_cols=43 Identities=19% Similarity=0.277 Sum_probs=34.3
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
.+..|++.++.|+.+..- .|....+|...+ |++..+|.+.+..
T Consensus 122 ~l~~L~~~~r~i~~l~~~---~~~~~~eIA~~l--gis~~tv~~~~~r 164 (179)
T PRK11924 122 CLDALPVKQREVFLLRYV---EGLSYREIAEIL--GVPVGTVKSRLRR 164 (179)
T ss_pred HHHhCCHHHHHHhhHHHH---cCCCHHHHHHHH--CCCHHHHHHHHHH
Confidence 356788888888766553 479999999999 9999988877654
No 458
>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=48.41 E-value=88 Score=21.51 Aligned_cols=65 Identities=9% Similarity=0.233 Sum_probs=38.2
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL 115 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~ 115 (233)
..+++.+.+ ++++++|++ .++++.+. ++. ...+++. |+.+-|+.|+. .
T Consensus 2 ~i~evA~~~--gvs~~tlR~----~~~~g~l~-~~~-~~~g~R~----------------------y~~~~l~~l~~--i 49 (67)
T cd04764 2 TIKEVSEII--GVKPHTLRY----YEKEFNLY-IPR-TENGRRY----------------------YTDEDIELLKK--I 49 (67)
T ss_pred CHHHHHHHH--CcCHHHHHH----HHHhcCCC-CCC-CCCCcee----------------------eCHHHHHHHHH--H
Confidence 567889999 999998874 56655553 121 2223333 34444555544 2
Q ss_pred HHhhhCCCCCHHHHHHHH
Q 026766 116 KQIIKLKVATLEGISDSI 133 (233)
Q Consensus 116 ~~i~~~~~~T~~~I~~~I 133 (233)
+.+.+. ..|+++|.+++
T Consensus 50 ~~l~~~-g~~l~~i~~~l 66 (67)
T cd04764 50 KTLLEK-GLSIKEIKEIL 66 (67)
T ss_pred HHHHHC-CCCHHHHHHHh
Confidence 334444 46688888776
No 459
>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=48.09 E-value=41 Score=21.37 Aligned_cols=27 Identities=4% Similarity=0.091 Sum_probs=21.6
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
+.+++.+.+ +++.++|. ..+++|+|..
T Consensus 2 ~~~e~a~~~--gv~~~tlr----~~~~~g~l~~ 28 (49)
T cd04761 2 TIGELAKLT--GVSPSTLR----YYERIGLLSP 28 (49)
T ss_pred cHHHHHHHH--CcCHHHHH----HHHHCCCCCC
Confidence 567888899 99988775 5689999863
No 460
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 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 3". 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: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=47.96 E-value=82 Score=21.45 Aligned_cols=43 Identities=12% Similarity=0.254 Sum_probs=36.3
Q ss_pred HHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 25 DVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 25 ~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
+++.+ +..|..+++|..+ +++-...--.|..|...|+.+.+-+
T Consensus 3 ~~~~~--~~~itv~~~rd~l--g~sRK~ai~lLE~lD~~g~T~R~gd 45 (50)
T PF09107_consen 3 ELLQK--NGEITVAEFRDLL--GLSRKYAIPLLEYLDREGITRRVGD 45 (50)
T ss_dssp HHHHT--TSSBEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHhc--CCcCcHHHHHHHH--CccHHHHHHHHHHHhccCCEEEeCC
Confidence 45555 5559999999999 9999999999999999999998764
No 461
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=47.85 E-value=1.4e+02 Score=25.96 Aligned_cols=60 Identities=23% Similarity=0.298 Sum_probs=45.0
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHh-hcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKREL-RVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM 81 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t-~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym 81 (233)
+.|-.|++++.+ .|+-..+.+.-..+ |-+|-.+.|.++|-.|++.|-|+.- .....|+|+
T Consensus 7 ~~e~ivl~~~~e-qNrP~ssq~v~~~lq~e~lgktavqk~Ld~La~~Gki~~K---~YGKqKIY~ 67 (201)
T KOG4603|consen 7 DAEGIVLRYLQE-QNRPYSSQDVFGNLQREHLGKTAVQKTLDQLAQQGKIKEK---MYGKQKIYF 67 (201)
T ss_pred ccHHHHHHHHHH-hcCCCchHHHHHHHHHHhccchHHHHHHHHHHHcCchhHH---hccceeeEe
Confidence 356688888765 35667777766665 3378999999999999999999762 245678994
No 462
>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=47.84 E-value=31 Score=25.15 Aligned_cols=46 Identities=15% Similarity=0.308 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeE
Q 026766 108 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQI 161 (233)
Q Consensus 108 ~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~i 161 (233)
......+.++.......+.++|++.+. ++.++++.+|-.|+.+|.|
T Consensus 45 ~i~~~~l~~l~~~y~~i~~~~ia~~l~--------~~~~~vE~~l~~~I~~~~i 90 (105)
T PF01399_consen 45 KIRRRNLRQLSKPYSSISISEIAKALQ--------LSEEEVESILIDLISNGLI 90 (105)
T ss_dssp HHHHHHHHHHHHC-SEEEHHHHHHHHT--------CCHHHHHHHHHHHHHTTSS
T ss_pred HHHHHHHHHHHHHhcccchHHHHHHhc--------cchHHHHHHHHHHHHCCCE
No 463
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=47.75 E-value=35 Score=29.27 Aligned_cols=43 Identities=16% Similarity=0.109 Sum_probs=34.6
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
.+..|++.|+.|+.+..- +|...++|...+ |++...|.++.+.
