Query psy8797
Match_columns 122
No_of_seqs 149 out of 328
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 19:31:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8797.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8797hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2577|consensus 100.0 3.9E-32 8.5E-37 228.3 7.3 107 16-122 20-133 (354)
2 PF02319 E2F_TDP: E2F/DP famil 99.9 3.2E-27 6.9E-32 158.1 6.4 66 57-122 1-71 (71)
3 KOG2578|consensus 99.9 1.4E-22 3E-27 169.6 4.1 70 53-122 17-86 (388)
4 KOG2578|consensus 99.6 3.3E-16 7.3E-21 131.4 6.1 121 2-122 85-237 (388)
5 KOG2829|consensus 98.2 2.5E-06 5.4E-11 71.7 6.4 61 59-122 43-125 (326)
6 PF01978 TrmB: Sugar-specific 96.8 0.0027 6E-08 40.8 4.7 51 68-120 12-62 (68)
7 PF08279 HTH_11: HTH domain; 96.1 0.022 4.8E-07 34.9 5.5 41 67-108 3-43 (55)
8 cd00092 HTH_CRP helix_turn_hel 95.9 0.036 7.8E-07 34.5 5.9 54 65-118 5-63 (67)
9 smart00420 HTH_DEOR helix_turn 95.8 0.034 7.4E-07 32.6 5.0 46 68-115 4-49 (53)
10 smart00346 HTH_ICLR helix_turn 95.7 0.046 1E-06 36.0 5.8 48 66-114 7-54 (91)
11 PF09339 HTH_IclR: IclR helix- 95.2 0.039 8.5E-07 33.9 4.1 46 67-113 6-51 (52)
12 smart00550 Zalpha Z-DNA-bindin 95.2 0.07 1.5E-06 34.9 5.4 55 66-120 8-62 (68)
13 PF13412 HTH_24: Winged helix- 94.8 0.1 2.2E-06 31.3 4.9 43 67-111 6-48 (48)
14 PF12802 MarR_2: MarR family; 94.7 0.11 2.3E-06 32.0 5.0 46 68-113 9-54 (62)
15 PF02082 Rrf2: Transcriptional 94.3 0.24 5.3E-06 33.0 6.4 49 65-113 9-58 (83)
16 smart00418 HTH_ARSR helix_turn 94.2 0.12 2.5E-06 30.7 4.3 37 78-114 8-44 (66)
17 TIGR02944 suf_reg_Xantho FeS a 94.0 0.15 3.2E-06 36.4 5.1 48 66-113 11-58 (130)
18 PF13730 HTH_36: Helix-turn-he 93.1 0.19 4.2E-06 30.6 3.9 29 82-110 27-55 (55)
19 PF01047 MarR: MarR family; I 92.7 0.24 5.2E-06 30.4 4.0 44 69-114 8-51 (59)
20 cd00090 HTH_ARSR Arsenical Res 92.5 0.45 9.8E-06 28.7 5.0 45 67-114 10-54 (78)
21 smart00419 HTH_CRP helix_turn_ 92.3 0.28 6.1E-06 28.4 3.7 38 80-118 8-45 (48)
22 PF09079 Cdc6_C: CDC6, C termi 92.2 0.12 2.5E-06 34.6 2.3 30 85-114 27-59 (85)
23 PF13463 HTH_27: Winged helix 92.0 0.52 1.1E-05 29.3 5.0 38 76-113 14-51 (68)
24 smart00345 HTH_GNTR helix_turn 91.9 0.55 1.2E-05 28.0 4.8 40 77-116 16-56 (60)
25 cd08768 Cdc6_C Winged-helix do 91.8 0.18 4E-06 33.2 2.8 22 92-113 44-65 (87)
26 PF00392 GntR: Bacterial regul 91.1 0.51 1.1E-05 29.9 4.3 40 77-116 20-60 (64)
27 TIGR00738 rrf2_super rrf2 fami 90.3 1.1 2.4E-05 31.6 5.8 36 78-113 23-58 (132)
28 PF01726 LexA_DNA_bind: LexA D 89.5 0.65 1.4E-05 30.5 3.8 47 69-115 14-61 (65)
29 PF01022 HTH_5: Bacterial regu 89.0 1.1 2.4E-05 26.9 4.3 41 69-112 7-47 (47)
30 COG3355 Predicted transcriptio 88.9 0.74 1.6E-05 34.4 4.2 44 69-114 33-76 (126)
31 PF09012 FeoC: FeoC like trans 88.7 0.37 8E-06 31.2 2.2 45 70-116 6-50 (69)
32 PRK10163 DNA-binding transcrip 88.5 1.4 3E-05 35.3 5.8 48 66-114 27-74 (271)
33 PF04182 B-block_TFIIIC: B-blo 88.1 1.2 2.5E-05 29.6 4.3 49 67-115 5-53 (75)
34 PRK09834 DNA-binding transcrip 87.1 1.7 3.7E-05 34.5 5.5 51 68-119 15-66 (263)
35 PF08220 HTH_DeoR: DeoR-like h 87.0 1.7 3.6E-05 27.4 4.4 45 68-114 4-48 (57)
36 TIGR00122 birA_repr_reg BirA b 86.9 1.6 3.5E-05 27.9 4.4 40 68-110 4-43 (69)
37 cd07377 WHTH_GntR Winged helix 86.8 2.9 6.2E-05 25.3 5.3 34 81-114 26-59 (66)
38 smart00344 HTH_ASNC helix_turn 86.3 1.6 3.5E-05 29.6 4.4 47 65-113 4-50 (108)
39 smart00347 HTH_MARR helix_turn 86.2 2.2 4.8E-05 27.6 4.8 44 68-113 14-57 (101)
40 COG1378 Predicted transcriptio 86.2 0.9 1.9E-05 36.8 3.5 36 79-114 29-64 (247)
41 PF12840 HTH_20: Helix-turn-he 86.1 1.2 2.7E-05 27.9 3.5 46 67-114 13-58 (61)
42 PF08784 RPA_C: Replication pr 85.8 1.9 4.1E-05 29.6 4.5 50 61-110 44-95 (102)
43 TIGR02716 C20_methyl_CrtF C-20 85.5 0.91 2E-05 36.5 3.2 40 78-118 21-60 (306)
44 TIGR01610 phage_O_Nterm phage 84.7 3.7 7.9E-05 28.3 5.6 37 78-114 45-81 (95)
45 TIGR02010 IscR iron-sulfur clu 84.0 3.1 6.7E-05 30.0 5.2 37 77-113 22-58 (135)
46 PF01325 Fe_dep_repress: Iron 83.9 4.7 0.0001 25.8 5.5 41 73-114 16-56 (60)
47 COG2739 Uncharacterized protei 83.9 1.3 2.8E-05 32.4 3.1 41 63-103 16-56 (105)
48 TIGR01764 excise DNA binding d 83.9 1.1 2.4E-05 25.7 2.3 23 81-103 2-24 (49)
49 PF13518 HTH_28: Helix-turn-he 83.7 1.4 3.1E-05 26.0 2.8 37 69-109 5-41 (52)
50 PF08280 HTH_Mga: M protein tr 83.2 2.7 5.9E-05 26.5 4.1 36 68-105 9-44 (59)
51 PRK11511 DNA-binding transcrip 82.9 3.2 7E-05 29.6 4.9 45 62-106 7-51 (127)
52 TIGR01889 Staph_reg_Sar staphy 82.8 3.2 7E-05 28.8 4.7 45 70-114 31-77 (109)
53 PRK09954 putative kinase; Prov 82.5 2.2 4.7E-05 35.0 4.3 46 66-113 5-50 (362)
54 PRK10857 DNA-binding transcrip 82.3 2.6 5.7E-05 32.1 4.4 38 76-113 21-58 (164)
55 TIGR02431 pcaR_pcaU beta-ketoa 82.1 3.4 7.5E-05 32.3 5.1 50 67-118 12-61 (248)
56 PF13545 HTH_Crp_2: Crp-like h 82.0 2.6 5.5E-05 26.8 3.7 36 80-115 28-63 (76)
57 PRK10219 DNA-binding transcrip 82.0 3.9 8.4E-05 27.9 4.8 43 64-106 5-47 (107)
58 COG1414 IclR Transcriptional r 81.0 4.5 9.7E-05 32.3 5.5 51 67-118 7-58 (246)
59 PRK00215 LexA repressor; Valid 80.9 3.7 7.9E-05 31.2 4.8 42 75-116 18-60 (205)
60 PRK15090 DNA-binding transcrip 80.4 4.7 0.0001 31.8 5.4 47 67-115 17-63 (257)
61 COG1474 CDC6 Cdc6-related prot 79.9 1.6 3.4E-05 37.2 2.7 30 83-112 304-333 (366)
62 TIGR02337 HpaR homoprotocatech 79.0 3.9 8.4E-05 28.4 4.1 43 69-113 33-75 (118)
63 TIGR02297 HpaA 4-hydroxyphenyl 78.6 3.8 8.2E-05 31.9 4.3 45 64-108 186-230 (287)
64 PRK11050 manganese transport r 78.4 8.9 0.00019 28.4 6.1 41 78-118 49-89 (152)
65 PF05732 RepL: Firmicute plasm 78.3 3.7 8.1E-05 31.4 4.1 39 80-118 75-113 (165)
66 TIGR02366 DHAK_reg probable di 77.9 4.1 8.8E-05 29.5 4.0 35 64-98 7-41 (176)
67 PRK11014 transcriptional repre 77.9 5.3 0.00012 29.0 4.7 41 75-115 20-60 (141)
68 COG3093 VapI Plasmid maintenan 77.5 2.2 4.7E-05 31.1 2.4 32 65-102 14-45 (104)
69 COG1510 Predicted transcriptio 77.3 4 8.6E-05 32.3 4.0 36 78-113 39-74 (177)
70 PF14394 DUF4423: Domain of un 76.9 6.6 0.00014 30.0 5.1 43 76-118 35-79 (171)
71 PHA02943 hypothetical protein; 76.9 6.2 0.00013 31.0 4.9 47 67-116 14-60 (165)
72 TIGR00498 lexA SOS regulatory 76.8 5.5 0.00012 30.1 4.6 48 68-115 10-61 (199)
73 cd07153 Fur_like Ferric uptake 76.3 7.7 0.00017 26.6 4.9 45 69-114 6-55 (116)
74 COG4519 Uncharacterized protei 75.6 6 0.00013 28.2 4.2 41 69-110 12-52 (95)
75 COG4189 Predicted transcriptio 75.0 4.9 0.00011 33.9 4.1 52 60-113 18-70 (308)
76 PF03374 ANT: Phage antirepres 74.6 5 0.00011 27.7 3.6 41 69-113 14-54 (111)
77 PF01853 MOZ_SAS: MOZ/SAS fami 73.9 6.8 0.00015 31.2 4.6 60 56-118 119-185 (188)
78 TIGR01884 cas_HTH CRISPR locus 73.3 10 0.00022 29.1 5.3 45 68-114 147-191 (203)
79 COG1846 MarR Transcriptional r 73.0 8.1 0.00018 25.5 4.2 44 69-114 27-70 (126)
80 PRK10411 DNA-binding transcrip 72.9 9.1 0.0002 30.4 5.2 47 67-115 7-53 (240)
81 PRK13509 transcriptional repre 72.8 6.9 0.00015 31.2 4.5 46 68-115 9-54 (251)
82 PRK10130 transcriptional regul 72.5 5.1 0.00011 33.8 3.8 43 63-105 239-281 (350)
83 PF09904 HTH_43: Winged helix- 72.1 5.5 0.00012 28.4 3.3 29 82-110 23-51 (90)
