Query 018790
Match_columns 350
No_of_seqs 169 out of 388
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 04:03:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018790.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018790hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2578 Transcription factor E 100.0 2E-72 4.4E-77 538.3 13.7 338 5-346 2-387 (388)
2 KOG2577 Transcription factor E 99.9 1.1E-22 2.3E-27 199.8 7.7 76 19-94 63-138 (354)
3 PF02319 E2F_TDP: E2F/DP famil 99.9 1.8E-22 3.9E-27 157.6 4.8 66 24-89 1-71 (71)
4 KOG2578 Transcription factor E 99.1 4E-11 8.6E-16 116.9 3.4 77 19-95 151-243 (388)
5 PF02319 E2F_TDP: E2F/DP famil 98.7 6.7E-09 1.5E-13 81.3 1.8 55 147-202 1-71 (71)
6 KOG2829 E2F-like protein [Tran 97.6 3.9E-05 8.4E-10 75.1 2.7 72 29-103 46-140 (326)
7 KOG2577 Transcription factor E 96.2 0.0065 1.4E-07 61.2 5.0 59 145-205 66-136 (354)
8 PF01978 TrmB: Sugar-specific 94.5 0.019 4.1E-07 43.6 1.5 43 46-88 21-63 (68)
9 cd00092 HTH_CRP helix_turn_hel 92.0 0.23 4.9E-06 36.5 3.8 54 32-85 5-63 (67)
10 PF08279 HTH_11: HTH domain; 90.8 0.29 6.4E-06 35.3 3.3 41 34-75 3-43 (55)
11 smart00346 HTH_ICLR helix_turn 90.8 0.35 7.5E-06 37.8 3.9 56 34-90 8-63 (91)
12 smart00420 HTH_DEOR helix_turn 90.1 0.31 6.8E-06 33.8 2.9 46 35-82 4-49 (53)
13 PF09339 HTH_IclR: IclR helix- 89.5 0.29 6.4E-06 35.5 2.4 46 34-80 6-51 (52)
14 smart00550 Zalpha Z-DNA-bindin 89.0 0.53 1.1E-05 36.4 3.6 55 33-87 8-62 (68)
15 PF13412 HTH_24: Winged helix- 86.4 0.79 1.7E-05 32.4 2.9 43 34-78 6-48 (48)
16 smart00418 HTH_ARSR helix_turn 84.0 0.93 2E-05 31.9 2.4 37 46-82 9-45 (66)
17 PF12802 MarR_2: MarR family; 84.0 1.1 2.4E-05 32.6 2.9 46 35-80 9-54 (62)
18 cd00090 HTH_ARSR Arsenical Res 83.4 2.7 5.8E-05 30.2 4.7 48 33-83 9-56 (78)
19 PF02082 Rrf2: Transcriptional 83.2 1.5 3.3E-05 34.6 3.6 50 31-80 8-58 (83)
20 PF13730 HTH_36: Helix-turn-he 83.2 1.4 3E-05 31.8 3.0 30 48-77 26-55 (55)
21 TIGR02944 suf_reg_Xantho FeS a 82.0 1.3 2.9E-05 37.4 3.0 48 33-80 11-58 (130)
22 PF00392 GntR: Bacterial regul 81.3 2.9 6.3E-05 31.3 4.3 50 34-83 7-60 (64)
23 smart00419 HTH_CRP helix_turn_ 79.9 1.2 2.7E-05 30.5 1.7 38 47-85 8-45 (48)
24 smart00345 HTH_GNTR helix_turn 78.4 2.4 5.2E-05 30.0 2.9 40 44-83 16-56 (60)
25 PF09079 Cdc6_C: CDC6, C termi 75.5 0.89 1.9E-05 35.9 -0.0 28 53-80 28-58 (85)
26 PF01047 MarR: MarR family; I 75.2 2.2 4.8E-05 30.9 2.0 43 36-80 8-50 (59)
27 TIGR00122 birA_repr_reg BirA b 74.6 4.1 8.9E-05 30.9 3.4 53 35-90 4-57 (69)
28 cd08768 Cdc6_C Winged-helix do 73.9 3 6.6E-05 32.5 2.7 22 59-80 44-65 (87)
29 PRK10163 DNA-binding transcrip 73.0 9.5 0.0002 36.4 6.3 56 34-90 28-83 (271)
30 COG1378 Predicted transcriptio 72.4 5.6 0.00012 38.2 4.5 54 47-101 30-83 (247)
31 PF01726 LexA_DNA_bind: LexA D 72.2 2.5 5.4E-05 32.8 1.7 46 36-81 14-60 (65)
32 TIGR00738 rrf2_super rrf2 fami 68.6 7.8 0.00017 32.4 4.2 36 45-80 23-58 (132)
33 PF04182 B-block_TFIIIC: B-blo 67.7 5.6 0.00012 31.2 2.9 49 34-82 5-53 (75)
34 PF09012 FeoC: FeoC like trans 67.6 4.3 9.2E-05 31.1 2.2 47 36-84 5-51 (69)
35 COG2894 MinD Septum formation 66.5 2.5 5.4E-05 41.3 0.8 30 46-75 39-68 (272)
36 cd07377 WHTH_GntR Winged helix 65.8 8.7 0.00019 27.6 3.4 34 48-81 26-59 (66)
37 PF09756 DDRGK: DDRGK domain; 64.4 9.3 0.0002 35.7 4.1 71 32-104 100-172 (188)
38 PF13518 HTH_28: Helix-turn-he 64.3 8.7 0.00019 26.9 3.1 38 35-76 4-41 (52)
39 PRK09834 DNA-binding transcrip 63.4 7.8 0.00017 36.7 3.5 52 35-87 15-67 (263)
40 PF08220 HTH_DeoR: DeoR-like h 60.8 9.5 0.00021 28.4 2.9 46 34-81 3-48 (57)
41 PF13463 HTH_27: Winged helix 60.5 8.9 0.00019 28.2 2.7 38 43-80 14-51 (68)
42 COG3355 Predicted transcriptio 60.3 8.5 0.00018 34.0 2.9 43 36-80 33-75 (126)
43 PF03376 Adeno_E3B: Adenovirus 59.4 4.7 0.0001 32.0 1.0 15 315-329 51-65 (67)
44 TIGR01764 excise DNA binding d 59.2 4.6 9.9E-05 27.5 0.9 22 48-69 2-23 (49)
45 TIGR02716 C20_methyl_CrtF C-20 58.4 5 0.00011 38.5 1.3 39 46-85 22-60 (306)
46 smart00347 HTH_MARR helix_turn 57.3 14 0.00031 28.3 3.5 45 34-80 13-57 (101)
47 PRK11511 DNA-binding transcrip 57.1 14 0.0003 31.5 3.6 46 28-73 6-51 (127)
48 PF04218 CENP-B_N: CENP-B N-te 56.9 19 0.00042 26.6 3.9 42 24-69 2-44 (53)
49 PF08784 RPA_C: Replication pr 56.0 12 0.00026 30.5 2.9 50 28-77 44-95 (102)
50 PF05732 RepL: Firmicute plasm 55.7 13 0.00029 33.6 3.5 48 45-92 73-126 (165)
51 PRK00215 LexA repressor; Valid 55.3 11 0.00024 34.2 2.9 48 36-83 12-60 (205)
52 smart00344 HTH_ASNC helix_turn 55.0 11 0.00024 30.4 2.6 45 33-79 5-49 (108)
53 PRK10219 DNA-binding transcrip 54.6 13 0.00028 30.1 2.9 41 31-71 5-45 (107)
54 PF01022 HTH_5: Bacterial regu 54.5 12 0.00026 26.5 2.5 41 36-79 7-47 (47)
55 TIGR02366 DHAK_reg probable di 54.0 12 0.00025 32.4 2.8 36 30-65 6-41 (176)
56 TIGR02431 pcaR_pcaU beta-ketoa 53.7 15 0.00032 34.4 3.5 50 35-86 13-62 (248)
57 TIGR01610 phage_O_Nterm phage 52.9 16 0.00036 29.7 3.3 37 45-81 45-81 (95)
58 PRK15090 DNA-binding transcrip 52.8 17 0.00037 34.2 3.8 55 34-90 17-71 (257)
59 PF13545 HTH_Crp_2: Crp-like h 52.8 9.3 0.0002 28.8 1.7 51 32-82 3-63 (76)
60 TIGR02010 IscR iron-sulfur clu 52.7 18 0.00039 31.1 3.6 43 45-87 23-67 (135)
61 TIGR02337 HpaR homoprotocatech 52.5 16 0.00034 30.2 3.2 44 36-81 33-76 (118)
62 PRK09954 putative kinase; Prov 51.3 13 0.00028 36.5 2.8 46 33-80 5-50 (362)
63 PF12840 HTH_20: Helix-turn-he 51.2 7.2 0.00016 28.9 0.8 46 34-81 13-58 (61)
64 TIGR00498 lexA SOS regulatory 51.1 15 0.00032 33.2 3.0 46 36-81 14-60 (199)
65 KOG2747 Histone acetyltransfer 50.7 30 0.00065 35.9 5.4 58 28-90 304-367 (396)
66 PRK10857 DNA-binding transcrip 49.6 23 0.0005 32.0 4.0 36 45-80 23-58 (164)
67 PRK09464 pdhR transcriptional 48.9 29 0.00063 32.3 4.7 60 27-86 9-74 (254)
68 PRK11414 colanic acid/biofilm 48.6 57 0.0012 29.7 6.5 61 27-87 10-74 (221)
69 PF08280 HTH_Mga: M protein tr 47.9 12 0.00025 28.0 1.5 36 35-72 9-44 (59)
70 TIGR03338 phnR_burk phosphonat 47.1 41 0.00089 30.2 5.2 57 27-83 10-70 (212)
71 COG1414 IclR Transcriptional r 47.0 22 0.00047 33.8 3.6 56 34-90 7-62 (246)
72 PHA02943 hypothetical protein; 47.0 17 0.00037 33.4 2.7 50 34-86 14-63 (165)
73 TIGR02297 HpaA 4-hydroxyphenyl 46.9 18 0.00038 33.8 2.9 45 31-75 186-230 (287)
74 PF02796 HTH_7: Helix-turn-hel 46.5 16 0.00034 25.9 1.9 33 33-69 11-43 (45)
75 TIGR01889 Staph_reg_Sar staphy 45.4 21 0.00046 29.4 2.9 49 42-90 38-89 (109)
76 COG2739 Uncharacterized protei 45.2 13 0.00028 32.0 1.6 39 31-69 17-55 (105)
77 COG1510 Predicted transcriptio 45.0 18 0.0004 33.7 2.6 35 46-80 40-74 (177)
78 COG1474 CDC6 Cdc6-related prot 43.8 13 0.00028 37.7 1.6 29 50-78 304-332 (366)
79 PF07354 Sp38: Zona-pellucida- 43.7 13 0.00029 36.7 1.6 16 196-211 13-28 (271)
80 PRK11014 transcriptional repre 41.8 23 0.0005 30.5 2.7 39 43-81 21-59 (141)
81 PRK11534 DNA-binding transcrip 41.7 23 0.00051 32.2 2.8 48 43-90 26-73 (224)
82 PRK11050 manganese transport r 41.2 39 0.00085 29.8 4.1 42 46-87 50-91 (152)
83 PF01853 MOZ_SAS: MOZ/SAS fami 40.8 35 0.00075 32.1 3.8 56 27-85 123-185 (188)
84 PRK11569 transcriptional repre 40.4 33 0.00072 32.7 3.8 55 34-89 31-85 (274)
85 PRK10411 DNA-binding transcrip 39.9 33 0.00071 32.5 3.6 55 34-90 7-61 (240)
86 PRK03837 transcriptional regul 39.3 58 0.0013 29.8 5.1 54 28-81 13-71 (241)
87 PF13551 HTH_29: Winged helix- 39.0 30 0.00064 27.5 2.7 27 49-75 14-40 (112)
88 PRK04984 fatty acid metabolism 38.8 42 0.00091 30.8 4.1 44 43-86 26-71 (239)
89 PRK14165 winged helix-turn-hel 38.5 35 0.00075 32.5 3.5 48 34-81 7-55 (217)
90 TIGR01884 cas_HTH CRISPR locus 38.1 34 0.00073 31.3 3.3 45 35-81 147-191 (203)
91 PRK13503 transcriptional activ 37.9 27 0.00059 32.3 2.7 39 31-69 171-209 (278)
92 PRK10130 transcriptional regul 37.6 29 0.00063 34.8 3.0 41 30-70 239-279 (350)
93 PRK10225 DNA-binding transcrip 37.6 61 0.0013 30.2 5.0 56 31-86 13-73 (257)
94 PF01325 Fe_dep_repress: Iron 37.2 38 0.00083 25.6 2.9 38 44-81 19-56 (60)
95 COG2186 FadR Transcriptional r 37.0 32 0.0007 32.5 3.1 55 32-86 15-74 (241)
96 PRK13509 transcriptional repre 36.3 32 0.0007 32.7 3.0 49 34-84 8-56 (251)
97 PF03444 HrcA_DNA-bdg: Winged 35.9 55 0.0012 26.8 3.8 48 32-80 9-56 (78)
98 PF03374 ANT: Phage antirepres 35.0 30 0.00065 28.4 2.2 41 36-80 14-54 (111)
99 PRK10421 DNA-binding transcrip 34.6 28 0.0006 32.5 2.2 43 43-85 21-65 (253)
100 COG1802 GntR Transcriptional r 34.5 34 0.00074 31.4 2.7 44 43-86 35-78 (230)
101 PRK03573 transcriptional regul 34.4 44 0.00095 28.4 3.2 34 47-80 46-79 (144)
102 cd07153 Fur_like Ferric uptake 34.1 41 0.00089 27.4 2.9 45 36-81 6-55 (116)
103 PLN03239 histone acetyltransfe 33.8 1.1E+02 0.0024 31.5 6.4 59 21-82 250-316 (351)
104 PRK15121 right oriC-binding tr 33.8 43 0.00094 31.9 3.4 45 31-75 5-49 (289)
105 COG1522 Lrp Transcriptional re 33.7 42 0.0009 28.5 3.0 50 29-80 6-55 (154)
106 PRK09975 DNA-binding transcrip 33.2 37 0.0008 30.1 2.7 39 28-66 12-50 (213)
107 PF05930 Phage_AlpA: Prophage 33.2 24 0.00051 25.6 1.2 24 46-69 2-25 (51)
108 PRK09685 DNA-binding transcrip 32.8 34 0.00074 32.2 2.5 38 32-69 198-236 (302)
109 PF04703 FaeA: FaeA-like prote 32.3 44 0.00095 25.9 2.6 43 36-79 5-47 (62)
110 COG1846 MarR Transcriptional r 32.2 40 0.00086 26.5 2.4 44 36-81 27-70 (126)
111 PRK09990 DNA-binding transcrip 32.0 83 0.0018 29.1 4.9 59 27-85 6-70 (251)
112 PRK11523 DNA-binding transcrip 31.8 80 0.0017 29.4 4.8 55 32-86 13-72 (253)
113 PF09904 HTH_43: Winged helix- 31.5 27 0.00059 29.3 1.4 29 49-77 23-51 (90)
114 TIGR02702 SufR_cyano iron-sulf 31.2 62 0.0013 29.6 3.8 45 34-80 4-48 (203)
115 PF02295 z-alpha: Adenosine de 31.2 76 0.0017 24.7 3.8 57 32-88 5-61 (66)
116 COG4519 Uncharacterized protei 31.1 44 0.00095 28.0 2.5 41 36-77 12-52 (95)
117 smart00529 HTH_DTXR Helix-turn 31.1 36 0.00078 26.7 2.0 33 50-82 2-34 (96)
118 PLN03238 probable histone acet 30.8 1.3E+02 0.0029 30.1 6.3 62 20-85 191-258 (290)
119 PF14947 HTH_45: Winged helix- 30.7 48 0.001 26.0 2.6 53 31-87 6-58 (77)
120 PF12728 HTH_17: Helix-turn-he 30.5 24 0.00052 24.9 0.8 22 48-69 2-23 (51)