T Consensus 180 ~l~~L~~~e~~i~~~~~~---~~~t~~eIA~~l--gis~~~V~~~~~~ 222 (231)
T TIGR02885 180 AISKLDERERQIIMLRYF---KDKTQTEVANML--GISQVQVSRLEKK 222 (231)
T ss_pred HHHcCCHHHHHHHHHHHH---cCCCHHHHHHHH--CcCHHHHHHHHHH
Confidence 456889999888877542 578999999999 9999998876544
No 464
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=47.62 E-value=49 Score=29.45 Aligned_cols=49 Identities=12% Similarity=0.191 Sum_probs=43.0
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 109 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 109 ~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
.=++.++.+|.+++.+|+.|+.+.+ ..|.+-|++=|+.|.=.|+|.++.
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l--------~vS~~TiRRdL~~Le~~g~l~r~~ 53 (252)
T PRK10906 5 QRHDAIIELVKQQGYVSTEELVEHF--------SVSPQTIRRDLNDLAEQNKILRHH 53 (252)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHh--------CCCHHHHHHHHHHHHHCCCEEEec
Confidence 4467789999999999999999966 488899999999999999998875
No 465
>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=47.61 E-value=20 Score=23.44 Aligned_cols=27 Identities=7% Similarity=0.226 Sum_probs=20.5
Q ss_pred hCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 30 KQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 30 aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
-=..|+..++|.+.+ |++.++|.|.|+
T Consensus 17 l~~~G~si~~IA~~~--gvsr~TvyR~l~ 43 (45)
T PF02796_consen 17 LYAEGMSIAEIAKQF--GVSRSTVYRYLN 43 (45)
T ss_dssp HHHTT--HHHHHHHT--TS-HHHHHHHHC
T ss_pred HHHCCCCHHHHHHHH--CcCHHHHHHHHh
Confidence 335569999999999 999999999885
No 466
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=47.55 E-value=46 Score=28.73 Aligned_cols=47 Identities=13% Similarity=0.186 Sum_probs=34.7
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCcee
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIKE 68 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK~ 68 (233)
|+-.+-..+..+.+.|+ +. .=.+++ +++|..|++.||.||+ -.|..+
T Consensus 3 m~l~~L~~f~~v~e~~s--~t--~AA~~L--~isqpavS~~I~~LE~~lg~~Lf~R 52 (290)
T PRK10837 3 ITLRQLEVFAEVLKSGS--TT--QASVML--ALSQSAVSAALTDLEGQLGVQLFDR 52 (290)
T ss_pred CcHHHHHHHHHHHHcCC--HH--HHHHHh--CCCccHHHHHHHHHHHHhCCccEee
Confidence 55566667777777776 33 335668 9999999999999997 455544
No 467
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=47.49 E-value=1e+02 Score=22.06 Aligned_cols=53 Identities=15% Similarity=0.211 Sum_probs=34.7
Q ss_pred HHHHHHHHHHh----hCCCcccHHHHHHH-------hhc-CCChHHHHHHHHHHHhCCCceeeec
Q 026766 19 HERLIYDVIRS----KQDMGIWTRDMKRE-------LRV-NLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 19 ~e~lVy~~I~~----aG~~GIw~~dik~~-------t~~-~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
++++++..+-. .|...+.+.++-.. .+. -+..+.+...|..||..|+|..-++
T Consensus 3 ~~Kl~L~Al~~~~~~~~~~~~~~~~vy~~Y~~~c~~~~~~~l~~~~~~~~l~~L~~~gli~~~~~ 67 (87)
T cd08768 3 HQKLVLLALLLLFKRGGEEEATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELEMLGLLETEVS 67 (87)
T ss_pred hHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHcCCeEEEEe
Confidence 45555554432 22344666665443 222 5788999999999999999977554
No 468
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=47.30 E-value=62 Score=28.57 Aligned_cols=46 Identities=13% Similarity=0.298 Sum_probs=40.2
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026766 111 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV 164 (233)
Q Consensus 111 ~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v 164 (233)
+..++.+|.+++.+|.+|+++.+ .+|+.-|+.-|+.|.-.|+|.+.
