Query 045382
Match_columns 191
No_of_seqs 118 out of 365
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 12:40:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045382.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045382hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2577 Transcription factor E 99.9 3.8E-25 8.2E-30 200.1 9.2 86 104-189 63-153 (354)
2 KOG2578 Transcription factor E 99.9 6E-25 1.3E-29 196.7 4.4 86 103-188 15-100 (388)
3 PF02319 E2F_TDP: E2F/DP famil 99.9 1.2E-24 2.6E-29 156.3 4.4 66 109-174 1-71 (71)
4 KOG2578 Transcription factor E 99.8 7.1E-20 1.5E-24 164.3 1.6 128 51-179 91-242 (388)
5 KOG2829 E2F-like protein [Tran 98.8 3E-09 6.5E-14 95.4 3.1 90 68-188 49-140 (326)
6 PF01978 TrmB: Sugar-specific 95.0 0.019 4.2E-07 39.7 2.5 43 131-173 21-63 (68)
7 cd00092 HTH_CRP helix_turn_hel 93.3 0.13 2.8E-06 34.5 3.6 54 117-170 5-63 (67)
8 PF08279 HTH_11: HTH domain; 92.4 0.15 3.2E-06 33.7 2.9 41 119-160 3-43 (55)
9 smart00346 HTH_ICLR helix_turn 92.1 0.21 4.5E-06 35.5 3.6 55 119-174 8-62 (91)
10 smart00420 HTH_DEOR helix_turn 91.9 0.17 3.6E-06 32.0 2.6 46 120-167 4-49 (53)
11 smart00550 Zalpha Z-DNA-bindin 90.9 0.29 6.3E-06 34.5 3.2 56 117-172 7-62 (68)
12 PF09339 HTH_IclR: IclR helix- 90.9 0.21 4.6E-06 33.1 2.4 45 120-165 7-51 (52)
13 smart00418 HTH_ARSR helix_turn 88.5 0.71 1.5E-05 29.4 3.4 37 131-167 9-45 (66)
14 PF02082 Rrf2: Transcriptional 87.6 0.67 1.4E-05 33.3 3.2 59 116-174 8-68 (83)
15 TIGR02944 suf_reg_Xantho FeS a 87.2 0.72 1.6E-05 35.5 3.3 48 118-165 11-58 (130)
16 cd00090 HTH_ARSR Arsenical Res 87.0 1.7 3.7E-05 28.3 4.7 46 119-167 10-55 (78)
17 COG1378 Predicted transcriptio 86.9 0.9 2E-05 39.8 4.2 36 132-167 30-65 (247)
18 PF13412 HTH_24: Winged helix- 86.6 0.83 1.8E-05 29.4 2.9 43 119-163 6-48 (48)
19 PF12802 MarR_2: MarR family; 85.2 0.87 1.9E-05 30.1 2.5 46 120-165 9-54 (62)
20 smart00419 HTH_CRP helix_turn_ 82.7 0.83 1.8E-05 28.5 1.5 38 132-170 8-45 (48)
21 PF00392 GntR: Bacterial regul 82.5 2.7 5.7E-05 28.7 4.1 50 118-167 6-59 (64)
22 cd08768 Cdc6_C Winged-helix do 82.4 1.1 2.4E-05 31.7 2.3 43 112-165 23-65 (87)
23 PF09079 Cdc6_C: CDC6, C termi 81.5 0.42 9E-06 34.4 -0.2 21 145-165 38-58 (85)
24 smart00345 HTH_GNTR helix_turn 81.3 2 4.3E-05 27.6 3.0 40 129-168 16-56 (60)
25 PF13730 HTH_36: Helix-turn-he 81.2 1.4 3.1E-05 28.8 2.3 30 133-162 26-55 (55)
26 PRK10163 DNA-binding transcrip 80.8 4.1 8.8E-05 35.4 5.6 56 119-175 28-83 (271)
27 PF04182 B-block_TFIIIC: B-blo 78.5 2.3 5.1E-05 30.4 2.9 49 119-167 5-53 (75)
28 PF01047 MarR: MarR family; I 77.6 1.6 3.5E-05 28.7 1.7 43 122-166 9-51 (59)
29 COG3355 Predicted transcriptio 77.3 3 6.6E-05 33.6 3.5 60 121-182 33-100 (126)
30 PF09012 FeoC: FeoC like trans 76.9 1.1 2.5E-05 31.3 0.8 46 121-168 5-50 (69)
31 TIGR00738 rrf2_super rrf2 fami 75.5 5.1 0.00011 30.4 4.2 36 130-165 23-58 (132)
32 PF01726 LexA_DNA_bind: LexA D 74.0 1.9 4.1E-05 30.5 1.3 46 121-166 14-60 (65)
33 PRK15090 DNA-binding transcrip 72.7 8.1 0.00018 33.0 5.2 54 119-174 17-70 (257)
34 cd07377 WHTH_GntR Winged helix 70.7 5.3 0.00011 26.0 2.9 34 133-166 26-59 (66)
35 TIGR00122 birA_repr_reg BirA b 69.4 3.8 8.2E-05 28.2 2.0 54 120-176 4-58 (69)
36 TIGR02716 C20_methyl_CrtF C-20 68.9 2.3 4.9E-05 37.1 1.0 36 131-166 22-57 (306)
37 PRK09834 DNA-binding transcrip 68.8 5.5 0.00012 34.3 3.3 51 121-172 16-67 (263)
38 PF08220 HTH_DeoR: DeoR-like h 68.5 5.6 0.00012 27.0 2.7 45 120-166 4-48 (57)
39 PF13463 HTH_27: Winged helix 68.0 4.6 0.0001 27.0 2.2 38 128-165 14-51 (68)
40 PHA02943 hypothetical protein; 65.4 11 0.00024 31.8 4.3 68 119-189 14-83 (165)
41 PF01022 HTH_5: Bacterial regu 64.9 6.4 0.00014 25.4 2.3 41 121-164 7-47 (47)
42 smart00347 HTH_MARR helix_turn 64.7 9.9 0.00021 26.5 3.5 44 120-165 14-57 (101)
43 TIGR01610 phage_O_Nterm phage 64.0 7.6 0.00017 28.9 2.9 46 129-176 44-89 (95)
44 PF12840 HTH_20: Helix-turn-he 64.0 6.4 0.00014 26.5 2.3 46 119-166 13-58 (61)
45 TIGR02010 IscR iron-sulfur clu 63.5 9 0.0002 29.9 3.3 44 129-172 22-67 (135)
46 PF05732 RepL: Firmicute plasm 63.1 9 0.00019 31.7 3.4 59 119-177 62-126 (165)
47 COG2894 MinD Septum formation 61.1 4.4 9.6E-05 36.4 1.3 28 133-160 41-68 (272)
48 TIGR02337 HpaR homoprotocatech 60.3 12 0.00026 28.0 3.4 44 121-166 33-76 (118)
49 PRK14165 winged helix-turn-hel 60.0 16 0.00035 31.7 4.5 40 128-167 17-56 (217)
50 PF08784 RPA_C: Replication pr 59.9 7.6 0.00017 28.7 2.2 50 113-162 44-95 (102)
51 PRK00215 LexA repressor; Valid 59.8 8 0.00017 31.8 2.5 42 127-168 18-60 (205)
52 PF13518 HTH_28: Helix-turn-he 59.6 7.7 0.00017 24.6 2.0 37 121-161 5-41 (52)
53 smart00344 HTH_ASNC helix_turn 58.4 8.6 0.00019 28.2 2.3 46 117-164 4-49 (108)
54 PF09756 DDRGK: DDRGK domain; 57.0 12 0.00027 31.9 3.3 59 117-177 100-160 (188)
55 PRK10857 DNA-binding transcrip 56.8 10 0.00023 31.1 2.7 36 129-164 22-57 (164)
56 TIGR02431 pcaR_pcaU beta-ketoa 56.6 17 0.00037 30.8 4.1 50 120-171 13-62 (248)
57 TIGR00498 lexA SOS regulatory 56.3 9.8 0.00021 31.1 2.5 46 121-166 14-60 (199)
58 TIGR02366 DHAK_reg probable di 55.9 8.5 0.00019 30.1 2.0 36 115-150 6-41 (176)
59 COG1414 IclR Transcriptional r 55.6 12 0.00027 32.2 3.1 55 119-174 7-61 (246)
60 PF13545 HTH_Crp_2: Crp-like h 55.6 7 0.00015 26.7 1.3 37 131-167 27-63 (76)
61 TIGR01764 excise DNA binding d 55.1 3.8 8.3E-05 25.3 -0.1 22 133-154 2-23 (49)
62 COG1474 CDC6 Cdc6-related prot 54.4 6.2 0.00013 36.4 1.1 29 135-163 304-332 (366)
63 PRK11511 DNA-binding transcrip 53.8 11 0.00024 29.1 2.3 44 115-158 8-51 (127)
64 PRK10219 DNA-binding transcrip 53.1 9.9 0.00022 27.9 1.9 41 116-156 5-45 (107)
65 PRK09954 putative kinase; Prov 52.5 9.5 0.00021 33.9 2.0 45 118-164 5-49 (362)
66 PRK09464 pdhR transcriptional 52.4 21 0.00046 30.0 4.0 59 112-170 9-73 (254)
67 KOG2747 Histone acetyltransfer 51.6 26 0.00057 33.3 4.8 58 113-175 304-367 (396)
68 PF01853 MOZ_SAS: MOZ/SAS fami 51.1 20 0.00043 30.8 3.6 46 121-169 138-184 (188)
69 TIGR01889 Staph_reg_Sar staphy 50.9 15 0.00033 27.5 2.6 49 127-175 38-89 (109)
70 TIGR03338 phnR_burk phosphonat 50.9 35 0.00076 27.8 4.9 40 128-167 30-69 (212)
71 PRK06266 transcription initiat 50.4 28 0.00062 29.1 4.4 52 120-173 26-84 (178)
72 TIGR02702 SufR_cyano iron-sulf 50.3 23 0.00049 29.4 3.8 52 119-172 4-61 (203)
73 PLN03239 histone acetyltransfe 50.1 33 0.00072 32.2 5.1 60 121-183 271-332 (351)
74 PRK11414 colanic acid/biofilm 49.6 19 0.0004 29.8 3.2 45 128-172 30-74 (221)
75 PRK11050 manganese transport r 48.8 26 0.00056 28.1 3.8 42 131-172 50-91 (152)
76 COG1510 Predicted transcriptio 48.8 17 0.00036 31.1 2.7 36 130-165 39-74 (177)
77 TIGR00373 conserved hypothetic 47.5 19 0.00042 29.4 2.9 42 131-172 27-75 (158)
78 PRK11014 transcriptional repre 46.5 18 0.0004 28.3 2.6 38 128-165 21-58 (141)
79 PF04218 CENP-B_N: CENP-B N-te 45.6 28 0.00061 23.4 3.0 42 109-154 2-44 (53)
80 PRK10411 DNA-binding transcrip 45.4 24 0.00051 30.4 3.3 54 120-175 8-61 (240)
81 PRK11569 transcriptional repre 45.3 26 0.00057 30.3 3.5 48 120-168 32-79 (274)
82 PLN03238 probable histone acet 45.1 44 0.00096 30.6 5.0 59 121-183 213-271 (290)
83 PF08280 HTH_Mga: M protein tr 44.8 13 0.00029 25.2 1.3 36 120-157 9-44 (59)
84 COG2186 FadR Transcriptional r 44.4 19 0.00041 30.9 2.5 56 116-171 14-74 (241)
85 PRK13509 transcriptional repre 44.3 20 0.00044 30.9 2.7 48 120-169 9-56 (251)
86 PRK11534 DNA-binding transcrip 43.0 22 0.00047 29.4 2.6 49 128-176 26-74 (224)
87 TIGR01884 cas_HTH CRISPR locus 42.1 30 0.00064 28.7 3.3 45 120-166 147-191 (203)
88 cd07153 Fur_like Ferric uptake 41.7 28 0.0006 25.8 2.8 44 121-165 6-54 (116)
89 PRK04984 fatty acid metabolism 40.9 36 0.00079 28.3 3.6 44 128-171 26-71 (239)
90 PF01325 Fe_dep_repress: Iron 40.7 36 0.00078 23.4 3.0 38 129-166 19-56 (60)
91 TIGR02297 HpaA 4-hydroxyphenyl 40.3 18 0.00039 30.5 1.7 46 116-161 186-231 (287)
92 PF02796 HTH_7: Helix-turn-hel 37.9 18 0.00039 23.3 1.1 33 118-154 11-43 (45)
93 PF03374 ANT: Phage antirepres 37.5 19 0.00041 26.8 1.3 41 121-165 14-54 (111)
94 PRK09975 DNA-binding transcrip 37.2 26 0.00057 28.1 2.2 38 114-151 13-50 (213)
95 COG2238 RPS19A Ribosomal prote 37.0 39 0.00084 28.2 3.1 60 131-190 66-140 (147)
96 PF02295 z-alpha: Adenosine de 36.9 52 0.0011 23.3 3.4 58 116-173 4-61 (66)
97 PRK10225 DNA-binding transcrip 36.8 66 0.0014 27.2 4.6 57 115-171 12-73 (257)
98 smart00529 HTH_DTXR Helix-turn 36.8 26 0.00057 24.9 1.9 33 135-167 2-34 (96)
99 PF14394 DUF4423: Domain of un 36.7 34 0.00074 28.3 2.8 59 129-187 36-102 (171)
100 PRK03837 transcriptional regul 36.6 58 0.0013 27.0 4.2 49 117-165 18-70 (241)
101 PRK03902 manganese transport t 36.5 58 0.0013 25.4 4.0 52 118-171 10-61 (142)
102 COG4189 Predicted transcriptio 36.5 35 0.00076 31.1 3.0 51 112-164 18-69 (308)
103 COG1522 Lrp Transcriptional re 36.3 35 0.00076 26.2 2.7 50 114-165 6-55 (154)
104 PF13551 HTH_29: Winged helix- 35.3 24 0.00053 25.3 1.5 27 134-160 14-40 (112)
105 PRK10421 DNA-binding transcrip 35.3 26 0.00056 29.6 1.9 43 128-170 21-65 (253)
106 COG1802 GntR Transcriptional r 35.3 33 0.00071 28.6 2.5 41 128-168 35-75 (230)
107 PRK03573 transcriptional regul 35.1 54 0.0012 25.2 3.6 34 132-165 46-79 (144)
108 PRK09391 fixK transcriptional 34.3 43 0.00094 27.8 3.1 39 133-171 180-218 (230)
109 TIGR02928 orc1/cdc6 family rep 34.1 12 0.00025 32.9 -0.4 32 137-168 319-353 (365)
110 COG1846 MarR Transcriptional r 34.1 36 0.00078 24.2 2.3 44 122-167 28-71 (126)
111 PF14947 HTH_45: Winged helix- 34.0 41 0.00088 24.0 2.5 53 116-172 6-58 (77)
112 PRK13503 transcriptional activ 33.5 27 0.00059 29.2 1.8 40 116-155 171-210 (278)
113 PRK09990 DNA-binding transcrip 32.8 81 0.0018 26.4 4.5 43 128-170 26-70 (251)
114 PLN00104 MYST -like histone ac 32.8 91 0.002 30.2 5.3 66 113-182 350-421 (450)
115 PF03444 HrcA_DNA-bdg: Winged 32.7 63 0.0014 24.1 3.4 49 116-165 8-56 (78)
116 PF09904 HTH_43: Winged helix- 32.5 20 0.00044 27.5 0.8 55 134-188 23-89 (90)
117 COG2739 Uncharacterized protei 32.4 19 0.0004 28.5 0.5 40 116-155 17-56 (105)
118 PRK11512 DNA-binding transcrip 32.1 32 0.00069 26.7 1.8 35 131-165 53-87 (144)
119 PF01710 HTH_Tnp_IS630: Transp 31.9 36 0.00077 26.2 2.0 44 119-167 60-103 (119)
120 PRK10130 transcriptional regul 31.9 27 0.00058 31.9 1.5 44 115-158 239-282 (350)
121 COG1514 LigT 2'-5' RNA ligase 31.8 33 0.00072 28.6 2.0 35 155-190 72-106 (180)
122 PRK10870 transcriptional repre 31.7 45 0.00097 27.3 2.7 40 127-166 66-105 (176)
123 PRK04214 rbn ribonuclease BN/u 31.1 53 0.0012 30.4 3.4 43 129-171 307-349 (412)
124 PF08222 HTH_CodY: CodY helix- 30.6 24 0.00052 25.4 0.8 36 131-166 3-38 (61)
125 PRK10402 DNA-binding transcrip 30.1 65 0.0014 26.6 3.4 55 117-172 151-208 (226)
126 PRK15121 right oriC-binding tr 29.8 38 0.00083 29.2 2.1 45 116-160 5-49 (289)
127 PRK11753 DNA-binding transcrip 28.6 56 0.0012 26.0 2.8 36 132-167 168-203 (211)