121 PF13384 HTH_23: Homeodomain-l 30.0 22 0.00048 24.9 0.5 28 48-75 18-45 (50)
122 COG4189 Predicted transcriptio 29.7 54 0.0012 32.5 3.2 50 28-79 19-69 (308)
123 PRK09391 fixK transcriptional 29.4 59 0.0013 29.9 3.4 39 48-86 180-218 (230)
124 PF01710 HTH_Tnp_IS630: Transp 29.3 55 0.0012 27.6 3.0 44 34-82 60-103 (119)
125 PRK10572 DNA-binding transcrip 28.3 48 0.001 31.1 2.7 42 32-73 184-225 (290)
126 PRK10870 transcriptional repre 28.3 49 0.0011 29.8 2.6 38 43-80 67-104 (176)
127 cd04762 HTH_MerR-trunc Helix-T 27.9 29 0.00063 23.1 0.8 23 48-70 1-23 (49)
128 COG3093 VapI Plasmid maintenan 27.8 25 0.00054 30.2 0.6 41 24-70 5-46 (104)
129 PRK04214 rbn ribonuclease BN/u 27.8 62 0.0013 33.0 3.5 58 44-102 307-364 (412)
130 PF00440 TetR_N: Bacterial reg 27.7 32 0.0007 24.2 1.1 31 36-66 5-35 (47)
131 smart00342 HTH_ARAC helix_turn 27.6 33 0.00072 25.1 1.2 28 48-75 2-29 (84)
132 TIGR02928 orc1/cdc6 family rep 26.9 18 0.00039 35.0 -0.5 32 52-83 319-353 (365)
133 PF12793 SgrR_N: Sugar transpo 26.9 73 0.0016 27.3 3.3 46 33-78 3-50 (115)
134 PF04297 UPF0122: Putative hel 26.7 33 0.00071 29.2 1.1 32 36-70 25-56 (101)
135 PRK11512 DNA-binding transcrip 25.9 38 0.00083 29.0 1.4 35 46-80 53-87 (144)
136 PF14394 DUF4423: Domain of un 25.3 71 0.0015 29.0 3.1 58 45-102 37-102 (171)
137 PRK09393 ftrA transcriptional 25.1 69 0.0015 30.9 3.2 43 31-73 218-260 (322)
138 PRK10371 DNA-binding transcrip 24.9 66 0.0014 31.1 3.0 40 32-71 192-231 (302)
139 PRK09802 DNA-binding transcrip 24.8 72 0.0016 30.7 3.2 52 32-85 18-69 (269)
140 TIGR02812 fadR_gamma fatty aci 24.2 1.1E+02 0.0023 28.1 4.1 44 43-86 25-70 (235)
141 PRK00080 ruvB Holliday junctio 24.0 91 0.002 30.3 3.8 56 28-83 256-313 (328)
142 KOG3054 Uncharacterized conser 24.0 1.5E+02 0.0033 29.4 5.2 72 31-104 200-273 (299)
143 PF02954 HTH_8: Bacterial regu 23.6 31 0.00068 24.0 0.4 35 30-67 3-38 (42)
144 PLN00104 MYST -like histone ac 23.4 2E+02 0.0042 30.6 6.2 65 21-89 343-413 (450)
145 smart00351 PAX Paired Box doma 23.3 75 0.0016 27.2 2.7 45 32-80 22-66 (125)
146 PRK03902 manganese transport t 23.1 1.2E+02 0.0026 26.0 4.0 46 34-81 11-56 (142)
147 PRK11886 bifunctional biotin-- 22.9 89 0.0019 30.5 3.5 52 34-87 7-59 (319)
148 PF08222 HTH_CodY: CodY helix- 22.7 36 0.00078 26.7 0.5 42 47-88 4-48 (61)
149 PF06830 Root_cap: Root cap; 22.4 31 0.00067 26.8 0.2 13 312-324 15-27 (57)
150 PRK11753 DNA-binding transcrip 22.4 88 0.0019 27.6 3.1 36 47-82 168-203 (211)
151 COG2150 Predicted regulator of 22.4 52 0.0011 30.5 1.6 35 46-80 40-74 (167)
152 PRK15185 transcriptional regul 22.4 81 0.0017 31.7 3.1 39 31-69 206-244 (309)
153 PTZ00064 histone acetyltransfe 22.2 67 0.0015 34.7 2.6 48 48-98 472-519 (552)
154 PRK13502 transcriptional activ 22.1 73 0.0016 29.7 2.6 40 31-70 176-215 (282)
155 PRK09978 DNA-binding transcrip 22.1 72 0.0016 31.4 2.6 39 31-69 142-180 (274)
156 cd00569 HTH_Hin_like Helix-tur 22.0 1.2E+02 0.0027 17.6 2.9 30 34-67 12-41 (42)
157 PF13542 HTH_Tnp_ISL3: Helix-t 22.0 63 0.0014 22.7 1.7 37 33-69 13-49 (52)
158 PRK09333 30S ribosomal protein 21.1 85 0.0018 28.6 2.7 35 47-81 67-115 (150)
159 cd04770 HTH_HMRTR Helix-Turn-H 20.9 59 0.0013 27.2 1.6 54 48-105 1-58 (123)
160 PRK10402 DNA-binding transcrip 20.5 1E+02 0.0022 28.1 3.2 36 47-82 169-204 (226)
161 PF09862 DUF2089: Protein of u 20.0 96 0.0021 27.0 2.7 37 34-73 39-79 (113)
No 1
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=100.00 E-value=2e-72 Score=538.33 Aligned_cols=338 Identities=41% Similarity=0.638 Sum_probs=272.3
Q ss_pred CCCcccCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCc
Q 018790 5 SSSAFGFREAEPDGKQFYSRKEKSLGLLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNL 84 (350)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~sRkeKSLg~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~ 84 (350)
++++.++.++.....+.|+||+||||.||++||.+|.......+.|+++|.+|||+||||||||||||+||++.|.+||+
T Consensus 2 ~~av~~s~d~~~l~lqvysrkekslgvlv~nfl~lynr~dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~Knq 81 (388)
T KOG2578|consen 2 GGAVNTSADEADLDLQVYSRKEKSLGVLVQNFLILYNRSDVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQ 81 (388)
T ss_pred CCceecccchhhccchhhccccchhhHHHHHHHHHhcCCCcceechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCc
Confidence 35667788888888999999999999999999999998888999999999999999999999999999999999999999
Q ss_pred eEEecCCChHHHHHHHHHhchhccccc----cCCCCCCCCCCCCcCCCCCCcCCCCC---------CCCCccccccccch
Q 018790 85 YSWQGFDAIPEALEVLKEEGLRENFNI----NGCTNSGNVLNDNENEGSTCTVTDGQ---------DSSSSKIESKREKS 151 (350)
Q Consensus 85 y~W~G~~nI~~tL~~Lkeeg~~e~~~~----~~~~k~~d~~dd~e~~~sP~~~s~sd---------~~~p~~~d~rkeKS 151 (350)
|.|.||+.||.+|.+|++||+++.+.. .+...+++ +++.|..+.|.+.+..+ .+.+.+.|+|++||
T Consensus 82 YsWkGf~aiPral~eLqeEgvke~l~~~~~~~~~~m~s~-e~~~ee~~~s~tstptd~s~~g~l~e~S~~~k~DnrkekS 160 (388)
T KOG2578|consen 82 YSWKGFGAIPRALFELQEEGVKEGLPERVLRVNSAMVSF-EEESEERGVSCTSTPTDQSTDGLLEERSRSSKRDNRKEKS 160 (388)
T ss_pred ccccchhhhhHHHHHHHHHHHhhcccceeeecccccccc-cccccccCCccccCCCCCCCCCcchhcCCCCcccchhhhH
Confidence 999999999999999999999998763 23333333 22333323333322222 23346788999999
Q ss_pred HHHHHHHHHHHHhcCCCc-eecHHHHHHHHcCCCCCCccccc-------------------------CCCCceeeccCCC
Q 018790 152 LWLLTQNFVKLFLCSDVD-MITLDSAAMALLGDSNNSTAMRK-------------------------SRKPAFRWLGWKG 205 (350)
Q Consensus 152 L~~LSQkFVmLFL~s~~~-~ISLdeAAkiL~gd~~~~~~~r~-------------------------~rKPaF~WlG~~~ 205 (350)
|++|||+|||||||++.. .||||.||+.|++|++++..||+ +|||||+|+|+++
T Consensus 161 L~lL~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~trkPafrwlG~~~ 240 (388)
T KOG2578|consen 161 LWLLAQNFVKLFLCSDDDILVSLDSAAKALLKDSEDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTRKPAFRWLGSKP 240 (388)
T ss_pred HHHHHHHHHHheeccccceEEeecHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhheeCCCc
Confidence 999999999999999876 99999999999999999988887 9999999999999
Q ss_pred CCCCC----CCCccCCCCcccccCCccccchhhcccccccccc-ccCCCCCCCCcccccCCCCCCcchhh-hhhhccCCC
Q 018790 206 NPCNR----SAGFLDLNEPKKRVFGTDITNLRLKKNKVDSLTE-KKSNPKLNVPKYFKHCNEESNPDESR-LEQHSKHKS 279 (350)
Q Consensus 206 ~~~~~----~~~~~~~~~~~k~~f~~~~t~~~~kr~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 279 (350)
.++.. +.+.+..+++|+|+|||+||||++||+|..|+.. +--.....+. +|......++... +.-..++..
T Consensus 241 ~~t~sf~~gs~sL~~~n~~K~rafgteItnvnakr~kSs~s~~en~~~~~~~~~---k~~~e~~~ye~~~~l~~~~~p~~ 317 (388)
T KOG2578|consen 241 IQTGSFFQGSRSLSEQNLPKPRAFGTEITNVNAKRNKSSCSSMENFMFAEVVTK---KHAAEKMRYEAFAQLSSRLKPLP 317 (388)
T ss_pred cccccccccchhHhhcCCCCcccCCccccchhhhhccCcchhhhhHHHHHhhhh---hccchhhhhhhhhhhhhccCCcc
Confidence 99984 8889999999999999999999999999966544 3222222333 4433322222111 123367788
Q ss_pred CCcccccCCC-CccccccCCCC--CCcccccchhhhhhhcCCcccchHHHHHHHHHHHHHHHHHHHhhcc
Q 018790 280 KGFVYGPFTP-ASISGIHDSRS--KNTKQVLDFASLASTFRPKYHNEAVNGLFGHYVEAWKSWYAEVGDK 346 (350)
Q Consensus 280 ~~~~~gpf~p-~~~~~~~~~~~--~~~~~~~d~e~la~~~~pqy~n~~l~~lf~hy~eawkswy~e~~~~ 346 (350)
++|+||||+| ++.+....-.+ ...++..++|+|++.|+|+|||.++..+|.||.+++.+-..+.++.
T Consensus 318 ~~~~~gp~~P~igt~~t~~~~~~~~~srr~f~ie~l~sdyqPsy~n~e~~~~~~~~~~~f~v~k~~~~r~ 387 (388)
T KOG2578|consen 318 MAYLFGPFLPEIGTSQTNKQFNFPATSRRLFNIEALTSDYQPSYCNSESKKFKQGTNSTFQVVKKGETRP 387 (388)
T ss_pred cccccCCCCCCCCCcchhhccCCCCCccccccchhcccccCccccChhhhhhhcccceeeeeeccccCCC
Confidence 8999999999 55544443223 4566899999999999999999999999999999998877766653
No 2
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=99.87 E-value=1.1e-22 Score=199.81 Aligned_cols=76 Identities=38% Similarity=0.622 Sum_probs=72.6
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecCCChH
Q 018790 19 KQFYSRKEKSLGLLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGFDAIP 94 (350)
Q Consensus 19 ~~~~sRkeKSLg~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~~nI~ 94 (350)
+....|.++|||+||+|||.+++.+|+++++|+.||+.|+|+|||||||+|||||||||+|+.||.++|+|.+...
T Consensus 63 ~~~~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L~VqKRRIYDITNVLEGI~LIeKksKN~IqW~G~~~~~ 138 (354)
T KOG2577|consen 63 PSESTRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVLNVQKRRIYDITNVLEGIGLIEKKSKNNIQWIGGDFNS 138 (354)
T ss_pred CCCcccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHhccccceeeehhhhhhcccceeeccccceeeecCCCcc
Confidence 5577999999999999999999999999999999999999999999999999999999999999999999987664
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=99.86 E-value=1.8e-22 Score=157.63 Aligned_cols=66 Identities=47% Similarity=0.919 Sum_probs=62.8
Q ss_pred CCCCcHHHHHHHHHHHHhhCCCceecHHHHHHHh---CC--ceeeehhhHHHHhhhhhhhhcCCCceEEec
Q 018790 24 RKEKSLGLLCSKFLKLYNRDGVESIGLDDAASRL---GV--ERRRIYDVVNILESIGVVARQAKNLYSWQG 89 (350)
Q Consensus 24 RkeKSLg~L~~kFl~l~~~~~~~~I~L~~aA~~L---gV--~RRRIYDIvNVLEslGli~K~~KN~y~W~G 89 (350)
|+++||+.||++||++|...+...++|+++|++| ++ +|||||||+||||++|+|+|..|+.|.|+|
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=99.10 E-value=4e-11 Score=116.85 Aligned_cols=77 Identities=35% Similarity=0.567 Sum_probs=67.3
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHhhCCCc-eecHHHHHHHhC----------CceeeehhhHHHHhhhhhhhhc-----CC
Q 018790 19 KQFYSRKEKSLGLLCSKFLKLYNRDGVE-SIGLDDAASRLG----------VERRRIYDVVNILESIGVVARQ-----AK 82 (350)
Q Consensus 19 ~~~~sRkeKSLg~L~~kFl~l~~~~~~~-~I~L~~aA~~Lg----------V~RRRIYDIvNVLEslGli~K~-----~K 82 (350)
.+...|+++||++||++||.++-+.+.. .|+||.||..|= .+-||+|||.|||-+++||+|. .|
T Consensus 151 ~k~DnrkekSL~lL~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~trk 230 (388)
T KOG2578|consen 151 SKRDNRKEKSLWLLAQNFVKLFLCSDDDILVSLDSAAKALLKDSEDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTRK 230 (388)
T ss_pred CcccchhhhHHHHHHHHHHHheeccccceEEeecHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHhhhhhhhccccccc
Confidence 4667899999999999999999888776 899999998773 3579999999999999999996 68
Q ss_pred CceEEecCCChHH
Q 018790 83 NLYSWQGFDAIPE 95 (350)
Q Consensus 83 N~y~W~G~~nI~~ 95 (350)
..|.|.|-..+..