84 PRK14165 winged helix-turn-hel 71.9 9.8 0.00021 30.5 5.1 37 78-114 19-55 (217)
85 PRK03573 transcriptional regul 71.9 10 0.00022 27.1 4.7 34 80-113 46-79 (144)
86 COG1522 Lrp Transcriptional re 71.8 11 0.00023 26.9 4.9 50 62-113 6-55 (154)
87 PF02796 HTH_7: Helix-turn-hel 71.7 7.7 0.00017 23.2 3.5 33 66-102 11-43 (45)
88 PRK11414 colanic acid/biofilm 71.5 7.5 0.00016 29.7 4.2 40 76-115 30-69 (221)
89 PF14947 HTH_45: Winged helix- 71.1 8.2 0.00018 25.5 3.9 47 68-118 10-56 (77)
90 PF13384 HTH_23: Homeodomain-l 71.1 6.5 0.00014 23.2 3.1 36 69-108 10-45 (50)
91 COG2894 MinD Septum formation 71.1 1.3 2.9E-05 36.9 0.0 27 81-107 41-67 (272)
92 PRK11569 transcriptional repre 71.0 29 0.00064 27.7 7.7 47 67-114 31-77 (274)
93 KOG2747|consensus 70.5 11 0.00025 33.1 5.5 56 60-120 303-364 (396)
94 TIGR02702 SufR_cyano iron-sulf 70.3 15 0.00033 28.1 5.7 45 67-113 4-48 (203)
95 PRK13503 transcriptional activ 70.0 8.6 0.00019 29.7 4.3 41 64-104 171-211 (278)
96 PF12728 HTH_17: Helix-turn-he 69.9 4.6 0.0001 24.1 2.2 23 81-103 2-24 (51)
97 PF02295 z-alpha: Adenosine de 68.9 24 0.00052 23.1 5.7 57 65-121 5-61 (66)
98 PF04297 UPF0122: Putative hel 68.7 4.6 9.9E-05 29.1 2.3 39 65-103 18-56 (101)
99 PF13551 HTH_29: Winged helix- 68.7 6.3 0.00014 26.3 2.9 27 82-108 14-40 (112)
100 PRK10870 transcriptional repre 68.7 11 0.00024 28.5 4.6 40 74-113 65-104 (176)
101 cd04762 HTH_MerR-trunc Helix-T 68.5 9 0.00019 21.5 3.2 23 81-103 1-23 (49)
102 PF03444 HrcA_DNA-bdg: Winged 68.1 16 0.00036 25.2 4.9 46 67-113 11-56 (78)
103 PF12793 SgrR_N: Sugar transpo 68.0 16 0.00034 26.4 5.1 49 65-113 2-52 (115)
104 PRK11534 DNA-binding transcrip 67.9 10 0.00022 28.9 4.3 40 76-115 26-65 (224)
105 PRK03837 transcriptional regul 67.7 7.7 0.00017 29.7 3.6 49 65-113 18-70 (241)
106 PRK09464 pdhR transcriptional 67.1 9.1 0.0002 29.8 3.9 54 60-113 9-67 (254)
107 PF05930 Phage_AlpA: Prophage 66.6 5.7 0.00012 24.3 2.2 24 79-102 2-25 (51)
108 TIGR03338 phnR_burk phosphonat 66.5 12 0.00025 28.2 4.3 39 76-114 30-68 (212)
109 PRK15121 right oriC-binding tr 66.3 12 0.00025 30.0 4.5 43 65-107 6-48 (289)
110 PRK11512 DNA-binding transcrip 65.7 7.9 0.00017 27.8 3.1 36 78-113 52-87 (144)
111 PF01638 HxlR: HxlR-like helix 65.7 11 0.00025 25.2 3.8 37 78-114 16-53 (90)
112 smart00529 HTH_DTXR Helix-turn 65.7 11 0.00025 24.8 3.7 32 83-114 2-33 (96)
113 PF05491 RuvB_C: Holliday junc 65.7 19 0.00041 24.8 4.8 59 60-118 4-64 (76)
114 PRK03902 manganese transport t 65.2 29 0.00062 25.0 6.0 46 67-114 11-56 (142)
115 PF09756 DDRGK: DDRGK domain; 65.0 12 0.00027 29.5 4.3 46 65-112 100-145 (188)
116 PF01475 FUR: Ferric uptake re 64.5 14 0.00029 25.8 4.1 48 68-116 12-64 (120)
117 PRK09685 DNA-binding transcrip 64.3 11 0.00024 29.6 4.0 38 65-102 198-236 (302)
118 PF02954 HTH_8: Bacterial regu 64.2 13 0.00028 21.9 3.4 38 62-101 2-39 (42)
119 PRK11169 leucine-responsive tr 64.0 21 0.00046 26.5 5.3 52 59-112 9-60 (164)
120 PRK09393 ftrA transcriptional 63.3 15 0.00032 29.7 4.6 44 64-107 218-261 (322)
121 PRK04984 fatty acid metabolism 63.0 12 0.00027 28.7 3.9 38 76-113 26-64 (239)
122 PF14178 YppF: YppF-like prote 62.8 21 0.00046 23.7 4.5 51 61-111 2-56 (60)
123 PF04703 FaeA: FaeA-like prote 62.7 19 0.00041 23.6 4.2 44 69-113 5-48 (62)
124 PRK10572 DNA-binding transcrip 62.7 13 0.00029 29.1 4.2 41 65-105 184-224 (290)
125 PRK00080 ruvB Holliday junctio 62.7 14 0.00029 30.2 4.3 58 60-117 255-314 (328)
126 PF01710 HTH_Tnp_IS630: Transp 62.6 15 0.00032 26.1 4.1 43 67-114 60-102 (119)
127 PRK09391 fixK transcriptional 62.5 28 0.0006 26.7 5.8 38 81-118 180-217 (230)
128 COG1802 GntR Transcriptional r 62.4 10 0.00022 29.2 3.4 38 76-113 35-72 (230)
129 PRK04214 rbn ribonuclease BN/u 62.4 21 0.00045 30.6 5.6 43 77-119 307-349 (412)
130 PRK10225 DNA-binding transcrip 61.5 13 0.00029 29.0 3.9 49 65-113 14-66 (257)
131 PRK11920 rirA iron-responsive 61.2 20 0.00043 26.7 4.7 44 70-113 14-57 (153)
132 PF09107 SelB-wing_3: Elongati 60.8 25 0.00054 22.0 4.4 38 78-115 8-45 (50)
133 PF09940 DUF2172: Domain of un 60.8 8.9 0.00019 33.7 3.1 35 77-111 352-386 (386)
134 PRK11886 bifunctional biotin-- 60.6 24 0.00053 28.7 5.5 44 67-112 7-51 (319)
135 COG1321 TroR Mn-dependent tran 60.6 22 0.00048 26.8 4.9 40 77-116 21-60 (154)
136 PRK09975 DNA-binding transcrip 60.0 17 0.00037 26.9 4.1 37 63-99 14-50 (213)
137 PRK09802 DNA-binding transcrip 59.2 20 0.00044 28.9 4.8 50 65-116 18-67 (269)
138 PRK09990 DNA-binding transcrip 59.1 16 0.00034 28.4 4.0 38 76-113 26-64 (251)
139 PRK06474 hypothetical protein; 59.1 25 0.00054 26.9 5.0 47 67-114 14-61 (178)
140 TIGR02928 orc1/cdc6 family rep 58.4 9.9 0.00022 30.7 2.8 30 85-114 319-351 (365)
141 TIGR02147 Fsuc_second hypothet 57.9 24 0.00052 29.1 5.0 42 77-118 134-177 (271)
142 PRK10402 DNA-binding transcrip 57.5 30 0.00065 26.4 5.2 36 80-115 169-204 (226)
143 PRK10421 DNA-binding transcrip 56.7 16 0.00034 28.6 3.6 38 76-113 21-59 (253)
144 smart00351 PAX Paired Box doma 56.1 23 0.0005 25.5 4.1 44 65-112 22-65 (125)
145 PRK09462 fur ferric uptake reg 56.1 33 0.00072 25.0 5.0 46 69-114 22-72 (148)
146 PF09862 DUF2089: Protein of u 56.0 20 0.00043 26.3 3.8 37 67-106 39-79 (113)
147 PRK15185 transcriptional regul 55.6 22 0.00048 30.1 4.5 40 64-103 206-245 (309)
148 PRK13626 transcriptional regul 55.2 26 0.00057 30.7 5.1 50 64-113 5-56 (552)
149 PRK13502 transcriptional activ 55.2 21 0.00046 27.8 4.1 40 64-103 176-215 (282)
150 PRK11642 exoribonuclease R; Pr 55.1 28 0.0006 33.0 5.5 50 68-118 23-76 (813)
151 PRK10371 DNA-binding transcrip 54.9 22 0.00048 28.8 4.3 43 65-107 192-234 (302)
152 PLN03239 histone acetyltransfe 54.6 49 0.0011 28.8 6.5 59 53-114 249-315 (351)
153 COG1373 Predicted ATPase (AAA+ 54.6 24 0.00053 30.2 4.7 50 64-113 220-270 (398)
154 PRK00411 cdc6 cell division co 54.5 12 0.00026 30.7 2.7 35 79-113 314-358 (394)
155 smart00342 HTH_ARAC helix_turn 54.3 15 0.00031 22.5 2.5 27 81-107 2-28 (84)
156 PRK11753 DNA-binding transcrip 53.5 48 0.001 24.4 5.6 36 80-115 168-203 (211)
157 PRK09978 DNA-binding transcrip 52.8 23 0.00051 29.3 4.2 39 64-102 142-180 (274)
158 PF13542 HTH_Tnp_ISL3: Helix-t 52.5 23 0.0005 20.9 3.1 38 65-102 12-49 (52)
159 PF04218 CENP-B_N: CENP-B N-te 52.2 12 0.00027 23.3 1.9 30 69-102 15-44 (53)
160 COG2207 AraC AraC-type DNA-bin 51.4 34 0.00074 22.5 4.2 42 68-109 24-65 (127)
161 TIGR00635 ruvB Holliday juncti 51.2 27 0.00059 27.6 4.2 56 62-117 236-293 (305)
162 PRK11179 DNA-binding transcrip 51.1 38 0.00083 24.8 4.7 50 62-113 7-56 (153)
163 TIGR02063 RNase_R ribonuclease 50.8 37 0.00081 31.1 5.5 53 67-119 5-61 (709)
164 PF10668 Phage_terminase: Phag 50.6 17 0.00038 23.9 2.5 22 71-93 14-35 (60)
165 PRK11523 DNA-binding transcrip 50.6 26 0.00056 27.3 3.9 47 67-113 15-65 (253)
166 PRK13501 transcriptional activ 50.5 28 0.00061 27.4 4.2 40 65-104 177-216 (290)
167 TIGR02812 fadR_gamma fatty aci 49.7 24 0.00052 27.1 3.6 38 76-113 25-63 (235)
168 COG2378 Predicted transcriptio 49.0 27 0.00058 29.0 4.0 39 70-110 14-52 (311)
169 PRK15186 AraC family transcrip 48.8 31 0.00068 28.4 4.3 39 65-103 182-220 (291)