128 KOG3054 Uncharacterized conser 28.5 1E+02 0.0022 28.2 4.6 60 116-177 200-261 (299)
129 TIGR02147 Fsuc_second hypothet 27.6 1.2E+02 0.0025 27.2 4.8 60 129-188 134-201 (271)
130 PF05930 Phage_AlpA: Prophage 27.4 22 0.00048 23.4 0.2 24 131-154 2-25 (51)
131 PF12728 HTH_17: Helix-turn-he 27.2 19 0.00042 23.1 -0.1 22 133-154 2-23 (51)
132 KOG4578 Uncharacterized conser 26.9 31 0.00067 32.7 1.1 44 105-148 359-402 (421)
133 PRK09685 DNA-binding transcrip 26.4 38 0.00083 28.8 1.5 38 117-154 198-236 (302)
134 PRK09333 30S ribosomal protein 26.1 61 0.0013 27.0 2.6 37 131-167 66-116 (150)
135 PRK00411 cdc6 cell division co 26.0 29 0.00062 30.9 0.7 33 132-164 315-357 (394)
136 PRK09802 DNA-binding transcrip 26.0 67 0.0015 28.1 3.0 50 119-170 20-69 (269)
137 PF02954 HTH_8: Bacterial regu 25.9 43 0.00093 21.2 1.3 35 114-151 2-37 (42)
138 PF01475 FUR: Ferric uptake re 25.7 50 0.0011 24.8 1.9 48 119-167 11-63 (120)
139 PRK11886 bifunctional biotin-- 25.6 74 0.0016 28.1 3.2 51 119-171 7-58 (319)
140 PF14830 Haemocyan_bet_s: Haem 25.5 34 0.00074 26.8 0.9 19 144-162 52-70 (103)
141 PF09862 DUF2089: Protein of u 25.4 41 0.00089 26.7 1.4 37 119-158 39-79 (113)
142 PTZ00064 histone acetyltransfe 25.4 84 0.0018 31.2 3.7 49 133-184 472-520 (552)
143 PRK00080 ruvB Holliday junctio 25.3 78 0.0017 27.9 3.3 56 113-168 256-313 (328)
144 PF04703 FaeA: FaeA-like prote 25.2 64 0.0014 22.8 2.2 52 121-173 5-59 (62)
145 PF13384 HTH_23: Homeodomain-l 25.2 21 0.00045 22.7 -0.3 28 133-160 18-45 (50)
146 TIGR02812 fadR_gamma fatty aci 24.9 86 0.0019 26.0 3.3 44 128-171 25-70 (235)
147 cd04762 HTH_MerR-trunc Helix-T 24.4 24 0.00051 21.3 -0.1 23 133-155 1-23 (49)
148 PRK11523 DNA-binding transcrip 24.0 1.3E+02 0.0028 25.4 4.3 54 117-170 13-71 (253)
149 TIGR02063 RNase_R ribonuclease 24.0 89 0.0019 31.1 3.7 53 120-172 6-62 (709)
150 COG4519 Uncharacterized protei 23.9 55 0.0012 25.2 1.7 41 121-162 12-52 (95)
151 PF09182 PuR_N: Bacterial puri 23.5 88 0.0019 23.0 2.7 31 121-151 9-39 (70)
152 PRK09393 ftrA transcriptional 23.1 62 0.0013 28.3 2.2 44 116-159 218-261 (322)
153 COG3093 VapI Plasmid maintenan 23.0 24 0.00053 27.7 -0.3 39 110-154 6-45 (104)
154 PRK10141 DNA-binding transcrip 23.0 1.7E+02 0.0036 23.0 4.4 51 120-172 20-70 (117)
155 PRK06474 hypothetical protein; 22.9 82 0.0018 26.0 2.8 46 119-165 14-60 (178)
156 cd00569 HTH_Hin_like Helix-tur 22.8 93 0.002 16.3 2.2 20 133-152 22-41 (42)
157 PF01090 Ribosomal_S19e: Ribos 22.5 1.2E+02 0.0027 24.8 3.7 55 132-186 66-136 (139)
158 PF00440 TetR_N: Bacterial reg 22.4 34 0.00074 21.8 0.4 30 121-150 5-34 (47)
159 PRK11642 exoribonuclease R; Pr 22.4 80 0.0017 32.4 3.1 50 121-171 24-77 (813)
160 TIGR00635 ruvB Holliday juncti 22.0 98 0.0021 26.5 3.2 52 118-169 240-293 (305)
161 PF02553 CbiN: Cobalt transpor 22.0 20 0.00043 26.6 -0.9 26 5-30 31-56 (74)
162 PHA00738 putative HTH transcri 21.9 1.4E+02 0.0031 23.6 3.8 54 119-174 15-68 (108)
163 COG1373 Predicted ATPase (AAA+ 21.8 75 0.0016 29.5 2.6 48 116-163 220-268 (398)
164 COG2150 Predicted regulator of 21.8 43 0.00093 28.4 0.9 30 131-160 40-69 (167)
165 PRK10572 DNA-binding transcrip 21.7 57 0.0012 27.7 1.7 42 117-158 184-225 (290)
166 TIGR03697 NtcA_cyano global ni 21.5 99 0.0021 24.2 2.9 43 132-175 143-185 (193)
167 PF12793 SgrR_N: Sugar transpo 21.4 98 0.0021 24.1 2.8 56 118-173 3-66 (115)
168 PHA02574 57B hypothetical prot 21.1 71 0.0015 26.2 2.0 32 156-190 68-99 (149)
169 smart00342 HTH_ARAC helix_turn 21.0 33 0.00071 22.7 0.0 27 133-159 2-28 (84)
170 PRK11169 leucine-responsive tr 21.0 1.2E+02 0.0026 24.3 3.4 52 111-164 9-60 (164)
171 PRK11920 rirA iron-responsive 20.9 77 0.0017 25.5 2.2 39 124-162 16-54 (153)
172 PRK10906 DNA-binding transcrip 20.2 84 0.0018 27.2 2.4 48 119-168 8-55 (252)
173 PF04297 UPF0122: Putative hel 20.2 39 0.00085 26.2 0.3 35 131-165 32-74 (101)
No 1
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=99.92 E-value=3.8e-25 Score=200.10 Aligned_cols=86 Identities=35% Similarity=0.563 Sum_probs=77.6
Q ss_pred CcCCCCCCCchHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecccch-----
Q 045382 104 HYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAI----- 178 (191)
Q Consensus 104 ~~~~~RkeKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~I----- 178 (191)
.....|.++||++||+|||.+++.++++++||+.||+.|+|+|||||||+|||||||||+|++||.++|+|.+..
T Consensus 63 ~~~~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L~VqKRRIYDITNVLEGI~LIeKksKN~IqW~G~~~~~~~~~ 142 (354)
T KOG2577|consen 63 PSESTRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVLNVQKRRIYDITNVLEGIGLIEKKSKNNIQWIGGDFNSTGGV 142 (354)
T ss_pred CCCcccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHhccccceeeehhhhhhcccceeeccccceeeecCCCcccccc
Confidence 356789999999999999999999999999999999999999999999999999999999999999999997654
Q ss_pred HHHHHHHHHHh
Q 045382 179 RGALQELKVLL 189 (191)
Q Consensus 179 ~~tLekLk~Ei 189 (191)
...++.|++|+
T Consensus 143 ~e~~~~l~~e~ 153 (354)
T KOG2577|consen 143 PERLNGLEAEV 153 (354)
T ss_pred HHHHHHHHHHH
Confidence 35556666665
No 2
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=99.90 E-value=6e-25 Score=196.66 Aligned_cols=86 Identities=66% Similarity=1.013 Sum_probs=83.0
Q ss_pred CCcCCCCCCCchHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecccchHHHH
Q 045382 103 RHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGAL 182 (191)
Q Consensus 103 ~~~~~~RkeKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~I~~tL 182 (191)
+.+.++||+||||.||++|+.++.......+.|+.+|.+|||+|||||||+||||+||+++|.+||+|.|.||++||.+|
T Consensus 15 ~lqvysrkekslgvlv~nfl~lynr~dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkGf~aiPral 94 (388)
T KOG2578|consen 15 DLQVYSRKEKSLGVLVQNFLILYNRSDVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKGFGAIPRAL 94 (388)
T ss_pred cchhhccccchhhHHHHHHHHHhcCCCcceechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCcccccchhhhhHHH
Confidence 35789999999999999999999888888999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHH
Q 045382 183 QELKVL 188 (191)
Q Consensus 183 ekLk~E 188 (191)
.+||+|
T Consensus 95 ~eLqeE 100 (388)
T KOG2578|consen 95 FELQEE 100 (388)
T ss_pred HHHHHH
Confidence 999998
No 3
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=99.90 E-value=1.2e-24 Score=156.28 Aligned_cols=66 Identities=48% Similarity=0.896 Sum_probs=62.7
Q ss_pred CCCCchHHHHHHHHHHHhhCCCceecHHHHHHHh---CC--eeeEeeehhhHhhhhcceeecCCCceEEec
Q 045382 109 RKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKL---GV--ERRRIYDIVNVLESVGVLTRRAKNKYTWKG 174 (191)
Q Consensus 109 RkeKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L---~V--~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G 174 (191)
|+++||+.+|++||++|...++..++++++|+.| ++ ++||||||+|||||+|+|+|.+|+.|.|+|
T Consensus 1 r~~~sL~~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~~~k~~~RRlYDI~NVLealgli~K~~k~~~~W~G 71 (71)
T PF02319_consen 1 RKEKSLKLLTQRFIQLFESSPDKSISLNEIADKLISENVKTQRRRLYDIINVLEALGLIEKQSKNSYKWIG 71 (71)
T ss_dssp TTTTHHHHHHHHHHHHHHHCCCTEEEHHHHHHHCHHHCCHHHCHHHHHHHHHHHHCTSEEEEETTEEEE--
T ss_pred CCcCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHcccccccccchhhHHHHHHHHhCceeecCCCceEecC
Confidence 7899999999999999999888999999999999 99 999999999999999999999999999998
No 4
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=99.77 E-value=7.1e-20 Score=164.26 Aligned_cols=128 Identities=29% Similarity=0.383 Sum_probs=100.1
Q ss_pred cccCcccc-CCcCCCCceee-cCccceecccccccccccCCCCCCCCCCCCCC------CCCcCCCCCCCchHHHHHHHH
Q 045382 51 FRSVPTLA-GGVEGNGNEIR-VGSLYKVTYSSLKSFTETMPQSSSSTKVQDPS------SRHYAYSRKQKSLGLLCSNFL 122 (191)
Q Consensus 51 ~r~~~~l~-~g~~~~~~~~~-~~~~~~~~~~~~~~~~e~m~~~~~~~~~~~~~------~~~~~~~RkeKSL~~Lt~kFI 122 (191)
=|.|-||+ |||+|.|.++. ..++.++++.+... +...+.++..++.+.|. ...+...|++|||++|||+||
T Consensus 91 Pral~eLqeEgvke~l~~~~~~~~~~m~s~e~~~e-e~~~s~tstptd~s~~g~l~e~S~~~k~DnrkekSL~lL~qnFv 169 (388)
T KOG2578|consen 91 PRALFELQEEGVKEGLPERVLRVNSAMVSFEEESE-ERGVSCTSTPTDQSTDGLLEERSRSSKRDNRKEKSLWLLAQNFV 169 (388)
T ss_pred hHHHHHHHHHHHhhcccceeeeccccccccccccc-ccCCccccCCCCCCCCCcchhcCCCCcccchhhhHHHHHHHHHH
Confidence 45678999 99999999986 66777777666554 32234444433332221 135788899999999999999
Q ss_pred HHHhhCCCc-eecHHHHHHHh----------CCeeeEeeehhhHhhhhcceeec-----CCCceEEecccchH
Q 045382 123 SLYNRDGVE-SIGLDDAASKL----------GVERRRIYDIVNVLESVGVLTRR-----AKNKYTWKGFKAIR 179 (191)
Q Consensus 123 ~l~~~~~~~-~i~L~~aA~~L----------~V~rRRIYDIiNVLEslgLI~K~-----~Kn~y~W~G~~~I~ 179 (191)
++|.+++.. .|+|+.||..| ..+.||||||.|||.+||||+|+ .|+.|+|.|-..+.
T Consensus 170 klflcs~~~~lvslD~Aak~Ll~ds~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~trkPafrwlG~~~~~ 242 (388)
T KOG2578|consen 170 KLFLCSDDDILVSLDSAAKALLKDSEDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTRKPAFRWLGSKPIQ 242 (388)
T ss_pred HheeccccceEEeecHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhheeCCCccc
Confidence 999988876 89999999887 34789999999999999999995 68999999977654
No 5
>KOG2829 consensus E2F-like protein [Transcription]
Probab=98.79 E-value=3e-09 Score=95.40 Aligned_cols=90 Identities=20% Similarity=0.312 Sum_probs=65.9
Q ss_pred eecCccceecccccccccccCCCCCCCCCCCCCCCCCcCCCCCCCchHHHHHHHHHHHhhCCC-ceecHHHHHHHhCCee
Q 045382 68 IRVGSLYKVTYSSLKSFTETMPQSSSSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGV-ESIGLDDAASKLGVER 146 (191)
Q Consensus 68 ~~~~~~~~~~~~~~~~~~e~m~~~~~~~~~~~~~~~~~~~~RkeKSL~~Lt~kFI~l~~~~~~-~~i~L~~aA~~L~V~r 146 (191)
|.+..|+|| +.++.+.| .+.+...|..|..... .-|..++-+--....|
T Consensus 49 fs~kVCeKv---e~Kg~TtY---------------------------neVADelVaef~~~n~~~~i~~n~~~yd~KNIR 98 (326)
T KOG2829|consen 49 FSMKVCEKV---ERKGTTTY---------------------------NEVADELVAEFAGANNYSHICPNEQEYDQKNIR 98 (326)
T ss_pred hhHHHHHHH---HhcCCccH---------------------------HHHHHHHHHHHhccccccccCccccccchHHHH
Confidence 679999999 77776666 6677777776654432 2455555554556679
Q ss_pred eEeeehhhHhhhhcceeecCCCceEEeccc-chHHHHHHHHHH
Q 045382 147 RRIYDIVNVLESVGVLTRRAKNKYTWKGFK-AIRGALQELKVL 188 (191)
Q Consensus 147 RRIYDIiNVLEslgLI~K~~Kn~y~W~G~~-~I~~tLekLk~E 188 (191)
||+||.+|||.+|.+|.|. |..|+|+|+. +-.+.+++|++|
T Consensus 99 RRVYDALNVlmAmnIIsKd-KKEIrW~GLP~~ss~dv~~le~E 140 (326)
T KOG2829|consen 99 RRVYDALNVLMAMNIISKD-KKEIRWIGLPATSSQDVSELEEE 140 (326)
T ss_pred HHHHHHHHHHHHHHHHhcc-cceeeeeccCccchHHHHHHHHH
Confidence 9999999999999999999 5579999986 233455555544
No 6
>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=95.02 E-value=0.019 Score=39.69 Aligned_cols=43 Identities=21% Similarity=0.459 Sum_probs=38.3
Q ss_pred ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEe
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWK 173 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~ 173 (191)
+..+..++|+.+++.+..+|+++|-|+..|+|++...+.+.|.