T Consensus 231 PafrwlG~~~~~t 243 (388)
T KOG2578|consen 231 PAFRWLGSKPIQT 243 (388)
T ss_pred chhheeCCCcccc
Confidence 8999999876654
No 5
>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=98.68 E-value=6.7e-09 Score=81.25 Aligned_cols=55 Identities=38% Similarity=0.657 Sum_probs=45.0
Q ss_pred cccchHHHHHHHHHHHHhcCCCceecHHHHHHHHcCCCCCCccccc----------------CCCCceeecc
Q 018790 147 KREKSLWLLTQNFVKLFLCSDVDMITLDSAAMALLGDSNNSTAMRK----------------SRKPAFRWLG 202 (350)
Q Consensus 147 rkeKSL~~LSQkFVmLFL~s~~~~ISLdeAAkiL~gd~~~~~~~r~----------------~rKPaF~WlG 202 (350)
|+++||+.||++||++|...+...++|++||+.|+.++.. +..|| .+||.|+|+|
T Consensus 1 r~~~sL~~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~~~k-~~~RRlYDI~NVLealgli~K~~k~~~~W~G 71 (71)
T PF02319_consen 1 RKEKSLKLLTQRFIQLFESSPDKSISLNEIADKLISENVK-TQRRRLYDIINVLEALGLIEKQSKNSYKWIG 71 (71)
T ss_dssp TTTTHHHHHHHHHHHHHHHCCCTEEEHHHHHHHCHHHCCH-HHCHHHHHHHHHHHHCTSEEEEETTEEEE--
T ss_pred CCcCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHcccccc-cccchhhHHHHHHHHhCceeecCCCceEecC
Confidence 5789999999999999999988999999999999877332 23333 6899999998
No 6
>KOG2829 consensus E2F-like protein [Transcription]
Probab=97.57 E-value=3.9e-05 Score=75.06 Aligned_cols=72 Identities=26% Similarity=0.466 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHhhCCCceecHHHHHHHhC----------------------CceeeehhhHHHHhhhhhhhhcCCCceE
Q 018790 29 LGLLCSKFLKLYNRDGVESIGLDDAASRLG----------------------VERRRIYDVVNILESIGVVARQAKNLYS 86 (350)
Q Consensus 29 Lg~L~~kFl~l~~~~~~~~I~L~~aA~~Lg----------------------V~RRRIYDIvNVLEslGli~K~~KN~y~ 86 (350)
|...+.+.-+-.+.. +..+-+++|..|- --|||+||.+|||-++.+|.|..| -+.
T Consensus 46 LRhfs~kVCeKve~K--g~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKdKK-EIr 122 (326)
T KOG2829|consen 46 LRHFSMKVCEKVERK--GTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKDKK-EIR 122 (326)
T ss_pred hhhhhHHHHHHHHhc--CCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcccc-eee
Confidence 555555555544443 4456666666541 249999999999999999999955 599
Q ss_pred EecCCC-hHHHHHHHHHh
Q 018790 87 WQGFDA-IPEALEVLKEE 103 (350)
Q Consensus 87 W~G~~n-I~~tL~~Lkee 103 (350)
|+|+.. -.+.+++|+++
T Consensus 123 W~GLP~~ss~dv~~le~E 140 (326)
T KOG2829|consen 123 WIGLPATSSQDVSELEEE 140 (326)
T ss_pred eeccCccchHHHHHHHHH
Confidence 999873 34456666644
No 7
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=96.20 E-value=0.0065 Score=61.16 Aligned_cols=59 Identities=29% Similarity=0.398 Sum_probs=47.4
Q ss_pred cccccchHHHHHHHHHHHHhcCCCceecHHHHHHHHcCCCCCCcc------------cccCCCCceeeccCCC
Q 018790 145 ESKREKSLWLLTQNFVKLFLCSDVDMITLDSAAMALLGDSNNSTA------------MRKSRKPAFRWLGWKG 205 (350)
Q Consensus 145 d~rkeKSL~~LSQkFVmLFL~s~~~~ISLdeAAkiL~gd~~~~~~------------~r~~rKPaF~WlG~~~ 205 (350)
.+|-++||++||++||.|.=.++..+|+|-.||+.|--- .-++ ..+.-|.-.+|+|..-
T Consensus 66 ~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L~Vq--KRRIYDITNVLEGI~LIeKksKN~IqW~G~~~ 136 (354)
T KOG2577|consen 66 STRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVLNVQ--KRRIYDITNVLEGIGLIEKKSKNNIQWIGGDF 136 (354)
T ss_pred cccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHhccc--cceeeehhhhhhcccceeeccccceeeecCCC
Confidence 368899999999999999999999999999999999432 1010 1227789999999863
No 8
>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=94.51 E-value=0.019 Score=43.56 Aligned_cols=43 Identities=23% Similarity=0.444 Sum_probs=38.5
Q ss_pred ceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEe
Q 018790 46 ESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQ 88 (350)
Q Consensus 46 ~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~ 88 (350)
+..+..++|+.+|+.|..+|++++-|+..|+|.+...+.+.|.
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 4689999999999999999999999999999999876666653
No 9
>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=92.03 E-value=0.23 Score=36.54 Aligned_cols=54 Identities=26% Similarity=0.363 Sum_probs=42.4
Q ss_pred HHHHHHHHHhhC-----CCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCce
Q 018790 32 LCSKFLKLYNRD-----GVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLY 85 (350)
Q Consensus 32 L~~kFl~l~~~~-----~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y 85 (350)
++.-|+.++... ....++..++|+.+|+.+.-++.+++.|+.-|+|.+...+.|
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 444555555443 235689999999999999999999999999999998764444
No 10
>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=90.83 E-value=0.29 Score=35.33 Aligned_cols=41 Identities=32% Similarity=0.391 Sum_probs=34.1
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhh
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIG 75 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslG 75 (350)
.+.+.++....+. ++..++|+.|+|.+|-|+--++.|+..|
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 11
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=90.79 E-value=0.35 Score=37.79 Aligned_cols=56 Identities=21% Similarity=0.322 Sum_probs=43.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecC
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGF 90 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~ 90 (350)
...++++...+ ..+++.++|+.+|+.+.-+|-+++.|+..|++.+...+.....|.
T Consensus 8 ~~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~ 63 (91)
T smart00346 8 LAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLGP 63 (91)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCCceeecH
Confidence 44566666553 369999999999999999999999999999999874443333443
No 12
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=90.15 E-value=0.31 Score=33.75 Aligned_cols=46 Identities=26% Similarity=0.408 Sum_probs=38.2
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCC
Q 018790 35 KFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAK 82 (350)
Q Consensus 35 kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~K 82 (350)
.++.++... ..+++.++|..|++.++-+|..+.-|+..|+|.+...
T Consensus 4 ~il~~l~~~--~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 4 QILELLAQQ--GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 355555554 3489999999999999999999999999999987643
No 13
>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=89.48 E-value=0.29 Score=35.46 Aligned_cols=46 Identities=22% Similarity=0.373 Sum_probs=37.5
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
-..|+++...+.. +++.++|+++|+.|=-+|-+++.|+..|++.+.
T Consensus 6 l~iL~~l~~~~~~-~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 6 LRILEALAESGGP-LTLSEIARALGLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHHCHHCTBSC-EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHHcCCCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence 3455666665444 799999999999999999999999999999874
No 14
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=88.95 E-value=0.53 Score=36.37 Aligned_cols=55 Identities=25% Similarity=0.371 Sum_probs=45.6
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEE
Q 018790 33 CSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSW 87 (350)
Q Consensus 33 ~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W 87 (350)
-.+.+.++...++..+.+.++|..||+.++-+.-++.-|+.-|+|.+...+.=.|
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 3567888887755459999999999999999999999999999999976442345
No 15
>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=86.42 E-value=0.79 Score=32.38 Aligned_cols=43 Identities=23% Similarity=0.411 Sum_probs=36.0
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhh
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVA 78 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~ 78 (350)
.+.|.++...|. ++..++|.++|+.+..++.+++-|+.-|+|+
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 567778877654 9999999999999999999999999999874
No 16
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=84.03 E-value=0.93 Score=31.87 Aligned_cols=37 Identities=16% Similarity=0.288 Sum_probs=33.4
Q ss_pred ceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCC
Q 018790 46 ESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAK 82 (350)
Q Consensus 46 ~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~K 82 (350)
..+++.+++..|++.+..++++++.|+.-|++....+
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 17
>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=84.01 E-value=1.1 Score=32.60 Aligned_cols=46 Identities=28% Similarity=0.458 Sum_probs=39.3
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 35 KFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 35 kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
..|.++...++..+.+.++|+.+++.+=.+--+++-||.-|+|.|.
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 3455666777667999999999999999999999999999999886
No 18
>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=83.40 E-value=2.7 Score=30.18 Aligned_cols=48 Identities=21% Similarity=0.369 Sum_probs=38.9
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCC
Q 018790 33 CSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKN 83 (350)
Q Consensus 33 ~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN 83 (350)
...++..+...+ ++..++|..+++.+.-++-+++.|+.-|+|.+....
T Consensus 9 ~~~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 9 RLRILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 344555555543 899999999999999999999999999999876433
No 19
>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=83.24 E-value=1.5 Score=34.58 Aligned_cols=50 Identities=16% Similarity=0.288 Sum_probs=39.5
Q ss_pred HHHHHHHHHHhhCCCc-eecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 31 LLCSKFLKLYNRDGVE-SIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~-~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
..+-+++-++-..+.. .+++.++|+++++..+.+..|++-|+--|+|+..
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence 3455666666655543 4999999999999999999999999999999754
No 20
>PF13730 HTH_36: Helix-turn-helix domain
Probab=83.22 E-value=1.4 Score=31.80 Aligned_cols=30 Identities=30% Similarity=0.478 Sum_probs=28.2
Q ss_pred ecHHHHHHHhCCceeeehhhHHHHhhhhhh
Q 018790 48 IGLDDAASRLGVERRRIYDVVNILESIGVV 77 (350)
Q Consensus 48 I~L~~aA~~LgV~RRRIYDIvNVLEslGli 77 (350)
-+.+.+|+.+|+.+|.|+-.++.||..|+|
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 389999999999999999999999999976
No 21
>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=81.97 E-value=1.3 Score=37.40 Aligned_cols=48 Identities=13% Similarity=0.277 Sum_probs=40.5
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 33 CSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 33 ~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
+-+.+.++...++..+++.++|.++++.+..++.|++.|+.-|+|...
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 344555665556678999999999999999999999999999999764
No 22
>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=81.30 E-value=2.9 Score=31.30 Aligned_cols=50 Identities=18% Similarity=0.305 Sum_probs=37.8
Q ss_pred HHHHHHHhh---CCCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCC
Q 018790 34 SKFLKLYNR---DGVESI-GLDDAASRLGVERRRIYDVVNILESIGVVARQAKN 83 (350)
Q Consensus 34 ~kFl~l~~~---~~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN 83 (350)
..+.+.+.. .++..+ +..++|++|+|.|.=+.+.++.|+.-|+|.+..+.
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~ 60 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPGR 60 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred HHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCc
Confidence 344444433 456788 99999999999999999999999999999877543
No 23
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=79.89 E-value=1.2 Score=30.50 Aligned_cols=38 Identities=21% Similarity=0.382 Sum_probs=33.7
Q ss_pred eecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCce
Q 018790 47 SIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLY 85 (350)
Q Consensus 47 ~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y 85 (350)
.++..++|+.+|+.+..+..+++.|+.-|++.+.. +.|
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 47889999999999999999999999999998764 444
No 24
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=78.39 E-value=2.4 Score=30.00 Aligned_cols=40 Identities=25% Similarity=0.429 Sum_probs=34.8
Q ss_pred CCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCC
Q 018790 44 GVESI-GLDDAASRLGVERRRIYDVVNILESIGVVARQAKN 83 (350)
Q Consensus 44 ~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN 83 (350)
++..+ +..++|+.+++.+=-+...++-|+.-|+|.+....
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 45556 89999999999999999999999999999876543
No 25
>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=75.50 E-value=0.89 Score=35.93 Aligned_cols=28 Identities=32% Similarity=0.546 Sum_probs=22.6
Q ss_pred HHHHhCC---ceeeehhhHHHHhhhhhhhhc
Q 018790 53 AASRLGV---ERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 53 aA~~LgV---~RRRIYDIvNVLEslGli~K~ 80 (350)
+|+.+|+ ..||++|+++-|+.+|+|...
T Consensus 28 lc~~~~~~pls~~r~~~~l~eL~~~gli~~~ 58 (85)
T PF09079_consen 28 LCESLGVDPLSYRRFSDYLSELEMLGLIESE 58 (85)
T ss_dssp HHHHTTS----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHcCCCCCCHHHHHHHHHHHHhCCCeEEE
Confidence 5556665 489999999999999999654
No 26
>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=75.21 E-value=2.2 Score=30.90 Aligned_cols=43 Identities=26% Similarity=0.550 Sum_probs=35.4
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
+|..+.+.++ +++.++|..+++.+--+-.+++-|+.-|+|+|.
T Consensus 8 iL~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 8 ILRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp HHHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence 3444455444 999999999999999999999999999999886
No 27
>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=74.59 E-value=4.1 Score=30.85 Aligned_cols=53 Identities=17% Similarity=0.219 Sum_probs=39.3
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhh-hhcCCCceEEecC
Q 018790 35 KFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVV-ARQAKNLYSWQGF 90 (350)
Q Consensus 35 kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli-~K~~KN~y~W~G~ 90 (350)
+.+.++.+. .++..++|++|||.++-|+.-+..|+.-|++ ...++..+.+.+.
T Consensus 4 ~il~~L~~~---~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~~~g~~l~~~~ 57 (69)
T TIGR00122 4 RLLALLADN---PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTVGKGYRLPPPI 57 (69)
T ss_pred HHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCCceEecCcc
Confidence 455565543 3679999999999999999999999998884 3335555555544
No 28
>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=73.92 E-value=3 Score=32.47 Aligned_cols=22 Identities=32% Similarity=0.635 Sum_probs=19.4
Q ss_pred CceeeehhhHHHHhhhhhhhhc
Q 018790 59 VERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 59 V~RRRIYDIvNVLEslGli~K~ 80 (350)
...||++||+|-||..|+|.-.
T Consensus 44 l~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEEE
Confidence 3589999999999999999754
No 29
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=73.03 E-value=9.5 Score=36.44 Aligned_cols=56 Identities=14% Similarity=0.280 Sum_probs=44.1
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecC
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGF 90 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~ 90 (350)
-..|+++.... ..+++.++|+.+|+.|=.+|.+++-|+..|++.+.....-...|.
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 44566665543 359999999999999999999999999999998875444445553
No 30
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=72.44 E-value=5.6 Score=38.24 Aligned_cols=54 Identities=24% Similarity=0.359 Sum_probs=40.0
Q ss_pred eecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecCCChHHHHHHHH
Q 018790 47 SIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGFDAIPEALEVLK 101 (350)
Q Consensus 47 ~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~~nI~~tL~~Lk 101 (350)
..+-.++|+..||.|=|+|||++-||.=|+|......--...-. .....|.+.+
T Consensus 30 ~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av-~p~~~i~~~~ 83 (247)
T COG1378 30 EATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAV-PPEELIERIK 83 (247)
T ss_pred CccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeC-CHHHHHHHHH
Confidence 46788999999999999999999999999999974443333322 2333455544
No 31
>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=72.17 E-value=2.5 Score=32.77 Aligned_cols=46 Identities=20% Similarity=0.345 Sum_probs=35.5
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCc-eeeehhhHHHHhhhhhhhhcC
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVE-RRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~-RRRIYDIvNVLEslGli~K~~ 81 (350)
||.-+....+..-++.++|+.||+. ..-+++-+..||.-|+|.+..