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l--------~VS~~TiRRdL~~L~~~~~l~r~ 51 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQL--------NVSKETIRRDLNELQTQGKILRN 51 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEe
Confidence 45688999999999999999998 37888899999999999999874
No 469
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=47.27 E-value=41 Score=27.15 Aligned_cols=42 Identities=12% Similarity=0.083 Sum_probs=31.5
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
+..||+.++.|+.+..- .|...++|...+ |++..+|...|..
T Consensus 110 l~~L~~~~r~v~~l~~~---~g~s~~eIA~~l--gis~~tV~~~l~R 151 (164)
T PRK12547 110 LNLLSADQREAIILIGA---SGFSYEDAAAIC--GCAVGTIKSRVSR 151 (164)
T ss_pred HHhCCHHHHHHHHHHHH---cCCCHHHHHHHh--CCCHHHHHHHHHH
Confidence 45677777777766544 678999999999 9998877665544
No 470
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=47.20 E-value=43 Score=26.65 Aligned_cols=43 Identities=12% Similarity=0.032 Sum_probs=32.6
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
.+..||+.++.|+.+..- .|...++|.+.+ |++.++|...|..
T Consensus 119 ~l~~L~~~~r~vl~l~~~---~g~s~~eIA~~l--~is~~tv~~~l~r 161 (170)
T TIGR02952 119 ALKILTPKQQHVIALRFG---QNLPIAEVARIL--GKTEGAVKILQFR 161 (170)
T ss_pred HHHhCCHHHHHHHHHHHh---cCCCHHHHHHHH--CCCHHHHHHHHHH
Confidence 345788888888877543 479999999999 9998877655543
No 471
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=47.14 E-value=83 Score=22.85 Aligned_cols=44 Identities=16% Similarity=0.194 Sum_probs=38.4
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHh
Q 026766 110 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALV 156 (233)
Q Consensus 110 l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv 156 (233)
.+....+|+.+++..|.+.|..-..+.| -..|+.+|+++.+.+.
T Consensus 18 ar~~~~k~l~~NPpine~mir~M~~QMG---~kpSekqi~Q~m~~mk 61 (64)
T PF03672_consen 18 ARKYMEKQLKENPPINEKMIRAMMMQMG---RKPSEKQIKQMMRSMK 61 (64)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHhC---CCccHHHHHHHHHHHH
Confidence 5677788998899999999999999999 4699999999998763
No 472
>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=47.13 E-value=39 Score=29.41 Aligned_cols=50 Identities=12% Similarity=0.314 Sum_probs=41.0
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI 66 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI 66 (233)
.++.....|+.++++....|+...+|..++ +.+.....-.|..||..|++
T Consensus 171 e~~~~~~~il~~~~~~~~g~vt~~~l~~~~--~ws~~~a~~~L~~~~~~G~l 220 (223)
T PF04157_consen 171 ELSKDQSRILELAEEENGGGVTASELAEKL--GWSVERAKEALEELEREGLL 220 (223)
T ss_dssp HH-HHHHHHHHHH--TTTSEEEHHHHHHHH--TB-HHHHHHHHHHHHHTTSE
T ss_pred hhhHHHHHHHHHHHhhcCCCCCHHHHHHHh--CCCHHHHHHHHHHHHhCCCE
Confidence 345667889999966677789999999999 99999999999999999986
No 473
>COG3177 Fic family protein [Function unknown]
Probab=47.05 E-value=42 Score=31.40 Aligned_cols=41 Identities=17% Similarity=0.235 Sum_probs=35.9
Q ss_pred hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026766 29 SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN 71 (233)
Q Consensus 29 ~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks 71 (233)
..-+.++...++...+ +++.++++|.|+.|.++|++.+++.
T Consensus 299 ~~~~~~~t~~~~~~~~--~~s~~Ta~r~l~~l~~~g~l~~~~~ 339 (348)
T COG3177 299 FGQEGYLTAAEIEAIL--GVSKATATRDLKELLELGILEEVKG 339 (348)
T ss_pred hccCCCccHHHHHHHh--CccHHHHHHHHHHHHhCCCeeecCC
Confidence 3445678999999999 9999999999999999999988664
No 474
>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=47.05 E-value=43 Score=26.09 Aligned_cols=43 Identities=21% Similarity=0.261 Sum_probs=32.7
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSL 60 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~L 60 (233)
+..|++.++.|+.+..- .|...++|...+ |++..+|...+...