T Consensus 21 ~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~ 63 (68)
T PF01978_consen 21 GPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYR 63 (68)
T ss_dssp CHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEE
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEE
Confidence 4699999999999999999999999999999999876666553
No 7
>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=93.25 E-value=0.13 Score=34.48 Aligned_cols=54 Identities=30% Similarity=0.422 Sum_probs=42.1
Q ss_pred HHHHHHHHHhhC-----CCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCce
Q 045382 117 LCSNFLSLYNRD-----GVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKY 170 (191)
Q Consensus 117 Lt~kFI~l~~~~-----~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y 170 (191)
++.-|+.++... ....++..++|+.+|+.+.-++.+++.|+.-|+|.+...+.|
T Consensus 5 ia~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~~~~~ 63 (67)
T cd00092 5 LASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKY 63 (67)
T ss_pred HHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCeE
Confidence 344455554432 345689999999999999999999999999999998864444
No 8
>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=92.41 E-value=0.15 Score=33.66 Aligned_cols=41 Identities=29% Similarity=0.358 Sum_probs=34.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhc
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVG 160 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslg 160 (191)
.+.+.++.++++. ++..++|+.|+|.+|=|+--++.|+..|
T Consensus 3 ~~il~~L~~~~~~-it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEP-ITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTS-BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCC-cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3567777555554 9999999999999999999999999998
No 9
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=92.08 E-value=0.21 Score=35.49 Aligned_cols=55 Identities=18% Similarity=0.325 Sum_probs=43.0
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEec
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKG 174 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G 174 (191)
...++++.+.+ ..+++.++|+.+++.+.-+|-+++.|+..|++.+...+.....|
T Consensus 8 ~~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~ 62 (91)
T smart00346 8 LAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLG 62 (91)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCCceeec
Confidence 44566666553 36999999999999999999999999999999987443333344
No 10
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=91.92 E-value=0.17 Score=31.98 Aligned_cols=46 Identities=33% Similarity=0.475 Sum_probs=38.4
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
.++.++..++ .+++.++++.+++.++-+|..++-|+..|+|.+..+
T Consensus 4 ~il~~l~~~~--~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 4 QILELLAQQG--KVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHcC--CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 3555665543 489999999999999999999999999999987644
No 11
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=90.91 E-value=0.29 Score=34.53 Aligned_cols=56 Identities=20% Similarity=0.369 Sum_probs=46.0
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEE
Q 045382 117 LCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTW 172 (191)
Q Consensus 117 Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W 172 (191)
.-++.++++...++..+...++|+.||+.++-+.-++.-|+.-|+|.+.+.+.=.|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 34677888887765459999999999999999999999999999999976432345
No 12
>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=90.89 E-value=0.21 Score=33.05 Aligned_cols=45 Identities=20% Similarity=0.376 Sum_probs=37.4
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
..++++..++. .+++.++|+++|+.|=-+|-+++.|+..|++++.
T Consensus 7 ~iL~~l~~~~~-~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 7 RILEALAESGG-PLTLSEIARALGLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHCHHCTBS-CEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHcCCC-CCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence 45566666654 3799999999999999999999999999999875
No 13
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=88.49 E-value=0.71 Score=29.44 Aligned_cols=37 Identities=16% Similarity=0.314 Sum_probs=33.4
Q ss_pred ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
..+++.+++..+++.+.-++++++.|+.-|++....+
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence 4579999999999999999999999999999987653
No 14
>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=87.60 E-value=0.67 Score=33.35 Aligned_cols=59 Identities=14% Similarity=0.191 Sum_probs=43.1
Q ss_pred HHHHHHHHHHhhCCCc-eecHHHHHHHhCCeeeEeeehhhHhhhhcceeec-CCCceEEec
Q 045382 116 LLCSNFLSLYNRDGVE-SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR-AKNKYTWKG 174 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~-~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~-~Kn~y~W~G 174 (191)
..+-+++-++...++. .+++.++|+.+++..+.+..|++-|+.-|+|+.. +++-=.|..
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~ 68 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLA 68 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEES
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeec
Confidence 4455666776655543 4999999999999999999999999999999754 333333333
No 15
>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=87.19 E-value=0.72 Score=35.51 Aligned_cols=48 Identities=15% Similarity=0.306 Sum_probs=40.7
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 118 CSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 118 t~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
+-+.+.++...++..+++.++|+++++.+..++.+++.|+.-|+|...
T Consensus 11 al~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 11 ATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 344556666566678999999999999999999999999999999864
No 16
>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=87.04 E-value=1.7 Score=28.25 Aligned_cols=46 Identities=20% Similarity=0.364 Sum_probs=37.7
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
..++.++...+ ++..++++.+++.+.-++-++|.|+.-|+|.+...
T Consensus 10 ~~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~ 55 (78)
T cd00090 10 LRILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRRE 55 (78)
T ss_pred HHHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEe
Confidence 44555555543 89999999999999999999999999999987543
No 17
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=86.92 E-value=0.9 Score=39.76 Aligned_cols=36 Identities=22% Similarity=0.415 Sum_probs=32.5
Q ss_pred eecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 132 SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 132 ~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
..+-.++|+..||++=|+|||++-||.=|+++.+..
T Consensus 30 ~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g 65 (247)
T COG1378 30 EATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEG 65 (247)
T ss_pred CccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCC
Confidence 467889999999999999999999999999988633
No 18
>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=86.57 E-value=0.83 Score=29.37 Aligned_cols=43 Identities=23% Similarity=0.404 Sum_probs=36.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhccee
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLT 163 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~ 163 (191)
.+.+.++.+++. ++..++|+.+|+.+..++.+++-|+.-|+|+
T Consensus 6 ~~Il~~l~~~~~--~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLRENPR--ITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHCTT--S-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCC--CCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 567778878755 9999999999999999999999999999985
No 19
>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=85.24 E-value=0.87 Score=30.13 Aligned_cols=46 Identities=26% Similarity=0.417 Sum_probs=38.9
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
..+.++...++..+.+.++|+.+++.+=.+--+++-|+.-|+|++.
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 3455566776667999999999999999999999999999999986
No 20
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=82.71 E-value=0.83 Score=28.51 Aligned_cols=38 Identities=21% Similarity=0.420 Sum_probs=33.7
Q ss_pred eecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCce
Q 045382 132 SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKY 170 (191)
Q Consensus 132 ~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y 170 (191)
.++..++|+.+++.+..+..+++.|+.-|++.+.. +.|
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~-~~~ 45 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG-GRI 45 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC-CEE
Confidence 47889999999999999999999999999999874 444
No 21
>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=82.51 E-value=2.7 Score=28.67 Aligned_cols=50 Identities=18% Similarity=0.293 Sum_probs=37.7
Q ss_pred HHHHHHHHhh---CCCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 118 CSNFLSLYNR---DGVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 118 t~kFI~l~~~---~~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
...+.+.+.. .++..+ +..++|++++|.+.=+.+.++.|+.-|+|++..+
T Consensus 6 ~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 6 YDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 3444444433 356678 9999999999999999999999999999987644
No 22
>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=82.44 E-value=1.1 Score=31.75 Aligned_cols=43 Identities=28% Similarity=0.474 Sum_probs=29.0
Q ss_pred CchHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 112 KSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 112 KSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
-+++.+-+.+-++|+..... -...||++|++|-|+.+|+|.-.
T Consensus 23 ~~~~~vy~~Y~~~c~~~~~~-----------~l~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 23 ATTGEVYEVYEELCEEIGVD-----------PLTQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred ccHHHHHHHHHHHHHHcCCC-----------CCcHHHHHHHHHHHHHcCCeEEE
Confidence 34455555555555543211 13679999999999999999753
No 23
>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=81.52 E-value=0.42 Score=34.42 Aligned_cols=21 Identities=29% Similarity=0.493 Sum_probs=18.2
Q ss_pred eeeEeeehhhHhhhhcceeec
Q 045382 145 ERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 145 ~rRRIYDIiNVLEslgLI~K~ 165 (191)
..||++|++|-|+.+|+|...
T Consensus 38 s~~r~~~~l~eL~~~gli~~~ 58 (85)
T PF09079_consen 38 SYRRFSDYLSELEMLGLIESE 58 (85)
T ss_dssp -HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHHHhCCCeEEE
Confidence 579999999999999999654
No 24
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=81.34 E-value=2 Score=27.61 Aligned_cols=40 Identities=25% Similarity=0.446 Sum_probs=34.5
Q ss_pred CCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCC
Q 045382 129 GVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKN 168 (191)
Q Consensus 129 ~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn 168 (191)
++..+ +..++|+.+++.+=-+...++.|+.-|+|.+....
T Consensus 16 ~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 16 PGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 34456 89999999999999999999999999999876543
No 25
>PF13730 HTH_36: Helix-turn-helix domain
Probab=81.24 E-value=1.4 Score=28.84 Aligned_cols=30 Identities=30% Similarity=0.487 Sum_probs=28.2
Q ss_pred ecHHHHHHHhCCeeeEeeehhhHhhhhcce
Q 045382 133 IGLDDAASKLGVERRRIYDIVNVLESVGVL 162 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDIiNVLEslgLI 162 (191)
-+.+.+|+.+|+.+|.++-.++.|+..|+|
T Consensus 26 pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 26 PSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 389999999999999999999999999986
No 26
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=80.76 E-value=4.1 Score=35.36 Aligned_cols=56 Identities=14% Similarity=0.291 Sum_probs=43.6
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecc
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGF 175 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~ 175 (191)
-..+++|...+ ..+.+.++|+.+|+.|=.+|.+++-|+..|++.+.....-.+.|.
T Consensus 28 l~IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG~ 83 (271)
T PRK10163 28 IAILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIGL 83 (271)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEecH
Confidence 34556665543 358999999999999999999999999999998865444444553
No 27
>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=78.53 E-value=2.3 Score=30.36 Aligned_cols=49 Identities=22% Similarity=0.367 Sum_probs=41.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
..+++.+..+...-+.-.+++..++...|-++=+++.|+..|||.|+.-
T Consensus 5 ~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 5 YCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred HHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 4567777666666677888899999999999999999999999999754
No 28
>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=77.56 E-value=1.6 Score=28.73 Aligned_cols=43 Identities=30% Similarity=0.519 Sum_probs=35.4
Q ss_pred HHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382 122 LSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 122 I~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~ 166 (191)
+..+.+.++ +++.++|+.+++.+--+-.+++-|+.-|+|+|..
T Consensus 9 L~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 9 LRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence 334445544 9999999999999999999999999999999863
No 29
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=77.25 E-value=3 Score=33.62 Aligned_cols=60 Identities=20% Similarity=0.304 Sum_probs=44.5
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCC--------ceEEecccchHHHH
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKN--------KYTWKGFKAIRGAL 182 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn--------~y~W~G~~~I~~tL 182 (191)
|..+++ .++..+.+++|+.|+..|=.+|=.+|=|...|+|+|...+ -|.|+-.+.+...+
T Consensus 33 ~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i 100 (126)
T COG3355 33 YKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKI 100 (126)
T ss_pred HHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHH
Confidence 344444 3467999999999999999999999999999999885322 34455555555444
No 30
>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=76.90 E-value=1.1 Score=31.25 Aligned_cols=46 Identities=11% Similarity=0.239 Sum_probs=36.2
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCC
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKN 168 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn 168 (191)
..+++.+. +.+++.++|.+|++...-+=+.+.+|+..|.|.|...+
T Consensus 5 i~~~l~~~--~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 5 IRDYLRER--GRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMS 50 (69)
T ss_dssp HHHHHHHS---SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE
T ss_pred HHHHHHHc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCC
Confidence 34455555 56999999999999999999999999999999987543
No 31
>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=75.47 E-value=5.1 Score=30.44 Aligned_cols=36 Identities=17% Similarity=0.377 Sum_probs=33.3
Q ss_pred CceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 130 VESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 130 ~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
...++..++|+.+++.+..+.+|++.|..-|+|...
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 348999999999999999999999999999999764
No 32
>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=74.02 E-value=1.9 Score=30.54 Aligned_cols=46 Identities=20% Similarity=0.325 Sum_probs=35.5
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCe-eeEeeehhhHhhhhcceeecC
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVE-RRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~-rRRIYDIiNVLEslgLI~K~~ 166 (191)
||.-+....+..-++.++|+.||+. ..-+++-+..||.-|+|++..
T Consensus 14 ~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 14 FIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGC
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCC
Confidence 5544444445567999999999998 999999999999999999874
No 33
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=72.68 E-value=8.1 Score=32.97 Aligned_cols=54 Identities=9% Similarity=0.319 Sum_probs=42.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEec
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKG 174 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G 174 (191)
-..++++... ..+++.++|+.+|+.|=-+|-+++.|+..|++.+...+.-...|
T Consensus 17 l~IL~~l~~~--~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG 70 (257)
T PRK15090 17 FGILQALGEE--REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSLT 70 (257)
T ss_pred HHHHHHhhcC--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEec
Confidence 3455556544 35899999999999999999999999999999987544434455
No 34
>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=70.67 E-value=5.3 Score=26.05 Aligned_cols=34 Identities=29% Similarity=0.476 Sum_probs=31.2
Q ss_pred ecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382 133 IGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~ 166 (191)
.+..++|+.+++.+=.+...++-|+.-|+|++..
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 4599999999999999999999999999998774
No 35
>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=69.36 E-value=3.8 Score=28.24 Aligned_cols=54 Identities=17% Similarity=0.183 Sum_probs=39.5
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcce-eecCCCceEEeccc
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVL-TRRAKNKYTWKGFK 176 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI-~K~~Kn~y~W~G~~ 176 (191)
+.+..+.+. .++..++|+.++|.++-++.-++.|+.-|++ ...++..+.+.+.+
T Consensus 4 ~il~~L~~~---~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~~~g~~l~~~~~ 58 (69)
T TIGR00122 4 RLLALLADN---PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTVGKGYRLPPPIP 58 (69)
T ss_pred HHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCCceEecCccc
Confidence 445555543 3669999999999999999999999999884 33355555555543
No 36
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=68.88 E-value=2.3 Score=37.08 Aligned_cols=36 Identities=17% Similarity=0.204 Sum_probs=33.4
Q ss_pred ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~ 166 (191)
+..+++++|.++++..|.++-+++.|.++|++++..
T Consensus 22 gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~ 57 (306)
T TIGR02716 22 GPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED 57 (306)
T ss_pred CCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC
Confidence 468999999999999999999999999999999863
No 37
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=68.79 E-value=5.5 Score=34.26 Aligned_cols=51 Identities=20% Similarity=0.299 Sum_probs=40.8
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC-CCceEE
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA-KNKYTW 172 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~-Kn~y~W 172 (191)
.++++..++ ..+++.++|+.+|+.|=-+|-+++-|+..|++.+.. .+.|..
T Consensus 16 iL~~l~~~~-~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~L 67 (263)
T PRK09834 16 VLRALNRLD-GGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFRL 67 (263)
T ss_pred HHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEEE
Confidence 445555443 349999999999999999999999999999999863 455654
No 38
>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=68.53 E-value=5.6 Score=26.98 Aligned_cols=45 Identities=24% Similarity=0.415 Sum_probs=36.5
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~ 166 (191)
+.++++.+. +.+++.++|+.|+|...=+.==+|.|+.-|+|.|..
T Consensus 4 ~Il~~l~~~--~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 4 QILELLKEK--GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHc--CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 456677665 569999999999998666666678999999998873
No 39
>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=68.03 E-value=4.6 Score=26.98 Aligned_cols=38 Identities=21% Similarity=0.433 Sum_probs=31.0
Q ss_pred CCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 128 DGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 128 ~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
..+..+.+.++|+.+++.+--+..+++-|+..|+|+|.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 35567899999999999999999999999999999876
No 40
>PHA02943 hypothetical protein; Provisional
Probab=65.39 E-value=11 Score=31.81 Aligned_cols=68 Identities=21% Similarity=0.196 Sum_probs=48.8
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCce-EE-ecccchHHHHHHHHHHh
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKY-TW-KGFKAIRGALQELKVLL 189 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y-~W-~G~~~I~~tLekLk~Ei 189 (191)
..+++++ . .+-.+..++|+.||+.--....++-|||.-|.|++...+.. .| .-.++-.+.+..+..||
T Consensus 14 ~eILE~L-k--~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~day~~~v~~~~Rel 83 (165)
T PHA02943 14 IKTLRLL-A--DGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDEDAYTNLVFEIKREL 83 (165)
T ss_pred HHHHHHH-h--cCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEEChHHHHHHHHHHHHHH
Confidence 4567777 3 34578999999999999999999999999999999766533 34 33344444455555554
No 41
>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=64.86 E-value=6.4 Score=25.43 Aligned_cols=41 Identities=17% Similarity=0.414 Sum_probs=33.7
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceee
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTR 164 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K 164 (191)
.+.++.+ +..++.++++.+++.+=-++-=+++|+..|+|+|
T Consensus 7 Il~~L~~---~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 7 ILKLLSE---GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHTT---SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHh---CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 4445544 4589999999999999999999999999999986
No 42
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=64.74 E-value=9.9 Score=26.46 Aligned_cols=44 Identities=23% Similarity=0.478 Sum_probs=36.7
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
..+.++...+ .++..+++..+++.+--++-+++-|+..|+|++.
T Consensus 14 ~il~~l~~~~--~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 14 LVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHcC--CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 3444454444 4899999999999999999999999999999876
No 43
>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=64.03 E-value=7.6 Score=28.85 Aligned_cols=46 Identities=15% Similarity=0.222 Sum_probs=37.6
Q ss_pred CCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEeccc
Q 045382 129 GVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFK 176 (191)
Q Consensus 129 ~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~ 176 (191)
....++-.++|+.+|+.|--+-.+++.|+..|+|.+..+ -.|.|+.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~--~~~~~~n 89 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGM--MGIVGVN 89 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecC--CceeecC
Confidence 345689999999999999999999999999999987642 3445543
No 44
>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=64.02 E-value=6.4 Score=26.54 Aligned_cols=46 Identities=17% Similarity=0.336 Sum_probs=37.2
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~ 166 (191)
.+.+.++... ...++.++|+.+++.+=-+|-=+++|+..|+|+...