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 4444444445567999999999998 999999999999999999874
No 32
>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=68.63 E-value=7.8 Score=32.45 Aligned_cols=36 Identities=19% Similarity=0.394 Sum_probs=33.4
Q ss_pred CceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 45 VESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 45 ~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
...+++.++|..+++.+..+++|+..|...|+|...
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 348999999999999999999999999999999864
No 33
>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=67.69 E-value=5.6 Score=31.16 Aligned_cols=49 Identities=24% Similarity=0.374 Sum_probs=41.8
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCC
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAK 82 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~K 82 (350)
..+|+.+-.....-+.-.+++..+|+.-|-++=++++|+..|+|.|+.-
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 4567777766666678889999999999999999999999999999854
No 34
>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=67.62 E-value=4.3 Score=31.10 Aligned_cols=47 Identities=11% Similarity=0.193 Sum_probs=36.2
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCc
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNL 84 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~ 84 (350)
..+++.. .+.+++.++|.+|++...-|=+++.+|+..|.|.+...+.
T Consensus 5 i~~~l~~--~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 5 IRDYLRE--RGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHHH--S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 3445555 3579999999999999999999999999999999875443
No 35
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=66.55 E-value=2.5 Score=41.28 Aligned_cols=30 Identities=33% Similarity=0.614 Sum_probs=24.6
Q ss_pred ceecHHHHHHHhCCceeeehhhHHHHhhhh
Q 018790 46 ESIGLDDAASRLGVERRRIYDVVNILESIG 75 (350)
Q Consensus 46 ~~I~L~~aA~~LgV~RRRIYDIvNVLEslG 75 (350)
..|.|..+=--||.++|-+||++||+|+=.
T Consensus 39 ~DiGLRNLDlimGlE~RiVYd~vdVi~g~~ 68 (272)
T COG2894 39 FDIGLRNLDLIMGLENRIVYDLVDVIEGEA 68 (272)
T ss_pred cCcCchhhhhhhcccceeeeeehhhhcCcc
Confidence 346666777789999999999999999754
No 36
>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=65.81 E-value=8.7 Score=27.57 Aligned_cols=34 Identities=29% Similarity=0.447 Sum_probs=31.2
Q ss_pred ecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 48 IGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 48 I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
.+..++|..+++.+=.+...++-|+.-|+|.+..
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 4599999999999999999999999999998764
No 37
>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=64.37 E-value=9.3 Score=35.71 Aligned_cols=71 Identities=15% Similarity=0.384 Sum_probs=35.9
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc--CCCceEEecCCChHHHHHHHHHhc
Q 018790 32 LCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ--AKNLYSWQGFDAIPEALEVLKEEG 104 (350)
Q Consensus 32 L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~--~KN~y~W~G~~nI~~tL~~Lkeeg 104 (350)
+.+.||+|+..+ .++.|+++|..||+..==+-|-|+-|+.-|.|+=+ ..+.|+++...-+...-.-++..|
T Consensus 100 lL~~Fi~yIK~~--Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~~~va~fi~~rG 172 (188)
T PF09756_consen 100 LLQEFINYIKEH--KVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEMEAVAKFIKQRG 172 (188)
T ss_dssp HHHHHHHHHHH---SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE-----------------
T ss_pred HHHHHHHHHHHc--ceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHHHHHHHHHHHcC
Confidence 788999999986 47999999999999766555555666666655443 466899988766665545455554
No 38
>PF13518 HTH_28: Helix-turn-helix domain
Probab=64.27 E-value=8.7 Score=26.86 Aligned_cols=38 Identities=18% Similarity=0.457 Sum_probs=30.8
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhh
Q 018790 35 KFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGV 76 (350)
Q Consensus 35 kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGl 76 (350)
+.|.++.+ +. ++.++|.++||.+..||.++.-++.-|+
T Consensus 4 ~iv~~~~~---g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 4 QIVELYLE---GE-SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHHc---CC-CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 34555653 22 9999999999999999999999998664
No 39
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=63.35 E-value=7.8 Score=36.73 Aligned_cols=52 Identities=21% Similarity=0.283 Sum_probs=41.4
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC-CCceEE
Q 018790 35 KFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA-KNLYSW 87 (350)
Q Consensus 35 kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~-KN~y~W 87 (350)
..|+++...+ ..+++.++|+++|+.|=-+|-+++-|+..|++.+.. .+.|..
T Consensus 15 ~iL~~l~~~~-~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~L 67 (263)
T PRK09834 15 MVLRALNRLD-GGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFRL 67 (263)
T ss_pred HHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEEE
Confidence 3455555443 349999999999999999999999999999999863 455654
No 40
>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=60.78 E-value=9.5 Score=28.37 Aligned_cols=46 Identities=24% Similarity=0.416 Sum_probs=37.6
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
...++++... +.+++.++|+.|+|...=|.==+|.|+.-|+|.|..
T Consensus 3 ~~Il~~l~~~--~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKEK--GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHc--CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 3456777664 579999999999999777777788999999998874
No 41
>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=60.51 E-value=8.9 Score=28.20 Aligned_cols=38 Identities=24% Similarity=0.462 Sum_probs=31.0
Q ss_pred CCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 43 DGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 43 ~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
.....+.+.++|..+++.+--+..+++-|+..|+|+|.
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 35667899999999999999999999999999999776
No 42
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=60.30 E-value=8.5 Score=33.96 Aligned_cols=43 Identities=23% Similarity=0.381 Sum_probs=36.8
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
|..+++ ..+..+.+++|+.|+..|=.+|=.++=|...|+|.|.
T Consensus 33 ~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Re 75 (126)
T COG3355 33 YKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVERE 75 (126)
T ss_pred HHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeee
Confidence 344443 3456999999999999999999999999999999986
No 43
>PF03376 Adeno_E3B: Adenovirus E3B protein; InterPro: IPR005041 Adenoviruses are medium-sized, non-enveloped viruses containing double-stranded DNA. They can cause a variety of diseases including pneumonia, cystitis, conjunctivitis and diarrhoea, all of which can be fatal to patients who are immunocompromised []. These viruses have many mechanisms to evade the host immune response, including several proteins which are expressed as part of the early transcription unit 3 (E3) []. One of the regions of E3, known as the E3B region, encodes three proteins known as 10.4K, 14.5K and 14.7K. Two of these proteins, 10.4K and 14.5K, form the RID complex (receptor internalisation and degradation) which protects the infected cell from host-induced lysis by clearing the the TNF and Fas receptors from the cell surface []. Other receptors, such as the epidermal growth factor receptor, are also known to be cleared by RID []. This entry represents the E3B region 10.4K protein, also known as the RID alpha subunit.; GO: 0016020 membrane
Probab=59.41 E-value=4.7 Score=32.03 Aligned_cols=15 Identities=27% Similarity=0.720 Sum_probs=12.4
Q ss_pred hcCCcccchHHHHHH
Q 018790 315 TFRPKYHNEAVNGLF 329 (350)
Q Consensus 315 ~~~pqy~n~~l~~lf 329 (350)
.|-||||||.+-.|.
T Consensus 51 RHhPqYrn~~iA~LL 65 (67)
T PF03376_consen 51 RHHPQYRNQQIAALL 65 (67)
T ss_pred HcCchhcCHHHHHHh
Confidence 467999999998874
No 44
>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=59.19 E-value=4.6 Score=27.46 Aligned_cols=22 Identities=27% Similarity=0.685 Sum_probs=20.2
Q ss_pred ecHHHHHHHhCCceeeehhhHH
Q 018790 48 IGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 48 I~L~~aA~~LgV~RRRIYDIvN 69 (350)
+++.++|+.|||.++.||..++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999885
No 45
>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=58.42 E-value=5 Score=38.52 Aligned_cols=39 Identities=15% Similarity=0.203 Sum_probs=34.7
Q ss_pred ceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCce
Q 018790 46 ESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLY 85 (350)
Q Consensus 46 ~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y 85 (350)
+..++.++|.++|+..|.++-++..|.++|++++.+ +.|
T Consensus 22 gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~-~~y 60 (306)
T TIGR02716 22 GPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED-GKW 60 (306)
T ss_pred CCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC-CcE
Confidence 468999999999999999999999999999999864 443
No 46
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=57.27 E-value=14 Score=28.35 Aligned_cols=45 Identities=27% Similarity=0.490 Sum_probs=37.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
...|.++...+ .++..++|..+++.+.-|+-+++-|+.-|+|.+.
T Consensus 13 ~~il~~l~~~~--~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 13 FLVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHcC--CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 34445555444 4899999999999999999999999999999876
No 47
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=57.11 E-value=14 Score=31.45 Aligned_cols=46 Identities=9% Similarity=0.147 Sum_probs=37.5
Q ss_pred cHHHHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhh
Q 018790 28 SLGLLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILES 73 (350)
Q Consensus 28 SLg~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEs 73 (350)
.-.....++++++..+....++|+++|+.+|+.+|.|.-++.-.-+
T Consensus 6 ~~~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G 51 (127)
T PRK11511 6 TDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETG 51 (127)
T ss_pred ccHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 3455678899999998888899999999999999988877664433
No 48
>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=56.88 E-value=19 Score=26.58 Aligned_cols=42 Identities=29% Similarity=0.376 Sum_probs=27.3
Q ss_pred CCCCcHHHHH-HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHH
Q 018790 24 RKEKSLGLLC-SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 24 RkeKSLg~L~-~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvN 69 (350)
|+.++|.+-- ...|.+++..+ +..++|.+|||.+.-|++|+.
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 4455555443 34666666654 799999999999999999985
No 49
>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=55.96 E-value=12 Score=30.48 Aligned_cols=50 Identities=22% Similarity=0.417 Sum_probs=38.6
Q ss_pred cHHHHHHHHHHHHhhCC--CceecHHHHHHHhCCceeeehhhHHHHhhhhhh
Q 018790 28 SLGLLCSKFLKLYNRDG--VESIGLDDAASRLGVERRRIYDVVNILESIGVV 77 (350)
Q Consensus 28 SLg~L~~kFl~l~~~~~--~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli 77 (350)
+|..+.++.++++...+ ..=+.+++++++|++....|.+++.-|..-|+|
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 68888999999988722 345999999999999888888888888887776
No 50
>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=55.72 E-value=13 Score=33.62 Aligned_cols=48 Identities=15% Similarity=0.299 Sum_probs=41.0
Q ss_pred CceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCce------EEecCCC
Q 018790 45 VESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLY------SWQGFDA 92 (350)
Q Consensus 45 ~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y------~W~G~~n 92 (350)
.-.++..++|..+|+.++-++..+..|+--++|.|...+.| .|.|...
T Consensus 73 ~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G~Y~iNP~~~~kG~~~ 126 (165)
T PF05732_consen 73 AVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAYMINPNFFFKGDRD 126 (165)
T ss_pred eEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeEEECcHHheeCcHH
Confidence 34578899999999999999999999999999999865655 6888743
No 51
>PRK00215 LexA repressor; Validated
Probab=55.26 E-value=11 Score=34.18 Aligned_cols=48 Identities=17% Similarity=0.233 Sum_probs=38.8
Q ss_pred HHHHHhhCCCceecHHHHHHHhCC-ceeeehhhHHHHhhhhhhhhcCCC
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGV-ERRRIYDVVNILESIGVVARQAKN 83 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV-~RRRIYDIvNVLEslGli~K~~KN 83 (350)
||..+....+...++.++|+.+|+ .+=-++.+++-|+.-|+|++....
T Consensus 12 ~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 12 FIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 333333344566899999999999 999999999999999999987544
No 52
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=55.04 E-value=11 Score=30.45 Aligned_cols=45 Identities=27% Similarity=0.410 Sum_probs=39.5
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhh
Q 018790 33 CSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVAR 79 (350)
Q Consensus 33 ~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K 79 (350)
=.+++.++...+ .++..++|+.+|+.+.-++..++-|+.-|+|.+
T Consensus 5 D~~il~~L~~~~--~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 5 DRKILEELQKDA--RISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHhC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence 357788887754 589999999999999999999999999999985
No 53
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=54.57 E-value=13 Score=30.12 Aligned_cols=41 Identities=7% Similarity=0.169 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHH
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNIL 71 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVL 71 (350)
.+..+++.++.......+++.++|..+|+.+|.+.-++.=.
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45677888888888888999999999999999888776543
No 54
>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=54.52 E-value=12 Score=26.47 Aligned_cols=41 Identities=22% Similarity=0.438 Sum_probs=33.5
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhh
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVAR 79 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K 79 (350)
.+.++.. +..++.++|+.+|+.+=-++-=+++|+..|+|++
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 4444444 4589999999999999999999999999999874
No 55
>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=54.02 E-value=12 Score=32.40 Aligned_cols=36 Identities=19% Similarity=0.350 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHhhCCCceecHHHHHHHhCCceeeeh
Q 018790 30 GLLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIY 65 (350)
Q Consensus 30 g~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIY 65 (350)
..|..-|++++...+-..|++.++|++-||.|.-+|
T Consensus 6 ~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY 41 (176)
T TIGR02366 6 KKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFY 41 (176)
T ss_pred HHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHH
Confidence 457788999999999999999999999999998876
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=53.69 E-value=15 Score=34.38 Aligned_cols=50 Identities=18% Similarity=0.319 Sum_probs=40.3
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceE
Q 018790 35 KFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYS 86 (350)
Q Consensus 35 kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~ 86 (350)
..|+++... ...+++.++|+++|+.|=.+|-+++-|+..|++.+.. ..|.
T Consensus 13 ~IL~~l~~~-~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~~-~~Y~ 62 (248)
T TIGR02431 13 AVIEAFGAE-RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSDG-RLFW 62 (248)
T ss_pred HHHHHHhcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC-CEEE
Confidence 455555544 3469999999999999999999999999999999853 4454
No 57
>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=52.93 E-value=16 Score=29.74 Aligned_cols=37 Identities=19% Similarity=0.283 Sum_probs=33.9
Q ss_pred CceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 45 VESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 45 ~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
...++-.++|..+|+.|.-+-.+++.||.-|+|.+..
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeec
Confidence 4578899999999999999999999999999999764
No 58
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=52.85 E-value=17 Score=34.18 Aligned_cols=55 Identities=15% Similarity=0.341 Sum_probs=43.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecC
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGF 90 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~ 90 (350)
-..|+++... ..+++.++|+++|+.|=-+|-+++.|+..|++.+...+.-...|.
T Consensus 17 l~IL~~l~~~--~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG~ 71 (257)
T PRK15090 17 FGILQALGEE--REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSLTL 71 (257)
T ss_pred HHHHHHhhcC--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEecH
Confidence 3455666543 358999999999999999999999999999999875544445553
No 59
>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=52.79 E-value=9.3 Score=28.80 Aligned_cols=51 Identities=24% Similarity=0.369 Sum_probs=40.2
Q ss_pred HHHHHHHHHhhCC----------CceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCC
Q 018790 32 LCSKFLKLYNRDG----------VESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAK 82 (350)
Q Consensus 32 L~~kFl~l~~~~~----------~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~K 82 (350)
+|.-++.++...+ ...++..++|..+|+.|+.+--+++-|+.-|+|+...+
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 4555666654422 13578999999999999999999999999999997644
No 60
>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=52.68 E-value=18 Score=31.07 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=35.9
Q ss_pred CceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc--CCCceEE
Q 018790 45 VESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ--AKNLYSW 87 (350)
Q Consensus 45 ~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~--~KN~y~W 87 (350)
...+++.++|+++++..+-+..|+..|.--|+|.-. ..+-|.+
T Consensus 23 ~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l 67 (135)
T TIGR02010 23 TGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQL 67 (135)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEec
Confidence 457999999999999999999999999999999743 2344443
No 61
>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=52.51 E-value=16 Score=30.18 Aligned_cols=44 Identities=20% Similarity=0.333 Sum_probs=36.5
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
.|..+... +.+++.++|..+++.+--+.=+++-||.-|+|.|..