170 PLN03238 probable histone acet 48.5 73 0.0016 27.0 6.5 57 53-113 191-253 (290)
171 PRK13500 transcriptional activ 48.1 27 0.00058 28.2 3.8 39 64-102 206-244 (312)
172 PRK09333 30S ribosomal protein 48.0 28 0.00061 26.8 3.6 38 78-115 65-116 (150)
173 PRK10906 DNA-binding transcrip 46.5 37 0.00081 27.1 4.4 45 67-113 8-52 (252)
174 PRK15044 transcriptional regul 46.1 34 0.00073 28.9 4.2 38 66-103 194-231 (295)
175 TIGR03697 NtcA_cyano global ni 45.4 65 0.0014 23.2 5.2 36 80-115 143-178 (193)
176 PF05225 HTH_psq: helix-turn-h 45.0 28 0.00061 21.0 2.7 24 80-103 16-39 (45)
177 PF01381 HTH_3: Helix-turn-hel 44.7 21 0.00045 21.1 2.1 23 81-103 10-32 (55)
178 PF00440 TetR_N: Bacterial reg 44.6 29 0.00062 20.5 2.6 29 70-98 6-34 (47)
179 COG2186 FadR Transcriptional r 44.5 22 0.00048 28.1 2.7 49 65-113 15-67 (241)
180 PF14830 Haemocyan_bet_s: Haem 44.3 8.4 0.00018 28.0 0.3 14 97-110 57-70 (103)
181 PF08221 HTH_9: RNA polymerase 44.2 84 0.0018 20.1 5.3 49 61-111 10-58 (62)
182 PRK10434 srlR DNA-bindng trans 42.6 47 0.001 26.5 4.3 45 68-114 9-53 (256)
183 COG1654 BirA Biotin operon rep 42.2 75 0.0016 21.8 4.7 44 67-110 6-49 (79)
184 PRK00118 putative DNA-binding 42.0 20 0.00042 25.8 1.9 34 80-113 33-74 (104)
185 PF12844 HTH_19: Helix-turn-he 41.9 23 0.0005 21.7 2.0 22 81-102 13-34 (64)
186 PF09182 PuR_N: Bacterial puri 41.9 56 0.0012 22.2 4.0 32 70-101 10-41 (70)
187 PRK12423 LexA repressor; Provi 41.9 56 0.0012 25.1 4.6 37 78-114 23-60 (202)
188 PF09035 Tn916-Xis: Excisionas 41.7 31 0.00068 23.0 2.7 24 79-102 12-35 (67)
189 PF08222 HTH_CodY: CodY helix- 41.7 26 0.00057 23.3 2.3 35 80-114 4-38 (61)
190 PF10141 ssDNA-exonuc_C: Singl 41.4 66 0.0014 24.8 4.9 46 68-113 102-149 (195)
191 PRK05638 threonine synthase; V 41.1 48 0.001 28.5 4.4 58 53-113 360-419 (442)
192 COG1349 GlpR Transcriptional r 40.5 51 0.0011 26.4 4.3 46 67-114 8-53 (253)
193 COG2512 Predicted membrane-ass 39.6 68 0.0015 26.3 4.9 59 61-120 192-250 (258)
194 TIGR02787 codY_Gpos GTP-sensin 39.5 72 0.0016 26.6 5.0 37 78-114 196-232 (251)
195 PF05584 Sulfolobus_pRN: Sulfo 39.5 99 0.0021 21.1 4.9 46 65-113 6-51 (72)
196 PF00165 HTH_AraC: Bacterial r 39.3 44 0.00095 19.1 2.8 29 74-102 2-30 (42)
197 PF04539 Sigma70_r3: Sigma-70 39.1 41 0.00088 21.4 2.9 39 69-107 9-47 (78)
198 PLN00104 MYST -like histone ac 39.0 1.3E+02 0.0028 27.1 6.8 56 54-113 343-404 (450)
199 COG3888 Predicted transcriptio 38.3 83 0.0018 27.0 5.3 58 64-121 4-64 (321)
200 cd06171 Sigma70_r4 Sigma70, re 37.3 50 0.0011 18.2 2.8 23 81-103 27-49 (55)
201 PF04545 Sigma70_r4: Sigma-70, 36.9 24 0.00052 20.9 1.5 24 78-101 18-41 (50)
202 COG1959 Predicted transcriptio 36.8 1.2E+02 0.0027 22.5 5.6 43 71-113 15-58 (150)
203 COG2150 Predicted regulator of 36.0 32 0.00069 27.1 2.3 28 80-107 41-68 (167)
204 cd00569 HTH_Hin_like Helix-tur 35.8 58 0.0012 15.8 3.1 20 81-100 22-41 (42)
205 PF00126 HTH_1: Bacterial regu 35.5 74 0.0016 19.6 3.6 44 68-116 6-52 (60)
206 PRK10736 hypothetical protein; 35.1 87 0.0019 27.2 5.1 43 78-120 319-361 (374)
207 PRK11161 fumarate/nitrate redu 34.4 68 0.0015 24.2 3.9 36 80-115 184-219 (235)
208 TIGR00373 conserved hypothetic 34.1 79 0.0017 23.8 4.2 34 78-111 26-59 (158)
209 PF04157 EAP30: EAP30/Vps36 fa 33.6 1.2E+02 0.0026 23.7 5.3 51 60-110 170-220 (223)
210 PF08765 Mor: Mor transcriptio 33.5 36 0.00079 23.8 2.1 26 81-106 73-98 (108)
211 PRK04172 pheS phenylalanyl-tRN 33.4 91 0.002 27.4 5.0 48 67-116 9-56 (489)
212 PRK06266 transcription initiat 33.3 1E+02 0.0022 23.8 4.7 42 68-111 26-67 (178)
213 COG4977 Transcriptional regula 33.2 45 0.00097 28.5 3.0 37 65-101 221-257 (328)
214 TIGR03613 RutR pyrimidine util 32.7 69 0.0015 23.4 3.6 37 64-100 12-48 (202)
215 cd04761 HTH_MerR-SF Helix-Turn 32.7 47 0.001 19.0 2.3 21 81-101 1-21 (49)
216 PRK09940 transcriptional regul 32.3 53 0.0011 26.9 3.2 36 67-102 137-172 (253)
217 PRK13756 tetracycline represso 32.3 87 0.0019 24.2 4.3 36 63-98 7-42 (205)
218 PHA00738 putative HTH transcri 32.2 1.5E+02 0.0033 21.7 5.2 48 67-116 15-62 (108)
219 PRK11639 zinc uptake transcrip 32.0 1.1E+02 0.0025 23.0 4.8 45 69-114 31-80 (169)
220 COG4565 CitB Response regulato 32.0 1E+02 0.0022 25.3 4.8 50 58-111 151-204 (224)
221 PRK09480 slmA division inhibit 31.4 89 0.0019 22.4 4.0 35 64-98 14-48 (194)
222 PF06056 Terminase_5: Putative 31.0 49 0.0011 21.1 2.3 22 81-102 14-35 (58)
223 KOG0416|consensus 30.6 25 0.00055 28.1 1.0 44 59-107 63-106 (189)
224 PF08020 DUF1706: Protein of u 30.4 69 0.0015 24.6 3.4 56 58-121 81-136 (166)
225 COG5027 SAS2 Histone acetyltra 29.3 1.1E+02 0.0023 27.2 4.6 54 60-116 305-364 (395)
226 PF05158 RNA_pol_Rpc34: RNA po 29.3 1.4E+02 0.0031 25.2 5.4 60 61-120 6-68 (327)
227 PRK10668 DNA-binding transcrip 29.2 1.1E+02 0.0023 22.7 4.2 35 64-98 15-49 (215)
228 PF11972 HTH_13: HTH DNA bindi 29.1 1.5E+02 0.0033 19.1 4.3 47 68-119 3-49 (54)
229 PRK09764 DNA-binding transcrip 29.0 96 0.0021 24.0 4.0 54 65-118 10-68 (240)
230 PRK13918 CRP/FNR family transc 29.0 89 0.0019 22.8 3.7 39 80-119 149-187 (202)
231 PF09607 BrkDBD: Brinker DNA-b 28.9 1.1E+02 0.0023 20.1 3.6 35 68-102 13-47 (58)
232 PF04492 Phage_rep_O: Bacterio 28.6 97 0.0021 21.9 3.6 39 76-114 50-88 (100)
233 PRK15008 HTH-type transcriptio 28.3 1.3E+02 0.0028 22.5 4.6 37 63-99 21-57 (212)
234 PRK14999 histidine utilization 28.1 1.9E+02 0.004 22.4 5.5 54 65-118 17-75 (241)
235 cd04895 ACT_ACR_1 ACT domain-c 28.0 34 0.00074 22.9 1.2 17 97-113 15-31 (72)
236 PF13443 HTH_26: Cro/C1-type H 28.0 51 0.0011 20.0 1.9 22 81-102 11-32 (63)
237 smart00421 HTH_LUXR helix_turn 27.7 66 0.0014 18.2 2.3 23 81-103 19-41 (58)
238 KOG2255|consensus 27.6 30 0.00065 28.3 1.0 30 82-113 63-92 (224)
239 TIGR01636 phage_rinA phage tra 27.6 1.1E+02 0.0025 22.1 4.0 37 66-103 87-123 (134)
240 PRK14996 TetR family transcrip 27.6 1E+02 0.0022 22.5 3.7 35 64-98 12-46 (192)
241 TIGR02018 his_ut_repres histid 27.2 1.9E+02 0.0042 22.1 5.4 48 66-113 7-58 (230)
242 PRK11402 DNA-binding transcrip 27.1 79 0.0017 24.4 3.2 54 65-118 14-72 (241)
243 TIGR02404 trehalos_R_Bsub treh 27.0 79 0.0017 24.2 3.2 52 67-118 7-63 (233)
244 COG0735 Fur Fe2+/Zn2+ uptake r 27.0 1.8E+02 0.0039 21.4 5.0 46 69-115 26-76 (145)
245 PTZ00064 histone acetyltransfe 26.9 2.5E+02 0.0055 26.0 6.7 35 81-118 472-506 (552)
246 PRK09392 ftrB transcriptional 26.9 2.2E+02 0.0047 21.4 5.6 36 83-120 176-211 (236)
247 smart00497 IENR1 Intron encode 26.7 66 0.0014 18.8 2.2 33 82-121 19-51 (53)
248 PF13601 HTH_34: Winged helix 26.4 1.3E+02 0.0029 20.0 3.9 36 78-113 12-47 (80)
249 PRK15431 ferrous iron transpor 26.1 1E+02 0.0023 21.3 3.3 37 78-114 14-50 (78)
250 PF05043 Mga: Mga helix-turn-h 26.0 98 0.0021 20.2 3.1 32 78-109 28-63 (87)
251 PF07381 DUF1495: Winged helix 25.8 1.3E+02 0.0027 21.2 3.8 27 66-92 11-37 (90)
252 PF10820 DUF2543: Protein of u 25.5 70 0.0015 22.3 2.4 25 83-107 54-78 (81)
253 PF02616 ScpA_ScpB: ScpA/B pro 25.5 85 0.0018 24.5 3.2 31 58-90 10-40 (242)
254 COG3311 AlpA Predicted transcr 25.3 64 0.0014 21.8 2.1 28 76-103 9-36 (70)
255 TIGR03384 betaine_BetI transcr 25.1 1.4E+02 0.0029 21.3 4.0 36 64-99 12-47 (189)