T Consensus 111 l~~L~~~~r~il~l~~~---~~~~~~eIA~~l--gis~~tv~~~~~ra 153 (161)
T TIGR02985 111 IEKLPEQCRKIFILSRF---EGKSYKEIAEEL--GISVKTVEYHISKA 153 (161)
T ss_pred HHHCCHHHHHHHHHHHH---cCCCHHHHHHHH--CCCHHHHHHHHHHH
Confidence 45678888877766332 478999999999 99999977666553
No 475
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=47.04 E-value=1.6e+02 Score=23.97 Aligned_cols=69 Identities=9% Similarity=0.102 Sum_probs=44.7
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026766 36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL 115 (233)
Q Consensus 36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~ 115 (233)
...++.+.+ |++.++|. .-|+.|||++.+ ...+.+.| +.+-|+.|+.+
T Consensus 2 ~I~e~a~~~--gvs~~TLR----~Ye~~GLl~p~r--~~~g~R~Y----------------------~~~~l~~l~~I-- 49 (134)
T cd04779 2 RIGQLAHLA--GVSKRTID----YYTNLGLLTPER--SDSNYRYY----------------------DETALDRLQLI-- 49 (134)
T ss_pred CHHHHHHHH--CcCHHHHH----HHHHCCCCCCcc--CCCCCeeE----------------------CHHHHHHHHHH--
Confidence 467888899 99988764 568999998533 12244444 33444444443
Q ss_pred HHhhhCCCCCHHHHHHHHHHhC
Q 026766 116 KQIIKLKVATLEGISDSIKRSG 137 (233)
Q Consensus 116 ~~i~~~~~~T~~~I~~~I~~~~ 137 (233)
.+++.. ..|+++|.+++....
T Consensus 50 ~~lr~~-G~sL~eI~~~l~~~~ 70 (134)
T cd04779 50 EHLKGQ-RLSLAEIKDQLEEVQ 70 (134)
T ss_pred HHHHHC-CCCHHHHHHHHHhhc
Confidence 344455 466999999998665
No 476
>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=47.00 E-value=92 Score=26.71 Aligned_cols=59 Identities=15% Similarity=0.233 Sum_probs=41.4
Q ss_pred CCCChHHHHHHHHHHhhCCCccc---------H--HHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIW---------T--RDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH 73 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw---------~--~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~ 73 (233)
-+|++-...|++.+-+--...-| . .+|..++ -+|+.++|+++|..|.+.|||..--|-+
T Consensus 39 lgl~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~-~G~s~~tlrR~l~~LveaGLI~rrDS~N 108 (177)
T PF03428_consen 39 LGLSDRALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERL-NGMSERTLRRHLARLVEAGLIVRRDSPN 108 (177)
T ss_pred cCCChhHHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHH-cCCCHHHHHHHHHHHHHCCCeeeccCCC
Confidence 46777777777766654444433 2 4455443 1799999999999999999998765544
No 477
>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=46.92 E-value=61 Score=22.72 Aligned_cols=38 Identities=13% Similarity=0.312 Sum_probs=28.0
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
.++.+++-..++++ .|+.+.++.+++ +++..+|++.++
T Consensus 3 ~~~g~~i~~~~~~~---~~~t~~~lA~~~--gis~~tis~~~~ 40 (78)
T TIGR02607 3 AHPGEILREEFLEP---LGLSIRALAKAL--GVSRSTLSRIVN 40 (78)
T ss_pred CCHHHHHHHHHHHH---cCCCHHHHHHHh--CCCHHHHHHHHc
Confidence 34556554455554 468999999999 999999998653
No 478
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=46.78 E-value=48 Score=28.79 Aligned_cols=38 Identities=16% Similarity=0.253 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
.+-..+..|.+.|+ ...-.+++ +++|..|++.||.||+
T Consensus 4 ~~L~~f~~v~~~gs----~s~AA~~L--~itqpavS~~Ik~LE~ 41 (291)
T TIGR03418 4 QALRVFESAARLAS----FTAAAREL--GSTQPAVSQQVKRLEE 41 (291)
T ss_pred HHHHHHHHHHHhCC----HHHHHHHh--CCCHHHHHHHHHHHHH
Confidence 34455666777776 33445778 9999999999999997
No 479
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=46.61 E-value=63 Score=21.02 Aligned_cols=36 Identities=19% Similarity=0.231 Sum_probs=28.2
Q ss_pred HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
++...++....+. ...+++.+.+ +++.++|.++++.