T Consensus 33 iL~~l~~~--~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 33 ILRILAEQ--GSMEFTQLANQACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred HHHHHHHc--CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence 44444443 348899999999999999999999999999999863
No 62
>PRK09954 putative kinase; Provisional
Probab=51.33 E-value=13 Score=36.48 Aligned_cols=46 Identities=20% Similarity=0.247 Sum_probs=40.1
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 33 CSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 33 ~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
-++.|+++.+++ .++..++|+.|+|.|..++..++=|+.-|+|.+.
T Consensus 5 ~~~il~~l~~~~--~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~ 50 (362)
T PRK09954 5 EKEILAILRRNP--LIQQNEIADILQISRSRVAAHIMDLMRKGRIKGK 50 (362)
T ss_pred HHHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCc
Confidence 456788888765 6999999999999999999999999999998653
No 63
>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=51.21 E-value=7.2 Score=28.94 Aligned_cols=46 Identities=17% Similarity=0.341 Sum_probs=36.8
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
.+++.++.. ....++.++|+.||+.+=-+|-=+++|+..|+|+...
T Consensus 13 ~~Il~~L~~--~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 13 LRILRLLAS--NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHHH--CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHhc--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 345666633 3458999999999999999999999999999998653
No 64
>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=51.11 E-value=15 Score=33.21 Aligned_cols=46 Identities=13% Similarity=0.198 Sum_probs=37.3
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCc-eeeehhhHHHHhhhhhhhhcC
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVE-RRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~-RRRIYDIvNVLEslGli~K~~ 81 (350)
||..+....+...++.++|+.||+. +=-++..+..||..|+|.+..
T Consensus 14 ~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 14 LIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred HHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCC
Confidence 3333333345568899999999998 999999999999999999975
No 65
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=50.68 E-value=30 Score=35.94 Aligned_cols=58 Identities=22% Similarity=0.406 Sum_probs=46.6
Q ss_pred cHHHHHHH------HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecC
Q 018790 28 SLGLLCSK------FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGF 90 (350)
Q Consensus 28 SLg~L~~k------Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~ 90 (350)
-||+|+-+ .++++....+..|+|+++|..-|+. .-|||+.|+.++++.... + |.|..-
T Consensus 304 DLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~---~~DIisTL~~L~m~~y~k-~-~~~~~~ 367 (396)
T KOG2747|consen 304 DLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIR---PDDIISTLQSLNMIKYYK-G-YIISIC 367 (396)
T ss_pred hhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCC---HHHHHHHHHhhCCccccC-C-eeEEEe
Confidence 47877744 6777777666669999999999985 579999999999998773 3 888765
No 66
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=49.55 E-value=23 Score=31.97 Aligned_cols=36 Identities=19% Similarity=0.309 Sum_probs=33.4
Q ss_pred CceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 45 VESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 45 ~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
...++++++|+++++..+-+..|++-|.--|+|.-.
T Consensus 23 ~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 23 AGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 457999999999999999999999999999999854
No 67
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=48.89 E-value=29 Score=32.25 Aligned_cols=60 Identities=17% Similarity=0.218 Sum_probs=44.9
Q ss_pred CcHHH-HHHHHHHHHhh---CCCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhhc-CCCceE
Q 018790 27 KSLGL-LCSKFLKLYNR---DGVESI-GLDDAASRLGVERRRIYDVVNILESIGVVARQ-AKNLYS 86 (350)
Q Consensus 27 KSLg~-L~~kFl~l~~~---~~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~-~KN~y~ 86 (350)
.++.. +...+.+.+.. .|+..+ +-.++|++|||.|=-+-+-+..|++.|+|+.. +++.|.
T Consensus 9 ~~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V 74 (254)
T PRK09464 9 PKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFV 74 (254)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCceeEE
Confidence 45554 44555555433 567778 89999999999999999999999999999755 444333
No 68
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=48.60 E-value=57 Score=29.67 Aligned_cols=61 Identities=13% Similarity=0.131 Sum_probs=45.3
Q ss_pred CcHHHHH-HHHHHHHhh---CCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEE
Q 018790 27 KSLGLLC-SKFLKLYNR---DGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSW 87 (350)
Q Consensus 27 KSLg~L~-~kFl~l~~~---~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W 87 (350)
.++.... ..+.+.+-. .|+..+.-.++|++|||.|=-+=+-+..|+..|||+.....-+.-
T Consensus 10 ~~~~e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g~~v 74 (221)
T PRK11414 10 ISLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTV 74 (221)
T ss_pred CCHHHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCceee
Confidence 3555433 444444432 578889999999999999999999999999999998765443433
No 69
>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=47.91 E-value=12 Score=28.04 Aligned_cols=36 Identities=31% Similarity=0.434 Sum_probs=27.1
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHh
Q 018790 35 KFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILE 72 (350)
Q Consensus 35 kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLE 72 (350)
+.++++-. ...+++.++|..||+..|-|..-++-|.
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 4568999999999999998876666665
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=47.09 E-value=41 Score=30.23 Aligned_cols=57 Identities=25% Similarity=0.318 Sum_probs=43.2
Q ss_pred CcHHHHHHHHH-HHHhh---CCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCC
Q 018790 27 KSLGLLCSKFL-KLYNR---DGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKN 83 (350)
Q Consensus 27 KSLg~L~~kFl-~l~~~---~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN 83 (350)
+++.......| +.+-. .|+..|+-.++|++|||.|=-+=+.+..|+.-|+|+...+.
T Consensus 10 ~~~~~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~ 70 (212)
T TIGR03338 10 SSLTTLVQDEIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNR 70 (212)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCC
Confidence 45554443333 33322 57888999999999999999999999999999999876443
No 71
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=46.97 E-value=22 Score=33.77 Aligned_cols=56 Identities=20% Similarity=0.290 Sum_probs=45.6
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecC
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGF 90 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~ 90 (350)
-..|+++...|. .+.+.++|+++|..|=-+|=+++.|+..|++.+...+.-...|.
T Consensus 7 l~iL~~l~~~~~-~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~ 62 (246)
T COG1414 7 LAILDLLAEGPG-GLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRLGP 62 (246)
T ss_pred HHHHHHHHhCCC-CCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEeehH
Confidence 346677776444 38999999999999999999999999999999998764445553
No 72
>PHA02943 hypothetical protein; Provisional
Probab=46.97 E-value=17 Score=33.45 Aligned_cols=50 Identities=20% Similarity=0.181 Sum_probs=41.9
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceE
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYS 86 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~ 86 (350)
..+|+++ ..+.-+..++|+.||+.--....++=|||.-|+|.+...+...
T Consensus 14 ~eILE~L---k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~t 63 (165)
T PHA02943 14 IKTLRLL---ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAA 63 (165)
T ss_pred HHHHHHH---hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceE
Confidence 4577777 3456789999999999999999999999999999998766443
No 73
>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=46.90 E-value=18 Score=33.77 Aligned_cols=45 Identities=22% Similarity=0.414 Sum_probs=37.8
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhh
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIG 75 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslG 75 (350)
.+..+++.++.++....++|+++|+.+|+.++.+..++.-..++.
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t 230 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSALS 230 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCC
Confidence 456889999988888889999999999999999998887655443
No 74
>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=46.46 E-value=16 Score=25.91 Aligned_cols=33 Identities=24% Similarity=0.559 Sum_probs=23.6
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHH
Q 018790 33 CSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 33 ~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvN 69 (350)
....++++.+. +++.++|..+||.|.=||=+.+
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 45666666653 8999999999999999987653
No 75
>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=45.38 E-value=21 Score=29.40 Aligned_cols=49 Identities=6% Similarity=0.191 Sum_probs=39.6
Q ss_pred hCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCC--C-ceEEecC
Q 018790 42 RDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAK--N-LYSWQGF 90 (350)
Q Consensus 42 ~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~K--N-~y~W~G~ 90 (350)
..+.+.+++.++|..+++.+=.+-=+++-||--|+|.|..- + +..++-.
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 34557799999999999999999999999999999998632 2 4555543
No 76
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.15 E-value=13 Score=31.96 Aligned_cols=39 Identities=26% Similarity=0.396 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHH
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvN 69 (350)
+||.+=..+++-.=..-++|.++|+.++|+|--|||-|+
T Consensus 17 LLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIK 55 (105)
T COG2739 17 LLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIK 55 (105)
T ss_pred HHhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHH
Confidence 456553333333222359999999999999999999765
No 77
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=45.01 E-value=18 Score=33.70 Aligned_cols=35 Identities=20% Similarity=0.357 Sum_probs=33.4
Q ss_pred ceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 46 ESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 46 ~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
.+++|+++++.||++|=++-=.+-+|++.++|.++
T Consensus 40 ~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 40 KPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred CCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhh
Confidence 56999999999999999999999999999999987
No 78
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=43.77 E-value=13 Score=37.70 Aligned_cols=29 Identities=31% Similarity=0.629 Sum_probs=25.8
Q ss_pred HHHHHHHhCCceeeehhhHHHHhhhhhhh
Q 018790 50 LDDAASRLGVERRRIYDVVNILESIGVVA 78 (350)
Q Consensus 50 L~~aA~~LgV~RRRIYDIvNVLEslGli~ 78 (350)
+..+++.+++.+||+|||+|-|+.+|+|.
T Consensus 304 y~~~~~~~~~~~~~~~~ii~~L~~lgiv~ 332 (366)
T COG1474 304 YESLCERLRTSQRRFSDIISELEGLGIVS 332 (366)
T ss_pred HHHHHhhhCchHHHHHHHHHHHHhcCeEE
Confidence 45677888889999999999999999997
No 79
>PF07354 Sp38: Zona-pellucida-binding protein (Sp38); InterPro: IPR010857 This family contains a number of zona-pellucida-binding proteins that seem to be restricted to mammals. These are sperm proteins that bind to the 90 kDa family of zona pellucida glycoproteins in a calcium-dependent manner []. These represent some of the specific molecules that mediate the first steps of gamete interaction, allowing fertilisation to occur [].; GO: 0007339 binding of sperm to zona pellucida, 0005576 extracellular region
Probab=43.67 E-value=13 Score=36.66 Aligned_cols=16 Identities=31% Similarity=0.848 Sum_probs=14.4
Q ss_pred CceeeccCCCCCCCCC
Q 018790 196 PAFRWLGWKGNPCNRS 211 (350)
Q Consensus 196 PaF~WlG~~~~~~~~~ 211 (350)
|.|.|+||+|+...+.
T Consensus 13 P~y~W~GP~g~~l~gn 28 (271)
T PF07354_consen 13 PTYLWTGPNGKPLSGN 28 (271)
T ss_pred CceEEECCCCcccCCC
Confidence 9999999999888776
No 80
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=41.79 E-value=23 Score=30.54 Aligned_cols=39 Identities=18% Similarity=0.298 Sum_probs=35.0
Q ss_pred CCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 43 DGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 43 ~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
.++..++..++|+++||.+.-+-.|+..|..-|+|....
T Consensus 21 ~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~ 59 (141)
T PRK11014 21 PEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVR 59 (141)
T ss_pred CCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEec
Confidence 455689999999999999999999999999999997654
No 81
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=41.72 E-value=23 Score=32.22 Aligned_cols=48 Identities=13% Similarity=0.113 Sum_probs=41.3
Q ss_pred CCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecC
Q 018790 43 DGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGF 90 (350)
Q Consensus 43 ~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~ 90 (350)
.|+..+...++|++|||.|==|=+.+..|+.-|+|+.....-+.-..+
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~ 73 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASM 73 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCC
Confidence 567889999999999999999999999999999998776555555554
No 82
>PRK11050 manganese transport regulator MntR; Provisional
Probab=41.19 E-value=39 Score=29.76 Aligned_cols=42 Identities=21% Similarity=0.193 Sum_probs=36.0
Q ss_pred ceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEE
Q 018790 46 ESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSW 87 (350)
Q Consensus 46 ~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W 87 (350)
+.+.+.++|..|++.+--+..+++-||.-|+|.+.....+.+
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 458999999999999999999999999999998865444444
No 83
>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=40.83 E-value=35 Score=32.09 Aligned_cols=56 Identities=20% Similarity=0.301 Sum_probs=38.8
Q ss_pred CcHHHHH------HHHHHHHhhCCCc-eecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCce
Q 018790 27 KSLGLLC------SKFLKLYNRDGVE-SIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLY 85 (350)
Q Consensus 27 KSLg~L~------~kFl~l~~~~~~~-~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y 85 (350)
.-||.++ ...++++...... .|+|++++...|+.. -||+..|+.+|++.....+.+
T Consensus 123 SdlG~~sY~sYW~~~i~~~L~~~~~~~~isi~~is~~Tgi~~---~DIi~tL~~l~~l~~~~~~~~ 185 (188)
T PF01853_consen 123 SDLGRLSYRSYWRRVILEYLLEFKGKKSISIKDISQETGIRP---EDIISTLQQLGMLKYYKGQHI 185 (188)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHTSSE--EEHHHHHHHH-BTH---HHHHHHHHHTT-EEEETTEEE
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCCCeEEHHHHHHHHCCCH---HHHHHHHHHCCCEEEECCcEE
Confidence 3466665 2356666655553 799999999999965 699999999999988755443
No 84
>PRK11569 transcriptional repressor IclR; Provisional
Probab=40.45 E-value=33 Score=32.72 Aligned_cols=55 Identities=16% Similarity=0.178 Sum_probs=42.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEec
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQG 89 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G 89 (350)
-..|+++... ...++|.++|+.+|..|=.+|=+++-|+..|++.+.......-.|
T Consensus 31 l~IL~~l~~~-~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~~~~Y~lG 85 (274)
T PRK11569 31 LKLLEWIAES-NGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGELGHWAIG 85 (274)
T ss_pred HHHHHHHHhC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEecC
Confidence 3455556553 345899999999999999999999999999999986543333344
No 85
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=39.90 E-value=33 Score=32.53 Aligned_cols=55 Identities=18% Similarity=0.195 Sum_probs=44.6
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecC
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGF 90 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~ 90 (350)
.+.++++... ..+.+.++|+.|+|..+.|.--++.|+.-|++.+....-+.+.+.
T Consensus 7 ~~Il~~l~~~--~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~Gga~~~~~~ 61 (240)
T PRK10411 7 QAIVDLLLNH--TSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHGRAKYIHRQ 61 (240)
T ss_pred HHHHHHHHHc--CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCeEEEecCC
Confidence 3456666654 469999999999999999999999999999998876666666554
No 86
>PRK03837 transcriptional regulator NanR; Provisional
Probab=39.34 E-value=58 Score=29.78 Aligned_cols=54 Identities=13% Similarity=0.217 Sum_probs=42.5
Q ss_pred cHHH-HHHHHHHHHhh---CCCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 28 SLGL-LCSKFLKLYNR---DGVESI-GLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 28 SLg~-L~~kFl~l~~~---~~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
++.. +...+.+.+.. .|+..+ +..++|++|||.|--+=+.+..|+.-|+|+...