256 PRK10141 DNA-binding transcrip 24.6 2.4E+02 0.0053 20.4 5.2 47 68-116 20-66 (117)
257 TIGR02607 antidote_HigA addict 24.4 67 0.0015 20.2 2.0 22 81-102 19-40 (78)
258 PRK01905 DNA-binding protein F 24.4 1.3E+02 0.0029 19.7 3.5 38 62-102 34-72 (77)
259 PF14502 HTH_41: Helix-turn-he 24.2 1.5E+02 0.0033 18.8 3.5 40 78-117 4-43 (48)
260 TIGR00637 ModE_repress ModE mo 24.0 1.4E+02 0.003 20.7 3.7 32 82-113 18-52 (99)
261 COG1309 AcrR Transcriptional r 23.5 1.5E+02 0.0032 19.6 3.7 30 69-98 21-50 (201)
262 cd06170 LuxR_C_like C-terminal 23.0 1.6E+02 0.0034 16.7 3.9 23 81-103 16-38 (57)
263 cd00093 HTH_XRE Helix-turn-hel 22.5 88 0.0019 16.7 2.1 23 80-102 12-34 (58)
264 PF10298 WhiA_N: WhiA N-termin 22.5 17 0.00037 24.3 -1.1 47 63-110 34-86 (86)
265 PF05344 DUF746: Domain of Unk 22.1 90 0.002 21.0 2.3 23 67-93 4-26 (65)
266 COG2188 PhnF Transcriptional r 21.9 1.1E+02 0.0025 23.9 3.3 38 80-117 31-69 (236)
267 TIGR03826 YvyF flagellar opero 21.9 1.6E+02 0.0035 22.1 4.0 34 68-101 34-67 (137)
268 COG1733 Predicted transcriptio 21.9 1.8E+02 0.0038 21.0 4.0 61 56-116 11-73 (120)
269 PF07453 NUMOD1: NUMOD1 domain 21.9 72 0.0016 17.9 1.6 18 82-99 18-35 (37)
270 PF01710 HTH_Tnp_IS630: Transp 21.5 1.9E+02 0.0041 20.4 4.1 41 65-110 7-47 (119)
271 PRK15340 transcriptional regul 21.4 1.8E+02 0.0039 23.3 4.4 40 69-108 114-153 (216)
272 PRK11552 putative DNA-binding 21.3 1E+02 0.0022 23.7 2.8 34 65-99 18-51 (225)
273 PHA00542 putative Cro-like pro 21.2 82 0.0018 21.0 2.0 23 81-103 32-54 (82)
274 PRK15481 transcriptional regul 21.1 1.5E+02 0.0031 24.8 3.9 38 76-113 24-62 (431)
275 PLN02913 dihydrofolate synthet 21.0 20 0.00044 31.6 -1.3 28 95-122 184-215 (510)
276 cd04898 ACT_ACR-like_4 ACT dom 20.9 38 0.00082 23.6 0.3 16 95-110 12-27 (77)
277 TIGR03879 near_KaiC_dom probab 20.5 1.1E+02 0.0024 20.8 2.5 46 65-112 19-64 (73)
278 TIGR03693 ocin_ThiF_like putat 20.2 1.4E+02 0.003 28.0 3.9 49 65-113 41-90 (637)
279 KOG2729|consensus 20.0 26 0.00057 26.7 -0.7 21 93-113 91-111 (137)
No 1
>KOG2577|consensus
Probab=99.97 E-value=3.9e-32 Score=228.26 Aligned_cols=107 Identities=55% Similarity=0.723 Sum_probs=88.6
Q ss_pred hhhhhhcCCCCCCC-CC--CccCCCccccc--cCC-CCCCCCC-CCCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHh
Q psy8797 16 NMVKRRLNLDQDDE-ES--PFKTPKSVKKM--RVN-PPTTPAK-EKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASE 88 (122)
Q Consensus 16 ~~~~r~~~l~~~~~-~~--~~~tp~~~~~~--~~~-~~~~~k~-~~~~R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~ 88 (122)
.++|++..+++... .. .+.+|.+.++. +.+ ++..+++ +.+.|+++|||+||+|||.|++++|+|++|||.||+
T Consensus 20 ~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~s~~~~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~ 99 (354)
T KOG2577|consen 20 LPAKEDSRLEEMDPQSVESGLPSPISPGSRMDRKPDSSKSSSSPSESTRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAE 99 (354)
T ss_pred cchhhhhhhhcccccccccCCCCCCCCCcccccCCCCcccccCCCCcccchhhHHHHHHHHHHHHHhCCCceeeHHHHHH
Confidence 67888888877433 11 14444444433 333 4455555 788999999999999999999999999999999999
Q ss_pred HhccchhhhhhHHHhhhhccceeeccCCceeecC
Q psy8797 89 SLDVQKRRIYDITNVLEGIGILEKKSKNNIQCKR 122 (122)
Q Consensus 89 ~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W~G 122 (122)
.|+|+|||||||||||||||||+|++||+|+|+|
T Consensus 100 ~L~VqKRRIYDITNVLEGI~LIeKksKN~IqW~G 133 (354)
T KOG2577|consen 100 VLNVQKRRIYDITNVLEGIGLIEKKSKNNIQWIG 133 (354)
T ss_pred Hhccccceeeehhhhhhcccceeeccccceeeec
Confidence 9999999999999999999999999999999998
No 2
>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=99.94 E-value=3.2e-27 Score=158.11 Aligned_cols=66 Identities=47% Similarity=0.790 Sum_probs=62.9
Q ss_pred CCcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHh---cc--chhhhhhHHHhhhhccceeeccCCceeecC
Q psy8797 57 RYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESL---DV--QKRRIYDITNVLEGIGILEKKSKNNIQCKR 122 (122)
Q Consensus 57 R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L---~v--~kRRiYDI~NVLE~igLI~K~~Kn~~~W~G 122 (122)
|+++||+.+|++|+++|...+++.++++++|+.| ++ ++||||||+|||||+|+|+|.+++.|.|+|
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 7899999999999999999999999999999999 99 999999999999999999999999999998
No 3
>KOG2578|consensus
Probab=99.86 E-value=1.4e-22 Score=169.60 Aligned_cols=70 Identities=40% Similarity=0.622 Sum_probs=67.4
Q ss_pred CCCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceeecC
Q psy8797 53 EKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCKR 122 (122)
Q Consensus 53 ~~~~R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W~G 122 (122)
.-++|++||||+||++|+.++..+....+.|++||.+|||+|||||||+||||+||+++|.+||.|.|.|
T Consensus 17 qvysrkekslgvlv~nfl~lynr~dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkG 86 (388)
T KOG2578|consen 17 QVYSRKEKSLGVLVQNFLILYNRSDVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKG 86 (388)
T ss_pred hhhccccchhhHHHHHHHHHhcCCCcceechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCcccccc
Confidence 4589999999999999999998888889999999999999999999999999999999999999999998
No 4
>KOG2578|consensus
Probab=99.63 E-value=3.3e-16 Score=131.43 Aligned_cols=121 Identities=28% Similarity=0.335 Sum_probs=88.2
Q ss_pred CchhhhHHHHhhcChhhhh-hcCCC-----C--------CCC--CCCccCCCccccccCCCCCCCCCCCCCCCcCcHHHH
Q psy8797 2 KGTIRIRLKLKFHSNMVKR-RLNLD-----Q--------DDE--ESPFKTPKSVKKMRVNPPTTPAKEKGTRYDTSLGLL 65 (122)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~r-~~~l~-----~--------~~~--~~~~~tp~~~~~~~~~~~~~~k~~~~~R~~kSLg~L 65 (122)
+|---||.+|....+..-+ .|.-- . +++ +|-..||+.+..+.+-+-.++.+....|+++||++|
T Consensus 85 kGf~aiPral~eLqeEgvke~l~~~~~~~~~~m~s~e~~~ee~~~s~tstptd~s~~g~l~e~S~~~k~DnrkekSL~lL 164 (388)
T KOG2578|consen 85 KGFGAIPRALFELQEEGVKEGLPERVLRVNSAMVSFEEESEERGVSCTSTPTDQSTDGLLEERSRSSKRDNRKEKSLWLL 164 (388)
T ss_pred cchhhhhHHHHHHHHHHHhhcccceeeecccccccccccccccCCccccCCCCCCCCCcchhcCCCCcccchhhhHHHHH
Confidence 5777899999988776533 22211 1 011 233455554422221112233345678899999999
Q ss_pred HHHHHHHHhhCCCC-cccHHHHHhHh----------ccchhhhhhHHHhhhhccceeec-----cCCceeecC
Q psy8797 66 TKKFVKLLQSSPQG-VVDLNVASESL----------DVQKRRIYDITNVLEGIGILEKK-----SKNNIQCKR 122 (122)
Q Consensus 66 t~kFi~ll~~sp~~-~idL~~aa~~L----------~v~kRRiYDI~NVLE~igLI~K~-----~Kn~~~W~G 122 (122)
|++||.+|.++++. .|.|+.||..| ..+-||||||.|||.+++||+|+ .|..|.|.|
T Consensus 165 ~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~trkPafrwlG 237 (388)
T KOG2578|consen 165 AQNFVKLFLCSDDDILVSLDSAAKALLKDSEDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTRKPAFRWLG 237 (388)
T ss_pred HHHHHHheeccccceEEeecHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhheeC
Confidence 99999999999987 89999999988 35889999999999999999998 688999987
No 5
>KOG2829|consensus
Probab=98.24 E-value=2.5e-06 Score=71.67 Aligned_cols=61 Identities=26% Similarity=0.427 Sum_probs=45.6
Q ss_pred cCcHHHHHHHHHHHHhhCCCCcccHHHHHhHh----------------------ccchhhhhhHHHhhhhccceeeccCC
Q psy8797 59 DTSLGLLTKKFVKLLQSSPQGVVDLNVASESL----------------------DVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 59 ~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L----------------------~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