T Consensus 15 ~~~~~i~~~~~~~-~s~~~vA~~~--~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 15 RLEQYILKLLRES-RSFKDVAREL--GVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHHhhc-CCHHHHHHHH--CCCHHHHHHHHHh
Confidence 3444455555554 7999999999 9999999999875
No 480
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=46.56 E-value=34 Score=28.22 Aligned_cols=44 Identities=16% Similarity=0.369 Sum_probs=31.6
Q ss_pred CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHH----HHHHHHHh
Q 026766 14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVT----KSIKSLQN 62 (233)
Q Consensus 14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~----k~LK~Le~ 62 (233)
..|++.++.|+.+-. -.|...++|...+ |++.++|. |++++|.+
T Consensus 140 ~~L~~~~~~v~~l~~---~~g~s~~EIA~~l--gis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 140 AQLPESQRQVLELAY---YEGLSQSEIAKRL--GIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred HhCCHHHhhhhhhhh---hcCCCHHHHHHHh--CCCHHHHHHHHHHHHHHHHH
Confidence 345666665554433 3479999999999 99988887 66666654
No 481
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=46.44 E-value=70 Score=23.01 Aligned_cols=38 Identities=8% Similarity=0.177 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHHHHhhh-------------CCCCCHHHHHHHHHHhCC
Q 026766 101 SLDTEFIKVVKSQCLKQIIK-------------LKVATLEGISDSIKRSGA 138 (233)
Q Consensus 101 e~D~efI~~l~~~~~~~i~~-------------~~~~T~~~I~~~I~~~~i 138 (233)
......++.|.+.+.+||++ +.-|++.||...+.+.||
T Consensus 23 ~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi 73 (77)
T PF07524_consen 23 SASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGI 73 (77)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 34577889999999999874 356778888888887776
No 482
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=46.40 E-value=54 Score=28.54 Aligned_cols=44 Identities=14% Similarity=0.211 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCce
Q 026766 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIK 67 (233)
Q Consensus 18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK 67 (233)
-.+..++..+.+.|+ ...=.+++ ++++..|++.||+||+ -.|+.
T Consensus 3 l~~l~~f~~v~~~~s----~t~AA~~L--~isQpavS~~I~~LE~~lg~~Lf~ 49 (292)
T TIGR03298 3 YRQLAALAAVVEEGS----FERAAAAL--SVTPSAVSQRIKALEERLGQPLLV 49 (292)
T ss_pred HHHHHHHHHHHHcCC----HHHHHHHh--CCCHHHHHHHHHHHHHHhCchhee
Confidence 345566667777776 33345678 9999999999999997 44554
No 483
>PRK15320 transcriptional activator SprB; Provisional
Probab=45.94 E-value=46 Score=29.81 Aligned_cols=48 Identities=10% Similarity=0.122 Sum_probs=39.5
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~ 68 (233)
.||+-|..|++++. +|..+++|.+++ ++...+|++-+..|-.|==++.
T Consensus 164 ~LSdREIEVL~LLA----kG~SNKEIAekL--~LS~KTVSTYKnRLLeKLgAkN 211 (251)
T PRK15320 164 GVTQAKYALLILLS----SGHPAIELAKKF--GLGTKTVSIYRKKVMYRLGMDS 211 (251)
T ss_pred CCCHHHHHHHHHHH----cCCCHHHHHHHh--ccchhhHHHHHHHHHHHcCCCC
Confidence 57888999999886 579999999999 9999999988888776543433
No 484
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=45.93 E-value=2.6e+02 Score=27.08 Aligned_cols=55 Identities=22% Similarity=0.228 Sum_probs=34.4
Q ss_pred HHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCC---------cccCCcccCCCCCHHHHHHHHHHH
Q 026766 54 TKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKE---------ISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 54 ~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~e---------iTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+++=+.+|+-|+|.--+.- + +....+.|-++ ..+||.|-..=-|.+|++.+.+..