T Consensus 13 ~~~~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~ 71 (241)
T PRK03837 13 KLSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISH 71 (241)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4443 44555555433 567788 899999999999999999999999999998753
No 87
>PF13551 HTH_29: Winged helix-turn helix
Probab=38.97 E-value=30 Score=27.48 Aligned_cols=27 Identities=30% Similarity=0.546 Sum_probs=25.8
Q ss_pred cHHHHHHHhCCceeeehhhHHHHhhhh
Q 018790 49 GLDDAASRLGVERRRIYDVVNILESIG 75 (350)
Q Consensus 49 ~L~~aA~~LgV~RRRIYDIvNVLEslG 75 (350)
++.++|..||+.++-+|.+++-++.=|
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 799999999999999999999998888
No 88
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=38.83 E-value=42 Score=30.80 Aligned_cols=44 Identities=18% Similarity=0.176 Sum_probs=37.9
Q ss_pred CCCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhhc-CCCceE
Q 018790 43 DGVESI-GLDDAASRLGVERRRIYDVVNILESIGVVARQ-AKNLYS 86 (350)
Q Consensus 43 ~~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~-~KN~y~ 86 (350)
.|+..+ +-.++|++|||.|=-|-+-+..|+.-|+|... +++.|.
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 567788 79999999999999999999999999999865 455554
No 89
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=38.54 E-value=35 Score=32.49 Aligned_cols=48 Identities=21% Similarity=0.279 Sum_probs=38.5
Q ss_pred HHHHHHHhh-CCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 34 SKFLKLYNR-DGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 34 ~kFl~l~~~-~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
-+-|.++.. .....++..++|+.|++.+..+.-++.-||.-|+|+|..
T Consensus 7 Lk~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~ 55 (217)
T PRK14165 7 LKKLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTI 55 (217)
T ss_pred HHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEE
Confidence 334444433 334469999999999999999999999999999999874
No 90
>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=38.12 E-value=34 Score=31.27 Aligned_cols=45 Identities=22% Similarity=0.345 Sum_probs=38.1
Q ss_pred HHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 35 KFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 35 kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
+.+.++... +.+++.++|+.+++.+-.++-.++-|+..|+|.+..
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 445555543 348999999999999999999999999999999986
No 91
>PRK13503 transcriptional activator RhaS; Provisional
Probab=37.88 E-value=27 Score=32.28 Aligned_cols=39 Identities=10% Similarity=0.161 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHH
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvN 69 (350)
....++++++.++....++|+++|+.+|+.++.+..++.
T Consensus 171 ~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 347788888888888899999999999999999877765
No 92
>PRK10130 transcriptional regulator EutR; Provisional
Probab=37.63 E-value=29 Score=34.83 Aligned_cols=41 Identities=20% Similarity=0.200 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHH
Q 018790 30 GLLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNI 70 (350)
Q Consensus 30 g~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNV 70 (350)
..+..+.++++..+....+++.++|..+||.+|.|+-.+.=
T Consensus 239 ~~~v~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~ 279 (350)
T PRK10130 239 RRLLSRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHA 279 (350)
T ss_pred HHHHHHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46778888888888888899999999999999999877743
No 93
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=37.60 E-value=61 Score=30.21 Aligned_cols=56 Identities=20% Similarity=0.248 Sum_probs=42.8
Q ss_pred HHHHHHHHHHhh---CCCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhhc-CCCceE
Q 018790 31 LLCSKFLKLYNR---DGVESI-GLDDAASRLGVERRRIYDVVNILESIGVVARQ-AKNLYS 86 (350)
Q Consensus 31 ~L~~kFl~l~~~---~~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~-~KN~y~ 86 (350)
.+...+.+.+-. .|+..+ +-.++|++|||.|==+=+.+..|+..|+|+.. +++.|.
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~V 73 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYV 73 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEEE
Confidence 344444444433 577888 69999999999999999999999999999755 444443
No 94
>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=37.16 E-value=38 Score=25.64 Aligned_cols=38 Identities=24% Similarity=0.352 Sum_probs=33.9
Q ss_pred CCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 44 GVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 44 ~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
..+.+...++|+.|+|.+=-+.+.++-|+.-|+|....
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 67789999999999999999999999999999998763
No 95
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=37.03 E-value=32 Score=32.47 Aligned_cols=55 Identities=20% Similarity=0.295 Sum_probs=41.2
Q ss_pred HHHHHHHHHhh---CCCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhh-cCCCceE
Q 018790 32 LCSKFLKLYNR---DGVESI-GLDDAASRLGVERRRIYDVVNILESIGVVAR-QAKNLYS 86 (350)
Q Consensus 32 L~~kFl~l~~~---~~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K-~~KN~y~ 86 (350)
+..++.+++.+ .|+..+ +=.++|++|||.|--|=+.+-+|+..|+|+- .+.+.|.
T Consensus 15 v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~Gt~V 74 (241)
T COG2186 15 VAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEIRQGSGTFV 74 (241)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCCceEe
Confidence 44555555544 233333 5789999999999999999999999999964 5666776
No 96
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=36.33 E-value=32 Score=32.66 Aligned_cols=49 Identities=16% Similarity=0.295 Sum_probs=38.6
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCc
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNL 84 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~ 84 (350)
.+.++++.. .+.+.+.++|+.|||...-|+--++.||..|+|.|...+-
T Consensus 8 ~~Il~~l~~--~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~gga 56 (251)
T PRK13509 8 QILLELLAQ--LGFVTVEKVIERLGISPATARRDINKLDESGKLKKVRNGA 56 (251)
T ss_pred HHHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCc
Confidence 345566665 3579999999999999887777789999999998865443
No 97
>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=35.88 E-value=55 Score=26.78 Aligned_cols=48 Identities=27% Similarity=0.407 Sum_probs=38.1
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 32 LCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 32 L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
+.+-.|+.|... +..|.=.++|+.|++.-=-|..+.-.||.+|+|+++
T Consensus 9 IL~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 9 ILKALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 334456666654 567888999999999888888899999999999865
No 98
>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=35.04 E-value=30 Score=28.35 Aligned_cols=41 Identities=22% Similarity=0.398 Sum_probs=31.3
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
|.+.+-.. ++.+++.++|..||+.+++++++ |...|++-+.
T Consensus 14 ~~d~~~~~-~~~~ti~~~AK~L~i~~~~l~~~---Lr~~g~l~~~ 54 (111)
T PF03374_consen 14 FYDAFVDS-DGLYTIREAAKLLGIGRNKLFQW---LREKGWLYRR 54 (111)
T ss_pred HHHHHHcC-CCCccHHHHHHHhCCCHHHHHHH---HHhCCceEEC
Confidence 44444444 37899999999999999988875 5667777774
No 99
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=34.63 E-value=28 Score=32.49 Aligned_cols=43 Identities=21% Similarity=0.309 Sum_probs=36.8
Q ss_pred CCCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhhc-CCCce
Q 018790 43 DGVESI-GLDDAASRLGVERRRIYDVVNILESIGVVARQ-AKNLY 85 (350)
Q Consensus 43 ~~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~-~KN~y 85 (350)
.|+..+ +-.++|++|||.|=-+=+-+..|+..|+|... +++.|
T Consensus 21 ~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~~G~~ 65 (253)
T PRK10421 21 EAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTF 65 (253)
T ss_pred CCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCeEE
Confidence 567788 69999999999999999999999999999754 44444
No 100
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=34.48 E-value=34 Score=31.40 Aligned_cols=44 Identities=23% Similarity=0.278 Sum_probs=39.2
Q ss_pred CCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceE
Q 018790 43 DGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYS 86 (350)
Q Consensus 43 ~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~ 86 (350)
.|+..++..++|.+|||.|--|=+.+..|++-|+|.....--+.
T Consensus 35 ~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~ 78 (230)
T COG1802 35 APGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAF 78 (230)
T ss_pred CCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCCCe
Confidence 68899999999999999999999999999999999998543333
No 101
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=34.44 E-value=44 Score=28.40 Aligned_cols=34 Identities=24% Similarity=0.399 Sum_probs=31.9
Q ss_pred eecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 47 SIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 47 ~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
.++..++|..+++.+--+--+++.||.-|+|+|.
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQ 79 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeee
Confidence 3678999999999999999999999999999997
No 102
>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=34.08 E-value=41 Score=27.42 Aligned_cols=45 Identities=18% Similarity=0.352 Sum_probs=36.8
Q ss_pred HHHHHhhCCCceecHHHHHHHh-----CCceeeehhhHHHHhhhhhhhhcC
Q 018790 36 FLKLYNRDGVESIGLDDAASRL-----GVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~L-----gV~RRRIYDIvNVLEslGli~K~~ 81 (350)
.++++... ...++.+++.++| .+.+=-+|-+++.|+..|+|.+..
T Consensus 6 Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~ 55 (116)
T cd07153 6 ILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIE 55 (116)
T ss_pred HHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEE
Confidence 45566554 4568999999988 578999999999999999999863
No 103
>PLN03239 histone acetyltransferase; Provisional
Probab=33.85 E-value=1.1e+02 Score=31.45 Aligned_cols=59 Identities=15% Similarity=0.186 Sum_probs=41.8
Q ss_pred CCCCCCCcHHHHHH------HHHHHHhhCC--CceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCC
Q 018790 21 FYSRKEKSLGLLCS------KFLKLYNRDG--VESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAK 82 (350)
Q Consensus 21 ~~sRkeKSLg~L~~------kFl~l~~~~~--~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~K 82 (350)
++.|-=.-||.+.- ..++++.... ...++|+++|...|+. .-||+..|+.+|++.....
T Consensus 250 ~PEkPLSdlG~~sY~~YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~---~~DIi~tL~~l~~l~~~~g 316 (351)
T PLN03239 250 SPEKPMSDLGQQAYIPYWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIM---AEDIVFALNQLGILKFING 316 (351)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHhCCC---HHHHHHHHHHCCcEEEECC
Confidence 34444446777662 2555554443 2579999999999995 5799999999999975433
No 104
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=33.82 E-value=43 Score=31.91 Aligned_cols=45 Identities=11% Similarity=0.168 Sum_probs=37.2
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhh
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIG 75 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslG 75 (350)
.+..+.+.++..+....++|+++|..+|+.+|.|.-++.-.-++.
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 456788899999888899999999999999998887776554443
No 105
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=33.73 E-value=42 Score=28.52 Aligned_cols=50 Identities=24% Similarity=0.365 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 29 LGLLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 29 Lg~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
|-.+=.+.|+.++.... +++.++|+++|+...-+...+.-||.-|+|.+.
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 34455677888877543 999999999999999999999999999999875
No 106
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=33.18 E-value=37 Score=30.09 Aligned_cols=39 Identities=26% Similarity=0.288 Sum_probs=33.7
Q ss_pred cHHHHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehh
Q 018790 28 SLGLLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYD 66 (350)
Q Consensus 28 SLg~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYD 66 (350)
.-..|.+..++++.+.+-..++++++|++.||.|.-||.
T Consensus 12 ~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~ 50 (213)
T PRK09975 12 TRQELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYW 50 (213)
T ss_pred HHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHH
Confidence 345677888899988887889999999999999999995
No 107
>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=33.17 E-value=24 Score=25.59 Aligned_cols=24 Identities=29% Similarity=0.588 Sum_probs=19.5
Q ss_pred ceecHHHHHHHhCCceeeehhhHH
Q 018790 46 ESIGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 46 ~~I~L~~aA~~LgV~RRRIYDIvN 69 (350)
..|++.++++.+|+.|.-||..++
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 368999999999999999999887
No 108
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=32.82 E-value=34 Score=32.20 Aligned_cols=38 Identities=21% Similarity=0.313 Sum_probs=30.4
Q ss_pred HHHHHHHHHhhCCCce-ecHHHHHHHhCCceeeehhhHH
Q 018790 32 LCSKFLKLYNRDGVES-IGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 32 L~~kFl~l~~~~~~~~-I~L~~aA~~LgV~RRRIYDIvN 69 (350)
...++++++.++-... +++.++|..+|+.+|.||-++-
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 3456777777665444 9999999999999999998875
No 109
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=32.30 E-value=44 Score=25.92 Aligned_cols=43 Identities=21% Similarity=0.244 Sum_probs=33.2
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhh
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVAR 79 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K 79 (350)
.++++... ...++-.++|+.+|+.+-..-=+++.||.-|.|++
T Consensus 5 Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~ 47 (62)
T PF04703_consen 5 ILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEGKVER 47 (62)
T ss_dssp HHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE
T ss_pred HHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 45555542 34588999999999998888888999999999986
No 110
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=32.20 E-value=40 Score=26.52 Aligned_cols=44 Identities=25% Similarity=0.428 Sum_probs=34.6
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
++..+...++... .++|..+++.+=-+--+++-||.-|+|.|..
T Consensus 27 ~L~~l~~~~~~~~--~~la~~l~i~~~~vt~~l~~Le~~glv~r~~ 70 (126)
T COG1846 27 VLLALYEAGGITV--KELAERLGLDRSTVTRLLKRLEDKGLIERLR 70 (126)
T ss_pred HHHHHHHhCCCcH--HHHHHHHCCCHHHHHHHHHHHHHCCCeeecC
Confidence 3444444444333 9999999999999999999999999999874
No 111
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=32.04 E-value=83 Score=29.15 Aligned_cols=59 Identities=10% Similarity=0.281 Sum_probs=43.8
Q ss_pred CcHHHHH-HHHHHHHhh---CCCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhhc-CCCce
Q 018790 27 KSLGLLC-SKFLKLYNR---DGVESI-GLDDAASRLGVERRRIYDVVNILESIGVVARQ-AKNLY 85 (350)
Q Consensus 27 KSLg~L~-~kFl~l~~~---~~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~-~KN~y 85 (350)
+++...+ ..+.+.+.. .|+..+ +-.++|++|||.|==+-+-+..|+..|+|+.. +++.|
T Consensus 6 ~~~~~~v~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~ 70 (251)
T PRK09990 6 RPIADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSF 70 (251)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeE
Confidence 4454433 334444433 577889 89999999999999999999999999999766 34433
No 112
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=31.81 E-value=80 Score=29.41 Aligned_cols=55 Identities=15% Similarity=0.135 Sum_probs=41.6
Q ss_pred HHHHHHHHHhh---CCCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhhc-CCCceE
Q 018790 32 LCSKFLKLYNR---DGVESI-GLDDAASRLGVERRRIYDVVNILESIGVVARQ-AKNLYS 86 (350)
Q Consensus 32 L~~kFl~l~~~---~~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~-~KN~y~ 86 (350)
+...+.+.+.. .|+..+ +-.++|++|||.|==+=+-+..|+..|+|+.. +++.|.
T Consensus 13 v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~V 72 (253)
T PRK11523 13 LAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHV 72 (253)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCeeEE
Confidence 34444444433 567788 58999999999999999999999999999755 444443
No 113
>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=31.53 E-value=27 Score=29.32 Aligned_cols=29 Identities=24% Similarity=0.448 Sum_probs=23.0
Q ss_pred cHHHHHHHhCCceeeehhhHHHHhhhhhh
Q 018790 49 GLDDAASRLGVERRRIYDVVNILESIGVV 77 (350)
Q Consensus 49 ~L~~aA~~LgV~RRRIYDIvNVLEslGli 77 (350)
++..+.+.-|..||-+.|+++.|..+|+.
T Consensus 23 nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~ 51 (90)
T PF09904_consen 23 NVPALMEATGMPRRTIQDTIKALPELGIE 51 (90)
T ss_dssp -HHHHHHHH---HHHHHHHHHGGGGGT-E
T ss_pred cHHHHHHHhCCCHhHHHHHHHHhhcCCeE
Confidence 89999999999999999999999999985
No 114
>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=31.17 E-value=62 Score=29.56 Aligned_cols=45 Identities=16% Similarity=0.251 Sum_probs=37.7
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
.+.|.++...+ .++..++|..||+.+=-+.-.++.|+.-|+|.+.