T Consensus 13 ~~Il~~L~~~--~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 13 LRILRLLASN--GPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHHHC--STBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHhcC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 4456666333 458999999999999999999999999999998764
No 45
>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=63.49 E-value=9 Score=29.88 Aligned_cols=44 Identities=14% Similarity=0.287 Sum_probs=36.4
Q ss_pred CCceecHHHHHHHhCCeeeEeeehhhHhhhhcceee--cCCCceEE
Q 045382 129 GVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTR--RAKNKYTW 172 (191)
Q Consensus 129 ~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K--~~Kn~y~W 172 (191)
....+++.++|+++++..+-+..|+..|.--|+|.- ...+-|.+
T Consensus 22 ~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l 67 (135)
T TIGR02010 22 ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQL 67 (135)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEec
Confidence 345799999999999999999999999999999964 33345554
No 46
>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=63.10 E-value=9 Score=31.68 Aligned_cols=59 Identities=19% Similarity=0.333 Sum_probs=45.9
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCce------EEecccc
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKY------TWKGFKA 177 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y------~W~G~~~ 177 (191)
.-+++.+.....-..+..++|+.+++.++-++..+..|+--++|.|...+.| .|.|...
T Consensus 62 ~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G~Y~iNP~~~~kG~~~ 126 (165)
T PF05732_consen 62 MYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAYMINPNFFFKGDRD 126 (165)
T ss_pred HHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeEEECcHHheeCcHH
Confidence 3344444444445678999999999999999999999999999999865544 6888653
No 47
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=61.06 E-value=4.4 Score=36.45 Aligned_cols=28 Identities=39% Similarity=0.726 Sum_probs=22.5
Q ss_pred ecHHHHHHHhCCeeeEeeehhhHhhhhc
Q 045382 133 IGLDDAASKLGVERRRIYDIVNVLESVG 160 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDIiNVLEslg 160 (191)
+-|..+=--+|.++|=+||.+||+++=.
T Consensus 41 iGLRNLDlimGlE~RiVYd~vdVi~g~~ 68 (272)
T COG2894 41 IGLRNLDLIMGLENRIVYDLVDVIEGEA 68 (272)
T ss_pred cCchhhhhhhcccceeeeeehhhhcCcc
Confidence 4455555678999999999999999754
No 48
>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=60.26 E-value=12 Score=28.04 Aligned_cols=44 Identities=25% Similarity=0.381 Sum_probs=36.3
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~ 166 (191)
.+..+..++ .+++.++|+.+++.+--+.=+++-||.-|+|++..
T Consensus 33 iL~~l~~~~--~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 33 ILRILAEQG--SMEFTQLANQACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHcC--CcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence 334444443 48899999999999999999999999999999863
No 49
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=59.96 E-value=16 Score=31.68 Aligned_cols=40 Identities=23% Similarity=0.306 Sum_probs=35.3
Q ss_pred CCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 128 DGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 128 ~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
..+..++..++|+.|++.+..+.-+++-||.-|+|+|...
T Consensus 17 ~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~ 56 (217)
T PRK14165 17 NNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIV 56 (217)
T ss_pred CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEc
Confidence 3345689999999999999999999999999999998743
No 50
>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=59.86 E-value=7.6 Score=28.72 Aligned_cols=50 Identities=20% Similarity=0.406 Sum_probs=39.3
Q ss_pred chHHHHHHHHHHHhhC--CCceecHHHHHHHhCCeeeEeeehhhHhhhhcce
Q 045382 113 SLGLLCSNFLSLYNRD--GVESIGLDDAASKLGVERRRIYDIVNVLESVGVL 162 (191)
Q Consensus 113 SL~~Lt~kFI~l~~~~--~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI 162 (191)
++..+.++.+.++++. .+.-+.+++++++|++....|.+++.-|..-|.|
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence 6788888888888762 2345999999999999999999999999988887
No 51
>PRK00215 LexA repressor; Validated
Probab=59.77 E-value=8 Score=31.83 Aligned_cols=42 Identities=17% Similarity=0.240 Sum_probs=36.1
Q ss_pred hCCCceecHHHHHHHhCC-eeeEeeehhhHhhhhcceeecCCC
Q 045382 127 RDGVESIGLDDAASKLGV-ERRRIYDIVNVLESVGVLTRRAKN 168 (191)
Q Consensus 127 ~~~~~~i~L~~aA~~L~V-~rRRIYDIiNVLEslgLI~K~~Kn 168 (191)
...+...++.++|+.+++ .+=-++.+++-|+.-|+|++....
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 344556899999999999 899999999999999999887544
No 52
>PF13518 HTH_28: Helix-turn-helix domain
Probab=59.62 E-value=7.7 Score=24.62 Aligned_cols=37 Identities=19% Similarity=0.476 Sum_probs=30.1
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcc
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGV 161 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgL 161 (191)
.|+++.+ +. ++.++|.++||.+..||.+++-++.-|+
T Consensus 5 iv~~~~~---g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 5 IVELYLE---GE-SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHc---CC-CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 4555553 22 9999999999999999999999998664
No 53
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=58.37 E-value=8.6 Score=28.17 Aligned_cols=46 Identities=26% Similarity=0.408 Sum_probs=39.9
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceee
Q 045382 117 LCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTR 164 (191)
Q Consensus 117 Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K 164 (191)
+=.+.+.++.+++ .++..++|+.+|+...-++..++-|+.-|+|.+
T Consensus 4 ~D~~il~~L~~~~--~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 4 IDRKILEELQKDA--RISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHHhC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence 3367788887764 589999999999999999999999999999985
No 54
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=56.95 E-value=12 Score=31.87 Aligned_cols=59 Identities=20% Similarity=0.424 Sum_probs=34.8
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec--CCCceEEecccc
Q 045382 117 LCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR--AKNKYTWKGFKA 177 (191)
Q Consensus 117 Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~--~Kn~y~W~G~~~ 177 (191)
+.+.||.|+..+ .++.|+++|..||+.-==+-|-|+-|+..|.|+=. ..+.|.++....
T Consensus 100 lL~~Fi~yIK~~--Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE 160 (188)
T PF09756_consen 100 LLQEFINYIKEH--KVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEE 160 (188)
T ss_dssp HHHHHHHHHHH---SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE-----
T ss_pred HHHHHHHHHHHc--ceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHH
Confidence 789999999998 57999999999999655444555566666655432 346788877543
No 55
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=56.75 E-value=10 Score=31.12 Aligned_cols=36 Identities=14% Similarity=0.304 Sum_probs=32.8
Q ss_pred CCceecHHHHHHHhCCeeeEeeehhhHhhhhcceee
Q 045382 129 GVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTR 164 (191)
Q Consensus 129 ~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K 164 (191)
+...++++++|+++++..+-+..|++-|.--|||.-
T Consensus 22 ~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s 57 (164)
T PRK10857 22 EAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSS 57 (164)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 345799999999999999999999999999999974
No 56
>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=56.58 E-value=17 Score=30.76 Aligned_cols=50 Identities=16% Similarity=0.277 Sum_probs=40.3
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceE
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYT 171 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~ 171 (191)
..++++...+ ..+++.++|+.+|+.|=.+|-+++-|+..|++.+.. ..|.
T Consensus 13 ~IL~~l~~~~-~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~~-~~Y~ 62 (248)
T TIGR02431 13 AVIEAFGAER-PRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSDG-RLFW 62 (248)
T ss_pred HHHHHHhcCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC-CEEE
Confidence 3455555443 469999999999999999999999999999999863 4454
No 57
>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=56.28 E-value=9.8 Score=31.14 Aligned_cols=46 Identities=13% Similarity=0.174 Sum_probs=37.1
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCe-eeEeeehhhHhhhhcceeecC
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVE-RRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~-rRRIYDIiNVLEslgLI~K~~ 166 (191)
||..+....+...++.++|+.+++. +=-++..++.|+..|+|++..
T Consensus 14 ~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 14 LIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred HHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCC
Confidence 3433334445568899999999998 999999999999999999874
No 58
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=55.91 E-value=8.5 Score=30.13 Aligned_cols=36 Identities=19% Similarity=0.354 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEee
Q 045382 115 GLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIY 150 (191)
Q Consensus 115 ~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIY 150 (191)
..|.+.|++++.+.+-..|+++++|++-||.|.-+|
T Consensus 6 ~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY 41 (176)
T TIGR02366 6 KKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFY 41 (176)
T ss_pred HHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHH
Confidence 457888999999999999999999999999988776
No 59
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=55.64 E-value=12 Score=32.22 Aligned_cols=55 Identities=16% Similarity=0.310 Sum_probs=44.5
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEec
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKG 174 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G 174 (191)
-..++++...+. .+.+.++|+++|..|=-+|=+++.|+..|++++...+.-.+.|
T Consensus 7 l~iL~~l~~~~~-~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg 61 (246)
T COG1414 7 LAILDLLAEGPG-GLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRLG 61 (246)
T ss_pred HHHHHHHHhCCC-CCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEeeh
Confidence 346677766443 4899999999999999999999999999999999876433455
No 60
>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=55.62 E-value=7 Score=26.74 Aligned_cols=37 Identities=22% Similarity=0.394 Sum_probs=33.5
Q ss_pred ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
..++..++|+.+|+.++.+--+++-|+.-|+|+...+
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 3578999999999999999999999999999997744
No 61
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=55.13 E-value=3.8 Score=25.28 Aligned_cols=22 Identities=27% Similarity=0.696 Sum_probs=20.0
Q ss_pred ecHHHHHHHhCCeeeEeeehhh
Q 045382 133 IGLDDAASKLGVERRRIYDIVN 154 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDIiN 154 (191)
+++.++|+.||+.++.||..++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999875
No 62
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=54.42 E-value=6.2 Score=36.39 Aligned_cols=29 Identities=28% Similarity=0.601 Sum_probs=25.1
Q ss_pred HHHHHHHhCCeeeEeeehhhHhhhhccee
Q 045382 135 LDDAASKLGVERRRIYDIVNVLESVGVLT 163 (191)
Q Consensus 135 L~~aA~~L~V~rRRIYDIiNVLEslgLI~ 163 (191)
+..+++.+++.+||+|||+|-|+.+|+|.
T Consensus 304 y~~~~~~~~~~~~~~~~ii~~L~~lgiv~ 332 (366)
T COG1474 304 YESLCERLRTSQRRFSDIISELEGLGIVS 332 (366)
T ss_pred HHHHHhhhCchHHHHHHHHHHHHhcCeEE
Confidence 45666777789999999999999999996
No 63
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=53.85 E-value=11 Score=29.11 Aligned_cols=44 Identities=7% Similarity=0.173 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhh
Q 045382 115 GLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLES 158 (191)
Q Consensus 115 ~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEs 158 (191)
.....++++++.++....++++++|+.+|+.+|.|.-++.---+
T Consensus 8 ~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G 51 (127)
T PRK11511 8 AITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETG 51 (127)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 56678899999988888899999999999988877666554433
No 64
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=53.12 E-value=9.9 Score=27.93 Aligned_cols=41 Identities=10% Similarity=0.201 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHh
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVL 156 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVL 156 (191)
.+..+++.++.++....+++.++|+.+++.+|.+.-+++=.
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46778888888888888999999999999888776555443
No 65
>PRK09954 putative kinase; Provisional
Probab=52.51 E-value=9.5 Score=33.87 Aligned_cols=45 Identities=20% Similarity=0.262 Sum_probs=39.6
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceee
Q 045382 118 CSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTR 164 (191)
Q Consensus 118 t~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K 164 (191)
-++.++++.+++ .++..++|+.|++.|..++..++=|+.-|+|++
T Consensus 5 ~~~il~~l~~~~--~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~ 49 (362)
T PRK09954 5 EKEILAILRRNP--LIQQNEIADILQISRSRVAAHIMDLMRKGRIKG 49 (362)
T ss_pred HHHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCC
Confidence 456778888775 699999999999999999999999999999964
No 66
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=52.45 E-value=21 Score=30.03 Aligned_cols=59 Identities=20% Similarity=0.263 Sum_probs=43.3
Q ss_pred CchHH-HHHHHHHHHhh---CCCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeec-CCCce
Q 045382 112 KSLGL-LCSNFLSLYNR---DGVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRR-AKNKY 170 (191)
Q Consensus 112 KSL~~-Lt~kFI~l~~~---~~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~-~Kn~y 170 (191)
.++.. +.+.+.+.+.. .|+..+ +-.++|++|||.|==+-+.+..|++.|+|+.. +++.|
T Consensus 9 ~~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~ 73 (254)
T PRK09464 9 PKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTF 73 (254)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCceeE
Confidence 34543 44445554433 356777 89999999999999999999999999999754 44433
No 67
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=51.65 E-value=26 Score=33.31 Aligned_cols=58 Identities=26% Similarity=0.422 Sum_probs=44.5
Q ss_pred chHHHHHH------HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecc
Q 045382 113 SLGLLCSN------FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGF 175 (191)
Q Consensus 113 SL~~Lt~k------FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~ 175 (191)
-||.|+-+ .++++....+..|+|+++|..-++. .-||++.|+.+++|... |+ |.|..-
T Consensus 304 DLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~---~~DIisTL~~L~m~~y~-k~-~~~~~~ 367 (396)
T KOG2747|consen 304 DLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIR---PDDIISTLQSLNMIKYY-KG-YIISIC 367 (396)
T ss_pred hhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCC---HHHHHHHHHhhCCcccc-CC-eeEEEe
Confidence 35666633 5666766665559999999999985 47999999999999876 44 888665
No 68
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=51.05 E-value=20 Score=30.82 Aligned_cols=46 Identities=22% Similarity=0.330 Sum_probs=33.6
Q ss_pred HHHHHhhCCCc-eecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCc
Q 045382 121 FLSLYNRDGVE-SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNK 169 (191)
Q Consensus 121 FI~l~~~~~~~-~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~ 169 (191)
.++++....+. .++++++++..++.+ -||+..|+.+|++.....+.
T Consensus 138 i~~~L~~~~~~~~isi~~is~~Tgi~~---~DIi~tL~~l~~l~~~~~~~ 184 (188)
T PF01853_consen 138 ILEYLLEFKGKKSISIKDISQETGIRP---EDIISTLQQLGMLKYYKGQH 184 (188)
T ss_dssp HHHHHHHTSSE--EEHHHHHHHH-BTH---HHHHHHHHHTT-EEEETTEE
T ss_pred HHHHHHhcCCCCeEEHHHHHHHHCCCH---HHHHHHHHHCCCEEEECCcE
Confidence 45555555544 799999999999975 69999999999998874443
No 69
>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=50.94 E-value=15 Score=27.46 Aligned_cols=49 Identities=10% Similarity=0.247 Sum_probs=39.5
Q ss_pred hCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCC---ceEEecc
Q 045382 127 RDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKN---KYTWKGF 175 (191)
Q Consensus 127 ~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn---~y~W~G~ 175 (191)
..+++.+++.++|..+++.+=.+-=+++-||.-|+|.|...+ ...++-+
T Consensus 38 ~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~l 89 (109)
T TIGR01889 38 ENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISI 89 (109)
T ss_pred hccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEE
Confidence 345567999999999999999999999999999999986432 3555443
No 70
>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=50.88 E-value=35 Score=27.76 Aligned_cols=40 Identities=23% Similarity=0.378 Sum_probs=35.9
Q ss_pred CCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 128 DGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 128 ~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
.|+..++-.++|+.|||.|==+=+.+..|+.-|+|+...+
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~ 69 (212)
T TIGR03338 30 PPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKN 69 (212)
T ss_pred CCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecC
Confidence 4678889999999999999999999999999999987644
No 71
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=50.42 E-value=28 Score=29.06 Aligned_cols=52 Identities=19% Similarity=0.328 Sum_probs=38.8
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhccee--e-----cCCCceEEe
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLT--R-----RAKNKYTWK 173 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~--K-----~~Kn~y~W~ 173 (191)
.++..+..+ +.++-+++|..||++.--+=-+++-|+.-|||. + .+...|.|.