T Consensus 228 ~~ad~~~e~~g~~~~c~~c---g---~~~~~~~~~~~~c~~Cg~~~~~~GPlW~GpL~d~~f~e~~l~~~ 291 (380)
T COG1867 228 RRADKLLENLGYIYHCSRC---G---EIVGSFREVDEKCPHCGGKVHLAGPLWLGPLHDEEFIEEMLEIA 291 (380)
T ss_pred hhHHHHHHhcCcEEEcccc---c---ceecccccccccCCcccccceeccCcccCcccCHHHHHHHHHHh
Confidence 3444556666666432211 1 44455555555 346998888888999999988844
No 485
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=45.86 E-value=50 Score=29.31 Aligned_cols=42 Identities=14% Similarity=0.274 Sum_probs=33.6
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
.++..+..++..|.+.|+ ...-.+++ +++|..|++.|++||+
T Consensus 6 ~~~~~~L~~F~av~e~gs----~s~AA~~L--~iSQpavS~~I~~LE~ 47 (312)
T PRK10341 6 LPKTQHLVVFQEVIRSGS----IGSAAKEL--GLTQPAVSKIINDIED 47 (312)
T ss_pred hccHHHHHHHHHHHHcCC----HHHHHHHh--CCChHHHHHHHHHHHH
Confidence 345677788888888888 33445678 9999999999999997
No 486
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=45.46 E-value=37 Score=33.15 Aligned_cols=54 Identities=26% Similarity=0.324 Sum_probs=46.1
Q ss_pred ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccC
Q 026766 17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHS 74 (233)
Q Consensus 17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~ 74 (233)
..+..+|+.+|-.++- +.--||+..+ .++..+|+++|.+|++.+|||...-+..
T Consensus 28 ~~~~~lild~llr~~~--v~Eedl~~ll--k~~~KqLR~li~~LredKlI~~~~r~E~ 81 (436)
T KOG2593|consen 28 GGEHVLILDALLRRQC--VREEDLKELL--KFNKKQLRKLIASLREDKLIKIRTRTET 81 (436)
T ss_pred cchhHHHHHHHHHhhh--cchHHHHHHh--cccHHHHHHHHHHhhhhhhhhhhhhhhc
Confidence 4466778888887766 7788999999 9999999999999999999998776653
No 487
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=45.36 E-value=54 Score=28.57 Aligned_cols=41 Identities=17% Similarity=0.217 Sum_probs=31.4
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
|+-.+...+..+.+.|+ +.. =.+++ +++|..|++.||+||+
T Consensus 2 m~l~~L~~f~~v~~~gs--~t~--AA~~L--~iSQ~avS~~i~~LE~ 42 (294)
T PRK13348 2 LDYKQLEALAAVVETGS--FER--AARRL--HVTPSAVSQRIKALEE 42 (294)
T ss_pred CCHHHHHHHHHHHHcCC--HHH--HHHHh--CCCchHHHHHHHHHHH
Confidence 44456667777777777 333 35678 9999999999999997
No 488
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=45.21 E-value=55 Score=26.59 Aligned_cols=54 Identities=9% Similarity=0.248 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026766 104 TEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME 163 (233)
Q Consensus 104 ~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~ 163 (233)
.+-++......+.||..+ .-|..+|.+.+.+.| ++.+.|+.+|.-|.-.|.|..
T Consensus 7 ~~~~~~a~~~al~~L~~r-~~s~~el~~kL~~kg-----~~~~~i~~vl~~l~~~~~ldD 60 (157)
T PRK00117 7 RRMYASARARALRLLARR-EHSRAELRRKLAAKG-----FSEEVIEAVLDRLKEEGLLDD 60 (157)
T ss_pred ccHHHHHHHHHHHHHccc-hhHHHHHHHHHHhcC-----CCHHHHHHHHHHHHHcCCCCH
Confidence 456778888999999877 456999999999988 678999999999998888754
No 489
>PRK06930 positive control sigma-like factor; Validated
Probab=45.19 E-value=41 Score=28.37 Aligned_cols=44 Identities=23% Similarity=0.348 Sum_probs=35.3
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQ 61 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le 61 (233)
+..||+.++.|+.+.. -.|...++|...+ |++.++|...++...