T Consensus 4 ~~IL~~L~~~~--~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQG--QATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 34666666543 3899999999999999999999999999999875
No 115
>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=31.15 E-value=76 Score=24.66 Aligned_cols=57 Identities=23% Similarity=0.292 Sum_probs=46.6
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEe
Q 018790 32 LCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQ 88 (350)
Q Consensus 32 L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~ 88 (350)
+-++.++++...++..+..-..+..|.++++.|==+..=|+.=|.|.|.+-+--.|.
T Consensus 5 ~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~~~~PP~W~ 61 (66)
T PF02295_consen 5 LEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKEGGTPPKWS 61 (66)
T ss_dssp HHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEECSSSTEEE
T ss_pred HHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeCCCCCCceE
Confidence 446677777766677788888999999999999999999999999999888888884
No 116
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.14 E-value=44 Score=27.95 Aligned_cols=41 Identities=24% Similarity=0.405 Sum_probs=33.7
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhh
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVV 77 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli 77 (350)
.+.++-+ ..+..++-++...-|-.||-+-|++-.|++||++
T Consensus 12 Yla~Li~-S~e~~nVP~lm~~TGwPRRT~QDvikAlpglgi~ 52 (95)
T COG4519 12 YLAYLID-SGETANVPELMAATGWPRRTAQDVIKALPGLGIV 52 (95)
T ss_pred HHHHHHh-ccccCChHHHHHHcCCchhHHHHHHHhCcCCCeE
Confidence 3444444 3457889999999999999999999999999987
No 117
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=31.09 E-value=36 Score=26.74 Aligned_cols=33 Identities=24% Similarity=0.329 Sum_probs=30.5
Q ss_pred HHHHHHHhCCceeeehhhHHHHhhhhhhhhcCC
Q 018790 50 LDDAASRLGVERRRIYDVVNILESIGVVARQAK 82 (350)
Q Consensus 50 L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~K 82 (350)
+.++|..|++.+=-++.++..|+.-|+|.+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 568999999999999999999999999999863
No 118
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=30.84 E-value=1.3e+02 Score=30.11 Aligned_cols=62 Identities=16% Similarity=0.169 Sum_probs=42.8
Q ss_pred CCCCCCCCcHHHHHH------HHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCce
Q 018790 20 QFYSRKEKSLGLLCS------KFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLY 85 (350)
Q Consensus 20 ~~~sRkeKSLg~L~~------kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y 85 (350)
.++.|-=.-||.+.- ..++.+.+ ....|+|++++...|+. .-||+..|+.+|++.....+.+
T Consensus 191 G~PEkPLSdlG~~sY~~YW~~~il~~L~~-~~~~isi~~is~~T~i~---~~Dii~tL~~l~~l~~~~g~~~ 258 (290)
T PLN03238 191 GTPERPLSDLGKVSFRSYWTRVLLEQLRD-VKGDVSIKDLSLATGIR---GEDIVSTLQSLNLIKYWKGQHV 258 (290)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHh-cCCCccHHHHHHHhCCC---HHHHHHHHHHCCcEEEECCcEE
Confidence 344444446777662 24555543 34679999999999995 5799999999999965433333
No 119
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=30.72 E-value=48 Score=25.97 Aligned_cols=53 Identities=11% Similarity=0.184 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEE
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSW 87 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W 87 (350)
.+....|..+. .+.....+++...++...++..+++-|+.-|+|++ ..+.|.=
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 34555666665 34577899999999999999999999999999966 5666655
No 120
>PF12728 HTH_17: Helix-turn-helix domain
Probab=30.45 E-value=24 Score=24.95 Aligned_cols=22 Identities=27% Similarity=0.593 Sum_probs=20.0
Q ss_pred ecHHHHHHHhCCceeeehhhHH
Q 018790 48 IGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 48 I~L~~aA~~LgV~RRRIYDIvN 69 (350)
+++.++|+-|||.+..||.+++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6789999999999999999885
No 121
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=29.99 E-value=22 Score=24.91 Aligned_cols=28 Identities=29% Similarity=0.509 Sum_probs=18.3
Q ss_pred ecHHHHHHHhCCceeeehhhHHHHhhhh
Q 018790 48 IGLDDAASRLGVERRRIYDVVNILESIG 75 (350)
Q Consensus 48 I~L~~aA~~LgV~RRRIYDIvNVLEslG 75 (350)
.+..++|..|||.++-+|.+++=++.-|
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 122
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=29.67 E-value=54 Score=32.49 Aligned_cols=50 Identities=20% Similarity=0.423 Sum_probs=39.7
Q ss_pred cHHHHH-HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhh
Q 018790 28 SLGLLC-SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVAR 79 (350)
Q Consensus 28 SLg~L~-~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K 79 (350)
+|+..+ -..|+++... +.++++++|+.||...--+--=+-|||-.|+|..
T Consensus 19 alaS~vRv~Il~lL~~k--~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT 69 (308)
T COG4189 19 ALASKVRVAILQLLHRK--GPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRT 69 (308)
T ss_pred HHHHHHHHHHHHHHHHh--CCCCHHHHHHHhCCchhhhhhhHHHHHhcCceee
Confidence 555555 3466777654 4589999999999999888888999999999964
No 123
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=29.45 E-value=59 Score=29.86 Aligned_cols=39 Identities=15% Similarity=0.253 Sum_probs=33.7
Q ss_pred ecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceE
Q 018790 48 IGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYS 86 (350)
Q Consensus 48 I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~ 86 (350)
++-.++|..||+.|.-+.=+++-|+.-|+|+..+.+++.
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 566899999999999999999999999999876545554
No 124
>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=29.25 E-value=55 Score=27.63 Aligned_cols=44 Identities=23% Similarity=0.418 Sum_probs=34.0
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCC
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAK 82 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~K 82 (350)
..|.+++...|+ +.|.++|.+|||....|+ ..|.-+|+.-|+..
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 456777777775 788999999999766555 67888899888743
No 125
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=28.33 E-value=48 Score=31.14 Aligned_cols=42 Identities=5% Similarity=0.050 Sum_probs=34.2
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhh
Q 018790 32 LCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILES 73 (350)
Q Consensus 32 L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEs 73 (350)
...+++.++..+....++|+++|+.+|+.+++|.-++-=--+
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 467788888888888999999999999999988776654433
No 126
>PRK10870 transcriptional repressor MprA; Provisional
Probab=28.29 E-value=49 Score=29.82 Aligned_cols=38 Identities=24% Similarity=0.323 Sum_probs=34.0
Q ss_pred CCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 43 DGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 43 ~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
.+...++..++|..+++.+=-+--+++-||.-|+|.|.
T Consensus 67 ~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~ 104 (176)
T PRK10870 67 QENHSIQPSELSCALGSSRTNATRIADELEKRGWIERR 104 (176)
T ss_pred CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 34567889999999999999999999999999999996
No 127
>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=27.94 E-value=29 Score=23.15 Aligned_cols=23 Identities=26% Similarity=0.276 Sum_probs=19.2
Q ss_pred ecHHHHHHHhCCceeeehhhHHH
Q 018790 48 IGLDDAASRLGVERRRIYDVVNI 70 (350)
Q Consensus 48 I~L~~aA~~LgV~RRRIYDIvNV 70 (350)
+++.++|..|||.++-||..+.-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 46789999999999998887663
No 128
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=27.77 E-value=25 Score=30.22 Aligned_cols=41 Identities=29% Similarity=0.406 Sum_probs=29.5
Q ss_pred CCCCcHHHHH-HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHH
Q 018790 24 RKEKSLGLLC-SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNI 70 (350)
Q Consensus 24 RkeKSLg~L~-~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNV 70 (350)
|+.-.-|++. ..|++- .-++..++|+.|||.|.+|-.|||=
T Consensus 5 ~~P~~PGEiL~eeflep------~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 5 RKPAHPGEILREEFLEP------LGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred CCCCCchHHHHHHHhcc------ccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 3344455533 455542 2388999999999999999999983
No 129
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=27.76 E-value=62 Score=33.04 Aligned_cols=58 Identities=16% Similarity=0.167 Sum_probs=44.3
Q ss_pred CCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecCCChHHHHHHHHH
Q 018790 44 GVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGFDAIPEALEVLKE 102 (350)
Q Consensus 44 ~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~~nI~~tL~~Lke 102 (350)
.+..++.+++++++++.-+.+-||+.-|+..|+|.+...+.|. .+.+-=.-+|.++.+
T Consensus 307 ~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~~~g~~~-l~rd~~~itL~dv~~ 364 (412)
T PRK04214 307 HGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRGERGQWV-LARDLDSVPLAELYE 364 (412)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEecCCCceE-ecCCHHhCcHHHHHH
Confidence 3457899999999999999999999999999999987666544 333322335666654
No 130
>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=27.68 E-value=32 Score=24.17 Aligned_cols=31 Identities=32% Similarity=0.631 Sum_probs=24.5
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehh
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYD 66 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYD 66 (350)
-++++...+-..++++++|++.||.+.-||-
T Consensus 5 a~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~ 35 (47)
T PF00440_consen 5 ALELFAEKGYEAVSIRDIARRAGVSKGSFYR 35 (47)
T ss_dssp HHHHHHHHHTTTSSHHHHHHHHTSCHHHHHH
T ss_pred HHHHHHHhCHHhCCHHHHHHHHccchhhHHH
Confidence 3455666666779999999999999988873
No 131
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=27.55 E-value=33 Score=25.05 Aligned_cols=28 Identities=21% Similarity=0.334 Sum_probs=23.8
Q ss_pred ecHHHHHHHhCCceeeehhhHHHHhhhh
Q 018790 48 IGLDDAASRLGVERRRIYDVVNILESIG 75 (350)
Q Consensus 48 I~L~~aA~~LgV~RRRIYDIvNVLEslG 75 (350)
++|+++|..+|+..+.|+.+++-.-++.
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~s 29 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGTT 29 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCcC
Confidence 6899999999999999999998664443
No 132
>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=26.94 E-value=18 Score=35.02 Aligned_cols=32 Identities=31% Similarity=0.669 Sum_probs=25.7
Q ss_pred HHHHHhC---CceeeehhhHHHHhhhhhhhhcCCC
Q 018790 52 DAASRLG---VERRRIYDVVNILESIGVVARQAKN 83 (350)
Q Consensus 52 ~aA~~Lg---V~RRRIYDIvNVLEslGli~K~~KN 83 (350)
.+|+.+| +..|++||+++-||.+|+|.....+
T Consensus 319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~~~ 353 (365)
T TIGR02928 319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAEERN 353 (365)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEEEc
Confidence 4566666 4589999999999999999876443
No 133
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=26.90 E-value=73 Score=27.26 Aligned_cols=46 Identities=20% Similarity=0.341 Sum_probs=37.0
Q ss_pred HHHHHHHHhhCC--CceecHHHHHHHhCCceeeehhhHHHHhhhhhhh
Q 018790 33 CSKFLKLYNRDG--VESIGLDDAASRLGVERRRIYDVVNILESIGVVA 78 (350)
Q Consensus 33 ~~kFl~l~~~~~--~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~ 78 (350)
...|..++...+ ...++|+++|+.|.+.+|-.==|++=|+..|.|.
T Consensus 3 ~~~y~~L~~~~~~~~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~ 50 (115)
T PF12793_consen 3 LEQYQRLWQHYGGQPVEVTLDELAELLFCSRRNARTLLKKMQEEGWIT 50 (115)
T ss_pred HHHHHHHHHHcCCCCcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 455666665544 4568999999999999999999999999988874
No 134
>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=26.72 E-value=33 Score=29.21 Aligned_cols=32 Identities=34% Similarity=0.722 Sum_probs=21.9
Q ss_pred HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHH
Q 018790 36 FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNI 70 (350)
Q Consensus 36 Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNV 70 (350)
.+++|-. ..++|.++|+.+||.|=-+||.+.-
T Consensus 25 ~l~lyy~---eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 25 ILELYYE---EDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp HHHHHCT---S---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHc---cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4444433 4599999999999999999998764
No 135
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=25.89 E-value=38 Score=28.97 Aligned_cols=35 Identities=20% Similarity=0.174 Sum_probs=33.0
Q ss_pred ceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 46 ESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 46 ~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
+.++..++|..+++.+=-+--+++-||.-|+|.|.
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 35899999999999999999999999999999987
No 136
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=25.28 E-value=71 Score=29.02 Aligned_cols=58 Identities=17% Similarity=0.258 Sum_probs=45.2
Q ss_pred CceecHHHHHHHh--CCceeeehhhHHHHhhhhhhhhcCCCceEE------ecCCChHHHHHHHHH
Q 018790 45 VESIGLDDAASRL--GVERRRIYDVVNILESIGVVARQAKNLYSW------QGFDAIPEALEVLKE 102 (350)
Q Consensus 45 ~~~I~L~~aA~~L--gV~RRRIYDIvNVLEslGli~K~~KN~y~W------~G~~nI~~tL~~Lke 102 (350)
+..-+...+|.++ +|.--.+=+.++.|+-+|+|+|.+.+.|.= .|.+..+.++..+..
T Consensus 37 ~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~~~~~~~avr~~h~ 102 (171)
T PF14394_consen 37 PFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTSSEIPSEAVRSYHK 102 (171)
T ss_pred CCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeCCCCCcHHHHHHHHH
Confidence 3344999999999 999999999999999999999997755433 234555667777663
No 137
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=25.09 E-value=69 Score=30.90 Aligned_cols=43 Identities=9% Similarity=0.039 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhh
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILES 73 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEs 73 (350)
....++++++..+....++|+++|+.+|+.+|.|.-.+.-.-+
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g 260 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATG 260 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 4567888999998888899999999999999999888775544
No 138
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=24.94 E-value=66 Score=31.12 Aligned_cols=40 Identities=10% Similarity=0.219 Sum_probs=33.6
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHH
Q 018790 32 LCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNIL 71 (350)
Q Consensus 32 L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVL 71 (350)
..++.+.++..+....+++.++|..+|+.+|.+.-++.--
T Consensus 192 ~i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~~ 231 (302)
T PRK10371 192 YVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRV 231 (302)
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4677888888877778999999999999999888777654
No 139
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=24.84 E-value=72 Score=30.72 Aligned_cols=52 Identities=19% Similarity=0.318 Sum_probs=39.7
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCce
Q 018790 32 LCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLY 85 (350)
Q Consensus 32 L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y 85 (350)
--.+.++++.+.+ .+++.++|+.|+|..+=|.==+..||.-|++.|.....+
T Consensus 18 R~~~Il~~L~~~~--~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~GGa~ 69 (269)
T PRK09802 18 RREQIIQRLRQQG--SVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGAL 69 (269)
T ss_pred HHHHHHHHHHHcC--CEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeCCEE
Confidence 3455677777754 399999999999987666555667899999999875543
No 140
>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=24.16 E-value=1.1e+02 Score=28.09 Aligned_cols=44 Identities=18% Similarity=0.176 Sum_probs=37.8
Q ss_pred CCCcee-cHHHHHHHhCCceeeehhhHHHHhhhhhhhhc-CCCceE
Q 018790 43 DGVESI-GLDDAASRLGVERRRIYDVVNILESIGVVARQ-AKNLYS 86 (350)
Q Consensus 43 ~~~~~I-~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~-~KN~y~ 86 (350)
.|+..+ +-.++|++|||.|==+=+-+-.|+.-|+|+.. +++.|.