...|..++.+..+-++. .+...-+++|..| .--|||+||..|||.++.+|.|. |.
T Consensus 43 g~gLRhfs~kVCeKve~--Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd-KK 119 (326)
T KOG2829|consen 43 GGGLRHFSMKVCEKVER--KGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD-KK 119 (326)
T ss_pred CcchhhhhHHHHHHHHh--cCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc-cc
Confidence 44477777776666654 3445556666655 23799999999999999999999 66
Q ss_pred ceeecC
Q psy8797 117 NIQCKR 122 (122)
Q Consensus 117 ~~~W~G 122 (122)
.|+|+|
T Consensus 120 EIrW~G 125 (326)
T KOG2829|consen 120 EIRWIG 125 (326)
T ss_pred eeeeec
Confidence 699998
No 6
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=96.83 E-value=0.0027 Score=40.79 Aligned_cols=51 Identities=20% Similarity=0.289 Sum_probs=41.9
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC 120 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W 120 (122)
+....+. ..+..+..++|+.+++.+..+|+++|-|+..|+|++...+.+.|
T Consensus 12 ~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y 62 (68)
T PF01978_consen 12 KVYLALL--KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVY 62 (68)
T ss_dssp HHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEE
T ss_pred HHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEE
Confidence 3444443 35678999999999999999999999999999999987666554
No 7
>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=96.14 E-value=0.022 Score=34.91 Aligned_cols=41 Identities=29% Similarity=0.353 Sum_probs=34.9
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIG 108 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ig 108 (122)
.+.+.++..+.+. +...++|+.|+|++|-+|.-++.|+..|
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 4567777666555 9999999999999999999999999998
No 8
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=95.94 E-value=0.036 Score=34.45 Aligned_cols=54 Identities=13% Similarity=0.191 Sum_probs=42.6
Q ss_pred HHHHHHHHHhhC-----CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 65 LTKKFVKLLQSS-----PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 65 Lt~kFi~ll~~s-----p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
++.-|+++.... .+..+...++|+.+++.+.-++.+++.|+.-|+|.+.....|
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 345789999999999999999999999999999998863444
No 9
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.77 E-value=0.034 Score=32.61 Aligned_cols=46 Identities=28% Similarity=0.353 Sum_probs=39.0
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
.++.++.+. +.+++.++|+.+++.++-+|..++-|+..|+|.+...
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 456666654 3489999999999999999999999999999998753
No 10
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=95.66 E-value=0.046 Score=36.02 Aligned_cols=48 Identities=23% Similarity=0.377 Sum_probs=40.7
Q ss_pred HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+...++++.+.+ +.+.+.++|+.+++.+.-+|-+++.|+..|+|.+..
T Consensus 7 ~~~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~ 54 (91)
T smart00346 7 GLAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG 54 (91)
T ss_pred HHHHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC
Confidence 345667776653 469999999999999999999999999999999874
No 11
>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=95.24 E-value=0.039 Score=33.94 Aligned_cols=46 Identities=17% Similarity=0.265 Sum_probs=38.4
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
-..++++..++.+ +.+.++|+.+++.+=-+|-+++.|+..|++++.
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 3456667766555 699999999999999999999999999999875
No 12
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=95.21 E-value=0.07 Score=34.94 Aligned_cols=55 Identities=16% Similarity=0.195 Sum_probs=46.2
Q ss_pred HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797 66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC 120 (122)
Q Consensus 66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W 120 (122)
-.+.+++|..+++..+.+.++|..||+.++-+.-++.-|+.-|+|.+.+-+-=.|
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 3678888888765458999999999999999999999999999999976442355
No 13
>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=94.77 E-value=0.1 Score=31.28 Aligned_cols=43 Identities=21% Similarity=0.450 Sum_probs=36.3
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcccee
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILE 111 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~ 111 (122)
.+.+.++.+.|. ++..++|+.+++.+..++.+++-|+.-|+|+
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 567788887555 9999999999999999999999999999985
No 14
>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=94.67 E-value=0.11 Score=32.04 Aligned_cols=46 Identities=22% Similarity=0.355 Sum_probs=40.3
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
..+.++...++..+.+.++|+.+++.+=.+--+++-||.-|+|++.
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 4566677777777899999999999999999999999999999987
No 15
>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=94.29 E-value=0.24 Score=32.99 Aligned_cols=49 Identities=20% Similarity=0.344 Sum_probs=40.0
Q ss_pred HHHHHHHHHhhCCCC-cccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 65 LTKKFVKLLQSSPQG-VVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~-~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.+-+++.++...+++ .+++.++|+.+++..+.+..|++-|+.-|+|+..
T Consensus 9 ~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 9 YALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence 455666777666654 4999999999999999999999999999999865
No 16
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=94.22 E-value=0.12 Score=30.74 Aligned_cols=37 Identities=16% Similarity=0.267 Sum_probs=33.6
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.+.++++++++.|++.+--++++++.|+.-|+|....
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeee
Confidence 4557899999999999999999999999999998764
No 17
>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=94.01 E-value=0.15 Score=36.43 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=41.3
Q ss_pred HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
+-+.+.++...+++.+++.++|+.+++.+..++.+++.|+.-|+|+..
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 334566666666788999999999999999999999999999999864
No 18
>PF13730 HTH_36: Helix-turn-helix domain
Probab=93.11 E-value=0.19 Score=30.63 Aligned_cols=29 Identities=21% Similarity=0.367 Sum_probs=27.8
Q ss_pred cHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797 82 DLNVASESLDVQKRRIYDITNVLEGIGIL 110 (122)
Q Consensus 82 dL~~aa~~L~v~kRRiYDI~NVLE~igLI 110 (122)
+...+|+.+|+.+|.++-.++.||..|+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 79999999999999999999999999986
No 19
>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=92.69 E-value=0.24 Score=30.36 Aligned_cols=44 Identities=18% Similarity=0.379 Sum_probs=36.1
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
++.++.+.++ +.+.++|+.+++.+--+-.+++-|+.-|+|+|..