T Consensus 112 l~~L~~rer~V~~L~~---~eg~s~~EIA~~l--giS~~tVk~~l~Ra~ 155 (170)
T PRK06930 112 LSVLTEREKEVYLMHR---GYGLSYSEIADYL--NIKKSTVQSMIERAE 155 (170)
T ss_pred HHhCCHHHHHHHHHHH---HcCCCHHHHHHHH--CcCHHHHHHHHHHHH
Confidence 5689999999987754 4568999999999 999988877665443
No 490
>PRK04158 transcriptional repressor CodY; Validated
Probab=45.15 E-value=24 Score=32.16 Aligned_cols=60 Identities=10% Similarity=0.256 Sum_probs=45.4
Q ss_pred CCCCCChHHHHHHHHHHh--hCCCcccHH-HHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccC
Q 026766 12 PSDSLTDHERLIYDVIRS--KQDMGIWTR-DMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHS 74 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~--aG~~GIw~~-dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~ 74 (233)
.++.|+=.|..-..+|.+ .|++|+-.+ -|..+. |++.+++-.+|++||+.|+|.+ +|.--
T Consensus 176 Ai~tLSySEleAv~hIf~eL~g~EG~lvASkiADrv--gITRSVIVNALRK~ESAGvIES-rSlGM 238 (256)
T PRK04158 176 AINTLSYSELEAVEHIFEELDGNEGLLVASKIADRV--GITRSVIVNALRKLESAGVIES-RSLGM 238 (256)
T ss_pred HHHhcCHhHHHHHHHHHHhcCCCcceEEeeeccccc--CCchhhhhhhhhhhhcccceee-ccCCC
Confidence 355677655554445543 799998764 577777 9999999999999999999987 56553
No 491
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=45.05 E-value=57 Score=28.70 Aligned_cols=41 Identities=12% Similarity=0.205 Sum_probs=31.7
Q ss_pred CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
++-.+..++..+.+.|+ +.. =.+++ +++|..|++.||+||+
T Consensus 2 ~~~~~L~~f~~v~e~~s--~s~--AA~~L--~isQpavS~~I~~LE~ 42 (300)
T PRK11074 2 WSEYSLEVVDAVARTGS--FSA--AAQEL--HRVPSAVSYTVRQLEE 42 (300)
T ss_pred CCHHHHHHHHHHHHhCC--HHH--HHHHh--CCCHHHHHHHHHHHHH
Confidence 34466677888888887 333 34667 9999999999999996
No 492
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=45.04 E-value=1.6e+02 Score=23.49 Aligned_cols=69 Identities=16% Similarity=0.199 Sum_probs=43.6
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026766 35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC 114 (233)
Q Consensus 35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~ 114 (233)
+.++++.+.+ |++.++| ..=|++|||++...-. .+.+. |+ .+=|..|+.+.
T Consensus 2 ~~I~e~a~~~--gvs~~tl----R~Ye~~GLl~p~~r~~-~gyR~-----------------Y~-----~~~l~~l~~I~ 52 (131)
T TIGR02043 2 FQIGELAKLC--GVTSDTL----RFYEKNGLIKPAGRTD-SGYRL-----------------YT-----DEDQKRLRFIL 52 (131)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCCcCC-CCcee-----------------cC-----HHHHHHHHHHH
Confidence 4578899999 9998865 4578899996532212 23333 33 34444444333
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 026766 115 LKQIIKLKVATLEGISDSIKR 135 (233)
Q Consensus 115 ~~~i~~~~~~T~~~I~~~I~~ 135 (233)
+++.. ..++++|.+++..
T Consensus 53 --~lr~~-G~sl~eI~~~l~~ 70 (131)
T TIGR02043 53 --KAKEL-GFTLDEIKELLSI 70 (131)
T ss_pred --HHHHc-CCCHHHHHHHHHh
Confidence 34455 4579999999974
No 493
>PRK04280 arginine repressor; Provisional
Probab=45.04 E-value=85 Score=26.02 Aligned_cols=57 Identities=21% Similarity=0.253 Sum_probs=0.0
Q ss_pred HHHHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026766 20 ERLIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE 84 (233)
Q Consensus 20 e~lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~ 84 (233)
+.+|.++|.+..- =.|.||...+ |...+|.+|+|=||.| |+|| +++-+ ++-.|.+.+
T Consensus 6 ~~~I~~iI~~~~I--~tQeeL~~~L~~~Gi~vTQATiSRDikeL---~lvK-v~~~~--G~~~Y~lp~ 65 (148)
T PRK04280 6 HIKIREIITNNEI--ETQDELVDRLREEGFNVTQATVSRDIKEL---HLVK-VPLPD--GRYKYSLPA 65 (148)
T ss_pred HHHHHHHHHhCCC--CCHHHHHHHHHHcCCCeehHHHHHHHHHc---CCEE-eecCC--CcEEEeecc
No 494
>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=44.99 E-value=52 Score=25.05 Aligned_cols=37 Identities=14% Similarity=0.222 Sum_probs=27.4
Q ss_pred CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
+|++- ..|..++ ++|++.++|.+.+ +++.++|.|..|
T Consensus 36 ~Ls~R-~~I~~ll----~~G~S~~eIA~~L--gISrsTIyRi~R 72 (88)
T TIGR02531 36 SLAQR-LQVAKML----KQGKTYSDIEAET--GASTATISRVKR 72 (88)
T ss_pred hhhHH-HHHHHHH----HCCCCHHHHHHHH--CcCHHHHHHHHH
Confidence 34444 3444443 4679999999999 999999999665
No 495
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=44.75 E-value=39 Score=27.46 Aligned_cols=43 Identities=16% Similarity=0.196 Sum_probs=32.3
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSL 60 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~L 60 (233)
+..|++.++.|+.+..- .|...++|...+ |++..+|...|...