T Consensus 26 ~Vl~~L~~~--g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~ 84 (178)
T PRK06266 26 EVLKALIKK--GEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWK 84 (178)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEE
Confidence 344444443 358999999999998777777899999999997 2 233578886
No 72
>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=50.27 E-value=23 Score=29.41 Aligned_cols=52 Identities=17% Similarity=0.340 Sum_probs=40.6
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec------CCCceEE
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR------AKNKYTW 172 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~------~Kn~y~W 172 (191)
.+.+.++...+ .++..++|+.|++.+=-+.-.++.|+.-|+|++. +++.+.|
T Consensus 4 ~~IL~~L~~~~--~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y 61 (203)
T TIGR02702 4 EDILSYLLKQG--QATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHY 61 (203)
T ss_pred HHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEE
Confidence 34566666553 3899999999999988888899999999999875 2455655
No 73
>PLN03239 histone acetyltransferase; Provisional
Probab=50.11 E-value=33 Score=32.17 Aligned_cols=60 Identities=17% Similarity=0.146 Sum_probs=40.6
Q ss_pred HHHHHhhCC--CceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecccchHHHHH
Q 045382 121 FLSLYNRDG--VESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQ 183 (191)
Q Consensus 121 FI~l~~~~~--~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~I~~tLe 183 (191)
.++++.... ...++|++++...++. .-||+..|+.+|++.....+.+.-+..+.|.+.++
T Consensus 271 il~~L~~~~~~~~~~si~dis~~Tgi~---~~DIi~tL~~l~~l~~~~g~~~i~~~~~~l~~~~~ 332 (351)
T PLN03239 271 IVDFLLNHSGNDSSLSIMDIAKKTSIM---AEDIVFALNQLGILKFINGIYFIAAEKGLLEELAE 332 (351)
T ss_pred HHHHHHhccCCCCCccHHHHHHHhCCC---HHHHHHHHHHCCcEEEECCeEEEEeCHHHHHHHHH
Confidence 444544432 2579999999999995 57999999999999765444444444444444433
No 74
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=49.57 E-value=19 Score=29.78 Aligned_cols=45 Identities=18% Similarity=0.174 Sum_probs=37.9
Q ss_pred CCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEE
Q 045382 128 DGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTW 172 (191)
Q Consensus 128 ~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W 172 (191)
.|+..+.-.++|++|||.|==+=+.+..|+..|||+.....-+..
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g~~v 74 (221)
T PRK11414 30 KPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTV 74 (221)
T ss_pred CCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCceee
Confidence 367788889999999999999999999999999998765443433
No 75
>PRK11050 manganese transport regulator MntR; Provisional
Probab=48.83 E-value=26 Score=28.09 Aligned_cols=42 Identities=19% Similarity=0.238 Sum_probs=36.3
Q ss_pred ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEE
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTW 172 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W 172 (191)
+.+.+.++|+.|++.+--+...++-|+.-|+|.+.....+.+
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~~~v~L 91 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYRGVFL 91 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCceEE
Confidence 358899999999999999999999999999999865444554
No 76
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=48.82 E-value=17 Score=31.14 Aligned_cols=36 Identities=17% Similarity=0.301 Sum_probs=33.6
Q ss_pred CceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 130 VESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 130 ~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
..+++|+++++.+|+.|=++-=.+-.|++.|+++++
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhh
Confidence 357999999999999999999999999999999875
No 77
>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=47.54 E-value=19 Score=29.38 Aligned_cols=42 Identities=17% Similarity=0.369 Sum_probs=35.0
Q ss_pred ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec-------CCCceEE
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR-------AKNKYTW 172 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~-------~Kn~y~W 172 (191)
+.++-+++|..||++.+-+=-+++.|.-.||+... +...|.|
T Consensus 27 ~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w 75 (158)
T TIGR00373 27 GEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTW 75 (158)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEE
Confidence 45899999999999999999999999999999421 3356777
No 78
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=46.50 E-value=18 Score=28.27 Aligned_cols=38 Identities=21% Similarity=0.331 Sum_probs=31.0
Q ss_pred CCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 128 DGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 128 ~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
.++..++..++|+.++|.+.-+-.|+..|..-|+|+..
T Consensus 21 ~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~ 58 (141)
T PRK11014 21 PEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAV 58 (141)
T ss_pred CCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEe
Confidence 34567899999999998888888888888888888554
No 79
>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=45.64 E-value=28 Score=23.40 Aligned_cols=42 Identities=29% Similarity=0.371 Sum_probs=25.6
Q ss_pred CCCCchHHHH-HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhh
Q 045382 109 RKQKSLGLLC-SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVN 154 (191)
Q Consensus 109 RkeKSL~~Lt-~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiN 154 (191)
|+-++|..-- ...|+.++..+ ...++|..|||.+.-|++|+.
T Consensus 2 rkR~~LTl~eK~~iI~~~e~g~----s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEEGE----SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHCTT-----HHHHHHHHT--CCHHHHHHH
T ss_pred CCCccCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHHH
Confidence 3444444333 33556665543 799999999999999999975
No 80
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=45.45 E-value=24 Score=30.41 Aligned_cols=54 Identities=19% Similarity=0.196 Sum_probs=43.3
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecc
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGF 175 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~ 175 (191)
+.++++.++ ..+...++|+.|+|..+-+.--++.|+.-|++.+.....+.+.+.
T Consensus 8 ~Il~~l~~~--~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~Gga~~~~~~ 61 (240)
T PRK10411 8 AIVDLLLNH--TSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHGRAKYIHRQ 61 (240)
T ss_pred HHHHHHHHc--CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCeEEEecCC
Confidence 456666654 469999999999999999999999999999998875555556543
No 81
>PRK11569 transcriptional repressor IclR; Provisional
Probab=45.35 E-value=26 Score=30.34 Aligned_cols=48 Identities=13% Similarity=0.258 Sum_probs=39.4
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCC
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKN 168 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn 168 (191)
..+++|... ...+.+.++|+.+|..|=-+|=+++-|+..|++++....
T Consensus 32 ~IL~~l~~~-~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~~ 79 (274)
T PRK11569 32 KLLEWIAES-NGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGEL 79 (274)
T ss_pred HHHHHHHhC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 345556554 345999999999999999999999999999999986443
No 82
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=45.08 E-value=44 Score=30.59 Aligned_cols=59 Identities=14% Similarity=0.172 Sum_probs=40.7
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecccchHHHHH
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQ 183 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~I~~tLe 183 (191)
.++++.+ ....++|++++...++. .-||+..|+.+|++.....+.+.-+..+.+...++
T Consensus 213 il~~L~~-~~~~isi~~is~~T~i~---~~Dii~tL~~l~~l~~~~g~~~i~~~~~~~~~~~~ 271 (290)
T PLN03238 213 LLEQLRD-VKGDVSIKDLSLATGIR---GEDIVSTLQSLNLIKYWKGQHVIHVDQRVLDEHWA 271 (290)
T ss_pred HHHHHHh-cCCCccHHHHHHHhCCC---HHHHHHHHHHCCcEEEECCcEEEEeCHHHHHHHHH
Confidence 3444433 34579999999999995 47999999999999765444444444444444443
No 83
>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=44.85 E-value=13 Score=25.24 Aligned_cols=36 Identities=31% Similarity=0.407 Sum_probs=26.6
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhh
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLE 157 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLE 157 (191)
+.++++.+ ...+++.++|+.|++..|-|..-+|-|.
T Consensus 9 ~Ll~~L~~--~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 9 KLLELLLK--NKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHH--HTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHc--CCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45666666 3468999999999999888876666665
No 84
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=44.41 E-value=19 Score=30.91 Aligned_cols=56 Identities=16% Similarity=0.252 Sum_probs=41.8
Q ss_pred HHHHHHHHHHhhC---CC-ceecHHHHHHHhCCeeeEeeehhhHhhhhccee-ecCCCceE
Q 045382 116 LLCSNFLSLYNRD---GV-ESIGLDDAASKLGVERRRIYDIVNVLESVGVLT-RRAKNKYT 171 (191)
Q Consensus 116 ~Lt~kFI~l~~~~---~~-~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~-K~~Kn~y~ 171 (191)
.+..++.+++.+. ++ ..=.=.++|++|||.|-=+=+.+-+|++.|+|+ |.+.+.|.
T Consensus 14 ~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~Gt~V 74 (241)
T COG2186 14 EVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEIRQGSGTFV 74 (241)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCCceEe
Confidence 4445555555443 22 334678999999999999999999999999995 45667776
No 85
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=44.35 E-value=20 Score=30.90 Aligned_cols=48 Identities=17% Similarity=0.257 Sum_probs=37.6
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCc
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNK 169 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~ 169 (191)
+.++++.+. +.+.+.++|+.|+|...-++--++.||..|+|.|..-+.
T Consensus 9 ~Il~~l~~~--~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~gga 56 (251)
T PRK13509 9 ILLELLAQL--GFVTVEKVIERLGISPATARRDINKLDESGKLKKVRNGA 56 (251)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCc
Confidence 345666654 569999999999998776666689999999999865444
No 86
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=42.98 E-value=22 Score=29.38 Aligned_cols=49 Identities=10% Similarity=0.119 Sum_probs=40.6
Q ss_pred CCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEeccc
Q 045382 128 DGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFK 176 (191)
Q Consensus 128 ~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~ 176 (191)
.|+..+...++|++|||.|-=+=+.+..|+.-|+|+.....-+.-..++
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~ 74 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMS 74 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCCC
Confidence 3677889999999999999999999999999999987655545555443
No 87
>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=42.08 E-value=30 Score=28.71 Aligned_cols=45 Identities=20% Similarity=0.327 Sum_probs=37.9
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~ 166 (191)
+.+.++.++ +.+++.++|+.+++.+-.++-.++-|+..|+|++..
T Consensus 147 ~IL~~l~~~--g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 147 KVLEVLKAE--GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 444555544 348999999999999999999999999999999886
No 88
>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=41.73 E-value=28 Score=25.77 Aligned_cols=44 Identities=14% Similarity=0.319 Sum_probs=35.6
Q ss_pred HHHHHhhCCCceecHHHHHHHh-----CCeeeEeeehhhHhhhhcceeec
Q 045382 121 FLSLYNRDGVESIGLDDAASKL-----GVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L-----~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
.++++... +..++.+++.+.+ .+.+=-+|-.++.|+..|+|.+.
T Consensus 6 Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~ 54 (116)
T cd07153 6 ILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREI 54 (116)
T ss_pred HHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEE
Confidence 45555554 3568999999888 57888899999999999999886
No 89
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=40.92 E-value=36 Score=28.27 Aligned_cols=44 Identities=18% Similarity=0.224 Sum_probs=37.4
Q ss_pred CCCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeec-CCCceE
Q 045382 128 DGVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRR-AKNKYT 171 (191)
Q Consensus 128 ~~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~-~Kn~y~ 171 (191)
.++..+ +-.++|++|||.|==+-+.+..|+.-|+|+.. +++.|.
T Consensus 26 ~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g~G~~V 71 (239)
T PRK04984 26 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKV 71 (239)
T ss_pred CCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeEe
Confidence 366778 79999999999999999999999999999754 555555
No 90
>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=40.71 E-value=36 Score=23.45 Aligned_cols=38 Identities=18% Similarity=0.323 Sum_probs=34.1
Q ss_pred CCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382 129 GVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 129 ~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~ 166 (191)
....+...++|+.|+|.+=-+.+.++-|+.-|+|....
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 56789999999999999999999999999999998764
No 91
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=40.34 E-value=18 Score=30.54 Aligned_cols=46 Identities=22% Similarity=0.366 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcc
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGV 161 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgL 161 (191)
.+..+++.++.++....++++++|+.+++.++.|..++.-..++..
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t~ 231 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSALSP 231 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCCH
Confidence 4568889999888878899999999999999999888876555443
No 92
>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=37.93 E-value=18 Score=23.30 Aligned_cols=33 Identities=24% Similarity=0.550 Sum_probs=22.5
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhh
Q 045382 118 CSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVN 154 (191)
Q Consensus 118 t~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiN 154 (191)
....++++.+. +++.++|..+||.|.=||=++|
T Consensus 11 ~~~i~~l~~~G----~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYAEG----MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHHTT------HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHHCC----CCHHHHHHHHCcCHHHHHHHHh
Confidence 45556666553 8899999999999988886653
No 93
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=37.53 E-value=19 Score=26.81 Aligned_cols=41 Identities=27% Similarity=0.479 Sum_probs=31.6
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
|.+-+.+.. ..+++.++|..|++.+++|+++ |...|++-+.
T Consensus 14 ~~d~~~~~~-~~~ti~~~AK~L~i~~~~l~~~---Lr~~g~l~~~ 54 (111)
T PF03374_consen 14 FYDAFVDSD-GLYTIREAAKLLGIGRNKLFQW---LREKGWLYRR 54 (111)
T ss_pred HHHHHHcCC-CCccHHHHHHHhCCCHHHHHHH---HHhCCceEEC
Confidence 445554443 6799999999999999988765 6678888773
No 94
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=37.20 E-value=26 Score=28.07 Aligned_cols=38 Identities=26% Similarity=0.301 Sum_probs=33.3
Q ss_pred hHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeee
Q 045382 114 LGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYD 151 (191)
Q Consensus 114 L~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYD 151 (191)
-..|.+..++++.+.+-..++++++|++.||.|.-||.
T Consensus 13 r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~ 50 (213)
T PRK09975 13 RQELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYW 50 (213)
T ss_pred HHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHH
Confidence 35677889999988887889999999999999999984
No 95
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=36.97 E-value=39 Score=28.18 Aligned_cols=60 Identities=23% Similarity=0.370 Sum_probs=45.7
Q ss_pred ceecHHHHHHHhCCeeeE--------------eeehhhHhhhhcceeecCC-CceEEecccchHHHHHHHHHHhc
Q 045382 131 ESIGLDDAASKLGVERRR--------------IYDIVNVLESVGVLTRRAK-NKYTWKGFKAIRGALQELKVLLR 190 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRR--------------IYDIiNVLEslgLI~K~~K-n~y~W~G~~~I~~tLekLk~Ei~ 190 (191)
+.+.+..++..+|-.+.| +=-|+.-||.+|+|+|..+ ..+.=.|.+-+..+..++.+|+-
T Consensus 66 gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~~GR~ltp~GrsllD~~a~ei~eel~ 140 (147)
T COG2238 66 GPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTPKGRVLTPKGRSLLDRIATEIKEELE 140 (147)
T ss_pred CchhHHHHHHHHCccccCCCCchhhhcCCchHHHHHHHHHHHCCceeecCCCceeCccchhHHHHHHHHHHHHhc
Confidence 567888888888765444 2248899999999999874 56667888888888788888763
No 96
>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=36.93 E-value=52 Score=23.31 Aligned_cols=58 Identities=17% Similarity=0.240 Sum_probs=45.9
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEe
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWK 173 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~ 173 (191)
.+-++.++++...++.....-..+..|+++++.|==++.=|+.=|.|.|.+-+--.|.
T Consensus 4 ~~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~~~~PP~W~ 61 (66)
T PF02295_consen 4 DLEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKEGGTPPKWS 61 (66)
T ss_dssp HHHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEECSSSTEEE
T ss_pred hHHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeCCCCCCceE
Confidence 3446677777666566788888888999999998888999999999999887777884
No 97
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=36.78 E-value=66 Score=27.17 Aligned_cols=57 Identities=19% Similarity=0.213 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHhh---CCCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeec-CCCceE
Q 045382 115 GLLCSNFLSLYNR---DGVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRR-AKNKYT 171 (191)
Q Consensus 115 ~~Lt~kFI~l~~~---~~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~-~Kn~y~ 171 (191)
..+...+.+.+.. .|+..+ +-.++|++|||.|==+=+.+..|++.|||+.. +++.+.
T Consensus 12 ~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~V 73 (257)
T PRK10225 12 QEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYV 73 (257)
T ss_pred HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEEE
Confidence 3444444444432 367788 69999999999999999999999999999754 444433
No 98
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=36.77 E-value=26 Score=24.92 Aligned_cols=33 Identities=18% Similarity=0.301 Sum_probs=30.1
Q ss_pred HHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 135 LDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 135 L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
+.++|+.+++.+=-++.++..|+.-|+|.+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 468999999999999999999999999999864
No 99
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=36.68 E-value=34 Score=28.26 Aligned_cols=59 Identities=15% Similarity=0.197 Sum_probs=42.8
Q ss_pred CCceecHHHHHHHh--CCeeeEeeehhhHhhhhcceeecCCCceEE------ecccchHHHHHHHHH
Q 045382 129 GVESIGLDDAASKL--GVERRRIYDIVNVLESVGVLTRRAKNKYTW------KGFKAIRGALQELKV 187 (191)
Q Consensus 129 ~~~~i~L~~aA~~L--~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W------~G~~~I~~tLekLk~ 187 (191)
.+..-+...+|+++ ++.--.+=+.++.|+-+|+|+|.+.+.|.= .|.+..+.++..++.