T Consensus 8 iL~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 8 ILRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence 3444555444 8999999999999999999999999999999873
No 20
>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=92.52 E-value=0.45 Score=28.74 Aligned_cols=45 Identities=20% Similarity=0.399 Sum_probs=37.8
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
..++..+...+ +...++++.+++.+.-++-++|.|+.-|+|....
T Consensus 10 ~~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 10 LRILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEE
Confidence 44555555544 8999999999999999999999999999998763
No 21
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=92.30 E-value=0.28 Score=28.44 Aligned_cols=38 Identities=16% Similarity=0.267 Sum_probs=33.7
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
.+...++|+.+++.+--++.+++.|+.-|++++.. +.|
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 46789999999999999999999999999999874 444
No 22
>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=92.25 E-value=0.12 Score=34.57 Aligned_cols=30 Identities=37% Similarity=0.472 Sum_probs=23.1
Q ss_pred HHHhHhcc---chhhhhhHHHhhhhccceeecc
Q psy8797 85 VASESLDV---QKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 85 ~aa~~L~v---~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.+|+.+++ ..||+||++|-|+.+|+|.-..
T Consensus 27 ~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 27 ELCESLGVDPLSYRRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp HHHHHTTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 34555554 7899999999999999997653
No 23
>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=92.04 E-value=0.52 Score=29.33 Aligned_cols=38 Identities=26% Similarity=0.393 Sum_probs=31.7
Q ss_pred CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 76 sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
..++.+.+.++|+.+++.+--+..+++-|+..|+|++.
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 36788899999999999999999999999999999887
No 24
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=91.92 E-value=0.55 Score=27.98 Aligned_cols=40 Identities=15% Similarity=0.316 Sum_probs=35.3
Q ss_pred CCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797 77 PQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 77 p~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
++..+ +..++|+.+++++=-+...++.|+.-|+|.+....
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 45566 89999999999999999999999999999877544
No 25
>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=91.84 E-value=0.18 Score=33.18 Aligned_cols=22 Identities=41% Similarity=0.685 Sum_probs=19.7
Q ss_pred cchhhhhhHHHhhhhccceeec
Q psy8797 92 VQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 92 v~kRRiYDI~NVLE~igLI~K~ 113 (122)
...||++|++|-||..|+|.-.
T Consensus 44 l~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEEE
Confidence 4789999999999999999754
No 26
>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=91.14 E-value=0.51 Score=29.87 Aligned_cols=40 Identities=18% Similarity=0.321 Sum_probs=34.1
Q ss_pred CCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797 77 PQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 77 p~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
++..+ +..++|+.++|++.=+.+.++.|+.-|+|+.....
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~ 60 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPGR 60 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCc
Confidence 56678 99999999999999999999999999999887543
No 27
>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=90.34 E-value=1.1 Score=31.58 Aligned_cols=36 Identities=19% Similarity=0.341 Sum_probs=33.4
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
...++..++|+.+++.+..+++|++.|+..|+|...
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 28
>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=89.53 E-value=0.65 Score=30.51 Aligned_cols=47 Identities=13% Similarity=0.186 Sum_probs=36.1
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccc-hhhhhhHHHhhhhccceeeccC
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQ-KRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~-kRRiYDI~NVLE~igLI~K~~K 115 (122)
||.-+....+..-.+.++|+.||+. ..-+++-+..||.-|+|++...
T Consensus 14 ~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 14 FIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp HHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence 4444444446677999999999996 9999999999999999998743
No 29
>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=88.97 E-value=1.1 Score=26.88 Aligned_cols=41 Identities=24% Similarity=0.413 Sum_probs=34.3
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceee
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEK 112 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K 112 (122)
.+.++.+ +..++.++|+.+++.+=-++-=+++|+..|+|+|
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 4444544 6689999999999999999999999999999986
No 30
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=88.94 E-value=0.74 Score=34.43 Aligned_cols=44 Identities=20% Similarity=0.413 Sum_probs=38.7
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
|..+++ +++..+.+++|+.|+..|=.+|=.+|=|...|+|.|.-
T Consensus 33 ~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 33 YKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeee
Confidence 445554 57889999999999999999999999999999999873
No 31
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=88.68 E-value=0.37 Score=31.24 Aligned_cols=45 Identities=16% Similarity=0.228 Sum_probs=35.6
Q ss_pred HHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797 70 VKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 70 i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
.+++.+ .+.+++.++|..|+++..-+=+.+.+|+.-|.|++...+
T Consensus 6 ~~~l~~--~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 6 RDYLRE--RGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMS 50 (69)
T ss_dssp HHHHHH--S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE
T ss_pred HHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCC
Confidence 344443 567999999999999999999999999999999987543
No 32
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=88.45 E-value=1.4 Score=35.35 Aligned_cols=48 Identities=19% Similarity=0.272 Sum_probs=40.3
Q ss_pred HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+-..+++|..++ ..+.+.++|+.+++.|=.+|.+++-|+..|++.+..
T Consensus 27 ~l~IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~ 74 (271)
T PRK10163 27 GIAILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDS 74 (271)
T ss_pred HHHHHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence 345667776553 458999999999999999999999999999998864
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=88.10 E-value=1.2 Score=29.58 Aligned_cols=49 Identities=20% Similarity=0.207 Sum_probs=40.6
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
..+++.+-.+...-+.-.+++..++...|-++=+++.|+..|||.|+.-
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 3566777666655566678889999999999999999999999999865
No 34
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=87.15 E-value=1.7 Score=34.52 Aligned_cols=51 Identities=10% Similarity=0.265 Sum_probs=40.9
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc-CCcee
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS-KNNIQ 119 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~-Kn~~~ 119 (122)
..+++|..++ ..+.+.++|+.+++.|=-+|-+++-|+..|++++.. .+.|.
T Consensus 15 ~iL~~l~~~~-~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~ 66 (263)
T PRK09834 15 MVLRALNRLD-GGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFR 66 (263)
T ss_pred HHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEE
Confidence 3556665543 348999999999999999999999999999999863 44454
No 35
>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=86.95 E-value=1.7 Score=27.40 Aligned_cols=45 Identities=24% Similarity=0.404 Sum_probs=37.7
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+.++++.+ .+.+.+.++|+.|+|+..=+.==+|.|+.-|+|.|..
T Consensus 4 ~Il~~l~~--~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 4 QILELLKE--KGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHH--cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 45677765 4679999999999998887777788999999999874
No 36
>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=86.94 E-value=1.6 Score=27.89 Aligned_cols=40 Identities=15% Similarity=0.237 Sum_probs=33.0
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGIL 110 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI 110 (122)
+.+.++.+. .+...++|+.++|+++-++.-++.|++-|++
T Consensus 4 ~il~~L~~~---~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~ 43 (69)
T TIGR00122 4 RLLALLADN---PFSGEKLGEALGMSRTAVNKHIQTLREWGVD 43 (69)
T ss_pred HHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 455665543 3569999999999999999999999998884
No 37
>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=86.77 E-value=2.9 Score=25.27 Aligned_cols=34 Identities=21% Similarity=0.338 Sum_probs=31.3
Q ss_pred ccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 81 VDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
....++|+.+++.+=.+...++-|+.-|+|++..
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 4599999999999999999999999999998774
No 38
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=86.33 E-value=1.6 Score=29.64 Aligned_cols=47 Identities=15% Similarity=0.280 Sum_probs=40.6
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
+=.+++.++++. +.+...++|+.+++...-++..++-|+.-|+|.+.
T Consensus 4 ~D~~il~~L~~~--~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKD--ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHh--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeece
Confidence 346788888875 45889999999999999999999999999999854
No 39
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=86.23 E-value=2.2 Score=27.57 Aligned_cols=44 Identities=14% Similarity=0.273 Sum_probs=36.9
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
..+.++...+ .+...++|+.+++.+--++-+++-|+.-|+|++.
T Consensus 14 ~il~~l~~~~--~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 14 LVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHcC--CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 3445555443 5889999999999999999999999999999876
No 40
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=86.18 E-value=0.9 Score=36.79 Aligned_cols=36 Identities=28% Similarity=0.433 Sum_probs=32.3
Q ss_pred CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+...-.++|+..||.+=|+|||++-||.=|+|+...
T Consensus 29 g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~ 64 (247)
T COG1378 29 GEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIE 64 (247)
T ss_pred CCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeC
Confidence 345778999999999999999999999999999873
No 41
>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=86.13 E-value=1.2 Score=27.87 Aligned_cols=46 Identities=20% Similarity=0.360 Sum_probs=37.6
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.+.+.++. .++..++.++|+.|++..=-+|-=+++|+..|+|+...
T Consensus 13 ~~Il~~L~--~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 13 LRILRLLA--SNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHH--HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHh--cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 34566662 35678999999999999999999999999999998763
No 42
>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=85.78 E-value=1.9 Score=29.59 Aligned_cols=50 Identities=16% Similarity=0.347 Sum_probs=40.7
Q ss_pred cHHHHHHHHHHHHhhCC--CCcccHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797 61 SLGLLTKKFVKLLQSSP--QGVVDLNVASESLDVQKRRIYDITNVLEGIGIL 110 (122)
Q Consensus 61 SLg~Lt~kFi~ll~~sp--~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI 110 (122)
+|..+.++.++++++.+ +.-+.+++++++|++....+.+++.-|..-|+|
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 78889999999998732 345899999999999999999999999999987
No 43
>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=85.51 E-value=0.91 Score=36.52 Aligned_cols=40 Identities=13% Similarity=0.196 Sum_probs=35.3
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
++..++.++|+++++..|.++-+.+.|.++|++++.. +.|
T Consensus 21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~-~~y 60 (306)
T TIGR02716 21 EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED-GKW 60 (306)
T ss_pred cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC-CcE
Confidence 3578999999999999999999999999999999864 444
No 44
>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=84.69 E-value=3.7 Score=28.28 Aligned_cols=37 Identities=19% Similarity=0.218 Sum_probs=33.7
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
...+.-.++|+.+++.|--+..+++.||.-|+|.+..