T Consensus 134 l~~L~~~~r~v~~l~~~---~g~s~~eIA~~l--gis~~~v~~~l~Ra 176 (187)
T TIGR02948 134 IQALPPKYRMVIVLKYM---EDLSLKEISEIL--DLPVGTVKTRIHRG 176 (187)
T ss_pred HHhCCHHHhHHhhhHHh---cCCCHHHHHHHH--CCCHHHHHHHHHHH
Confidence 44677777777755332 589999999999 99998887776543
No 496
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=44.61 E-value=51 Score=26.76 Aligned_cols=42 Identities=10% Similarity=0.078 Sum_probs=32.3
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~ 59 (233)
+..|++.++.|+.+..- .|...++|...+ +++..+|.+.+..
T Consensus 138 l~~L~~~~r~vi~l~~~---~g~s~~eIA~~l--gis~~~v~~~l~R 179 (189)
T TIGR02984 138 LAKLPEDYREVILLRHL---EGLSFAEVAERM--DRSEGAVSMLWVR 179 (189)
T ss_pred HHcCCHHHHHHHHHHHh---cCCCHHHHHHHH--CcCHHHHHHHHHH
Confidence 34678877777765442 789999999999 9999888766543
No 497
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=44.57 E-value=49 Score=29.88 Aligned_cols=44 Identities=16% Similarity=0.137 Sum_probs=35.1
Q ss_pred CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 026766 12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIK 58 (233)
Q Consensus 12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK 58 (233)
.+..|++.|+.|+.+---. .+|...++|...+ |++...|+++.+
T Consensus 227 al~~L~~rEr~VL~lry~~-~~~~Tl~EIA~~l--gvS~~rVrqi~~ 270 (284)
T PRK06596 227 ALEGLDERSRDIIEARWLD-DDKSTLQELAAEY--GVSAERVRQIEK 270 (284)
T ss_pred HHhcCCHHHHHHHHHHhcC-CCCcCHHHHHHHH--CCCHHHHHHHHH
Confidence 4568999999998876532 2789999999999 999988875544
No 498
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.30 E-value=84 Score=24.09 Aligned_cols=51 Identities=14% Similarity=0.104 Sum_probs=40.0
Q ss_pred CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCC-ChHHHHHHHHHHHhCCCce
Q 026766 13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNL-PDNIVTKSIKSLQNKSLIK 67 (233)
Q Consensus 13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l-~~~~v~k~LK~Le~k~lIK 67 (233)
.+..|+|.++ ++++..-..|.+.++|.++. ++ +++++.+=.+++.+.+...
T Consensus 5 ~r~~s~EfK~--~iv~~~~~~g~sv~~vAr~~--gv~~~~~l~~W~~~~~~~~~~~ 56 (116)
T COG2963 5 RKKYSPEFKL--EAVALYLRGGDTVSEVAREF--GIVSATQLYKWRIQLQKGGGLA 56 (116)
T ss_pred cccCCHHHHH--HHHHHHHhcCccHHHHHHHh--CCCChHHHHHHHHHHHHccccc
Confidence 5667777663 45555666667999999999 96 9999999999999877653
No 499
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=44.18 E-value=86 Score=20.23 Aligned_cols=35 Identities=6% Similarity=0.218 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026766 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165 (233)
Q Consensus 123 ~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~ 165 (233)
.+|..++++.+ .+|..-|...|+.|+-+|.|+...
T Consensus 20 l~s~~~la~~~--------~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 20 LPSERELAAQL--------GVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEEec
Confidence 45888888877 367889999999999999998754
No 500
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=44.08 E-value=54 Score=29.20 Aligned_cols=39 Identities=18% Similarity=0.191 Sum_probs=28.0
Q ss_pred hHHHHHHHHHHhhC-CCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026766 18 DHERLIYDVIRSKQ-DMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62 (233)
Q Consensus 18 ~~e~lVy~~I~~aG-~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~ 62 (233)
-.+..++..+-+.| + ...=.+++ +++|..|++.||+||+
T Consensus 3 ~~~L~~F~~v~~~~~S----~s~AA~~L--~isQpavS~~I~~LE~ 42 (309)
T PRK12683 3 FQQLRIIREAVRQNFN----LTEVANAL--YTSQSGVSKQIKDLED 42 (309)
T ss_pred HHHHHHHHHHHHccCC----HHHHHHHh--cCCcHHHHHHHHHHHH
Confidence 34555565555554 5 33445678 9999999999999997
Done!