T Consensus 36 ~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~~~~~~~avr~~h~ 102 (171)
T PF14394_consen 36 MPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTSSEIPSEAVRSYHK 102 (171)
T ss_pred CCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeCCCCCcHHHHHHHHH
Confidence 34445999999999 999999999999999999999987744432 233444455544443
No 100
>PRK03837 transcriptional regulator NanR; Provisional
Probab=36.60 E-value=58 Score=26.96 Aligned_cols=49 Identities=10% Similarity=0.198 Sum_probs=39.4
Q ss_pred HHHHHHHHHhh---CCCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 117 LCSNFLSLYNR---DGVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 117 Lt~kFI~l~~~---~~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
+.+.+.+.+.. .|+..+ +..++|++|||.|-=+=+.+..|+.-|+|+..
T Consensus 18 v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 18 VEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS 70 (241)
T ss_pred HHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 44444444433 356778 89999999999999999999999999999865
No 101
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=36.51 E-value=58 Score=25.36 Aligned_cols=52 Identities=15% Similarity=0.142 Sum_probs=38.7
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceE
Q 045382 118 CSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYT 171 (191)
Q Consensus 118 t~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~ 171 (191)
.+.|..+.... +.+.+.++|+.|+|.+=-+--.++-|+.-|+|.+.....|.
T Consensus 10 L~~I~~l~~~~--~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~~~~i~ 61 (142)
T PRK03902 10 IEQIYLLIEEK--GYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEKYRGLV 61 (142)
T ss_pred HHHHHHHHhcC--CCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEecCceEE
Confidence 33344444433 45789999999999999999999999999999876433333
No 102
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=36.48 E-value=35 Score=31.06 Aligned_cols=51 Identities=24% Similarity=0.434 Sum_probs=40.0
Q ss_pred CchHHHH-HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceee
Q 045382 112 KSLGLLC-SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTR 164 (191)
Q Consensus 112 KSL~~Lt-~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K 164 (191)
++|++.+ -+.++++... ..++++++|+.||..+--+--=+.|||-.|||+.
T Consensus 18 kalaS~vRv~Il~lL~~k--~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT 69 (308)
T COG4189 18 KALASKVRVAILQLLHRK--GPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRT 69 (308)
T ss_pred HHHHHHHHHHHHHHHHHh--CCCCHHHHHHHhCCchhhhhhhHHHHHhcCceee
Confidence 3556555 3466666655 3589999999999999888888999999999953
No 103
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=36.25 E-value=35 Score=26.23 Aligned_cols=50 Identities=22% Similarity=0.323 Sum_probs=42.2
Q ss_pred hHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 114 LGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 114 L~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
|..+=.+.++.++.+.. +.+.++|+++|+...-+...+.-|+.-|+|.+-
T Consensus 6 lD~~D~~IL~~L~~d~r--~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 6 LDDIDRRILRLLQEDAR--ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred ccHHHHHHHHHHHHhCC--CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeE
Confidence 34555778888887643 999999999999999999999999999999774
No 104
>PF13551 HTH_29: Winged helix-turn helix
Probab=35.30 E-value=24 Score=25.32 Aligned_cols=27 Identities=26% Similarity=0.551 Sum_probs=25.9
Q ss_pred cHHHHHHHhCCeeeEeeehhhHhhhhc
Q 045382 134 GLDDAASKLGVERRRIYDIVNVLESVG 160 (191)
Q Consensus 134 ~L~~aA~~L~V~rRRIYDIiNVLEslg 160 (191)
++.++|..+|+.++-+|.+++-++.=|
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 799999999999999999999999888
No 105
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=35.29 E-value=26 Score=29.61 Aligned_cols=43 Identities=26% Similarity=0.363 Sum_probs=36.1
Q ss_pred CCCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeec-CCCce
Q 045382 128 DGVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRR-AKNKY 170 (191)
Q Consensus 128 ~~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~-~Kn~y 170 (191)
.|+..+ +-.++|++|||.|==+=+.+..|+..|+|+.. +++.|
T Consensus 21 ~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~~G~~ 65 (253)
T PRK10421 21 EAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTF 65 (253)
T ss_pred CCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCeEE
Confidence 466778 79999999999999999999999999999744 44444
No 106
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=35.26 E-value=33 Score=28.59 Aligned_cols=41 Identities=22% Similarity=0.359 Sum_probs=37.6
Q ss_pred CCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCC
Q 045382 128 DGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKN 168 (191)
Q Consensus 128 ~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn 168 (191)
.|+..++..++|.+|||.|--|=+.+..|++-|+|+.....
T Consensus 35 ~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~r 75 (230)
T COG1802 35 APGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNR 75 (230)
T ss_pred CCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCC
Confidence 47889999999999999999999999999999999988443
No 107
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=35.10 E-value=54 Score=25.21 Aligned_cols=34 Identities=21% Similarity=0.392 Sum_probs=31.8
Q ss_pred eecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 132 SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 132 ~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
.++..++|+.+++.+=-+--+++.||.-|+|+|.
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQ 79 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeee
Confidence 3678999999999999999999999999999986
No 108
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=34.29 E-value=43 Score=27.83 Aligned_cols=39 Identities=15% Similarity=0.254 Sum_probs=34.1
Q ss_pred ecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceE
Q 045382 133 IGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYT 171 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~ 171 (191)
++-.++|..||+.|.-+.=+++-|+.-|+|+..+.+++.
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 566899999999999999999999999999877555555
No 109
>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=34.12 E-value=12 Score=32.88 Aligned_cols=32 Identities=28% Similarity=0.655 Sum_probs=24.5
Q ss_pred HHHHHhC---CeeeEeeehhhHhhhhcceeecCCC
Q 045382 137 DAASKLG---VERRRIYDIVNVLESVGVLTRRAKN 168 (191)
Q Consensus 137 ~aA~~L~---V~rRRIYDIiNVLEslgLI~K~~Kn 168 (191)
.+|+.+| +..|++||+++-|+.+|+|+-...+
T Consensus 319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~~~ 353 (365)
T TIGR02928 319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAEERN 353 (365)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEEEc
Confidence 3445555 4679999999999999999876433
No 110
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=34.06 E-value=36 Score=24.17 Aligned_cols=44 Identities=23% Similarity=0.422 Sum_probs=34.4
Q ss_pred HHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 122 LSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 122 I~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
+..+...++... .++|+.+++.+=-+--+++-||.-|+|.+...
T Consensus 28 L~~l~~~~~~~~--~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~ 71 (126)
T COG1846 28 LLALYEAGGITV--KELAERLGLDRSTVTRLLKRLEDKGLIERLRD 71 (126)
T ss_pred HHHHHHhCCCcH--HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 333444444333 99999999999999999999999999988643
No 111
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=33.98 E-value=41 Score=23.97 Aligned_cols=53 Identities=13% Similarity=0.223 Sum_probs=38.7
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEE
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTW 172 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W 172 (191)
.+....++.+. .+.....+++...+....++..++|-|+.-|+|++ ..+.|.=
T Consensus 6 ~Ii~~IL~~l~---~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~-~~~~Y~l 58 (77)
T PF14947_consen 6 EIIFDILKILS---KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK-KDGKYRL 58 (77)
T ss_dssp HHHHHHHHHH----TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE-ETTEEEE
T ss_pred HHHHHHHHHHH---cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC-CCCEEEE
Confidence 45555666665 34577889999999999999999999999999977 5667766
No 112
>PRK13503 transcriptional activator RhaS; Provisional
Probab=33.52 E-value=27 Score=29.19 Aligned_cols=40 Identities=10% Similarity=0.147 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhH
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNV 155 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNV 155 (191)
...+++++++.++....++|+++|+.+++.++.+..++.=
T Consensus 171 ~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~ 210 (278)
T PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQ 210 (278)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578899999988888999999999999988887766653
No 113
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=32.81 E-value=81 Score=26.44 Aligned_cols=43 Identities=16% Similarity=0.328 Sum_probs=36.6
Q ss_pred CCCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeec-CCCce
Q 045382 128 DGVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRR-AKNKY 170 (191)
Q Consensus 128 ~~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~-~Kn~y 170 (191)
.|+..+ +-.++|+.|||.|==+-+.+..|+..|||+.. +++.|
T Consensus 26 ~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~ 70 (251)
T PRK09990 26 KVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSF 70 (251)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeE
Confidence 367788 89999999999999999999999999999765 33433
No 114
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=32.76 E-value=91 Score=30.20 Aligned_cols=66 Identities=20% Similarity=0.357 Sum_probs=43.6
Q ss_pred chHHHH-HH-----HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecccchHHHH
Q 045382 113 SLGLLC-SN-----FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGAL 182 (191)
Q Consensus 113 SL~~Lt-~k-----FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~I~~tL 182 (191)
-||.++ .. .++++... ...++|++++...++. .-||+..|+.+|++.......+.-+..+.|...+
T Consensus 350 dlG~~sY~~YW~~~i~~~L~~~-~~~~si~~is~~T~i~---~~Dii~tL~~l~~l~~~kg~~~i~~~~~~i~~~~ 421 (450)
T PLN00104 350 DLGLVSYRGYWTRVLLEILKKH-KGNISIKELSDMTAIK---AEDIVSTLQSLNLIQYRKGQHVICADPKVLEEHL 421 (450)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc-CCCccHHHHHHHhCCC---HHHHHHHHHHCCCEEecCCcEEEEECHHHHHHHH
Confidence 456555 22 44455444 3479999999999995 4799999999999986533444444444444433
No 115
>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=32.73 E-value=63 Score=24.13 Aligned_cols=49 Identities=22% Similarity=0.353 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
.+.+..|+.|.+. +..|.=.++|+.|++.-=-|-.+.-.||.+|+|+++
T Consensus 8 ~IL~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 8 EILKALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 3445566666655 457888888999998776677788889999999875
No 116
>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=32.54 E-value=20 Score=27.52 Aligned_cols=55 Identities=27% Similarity=0.443 Sum_probs=33.9
Q ss_pred cHHHHHHHhCCeeeEeeehhhHhhhhcceee-------cCCCceE---Eecc--cchHHHHHHHHHH
Q 045382 134 GLDDAASKLGVERRRIYDIVNVLESVGVLTR-------RAKNKYT---WKGF--KAIRGALQELKVL 188 (191)
Q Consensus 134 ~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K-------~~Kn~y~---W~G~--~~I~~tLekLk~E 188 (191)
++..+-+.-|..||-+.|.++.|..+|+.-. ..-+.|. |=-+ +-|...++.+++-
T Consensus 23 nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~~Fvq~G~R~~~GyY~i~~WG~id~~wi~~~~~~i~~~ 89 (90)
T PF09904_consen 23 NVPALMEATGMPRRTIQDTIKALPELGIECEFVQDGERNNAGYYRISDWGPIDRKWIADHLQEIKAA 89 (90)
T ss_dssp -HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEEE-TTB-HHHHHHHHHHHHHH
T ss_pred cHHHHHHHhCCCHhHHHHHHHHhhcCCeEEEEEecCccCCCCcEEeeecCCCCHHHHHHHHHHHHhh
Confidence 8999999999999999999999999998632 2223455 4222 3466667766654
No 117
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.42 E-value=19 Score=28.49 Aligned_cols=40 Identities=23% Similarity=0.352 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhH
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNV 155 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNV 155 (191)
+||.+=..+++-.=..-+++.++|+.++|.|--|||=|+-
T Consensus 17 LLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr 56 (105)
T COG2739 17 LLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKR 56 (105)
T ss_pred HHhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHH
Confidence 5565544444332223489999999999999999997763
No 118
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=32.10 E-value=32 Score=26.72 Aligned_cols=35 Identities=17% Similarity=0.172 Sum_probs=32.8
Q ss_pred ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
..++..++|+.+++.+=-+--+++-||.-|+|.|.
T Consensus 53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~ 87 (144)
T PRK11512 53 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL 87 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 35999999999999999999999999999999986
No 119
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=31.90 E-value=36 Score=26.15 Aligned_cols=44 Identities=20% Similarity=0.413 Sum_probs=34.0
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
+.|.+++.++|+ +.+.++|..|+|...-|+ ..|.-+|+.-|+..
T Consensus 60 ~~L~~~v~~~pd--~tl~Ela~~l~Vs~~ti~---~~Lkrlg~t~KK~~ 103 (119)
T PF01710_consen 60 DELKALVEENPD--ATLRELAERLGVSPSTIW---RALKRLGITRKKKT 103 (119)
T ss_pred HHHHHHHHHCCC--cCHHHHHHHcCCCHHHHH---HHHHHcCchhccCc
Confidence 557777788877 788999999999665554 67888899888743
No 120
>PRK10130 transcriptional regulator EutR; Provisional
Probab=31.86 E-value=27 Score=31.91 Aligned_cols=44 Identities=18% Similarity=0.164 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhh
Q 045382 115 GLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLES 158 (191)
Q Consensus 115 ~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEs 158 (191)
..+..+..+++.++....+++.++|+.+++.+|-|+-.+.=..+
T Consensus 239 ~~~v~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~G 282 (350)
T PRK10130 239 RRLLSRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHAILG 282 (350)
T ss_pred HHHHHHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHHHHC
Confidence 56778888998888888899999999999999998877744333
No 121
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=31.78 E-value=33 Score=28.62 Aligned_cols=35 Identities=20% Similarity=0.427 Sum_probs=29.7
Q ss_pred HhhhhcceeecCCCceEEecccchHHHHHHHHHHhc
Q 045382 155 VLESVGVLTRRAKNKYTWKGFKAIRGALQELKVLLR 190 (191)
Q Consensus 155 VLEslgLI~K~~Kn~y~W~G~~~I~~tLekLk~Ei~ 190 (191)
-|.++|.--..+.+.+.|.|..+ ...|.+|+++|+
T Consensus 72 ~l~g~g~F~~~~~~rvi~~~v~~-~~~L~~L~~~l~ 106 (180)
T COG1514 72 TLDGAGSFPNPRRPRVIWVGVEE-TEELRALAEELE 106 (180)
T ss_pred EEeeEcccCCCCCCcEEEEcCCC-cHHHHHHHHHHH
Confidence 37788888888889999999998 788888888875
No 122
>PRK10870 transcriptional repressor MprA; Provisional
Probab=31.68 E-value=45 Score=27.30 Aligned_cols=40 Identities=28% Similarity=0.348 Sum_probs=34.6
Q ss_pred hCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382 127 RDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 127 ~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~ 166 (191)
..++..++..++|+.+++.+=-+-=+++-|+.-|+|+|..
T Consensus 66 ~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~ 105 (176)
T PRK10870 66 SQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRE 105 (176)
T ss_pred cCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 3345678999999999999988888999999999999863
No 123
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=31.14 E-value=53 Score=30.43 Aligned_cols=43 Identities=12% Similarity=0.270 Sum_probs=37.6
Q ss_pred CCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceE
Q 045382 129 GVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYT 171 (191)
Q Consensus 129 ~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~ 171 (191)
.+..++.+++++++++.-+.+-||++-|+..|+|.+...+.|.
T Consensus 307 ~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~~~g~~~ 349 (412)
T PRK04214 307 HGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRGERGQWV 349 (412)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEecCCCceE
Confidence 3457899999999999999999999999999999987666544
No 124
>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=30.56 E-value=24 Score=25.39 Aligned_cols=36 Identities=28% Similarity=0.463 Sum_probs=26.8
Q ss_pred ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~ 166 (191)
+.+.-..+|++.|+.|.-|-.-+-=||+.|+|+-.+
T Consensus 3 g~lvas~iAd~~GiTRSvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 3 GRLVASKIADRVGITRSVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp EEE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred ceehHHHHHHHhCccHHHHHHHHHHHHhcCceeecc
Confidence 345667899999999988877777899999998653
No 125
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=30.07 E-value=65 Score=26.59 Aligned_cols=55 Identities=18% Similarity=0.201 Sum_probs=40.3
Q ss_pred HHHHHHHHHhh---CCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEE
Q 045382 117 LCSNFLSLYNR---DGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTW 172 (191)
Q Consensus 117 Lt~kFI~l~~~---~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W 172 (191)
+-+++..++.. ......+-.++|+.||+.|+-+.=+++-|+--|+|++.++ .+.=
T Consensus 151 ~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~-~i~I 208 (226)
T PRK10402 151 LENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKR-GYLI 208 (226)
T ss_pred HHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCC-EEEE
Confidence 34555555432 1222357799999999999999999999999999999754 4543
No 126
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=29.78 E-value=38 Score=29.24 Aligned_cols=45 Identities=13% Similarity=0.201 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhc
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVG 160 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslg 160 (191)
....+.+.++.++....++|+++|+.+|+.+|.|.-++.-.-++.