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 4567889999999999999999999999999999764
No 45
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=84.03 E-value=3.1 Score=30.04 Aligned_cols=37 Identities=19% Similarity=0.217 Sum_probs=33.5
Q ss_pred CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.++.+.+.++|+.+++..+-+..|+..|.-.|+|.-.
T Consensus 22 ~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~ 58 (135)
T TIGR02010 22 ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSV 58 (135)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence 3458999999999999999999999999999999743
No 46
>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=83.94 E-value=4.7 Score=25.83 Aligned_cols=41 Identities=22% Similarity=0.297 Sum_probs=36.2
Q ss_pred HhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 73 LQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 73 l~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+.+ .++.+...++|+.|+|.+=-..+.++-|+.-|+|....
T Consensus 16 l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 16 LSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 344 78899999999999999999999999999999998874
No 47
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.89 E-value=1.3 Score=32.42 Aligned_cols=41 Identities=29% Similarity=0.332 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHh
Q psy8797 63 GLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 63 g~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NV 103 (122)
++||.+=..++.-.-..-++|.++|+.++|+|-.|||=|+-
T Consensus 16 sLLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr 56 (105)
T COG2739 16 SLLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKR 56 (105)
T ss_pred HHHhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHH
Confidence 35777766665555555689999999999999999997763
No 48
>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=83.85 E-value=1.1 Score=25.71 Aligned_cols=23 Identities=26% Similarity=0.440 Sum_probs=20.6
Q ss_pred ccHHHHHhHhccchhhhhhHHHh
Q psy8797 81 VDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NV 103 (122)
+++.++|+.|++.+..||..++-
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 57899999999999999999863
No 49
>PF13518 HTH_28: Helix-turn-helix domain
Probab=83.73 E-value=1.4 Score=26.02 Aligned_cols=37 Identities=16% Similarity=0.316 Sum_probs=30.3
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccc
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGI 109 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igL 109 (122)
.|+++.+ +. ++.++|..++|.+..+|.+++-++.-|+
T Consensus 5 iv~~~~~---g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 5 IVELYLE---GE-SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHc---CC-CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 4555553 33 9999999999999999999999988664
No 50
>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=83.25 E-value=2.7 Score=26.54 Aligned_cols=36 Identities=25% Similarity=0.377 Sum_probs=28.0
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhh
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLE 105 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE 105 (122)
+.++++.. +..+.+.++|+.|+++.|-|..-+|-|.
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 46677766 5668999999999999999877776665
No 51
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=82.95 E-value=3.2 Score=29.64 Aligned_cols=45 Identities=11% Similarity=0.143 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhh
Q psy8797 62 LGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEG 106 (122)
Q Consensus 62 Lg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ 106 (122)
-.....++++++.++....++++++|+.+++..|.|.-+..---|
T Consensus 7 ~~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G 51 (127)
T PRK11511 7 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETG 51 (127)
T ss_pred cHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 345668899999999999999999999999999888766654433
No 52
>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=82.78 E-value=3.2 Score=28.81 Aligned_cols=45 Identities=18% Similarity=0.276 Sum_probs=38.9
Q ss_pred HHHHh--hCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 70 VKLLQ--SSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 70 i~ll~--~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+.++. .++++.+.+.++|+.+++.+=.+-=+++-||.-|+|.|..
T Consensus 31 L~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 31 LYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred HHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 44444 5567889999999999999999999999999999999873
No 53
>PRK09954 putative kinase; Provisional
Probab=82.49 E-value=2.2 Score=34.98 Aligned_cols=46 Identities=20% Similarity=0.349 Sum_probs=40.2
Q ss_pred HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
-++.++++++++ .++..++|+.|++.+..++..++-|+.-|+|+..
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 456888888655 7999999999999999999999999999999654
No 54
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=82.26 E-value=2.6 Score=32.06 Aligned_cols=38 Identities=21% Similarity=0.204 Sum_probs=34.4
Q ss_pred CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 76 sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
..+..+.+.++|+.+++..+-+..|++-|.--|||.-.
T Consensus 21 ~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 21 SEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 34568999999999999999999999999999999854
No 55
>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=82.11 E-value=3.4 Score=32.31 Aligned_cols=50 Identities=8% Similarity=0.116 Sum_probs=40.8
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
-..+++|..+ ...+.+.++|+.+++.|=.+|-+++-|+..|++++.. ..|
T Consensus 12 l~IL~~l~~~-~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~~-~~Y 61 (248)
T TIGR02431 12 LAVIEAFGAE-RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSDG-RLF 61 (248)
T ss_pred HHHHHHHhcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC-CEE
Confidence 3456666554 4568999999999999999999999999999999863 344
No 56
>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=82.01 E-value=2.6 Score=26.77 Aligned_cols=36 Identities=22% Similarity=0.296 Sum_probs=33.1
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
.++..++|+.+|+.+..+--+++-|+.-|+|+...+
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 578999999999999999999999999999997744
No 57
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=82.00 E-value=3.9 Score=27.85 Aligned_cols=43 Identities=5% Similarity=0.145 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhh
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEG 106 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ 106 (122)
.+..+++.++.+.....+++.++|+.++++.|.|.-+++=.-|
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g 47 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTH 47 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHC
Confidence 3567788899888888999999999999999888766654433
No 58
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=80.96 E-value=4.5 Score=32.25 Aligned_cols=51 Identities=22% Similarity=0.406 Sum_probs=43.4
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC-ce
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN-NI 118 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn-~~ 118 (122)
-..+++|...|.+ +.+.++|+.+|..|=-.|=+.+.|+..|++++...+ .|
T Consensus 7 l~iL~~l~~~~~~-l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y 58 (246)
T COG1414 7 LAILDLLAEGPGG-LSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRY 58 (246)
T ss_pred HHHHHHHHhCCCC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcE
Confidence 3567777775544 889999999999999999999999999999999865 44
No 59
>PRK00215 LexA repressor; Validated
Probab=80.87 E-value=3.7 Score=31.24 Aligned_cols=42 Identities=10% Similarity=0.133 Sum_probs=36.4
Q ss_pred hCCCCcccHHHHHhHhcc-chhhhhhHHHhhhhccceeeccCC
Q psy8797 75 SSPQGVVDLNVASESLDV-QKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 75 ~sp~~~idL~~aa~~L~v-~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
...+....+.++|+.+++ .+=-++.+++-||.-|+|++....
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 334566899999999999 999999999999999999887543
No 60
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=80.38 E-value=4.7 Score=31.76 Aligned_cols=47 Identities=11% Similarity=0.274 Sum_probs=39.5
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
-..+++|... ..+.+.++|+.+++.|=-+|-+++.|+..|++++...
T Consensus 17 l~IL~~l~~~--~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~ 63 (257)
T PRK15090 17 FGILQALGEE--REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGE 63 (257)
T ss_pred HHHHHHhhcC--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence 4466666543 3589999999999999999999999999999998643
No 61
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=79.87 E-value=1.6 Score=37.22 Aligned_cols=30 Identities=37% Similarity=0.583 Sum_probs=26.7
Q ss_pred HHHHHhHhccchhhhhhHHHhhhhccceee
Q psy8797 83 LNVASESLDVQKRRIYDITNVLEGIGILEK 112 (122)
Q Consensus 83 L~~aa~~L~v~kRRiYDI~NVLE~igLI~K 112 (122)
+..+++.++++.|++|||+|-|+.+|+|.-
T Consensus 304 y~~~~~~~~~~~~~~~~ii~~L~~lgiv~~ 333 (366)
T COG1474 304 YESLCERLRTSQRRFSDIISELEGLGIVSA 333 (366)
T ss_pred HHHHHhhhCchHHHHHHHHHHHHhcCeEEe
Confidence 567788888899999999999999999973
No 62
>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=79.03 E-value=3.9 Score=28.41 Aligned_cols=43 Identities=16% Similarity=0.323 Sum_probs=36.0
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
++..+.. ++.+.+.++|+.+++.+--++=+++-||.-|+|++.
T Consensus 33 iL~~l~~--~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~ 75 (118)
T TIGR02337 33 ILRILAE--QGSMEFTQLANQACILRPSLTGILARLERDGLVTRL 75 (118)
T ss_pred HHHHHHH--cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEec
Confidence 3344443 345889999999999999999999999999999986
No 63
>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=78.62 E-value=3.8 Score=31.95 Aligned_cols=45 Identities=18% Similarity=0.318 Sum_probs=38.8
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIG 108 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ig 108 (122)
.+..+|+.++.+++...++|+++|+.++++++.|..++.-..|+.
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 356889999999998999999999999999999998887665544
No 64
>PRK11050 manganese transport regulator MntR; Provisional
Probab=78.41 E-value=8.9 Score=28.41 Aligned_cols=41 Identities=15% Similarity=0.191 Sum_probs=35.5
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
++.+.+.++|+.|++.+--+..+++-||.-|+|.+.....+
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~~~v 89 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYRGV 89 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCce
Confidence 45678999999999999999999999999999998654434
No 65
>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=78.34 E-value=3.7 Score=31.39 Aligned_cols=39 Identities=21% Similarity=0.232 Sum_probs=35.2
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
..+..++|+.+++++.-++..++.|+--++|.|...+.|
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G~Y 113 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAY 113 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeE
Confidence 567889999999999999999999999999999865654
No 66
>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=77.93 E-value=4.1 Score=29.50 Aligned_cols=35 Identities=11% Similarity=0.325 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhh
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIY 98 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiY 98 (122)
.+..-|++|+.+.+=..+.++++|++-||.|.-+|
T Consensus 7 ~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY 41 (176)
T TIGR02366 7 KIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFY 41 (176)
T ss_pred HHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHH
Confidence 46778999999999999999999999999999887
No 67
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=77.91 E-value=5.3 Score=28.95 Aligned_cols=41 Identities=15% Similarity=0.208 Sum_probs=35.8
Q ss_pred hCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 75 SSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 75 ~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
..++..++..++|+.++|++.-+-.|+..|+.-|+|+-...