T Consensus 25 ~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~~G~~V 70 (235)
T TIGR02812 25 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKV 70 (235)
T ss_pred CCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCccEe
Confidence 577889 89999999999999999999999999999765 445443
No 141
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=24.05 E-value=91 Score=30.33 Aligned_cols=56 Identities=32% Similarity=0.493 Sum_probs=44.8
Q ss_pred cHHHHHHHHHH-HHhhCCCceecHHHHHHHhCCceeeehhhHH-HHhhhhhhhhcCCC
Q 018790 28 SLGLLCSKFLK-LYNRDGVESIGLDDAASRLGVERRRIYDVVN-ILESIGVVARQAKN 83 (350)
Q Consensus 28 SLg~L~~kFl~-l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvN-VLEslGli~K~~KN 83 (350)
.|.....+++. ++..-.+..+.++.+|..||.....+-|++- .|-..|+|.+....
T Consensus 256 ~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 313 (328)
T PRK00080 256 GLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRG 313 (328)
T ss_pred CCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCch
Confidence 45566777776 5566566689999999999999998888888 88888999877654
No 142
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.03 E-value=1.5e+02 Score=29.44 Aligned_cols=72 Identities=17% Similarity=0.371 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc--CCCceEEecCCChHHHHHHHHHhc
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ--AKNLYSWQGFDAIPEALEVLKEEG 104 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~--~KN~y~W~G~~nI~~tL~~Lkeeg 104 (350)
.|...||+|+.... ++.|+++|..+|..---..+=|.-|-.=|+++-+ +.++|+++...-+...-.-++..|
T Consensus 200 nll~eFv~YIk~nK--vV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~eEl~AVAkfIkqrG 273 (299)
T KOG3054|consen 200 NLLSEFVEYIKKNK--VVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISMEELAAVAKFIKQRG 273 (299)
T ss_pred HHHHHHHHHHHhcC--eeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecHHHHHHHHHHHHHcC
Confidence 57889999999864 6999999999998533222222233334555543 567899987655544434444444
No 143
>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=23.62 E-value=31 Score=24.04 Aligned_cols=35 Identities=26% Similarity=0.427 Sum_probs=21.3
Q ss_pred HHHHHHHHHH-HhhCCCceecHHHHHHHhCCceeeehhh
Q 018790 30 GLLCSKFLKL-YNRDGVESIGLDDAASRLGVERRRIYDV 67 (350)
Q Consensus 30 g~L~~kFl~l-~~~~~~~~I~L~~aA~~LgV~RRRIYDI 67 (350)
..+=+.+|.. +.... -++..+|..||+.|+-||.=
T Consensus 3 ~~~E~~~i~~aL~~~~---gn~~~aA~~Lgisr~tL~~k 38 (42)
T PF02954_consen 3 EEFEKQLIRQALERCG---GNVSKAARLLGISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHHHHTT---T-HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHHHHhC---CCHHHHHHHHCCCHHHHHHH
Confidence 3344445543 33332 25689999999999988853
No 144
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=23.37 E-value=2e+02 Score=30.63 Aligned_cols=65 Identities=15% Similarity=0.288 Sum_probs=44.6
Q ss_pred CCCCCCCcHHHHHHH------HHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEec
Q 018790 21 FYSRKEKSLGLLCSK------FLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQG 89 (350)
Q Consensus 21 ~~sRkeKSLg~L~~k------Fl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G 89 (350)
++.|-=.-||.++-+ .++++... ...++|++++...++. .-||+..|+.+||+.......+.-+.
T Consensus 343 ~PEkPLSdlG~~sY~~YW~~~i~~~L~~~-~~~~si~~is~~T~i~---~~Dii~tL~~l~~l~~~kg~~~i~~~ 413 (450)
T PLN00104 343 TPERPLSDLGLVSYRGYWTRVLLEILKKH-KGNISIKELSDMTAIK---AEDIVSTLQSLNLIQYRKGQHVICAD 413 (450)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHhc-CCCccHHHHHHHhCCC---HHHHHHHHHHCCCEEecCCcEEEEEC
Confidence 344444467777632 55555543 3579999999999995 57999999999999765333334343
No 145
>smart00351 PAX Paired Box domain.
Probab=23.28 E-value=75 Score=27.18 Aligned_cols=45 Identities=11% Similarity=0.138 Sum_probs=36.4
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 32 LCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 32 L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
+=.++|.++... .+..++|.+|||.+.-+|-|++=...-|.+.-.
T Consensus 22 ~R~riv~~~~~G----~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk 66 (125)
T smart00351 22 ERQRIVELAQNG----VRPCDISRQLCVSHGCVSKILGRYYETGSIRPG 66 (125)
T ss_pred HHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCc
Confidence 446788888642 578899999999999999999999888876543
No 146
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=23.14 E-value=1.2e+02 Score=25.96 Aligned_cols=46 Identities=15% Similarity=0.154 Sum_probs=36.4
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGVVARQA 81 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~ 81 (350)
..|..+... .+.+.+.++|..|+|.+=-+-.+++-|+.-|+|.+..
T Consensus 11 ~~I~~l~~~--~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 11 EQIYLLIEE--KGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred HHHHHHHhc--CCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEec
Confidence 333444433 3457899999999999999999999999999998653
No 147
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=22.86 E-value=89 Score=30.47 Aligned_cols=52 Identities=19% Similarity=0.292 Sum_probs=39.2
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHHHhhhhh-hhhcCCCceEE
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNILESIGV-VARQAKNLYSW 87 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNVLEslGl-i~K~~KN~y~W 87 (350)
.+.+.++.+ +..++..++|++|||.|.-++-.+..|+..|+ |.......|..
T Consensus 7 ~~il~~L~~--~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~~~~Gy~L 59 (319)
T PRK11886 7 LQLLSLLAD--GDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSVKGKGYRL 59 (319)
T ss_pred HHHHHHHHc--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEecCCeEEe
Confidence 356666655 35688889999999999999999999999999 44332223544
No 148
>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=22.70 E-value=36 Score=26.70 Aligned_cols=42 Identities=29% Similarity=0.420 Sum_probs=29.5
Q ss_pred eecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcC---CCceEEe
Q 018790 47 SIGLDDAASRLGVERRRIYDVVNILESIGVVARQA---KNLYSWQ 88 (350)
Q Consensus 47 ~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~---KN~y~W~ 88 (350)
.+.-..+|++.|+.|.-|-.-+-=||+.|+|+-.+ |+.|.=.
T Consensus 4 ~lvas~iAd~~GiTRSvIVNALRKleSaGvIesrSlGmKGT~ikv 48 (61)
T PF08222_consen 4 RLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKV 48 (61)
T ss_dssp EE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEEETTSS-EEEEE
T ss_pred eehHHHHHHHhCccHHHHHHHHHHHHhcCceeecccCCCceeeee
Confidence 45567899999999998888888899999998654 3555443
No 149
>PF06830 Root_cap: Root cap; InterPro: IPR009646 The cells at the periphery of the root cap are continuously sloughed off from the root into the mucilage, and are thought to be programmed to die [].This family represents a conserved region approximately 60 residues in length within plant root cap proteins, which may be involved in the process.
Probab=22.42 E-value=31 Score=26.77 Aligned_cols=13 Identities=46% Similarity=0.879 Sum_probs=11.4
Q ss_pred hhhhcCCcccchH
Q 018790 312 LASTFRPKYHNEA 324 (350)
Q Consensus 312 la~~~~pqy~n~~ 324 (350)
|-+||||-|.|++
T Consensus 15 LGQTYr~~yvn~v 27 (57)
T PF06830_consen 15 LGQTYRPDYVNPV 27 (57)
T ss_pred ccccccCCccccc
Confidence 6789999999984
No 150
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=22.41 E-value=88 Score=27.56 Aligned_cols=36 Identities=22% Similarity=0.408 Sum_probs=32.3
Q ss_pred eecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCC
Q 018790 47 SIGLDDAASRLGVERRRIYDVVNILESIGVVARQAK 82 (350)
Q Consensus 47 ~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~K 82 (350)
.++-.++|..||+.|+.+.=+++-|+.-|+|....+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~ 203 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGK 203 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 577799999999999999999999999999987644
No 151
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=22.39 E-value=52 Score=30.48 Aligned_cols=35 Identities=29% Similarity=0.445 Sum_probs=29.8
Q ss_pred ceecHHHHHHHhCCceeeehhhHHHHhhhhhhhhc
Q 018790 46 ESIGLDDAASRLGVERRRIYDVVNILESIGVVARQ 80 (350)
Q Consensus 46 ~~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~ 80 (350)
-.|....+|+.+||.||-+|+.++-.|+=.-+.+.
T Consensus 40 IEI~~t~iAka~gVdRrvV~~Ti~~I~sd~~L~~i 74 (167)
T COG2150 40 IEIPITKIAKATGVDRRVVYATIELIESDEELRRI 74 (167)
T ss_pred EEechHHHHHHhCcchHhHHHHHHHHhcCHHHHHH
Confidence 46899999999999999999999988876666554
No 152
>PRK15185 transcriptional regulator HilD; Provisional
Probab=22.35 E-value=81 Score=31.74 Aligned_cols=39 Identities=10% Similarity=0.117 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHH
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvN 69 (350)
.++.++..++..++...++++++|+.+|+.+|.|+-.+.
T Consensus 206 ~~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK 244 (309)
T PRK15185 206 TLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLA 244 (309)
T ss_pred HHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 466788888888888999999999999999999877654
No 153
>PTZ00064 histone acetyltransferase; Provisional
Probab=22.21 E-value=67 Score=34.65 Aligned_cols=48 Identities=19% Similarity=0.303 Sum_probs=36.3
Q ss_pred ecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCCCceEEecCCChHHHHH
Q 018790 48 IGLDDAASRLGVERRRIYDVVNILESIGVVARQAKNLYSWQGFDAIPEALE 98 (350)
Q Consensus 48 I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~KN~y~W~G~~nI~~tL~ 98 (350)
|+|++++...|+. ..||+..|+.+||+.......+.-.-..-|...++
T Consensus 472 iSI~dIS~~TgI~---~eDII~TLq~L~llky~kgq~~I~~~~~~ie~~~~ 519 (552)
T PTZ00064 472 KFIDNVVRSTGIR---REDVIRILEENGIMRNIKDQHYIFCNQEFLKGIVK 519 (552)
T ss_pred ccHHHHHHHhCCC---HHHHHHHHHHCCcEEEeCCCEEEEECHHHHHHHHH
Confidence 8999999999995 57999999999999876555555554443444433
No 154
>PRK13502 transcriptional activator RhaR; Provisional
Probab=22.10 E-value=73 Score=29.73 Aligned_cols=40 Identities=13% Similarity=0.081 Sum_probs=33.1
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHHH
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVNI 70 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvNV 70 (350)
.+..++++++.++-...++++++|..+|+..|.|.-++--
T Consensus 176 ~~~~~~~~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~ 215 (282)
T PRK13502 176 TLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRA 215 (282)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3567888888887777799999999999999998877653
No 155
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=22.06 E-value=72 Score=31.36 Aligned_cols=39 Identities=13% Similarity=0.075 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHH
Q 018790 31 LLCSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 31 ~L~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvN 69 (350)
....++++++.++....++|+++|..+|+.+|-|+-++.
T Consensus 142 ~~~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk 180 (274)
T PRK09978 142 NMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLR 180 (274)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 356788999999888899999999999999998776663
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=21.99 E-value=1.2e+02 Score=17.57 Aligned_cols=30 Identities=27% Similarity=0.429 Sum_probs=21.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCceeeehhh
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVERRRIYDV 67 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDI 67 (350)
..++.++... .++.++|..+|+.+.-||-+
T Consensus 12 ~~i~~~~~~~----~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 12 EEARRLLAAG----ESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHHHHHHHcC----CCHHHHHHHHCCCHHHHHHh
Confidence 3445555432 48999999999998877754
No 157
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=21.99 E-value=63 Score=22.72 Aligned_cols=37 Identities=19% Similarity=0.217 Sum_probs=22.6
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHhCCceeeehhhHH
Q 018790 33 CSKFLKLYNRDGVESIGLDDAASRLGVERRRIYDVVN 69 (350)
Q Consensus 33 ~~kFl~l~~~~~~~~I~L~~aA~~LgV~RRRIYDIvN 69 (350)
+.+|.+++...-....++.++|..+||.--.+..|++
T Consensus 13 T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 13 TKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 4444444433222237999999999998555555543
No 158
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=21.12 E-value=85 Score=28.59 Aligned_cols=35 Identities=23% Similarity=0.498 Sum_probs=30.1
Q ss_pred eecHHHHHHHhCCceee--------------ehhhHHHHhhhhhhhhcC
Q 018790 47 SIGLDDAASRLGVERRR--------------IYDVVNILESIGVVARQA 81 (350)
Q Consensus 47 ~I~L~~aA~~LgV~RRR--------------IYDIvNVLEslGli~K~~ 81 (350)
.|.+..++..+|..+|| |=-++..||.+|+|++..
T Consensus 67 pvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 67 PVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred CccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 58899999999997664 778999999999999875
No 159
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.91 E-value=59 Score=27.22 Aligned_cols=54 Identities=20% Similarity=0.355 Sum_probs=40.1
Q ss_pred ecHHHHHHHhCCceeeehhhHHHHhhhhhhh--hcCCCceEEecCCChHH--HHHHHHHhch
Q 018790 48 IGLDDAASRLGVERRRIYDVVNILESIGVVA--RQAKNLYSWQGFDAIPE--ALEVLKEEGL 105 (350)
Q Consensus 48 I~L~~aA~~LgV~RRRIYDIvNVLEslGli~--K~~KN~y~W~G~~nI~~--tL~~Lkeeg~ 105 (350)
+++.++|..+||..+-| --.|..|++. +...|.|.+.....+.. .|..|++.|+
T Consensus 1 ~~I~eva~~~gvs~~tL----RyYe~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~ 58 (123)
T cd04770 1 MKIGELAKAAGVSPDTI----RYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGF 58 (123)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCC
Confidence 36889999999998744 3478889996 34567899988776654 5666777663
No 160
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=20.46 E-value=1e+02 Score=28.07 Aligned_cols=36 Identities=22% Similarity=0.249 Sum_probs=32.5
Q ss_pred eecHHHHHHHhCCceeeehhhHHHHhhhhhhhhcCC
Q 018790 47 SIGLDDAASRLGVERRRIYDVVNILESIGVVARQAK 82 (350)
Q Consensus 47 ~I~L~~aA~~LgV~RRRIYDIvNVLEslGli~K~~K 82 (350)
.++-.++|..||+.|+-+.=+++-|+--|+|++..+
T Consensus 169 ~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~ 204 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKR 204 (226)
T ss_pred cchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCC
Confidence 357799999999999999999999999999998754
No 161
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.01 E-value=96 Score=26.97 Aligned_cols=37 Identities=24% Similarity=0.513 Sum_probs=28.6
Q ss_pred HHHHHHHhhCCCceecHHHHHHHhCCc----eeeehhhHHHHhh
Q 018790 34 SKFLKLYNRDGVESIGLDDAASRLGVE----RRRIYDVVNILES 73 (350)
Q Consensus 34 ~kFl~l~~~~~~~~I~L~~aA~~LgV~----RRRIYDIvNVLEs 73 (350)
..||..|-...+ +|.+++..|||. |-||.+|+..|..
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 568877766544 699999999996 8899998766543
Done!