T Consensus 5 ~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~s 49 (289)
T PRK15121 5 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHA 49 (289)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 456788889998888889999999999998887776666554433
No 127
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=28.56 E-value=56 Score=26.02 Aligned_cols=36 Identities=19% Similarity=0.398 Sum_probs=32.7
Q ss_pred eecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382 132 SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 132 ~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
.++-.++|..+|+.++.+.=+++-|+.-|+|+..++
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~ 203 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGK 203 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 577799999999999999999999999999987754
No 128
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.50 E-value=1e+02 Score=28.17 Aligned_cols=60 Identities=22% Similarity=0.396 Sum_probs=39.0
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec--CCCceEEecccc
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR--AKNKYTWKGFKA 177 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~--~Kn~y~W~G~~~ 177 (191)
.|...||+|+..++ .+.|+++|..+|..---..+=|.-|..=|+++-+ ..++|.++....
T Consensus 200 nll~eFv~YIk~nK--vV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~eE 261 (299)
T KOG3054|consen 200 NLLSEFVEYIKKNK--VVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISMEE 261 (299)
T ss_pred HHHHHHHHHHHhcC--eeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecHHH
Confidence 47788999999874 5999999999987432222222233344555443 456788887543
No 129
>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=27.63 E-value=1.2e+02 Score=27.18 Aligned_cols=60 Identities=13% Similarity=0.196 Sum_probs=42.0
Q ss_pred CCceecHHHHHHHhC--CeeeEeeehhhHhhhhcceeecCCCceEE------ecccchHHHHHHHHHH
Q 045382 129 GVESIGLDDAASKLG--VERRRIYDIVNVLESVGVLTRRAKNKYTW------KGFKAIRGALQELKVL 188 (191)
Q Consensus 129 ~~~~i~L~~aA~~L~--V~rRRIYDIiNVLEslgLI~K~~Kn~y~W------~G~~~I~~tLekLk~E 188 (191)
.++.-+...+|++++ |.--.+=|.++.|+-+|+|+|.+.+.|.= .|.+..+.++..++.+
T Consensus 134 ~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y~~t~~~l~~~~~~~~~avr~~h~q 201 (271)
T TIGR02147 134 MPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFYKQTDKAVSTGDEVIPLAVRQYQKQ 201 (271)
T ss_pred CCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcEEeecceeecCCccchHHHHHHHHH
Confidence 344557889999998 77788889999999999999986653332 2344444555555433
No 130
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=27.37 E-value=22 Score=23.40 Aligned_cols=24 Identities=29% Similarity=0.603 Sum_probs=19.4
Q ss_pred ceecHHHHHHHhCCeeeEeeehhh
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVN 154 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiN 154 (191)
..+++.++++.+|+.+.-||..++
T Consensus 2 rll~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 2 RLLRIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp -EE-HHHHHHHHSS-HHHHHHHHH
T ss_pred ccccHHHHHHHHCCCHHHHHHHHh
Confidence 468999999999999999999877
No 131
>PF12728 HTH_17: Helix-turn-helix domain
Probab=27.16 E-value=19 Score=23.08 Aligned_cols=22 Identities=27% Similarity=0.607 Sum_probs=19.7
Q ss_pred ecHHHHHHHhCCeeeEeeehhh
Q 045382 133 IGLDDAASKLGVERRRIYDIVN 154 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDIiN 154 (191)
+++.++|+.|||.+.-||.+++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999998885
No 132
>KOG4578 consensus Uncharacterized conserved protein, contains KAZAL and TY domains [General function prediction only]
Probab=26.89 E-value=31 Score=32.69 Aligned_cols=44 Identities=23% Similarity=0.254 Sum_probs=36.4
Q ss_pred cCCCCCCCchHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeE
Q 045382 105 YAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRR 148 (191)
Q Consensus 105 ~~~~RkeKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRR 148 (191)
+.+-++-+-+..-.++|.+||.-+.+..|+|++.-.-|++.++|
T Consensus 359 K~~l~k~s~~rkC~rk~~~yCDlNkDKkISl~Ew~~CL~~~~~~ 402 (421)
T KOG4578|consen 359 KRVLLKKSKPRKCSRKFFKYCDLNKDKKISLDEWRGCLGVEKER 402 (421)
T ss_pred HHHHHhhccHHHHhhhcchhcccCCCceecHHHHhhhhcccccc
Confidence 33445556667778899999999999999999999999998876
No 133
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=26.39 E-value=38 Score=28.83 Aligned_cols=38 Identities=18% Similarity=0.321 Sum_probs=30.9
Q ss_pred HHHHHHHHHhhCCCce-ecHHHHHHHhCCeeeEeeehhh
Q 045382 117 LCSNFLSLYNRDGVES-IGLDDAASKLGVERRRIYDIVN 154 (191)
Q Consensus 117 Lt~kFI~l~~~~~~~~-i~L~~aA~~L~V~rRRIYDIiN 154 (191)
...+.+.++.++-... +++.++|..+|+.+|.||-++-
T Consensus 198 ~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk 236 (302)
T PRK09685 198 QFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFA 236 (302)
T ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4457777877765444 9999999999999999998875
No 134
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=26.15 E-value=61 Score=26.96 Aligned_cols=37 Identities=24% Similarity=0.497 Sum_probs=30.6
Q ss_pred ceecHHHHHHHhCCeeeE--------------eeehhhHhhhhcceeecCC
Q 045382 131 ESIGLDDAASKLGVERRR--------------IYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRR--------------IYDIiNVLEslgLI~K~~K 167 (191)
+.+-+..++..+|..+|| +=-++..||.+|+|++...
T Consensus 66 gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~~ 116 (150)
T PRK09333 66 GPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTKK 116 (150)
T ss_pred CCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCCC
Confidence 358899999999986664 6679999999999998753
No 135
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=26.01 E-value=29 Score=30.87 Aligned_cols=33 Identities=24% Similarity=0.577 Sum_probs=25.7
Q ss_pred eecHHHHH-------HHhCCe---eeEeeehhhHhhhhcceee
Q 045382 132 SIGLDDAA-------SKLGVE---RRRIYDIVNVLESVGVLTR 164 (191)
Q Consensus 132 ~i~L~~aA-------~~L~V~---rRRIYDIiNVLEslgLI~K 164 (191)
.+...++. +.+++. +|+++|++|-|+..|||+-
T Consensus 315 ~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~~~glI~~ 357 (394)
T PRK00411 315 EVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIINT 357 (394)
T ss_pred cccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHHhcCCeEE
Confidence 45666555 446774 4999999999999999974
No 136
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=25.99 E-value=67 Score=28.11 Aligned_cols=50 Identities=20% Similarity=0.331 Sum_probs=37.2
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCce
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKY 170 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y 170 (191)
.+.++++++.+ .+.+.++|+.|+|..+=+.==++.||.-|++.|......
T Consensus 20 ~~Il~~L~~~~--~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~GGa~ 69 (269)
T PRK09802 20 EQIIQRLRQQG--SVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGAL 69 (269)
T ss_pred HHHHHHHHHcC--CEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeCCEE
Confidence 44566677764 499999999999975544434567899999999865544
No 137
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=25.94 E-value=43 Score=21.22 Aligned_cols=35 Identities=29% Similarity=0.426 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHH-hhCCCceecHHHHHHHhCCeeeEeee
Q 045382 114 LGLLCSNFLSLY-NRDGVESIGLDDAASKLGVERRRIYD 151 (191)
Q Consensus 114 L~~Lt~kFI~l~-~~~~~~~i~L~~aA~~L~V~rRRIYD 151 (191)
|..+=+.+|... .... -++..+|..||+.|+-||.
T Consensus 2 l~~~E~~~i~~aL~~~~---gn~~~aA~~Lgisr~tL~~ 37 (42)
T PF02954_consen 2 LEEFEKQLIRQALERCG---GNVSKAARLLGISRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHHHHHHTT---T-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHHHHHhC---CCHHHHHHHHCCCHHHHHH
Confidence 344445555553 3333 2578999999999987774
No 138
>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=25.72 E-value=50 Score=24.80 Aligned_cols=48 Identities=17% Similarity=0.324 Sum_probs=36.4
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhC-----CeeeEeeehhhHhhhhcceeecCC
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLG-----VERRRIYDIVNVLESVGVLTRRAK 167 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~-----V~rRRIYDIiNVLEslgLI~K~~K 167 (191)
...++++.+.+. .++.+++.+.|. +.+==||-.++.|+..|+|.+...
T Consensus 11 ~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~ 63 (120)
T PF01475_consen 11 LAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEF 63 (120)
T ss_dssp HHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEc
Confidence 346677777665 799999998884 444459999999999999988643
No 139
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=25.61 E-value=74 Score=28.13 Aligned_cols=51 Identities=22% Similarity=0.352 Sum_probs=38.6
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcc-eeecCCCceE
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGV-LTRRAKNKYT 171 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgL-I~K~~Kn~y~ 171 (191)
.+.+.++.+. ..++..++|++|++.|.-++-.+..|+..|+ |.......|.
T Consensus 7 ~~il~~L~~~--~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~~~~Gy~ 58 (319)
T PRK11886 7 LQLLSLLADG--DFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSVKGKGYR 58 (319)
T ss_pred HHHHHHHHcC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEecCCeEE
Confidence 3556666553 5688889999999999999999999999999 5443322344
No 140
>PF14830 Haemocyan_bet_s: Haemocyanin beta-sandwich; PDB: 1JS8_B 3QJO_A 1LNL_A.
Probab=25.46 E-value=34 Score=26.79 Aligned_cols=19 Identities=32% Similarity=0.593 Sum_probs=11.8
Q ss_pred CeeeEeeehhhHhhhhcce
Q 045382 144 VERRRIYDIVNVLESVGVL 162 (191)
Q Consensus 144 V~rRRIYDIiNVLEslgLI 162 (191)
+.|==-|||+.+|+.+||=
T Consensus 52 FdRlykydIT~~l~~l~l~ 70 (103)
T PF14830_consen 52 FDRLYKYDITDALKKLGLH 70 (103)
T ss_dssp -SS-EEEE-HHHHHHCT--
T ss_pred cCccchhhHHHHHHHcCCC
Confidence 3444569999999999986
No 141
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=25.41 E-value=41 Score=26.68 Aligned_cols=37 Identities=24% Similarity=0.482 Sum_probs=29.6
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCC----eeeEeeehhhHhhh
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGV----ERRRIYDIVNVLES 158 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V----~rRRIYDIiNVLEs 158 (191)
+.||..|-.+.+ +|.+++..||| .|-||.+|+..|..
T Consensus 39 ~~Fi~~Fi~~rG---nlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 39 LEFIKLFIKNRG---NLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHHHHHHHhcC---CHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 679988876655 69999999999 48999998776554
No 142
>PTZ00064 histone acetyltransferase; Provisional
Probab=25.39 E-value=84 Score=31.19 Aligned_cols=49 Identities=16% Similarity=0.392 Sum_probs=38.3
Q ss_pred ecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecccchHHHHHH
Q 045382 133 IGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQE 184 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~I~~tLek 184 (191)
++|++++...++. ..||+..|+.+|++.......+.-.-.+.|.+.+++
T Consensus 472 iSI~dIS~~TgI~---~eDII~TLq~L~llky~kgq~~I~~~~~~ie~~~~~ 520 (552)
T PTZ00064 472 KFIDNVVRSTGIR---REDVIRILEENGIMRNIKDQHYIFCNQEFLKGIVKR 520 (552)
T ss_pred ccHHHHHHHhCCC---HHHHHHHHHHCCcEEEeCCCEEEEECHHHHHHHHHH
Confidence 8999999999995 579999999999999775666666655555555443
No 143
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=25.32 E-value=78 Score=27.92 Aligned_cols=56 Identities=29% Similarity=0.459 Sum_probs=43.7
Q ss_pred chHHHHHHHHH-HHhhCCCceecHHHHHHHhCCeeeEeeehhh-HhhhhcceeecCCC
Q 045382 113 SLGLLCSNFLS-LYNRDGVESIGLDDAASKLGVERRRIYDIVN-VLESVGVLTRRAKN 168 (191)
Q Consensus 113 SL~~Lt~kFI~-l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiN-VLEslgLI~K~~Kn 168 (191)
.|.....+++. +...-.+..+.++.+|..||....-+-|++- .|-..|+|++..++
T Consensus 256 ~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 313 (328)
T PRK00080 256 GLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRG 313 (328)
T ss_pred CCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCch
Confidence 45556667776 4555456679999999999999998888888 88889999877654
No 144
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=25.23 E-value=64 Score=22.80 Aligned_cols=52 Identities=19% Similarity=0.304 Sum_probs=35.1
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceee--cCCCc-eEEe
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTR--RAKNK-YTWK 173 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K--~~Kn~-y~W~ 173 (191)
.++++... +..+.-.++|+.+|+.+--.-=+++.||.-|.|++ .+++. -.|.
T Consensus 5 Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~ 59 (62)
T PF04703_consen 5 ILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKSTYWR 59 (62)
T ss_dssp HHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-EEE
T ss_pred HHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcceeee
Confidence 34555442 34588999999999987666678999999999986 33332 3574
No 145
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.21 E-value=21 Score=22.70 Aligned_cols=28 Identities=25% Similarity=0.509 Sum_probs=18.1
Q ss_pred ecHHHHHHHhCCeeeEeeehhhHhhhhc
Q 045382 133 IGLDDAASKLGVERRRIYDIVNVLESVG 160 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDIiNVLEslg 160 (191)
.+..++|..|||.++-+|.+++=++.-|
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT------
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 7899999999999999999988765444
No 146
>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=24.93 E-value=86 Score=26.01 Aligned_cols=44 Identities=18% Similarity=0.224 Sum_probs=37.2
Q ss_pred CCCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeec-CCCceE
Q 045382 128 DGVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRR-AKNKYT 171 (191)
Q Consensus 128 ~~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~-~Kn~y~ 171 (191)
.|+..+ +-.++|++|||.|==+=+.+..|+.-|+|+.. +++.+.
T Consensus 25 ~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~~G~~V 70 (235)
T TIGR02812 25 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKV 70 (235)
T ss_pred CCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCccEe
Confidence 467788 89999999999999999999999999999754 445544
No 147
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=24.40 E-value=24 Score=21.34 Aligned_cols=23 Identities=26% Similarity=0.300 Sum_probs=18.7
Q ss_pred ecHHHHHHHhCCeeeEeeehhhH
Q 045382 133 IGLDDAASKLGVERRRIYDIVNV 155 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDIiNV 155 (191)
+++.++|+.|||.++-||..+.-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 46789999999999888877663
No 148
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=24.00 E-value=1.3e+02 Score=25.37 Aligned_cols=54 Identities=15% Similarity=0.114 Sum_probs=40.0
Q ss_pred HHHHHHHHHhh---CCCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeec-CCCce
Q 045382 117 LCSNFLSLYNR---DGVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRR-AKNKY 170 (191)
Q Consensus 117 Lt~kFI~l~~~---~~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~-~Kn~y 170 (191)
+.+.+.+.+.. .|+..+ +-.++|++|||.|==+=+.+..|+..|+|+.. +++.+
T Consensus 13 v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~ 71 (253)
T PRK11523 13 LAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIH 71 (253)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCeeE
Confidence 33444444432 366778 58899999999999999999999999999654 44443
No 149
>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=23.97 E-value=89 Score=31.10 Aligned_cols=53 Identities=15% Similarity=0.324 Sum_probs=43.4
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCe----eeEeeehhhHhhhhcceeecCCCceEE
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVE----RRRIYDIVNVLESVGVLTRRAKNKYTW 172 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~----rRRIYDIiNVLEslgLI~K~~Kn~y~W 172 (191)
+.++++.+.+...+...+++..|++. +.-++.+++-|+.-|.|.+..++.|..
T Consensus 6 ~il~~l~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~~~~~~~~ 62 (709)
T TIGR02063 6 LILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYAL 62 (709)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEec
Confidence 46777777777889999999999985 345999999999999999876666654
No 150
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.92 E-value=55 Score=25.18 Aligned_cols=41 Identities=20% Similarity=0.404 Sum_probs=33.1
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcce
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVL 162 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI 162 (191)
.+.++-++ .+..++-++-..-|-.||-+-|++..|++||++
T Consensus 12 Yla~Li~S-~e~~nVP~lm~~TGwPRRT~QDvikAlpglgi~ 52 (95)
T COG4519 12 YLAYLIDS-GETANVPELMAATGWPRRTAQDVIKALPGLGIV 52 (95)
T ss_pred HHHHHHhc-cccCChHHHHHHcCCchhHHHHHHHhCcCCCeE
Confidence 34444444 346788888888999999999999999999997
No 151
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=23.51 E-value=88 Score=23.02 Aligned_cols=31 Identities=16% Similarity=0.207 Sum_probs=21.8
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEeee
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIYD 151 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYD 151 (191)
..+++.++|+..++|...|+++++-|=-|-|
T Consensus 9 it~~L~~~P~~lisL~~Fae~f~~AKSsISE 39 (70)
T PF09182_consen 9 ITKYLLENPNKLISLTYFAERFGAAKSSISE 39 (70)
T ss_dssp HHHHHHTSTT--EEHHHHHHHHT--HHHHHH
T ss_pred HHHHHHcCCcceEcHHHHHHHhcccccchHH
Confidence 3456778999999999999999987766654
No 152
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=23.08 E-value=62 Score=28.30 Aligned_cols=44 Identities=7% Similarity=0.037 Sum_probs=35.8
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhh
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESV 159 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEsl 159 (191)
....++++++.++....++++++|+.+++..|.|.-.++-..++
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~ 261 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGM 261 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCc
Confidence 45678889999888888999999999999888887777655443
No 153
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=23.04 E-value=24 Score=27.71 Aligned_cols=39 Identities=28% Similarity=0.451 Sum_probs=28.6
Q ss_pred CCCchHHHH-HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhh
Q 045382 110 KQKSLGLLC-SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVN 154 (191)
Q Consensus 110 keKSL~~Lt-~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiN 154 (191)
+.-.-|++. ..|++.+ -++..++|+.|||.+.+|-+|+|
T Consensus 6 ~P~~PGEiL~eeflep~------glt~~~lA~~lgV~r~~is~lin 45 (104)
T COG3093 6 KPAHPGEILREEFLEPL------GLTQTELAEALGVTRNTISELIN 45 (104)
T ss_pred CCCCchHHHHHHHhccc------cCCHHHHHHHhCCCHHHHHHHHc
Confidence 333445544 5565532 37899999999999999999988
No 154
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=22.99 E-value=1.7e+02 Score=22.97 Aligned_cols=51 Identities=18% Similarity=0.304 Sum_probs=37.7
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEE
Q 045382 120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTW 172 (191)
Q Consensus 120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W 172 (191)
+.+.++... +..++.++++.+++.+=-+-==++||+..|||.....+...+
T Consensus 20 ~IL~~L~~~--~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~ 70 (117)
T PRK10141 20 GIVLLLRES--GELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVH 70 (117)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEE
Confidence 455555443 348889999999998888888899999999997655544333
No 155
>PRK06474 hypothetical protein; Provisional
Probab=22.91 E-value=82 Score=26.03 Aligned_cols=46 Identities=13% Similarity=0.191 Sum_probs=37.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHh-CCeeeEeeehhhHhhhhcceeec
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKL-GVERRRIYDIVNVLESVGVLTRR 165 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L-~V~rRRIYDIiNVLEslgLI~K~ 165 (191)
.+.++++...+. .++..+++..+ ++.+=-+|=.+++|+-.|+|.+.
T Consensus 14 ~~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~ 60 (178)
T PRK06474 14 MKICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVV 60 (178)
T ss_pred HHHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEe
Confidence 345666666543 38999999999 68888999999999999999864
No 156
>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=22.82 E-value=93 Score=16.29 Aligned_cols=20 Identities=30% Similarity=0.569 Sum_probs=15.6
Q ss_pred ecHHHHHHHhCCeeeEeeeh
Q 045382 133 IGLDDAASKLGVERRRIYDI 152 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDI 152 (191)
.++.++|..+++.+.-+|-+
T Consensus 22 ~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 22 ESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHCCCHHHHHHh
Confidence 48899999999887766643
No 157
>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=22.47 E-value=1.2e+02 Score=24.81 Aligned_cols=55 Identities=24% Similarity=0.407 Sum_probs=35.4
Q ss_pred eecHHHHHHHhCCeeeE--------------eeehhhHhhhhcceeecCCC--ceEEecccchHHHHHHHH
Q 045382 132 SIGLDDAASKLGVERRR--------------IYDIVNVLESVGVLTRRAKN--KYTWKGFKAIRGALQELK 186 (191)
Q Consensus 132 ~i~L~~aA~~L~V~rRR--------------IYDIiNVLEslgLI~K~~Kn--~y~W~G~~~I~~tLekLk 186 (191)
.+.+..++..+|-.+|| |=-|+.-||.+|+|+|..++ .+.=.|.+-+...-.++.
T Consensus 66 ~~GV~~lr~~YGg~k~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~lD~iA~~v~ 136 (139)
T PF01090_consen 66 PVGVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDLDRIAGQVA 136 (139)
T ss_dssp SB-HHHHHHHH--EEEETSSCCEE--CHHHHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHHHHHHHHHH
T ss_pred CcchHHHHHHhCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHHHHHHHHHH
Confidence 58899999999998887 45689999999999998543 344345443333333333
No 158
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=22.41 E-value=34 Score=21.81 Aligned_cols=30 Identities=30% Similarity=0.622 Sum_probs=23.5
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCeeeEee
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVERRRIY 150 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIY 150 (191)
-++++.+.+-..++++++|++.|+.+.-||
T Consensus 5 a~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y 34 (47)
T PF00440_consen 5 ALELFAEKGYEAVSIRDIARRAGVSKGSFY 34 (47)
T ss_dssp HHHHHHHHHTTTSSHHHHHHHHTSCHHHHH
T ss_pred HHHHHHHhCHHhCCHHHHHHHHccchhhHH
Confidence 345566666677999999999999887776
No 159
>PRK11642 exoribonuclease R; Provisional
Probab=22.37 E-value=80 Score=32.42 Aligned_cols=50 Identities=16% Similarity=0.254 Sum_probs=40.0
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCe----eeEeeehhhHhhhhcceeecCCCceE
Q 045382 121 FLSLYNRDGVESIGLDDAASKLGVE----RRRIYDIVNVLESVGVLTRRAKNKYT 171 (191)
Q Consensus 121 FI~l~~~~~~~~i~L~~aA~~L~V~----rRRIYDIiNVLEslgLI~K~~Kn~y~ 171 (191)
.++++.+.+ ..+++.+++..|++. +..|..+++-|+..|.|.+..++.|.
T Consensus 24 Il~~l~~~~-~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~~~~~~ 77 (813)
T PRK11642 24 ILEHLTKRE-KPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYA 77 (813)
T ss_pred HHHHHHhcC-CCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEe
Confidence 455565533 789999999999996 35599999999999999987666663
No 160
>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=22.00 E-value=98 Score=26.50 Aligned_cols=52 Identities=27% Similarity=0.399 Sum_probs=37.7
Q ss_pred HHHHHH-HHhhCCCceecHHHHHHHhCCeeeEeeehhh-HhhhhcceeecCCCc
Q 045382 118 CSNFLS-LYNRDGVESIGLDDAASKLGVERRRIYDIVN-VLESVGVLTRRAKNK 169 (191)
Q Consensus 118 t~kFI~-l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiN-VLEslgLI~K~~Kn~ 169 (191)
-+.++. +.....+..+.+.++|..||+....+..++- .|-..|+|.+.+.+.
T Consensus 240 ~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~~g~ 293 (305)
T TIGR00635 240 DRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGR 293 (305)
T ss_pred HHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCCchh
Confidence 333444 3333334458899999999999998888777 788889998776554
No 161
>PF02553 CbiN: Cobalt transport protein component CbiN; InterPro: IPR003705 The cobalt transport protein CbiN is part of the active cobalt transport system involved in uptake of cobalt in to the cell involved with cobalamin biosynthesis (vitamin B12). It has been suggested that CbiN may function as the periplasmic binding protein component of the active cobalt transport system [].; GO: 0015087 cobalt ion transmembrane transporter activity, 0006824 cobalt ion transport, 0009236 cobalamin biosynthetic process, 0016020 membrane
Probab=21.99 E-value=20 Score=26.58 Aligned_cols=26 Identities=23% Similarity=0.524 Sum_probs=20.0
Q ss_pred ccCCCcCceeeeeecCCCCCCCCccC
Q 045382 5 YGDKDGMEMTGVARASDRYQPWPMEL 30 (191)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 (191)
+|.+||.+......++.-|+||=..+
T Consensus 31 ~GGaD~~A~~~I~~~~p~Y~PWf~pl 56 (74)
T PF02553_consen 31 FGGADDQAEEMIEEIDPDYEPWFEPL 56 (74)
T ss_pred ccCccHHHHHHHHHhCCCCCcccccc
Confidence 67677777777777888999997744
No 162
>PHA00738 putative HTH transcription regulator
Probab=21.89 E-value=1.4e+02 Score=23.56 Aligned_cols=54 Identities=9% Similarity=0.132 Sum_probs=38.9
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEec
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKG 174 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G 174 (191)
++.+.++...+ .....++++.+++.+=.+-==+.||+..|||+....+...+.-
T Consensus 15 r~IL~lL~~~e--~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~ 68 (108)
T PHA00738 15 RKILELIAENY--ILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAK 68 (108)
T ss_pred HHHHHHHHHcC--CccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEE
Confidence 34556665543 3788889999998887777788999999999765555444433
No 163
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=21.81 E-value=75 Score=29.46 Aligned_cols=48 Identities=21% Similarity=0.243 Sum_probs=44.4
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHh-CCeeeEeeehhhHhhhhccee
Q 045382 116 LLCSNFLSLYNRDGVESIGLDDAASKL-GVERRRIYDIVNVLESVGVLT 163 (191)
Q Consensus 116 ~Lt~kFI~l~~~~~~~~i~L~~aA~~L-~V~rRRIYDIiNVLEslgLI~ 163 (191)
.+.++++.++..+.+..++.+.+|+.+ ++.++-++.-++.||..-++-
T Consensus 220 ~~~k~i~~~l~~~~g~~~s~~~la~~l~~is~~Ti~~Yl~~le~~fll~ 268 (398)
T COG1373 220 DLMKRILRFLASNIGSPISYSSLARELKGISKDTIRKYLSYLEDAFLLF 268 (398)
T ss_pred HHHHHHHHHHHhhcCCccCHHHHHHHHhccchHHHHHHHHHHHHhhheE
Confidence 677889999888888999999999999 799999999999999999985
No 164
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=21.78 E-value=43 Score=28.45 Aligned_cols=30 Identities=30% Similarity=0.490 Sum_probs=25.4
Q ss_pred ceecHHHHHHHhCCeeeEeeehhhHhhhhc
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVNVLESVG 160 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslg 160 (191)
-.|...++|+..||.||-+|+.+|-.++=.
T Consensus 40 IEI~~t~iAka~gVdRrvV~~Ti~~I~sd~ 69 (167)
T COG2150 40 IEIPITKIAKATGVDRRVVYATIELIESDE 69 (167)
T ss_pred EEechHHHHHHhCcchHhHHHHHHHHhcCH
Confidence 458999999999999999999998766533
No 165
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=21.70 E-value=57 Score=27.72 Aligned_cols=42 Identities=5% Similarity=0.048 Sum_probs=33.7
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhh
Q 045382 117 LCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLES 158 (191)
Q Consensus 117 Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEs 158 (191)
...+++.++..+....++++++|+.+++.+++|.-++.=--+
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G 225 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLG 225 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHC
Confidence 467788888888888999999999999988887766654433
No 166
>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=21.53 E-value=99 Score=24.15 Aligned_cols=43 Identities=16% Similarity=0.184 Sum_probs=36.6
Q ss_pred eecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecc
Q 045382 132 SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGF 175 (191)
Q Consensus 132 ~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~ 175 (191)
.++-.++|+.+|+.|.-+.-+++-|+.-|+|+... +.+...-.
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~-~~i~I~d~ 185 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHK-KKITVHDP 185 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecC-CEEEEeCH
Confidence 47889999999999999999999999999998874 45665433
No 167
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=21.37 E-value=98 Score=24.10 Aligned_cols=56 Identities=21% Similarity=0.356 Sum_probs=41.6
Q ss_pred HHHHHHHHhhCC--CceecHHHHHHHhCCeeeEeeehhhHhhhhccee------ecCCCceEEe
Q 045382 118 CSNFLSLYNRDG--VESIGLDDAASKLGVERRRIYDIVNVLESVGVLT------RRAKNKYTWK 173 (191)
Q Consensus 118 t~kFI~l~~~~~--~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~------K~~Kn~y~W~ 173 (191)
.+.|..++..-+ ...++|+++|+.|...+|-.==|++=|+..|.|+ |..+..+.|.
T Consensus 3 ~~~y~~L~~~~~~~~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L~~l 66 (115)
T PF12793_consen 3 LEQYQRLWQHYGGQPVEVTLDELAELLFCSRRNARTLLKKMQEEGWITWQPGRGRGNRSQLTFL 66 (115)
T ss_pred HHHHHHHHHHcCCCCcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeCCCCCCCCCeeEEe
Confidence 345555554433 4568999999999999999999999999999885 3344556663
No 168
>PHA02574 57B hypothetical protein; Provisional
Probab=21.09 E-value=71 Score=26.18 Aligned_cols=32 Identities=13% Similarity=-0.036 Sum_probs=24.1
Q ss_pred hhhhcceeecCCCceEEecccchHHHHHHHHHHhc
Q 045382 156 LESVGVLTRRAKNKYTWKGFKAIRGALQELKVLLR 190 (191)
Q Consensus 156 LEslgLI~K~~Kn~y~W~G~~~I~~tLekLk~Ei~ 190 (191)
|.++|+-... ++.+.|.|.+ +..|..|..+++
T Consensus 68 l~glG~F~~~-~~rvlWlg~~--~~~L~~L~~~l~ 99 (149)
T PHA02574 68 SGHLEVWETQ-DKNALVLVLE--SEYLQCRHKYAR 99 (149)
T ss_pred eccccccCCC-CCCEEEEEeC--CHHHHHHHHHHH
Confidence 5677777432 3679999997 788888888775
No 169
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=20.97 E-value=33 Score=22.68 Aligned_cols=27 Identities=22% Similarity=0.386 Sum_probs=21.7
Q ss_pred ecHHHHHHHhCCeeeEeeehhhHhhhh
Q 045382 133 IGLDDAASKLGVERRRIYDIVNVLESV 159 (191)
Q Consensus 133 i~L~~aA~~L~V~rRRIYDIiNVLEsl 159 (191)
++++++|+.+|+..+.|+.+++-..++
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~ 28 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGT 28 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCc
Confidence 678899999999988888888765443
No 170
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=20.96 E-value=1.2e+02 Score=24.28 Aligned_cols=52 Identities=21% Similarity=0.294 Sum_probs=43.5
Q ss_pred CCchHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceee
Q 045382 111 QKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTR 164 (191)
Q Consensus 111 eKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K 164 (191)
.+.|..+=.+.|..++.+ ..++..++|+++|+..--+..=++=|+.-|+|++
T Consensus 9 ~~~lD~~D~~IL~~Lq~d--~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 9 GKDLDRIDRNILNELQKD--GRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred hhhHHHHHHHHHHHhccC--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 345677778899988876 4588999999999988777778899999999975
No 171
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=20.89 E-value=77 Score=25.51 Aligned_cols=39 Identities=15% Similarity=0.263 Sum_probs=21.8
Q ss_pred HHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcce
Q 045382 124 LYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVL 162 (191)
Q Consensus 124 l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI 162 (191)
++...++..+++.++|+++++.+.-+.=|+.-|.--|+|
T Consensus 16 ~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv 54 (153)
T PRK11920 16 YCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLV 54 (153)
T ss_pred HHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 343444556788888888865444444444444444444
No 172
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=20.21 E-value=84 Score=27.23 Aligned_cols=48 Identities=13% Similarity=0.202 Sum_probs=36.2
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCC
Q 045382 119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKN 168 (191)
Q Consensus 119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn 168 (191)
++.++++.+. +.+++.++|+.|+|..-=|+==+..||.-|++.|..-+
T Consensus 8 ~~Il~~l~~~--~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~~GG 55 (252)
T PRK10906 8 DAIIELVKQQ--GYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRHHGG 55 (252)
T ss_pred HHHHHHHHHc--CCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 3456667665 46999999999999755554448899999999987444
No 173
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=20.17 E-value=39 Score=26.24 Aligned_cols=35 Identities=29% Similarity=0.620 Sum_probs=23.2
Q ss_pred ceecHHHHHHHhCCeeeEeeehhhH--------hhhhcceeec
Q 045382 131 ESIGLDDAASKLGVERRRIYDIVNV--------LESVGVLTRR 165 (191)
Q Consensus 131 ~~i~L~~aA~~L~V~rRRIYDIiNV--------LEslgLI~K~ 165 (191)
.-+++.++|+.+||.|=-+||.++- =+.+|+++|.
T Consensus 32 eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL~l~~k~ 74 (101)
T PF04297_consen 32 EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKLGLVEKF 74 (101)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH-HHHHH
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhhHHHH
Confidence 4599999999999999999998754 2345666554
Done!