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G 60 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRG 60 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecC
Confidence 34567899999999999999999999999999999976643
No 68
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=77.45 E-value=2.2 Score=31.12 Aligned_cols=32 Identities=25% Similarity=0.432 Sum_probs=26.9
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHH
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
|...|++-+. ++..++|+.|||.+.+|-+|+|
T Consensus 14 L~eeflep~g------lt~~~lA~~lgV~r~~is~lin 45 (104)
T COG3093 14 LREEFLEPLG------LTQTELAEALGVTRNTISELIN 45 (104)
T ss_pred HHHHHhcccc------CCHHHHHHHhCCCHHHHHHHHc
Confidence 4566776443 7899999999999999999998
No 69
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=77.30 E-value=4 Score=32.34 Aligned_cols=36 Identities=17% Similarity=0.206 Sum_probs=34.2
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
..++.|+++++.||++|=++.=.+-.|++.||++++
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhh
Confidence 568999999999999999999999999999999987
No 70
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=76.93 E-value=6.6 Score=30.03 Aligned_cols=43 Identities=16% Similarity=0.237 Sum_probs=37.6
Q ss_pred CCCCcccHHHHHhHh--ccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 76 SPQGVVDLNVASESL--DVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 76 sp~~~idL~~aa~~L--~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
-+++.-|..++|..+ ++.--.+=|.++.|+-+|+|+|.+.+.|
T Consensus 35 l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y 79 (171)
T PF14394_consen 35 LMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKY 79 (171)
T ss_pred cCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcE
Confidence 345666999999999 9999999999999999999999976554
No 71
>PHA02943 hypothetical protein; Provisional
Probab=76.85 E-value=6.2 Score=30.95 Aligned_cols=47 Identities=19% Similarity=0.184 Sum_probs=40.9
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
..+++++ ..|.....++|+.||++--....++-|||.-|.|++....
T Consensus 14 ~eILE~L---k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G 60 (165)
T PHA02943 14 IKTLRLL---ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIG 60 (165)
T ss_pred HHHHHHH---hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeec
Confidence 4578888 4667789999999999999999999999999999998554
No 72
>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=76.83 E-value=5.5 Score=30.14 Aligned_cols=48 Identities=13% Similarity=0.203 Sum_probs=38.2
Q ss_pred HHHHHHh---hCCCCcccHHHHHhHhccc-hhhhhhHHHhhhhccceeeccC
Q psy8797 68 KFVKLLQ---SSPQGVVDLNVASESLDVQ-KRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 68 kFi~ll~---~sp~~~idL~~aa~~L~v~-kRRiYDI~NVLE~igLI~K~~K 115 (122)
+.++++. ...+....+.++|+.+++. +=-++..++.||..|+|++...
T Consensus 10 ~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~ 61 (199)
T TIGR00498 10 EVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPG 61 (199)
T ss_pred HHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCC
Confidence 3444444 3345557899999999998 9999999999999999998743
No 73
>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=76.35 E-value=7.7 Score=26.60 Aligned_cols=45 Identities=20% Similarity=0.369 Sum_probs=37.9
Q ss_pred HHHHHhhCCCCcccHHHHHhHh-----ccchhhhhhHHHhhhhccceeecc
Q psy8797 69 FVKLLQSSPQGVVDLNVASESL-----DVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L-----~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.++++..+ +..++.+++.+.| ++.+=-+|-+++.|+..|+|.+..
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 45666665 5778999999988 578999999999999999999873
No 74
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.61 E-value=6 Score=28.22 Aligned_cols=41 Identities=20% Similarity=0.354 Sum_probs=34.2
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGIL 110 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI 110 (122)
++.++-++ .+..++-++.+..|-.||-+-|++..|++||++
T Consensus 12 Yla~Li~S-~e~~nVP~lm~~TGwPRRT~QDvikAlpglgi~ 52 (95)
T COG4519 12 YLAYLIDS-GETANVPELMAATGWPRRTAQDVIKALPGLGIV 52 (95)
T ss_pred HHHHHHhc-cccCChHHHHHHcCCchhHHHHHHHhCcCCCeE
Confidence 44555544 666788899999999999999999999999986
No 75
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=74.98 E-value=4.9 Score=33.91 Aligned_cols=52 Identities=21% Similarity=0.381 Sum_probs=41.3
Q ss_pred CcHHHHH-HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 60 TSLGLLT-KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 60 kSLg~Lt-~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
++|+..+ -..++++.. .+.+++|++|+.|+..+--+--=+.|||-.|||+-.
T Consensus 18 kalaS~vRv~Il~lL~~--k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 18 KALASKVRVAILQLLHR--KGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHHH--hCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeee
Confidence 4555555 346677764 466899999999999999999999999999999643
No 76
>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=74.57 E-value=5 Score=27.68 Aligned_cols=41 Identities=20% Similarity=0.426 Sum_probs=33.5
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
|.+-+.++ ++.+.+.++|..|++..+.|+++ |...|++-+.
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 55555554 58899999999999999999876 6678888884
No 77
>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=73.95 E-value=6.8 Score=31.15 Aligned_cols=60 Identities=20% Similarity=0.300 Sum_probs=41.9
Q ss_pred CCCcCcHHHHH------HHHHHHHhhCCCC-cccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 56 TRYDTSLGLLT------KKFVKLLQSSPQG-VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 56 ~R~~kSLg~Lt------~kFi~ll~~sp~~-~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
.|-=.-||.++ ...++++....+. .++++++++..++.. -||+..|+.+|++.....+.+
T Consensus 119 ErPLSdlG~~sY~sYW~~~i~~~L~~~~~~~~isi~~is~~Tgi~~---~DIi~tL~~l~~l~~~~~~~~ 185 (188)
T PF01853_consen 119 ERPLSDLGRLSYRSYWRRVILEYLLEFKGKKSISIKDISQETGIRP---EDIISTLQQLGMLKYYKGQHI 185 (188)
T ss_dssp -SS--HHHHHHHHHHHHHHHHHHHHHTSSE--EEHHHHHHHH-BTH---HHHHHHHHHTT-EEEETTEEE
T ss_pred cCccCHHHHHHHHHHHHHHHHHHHHhcCCCCeEEHHHHHHHHCCCH---HHHHHHHHHCCCEEEECCcEE
Confidence 34445567664 4477777776665 899999999999965 699999999999998865544
No 78
>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=73.32 E-value=10 Score=29.10 Aligned_cols=45 Identities=22% Similarity=0.309 Sum_probs=37.9
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+.+.++.++ +.+.+.++|+.+++.+-.++-.++-|+..|+|++..
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 344555543 458999999999999999999999999999999986
No 79
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=72.98 E-value=8.1 Score=25.45 Aligned_cols=44 Identities=18% Similarity=0.250 Sum_probs=35.1
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
++..+...++... .++|+.+++.+=-+.-+++-||.-|+|++..
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 3444445444333 8999999999999999999999999999873
No 80
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=72.91 E-value=9.1 Score=30.44 Aligned_cols=47 Identities=23% Similarity=0.277 Sum_probs=39.1
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
.+.++++.+ ++.+...++|+.|+|+.+-+.--++.|+.-|++.+...
T Consensus 7 ~~Il~~l~~--~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~G 53 (240)
T PRK10411 7 QAIVDLLLN--HTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHG 53 (240)
T ss_pred HHHHHHHHH--cCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence 345667764 45799999999999999999999999999999987643
No 81
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=72.83 E-value=6.9 Score=31.23 Aligned_cols=46 Identities=24% Similarity=0.283 Sum_probs=37.7
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
+.++++.+ .+.+.+.++|+.|+|+..-++--++.||..|+|.+..-
T Consensus 9 ~Il~~l~~--~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~g 54 (251)
T PRK13509 9 ILLELLAQ--LGFVTVEKVIERLGISPATARRDINKLDESGKLKKVRN 54 (251)
T ss_pred HHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence 45566664 67799999999999988888777899999999998643
No 82
>PRK10130 transcriptional regulator EutR; Provisional
Probab=72.52 E-value=5.1 Score=33.78 Aligned_cols=43 Identities=12% Similarity=0.094 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhh
Q psy8797 63 GLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLE 105 (122)
Q Consensus 63 g~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE 105 (122)
..+..++.+++.++.+..+++.++|+.+++++|-|+-.+.=.-
T Consensus 239 ~~~v~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~ 281 (350)
T PRK10130 239 RRLLSRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHAIL 281 (350)
T ss_pred HHHHHHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4577888999999999999999999999999999987764433
No 83
>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=72.12 E-value=5.5 Score=28.39 Aligned_cols=29 Identities=24% Similarity=0.377 Sum_probs=22.7
Q ss_pred cHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797 82 DLNVASESLDVQKRRIYDITNVLEGIGIL 110 (122)
Q Consensus 82 dL~~aa~~L~v~kRRiYDI~NVLE~igLI 110 (122)
++..+.+..|..+|-+.|.++.|..+|+.
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 88899999999999999999999999975
No 84
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=71.91 E-value=9.8 Score=30.52 Aligned_cols=37 Identities=11% Similarity=0.091 Sum_probs=34.0
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+..+...++|+.|++.+..+.-+++-||.-|+|++..
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~ 55 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTI 55 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEE
Confidence 4468899999999999999999999999999999874
No 85
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=71.90 E-value=10 Score=27.09 Aligned_cols=34 Identities=9% Similarity=0.227 Sum_probs=31.8
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.+...++|+.+++.+=-+--+++-||.-|+|++.
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQ 79 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeee
Confidence 3578999999999999999999999999999997
No 86
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=71.79 E-value=11 Score=26.90 Aligned_cols=50 Identities=16% Similarity=0.281 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 62 LGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 62 Lg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
|-.+=.+.+++++. ++...+.++|+.+|++.--+...+.-||.-|+|.+.
T Consensus 6 lD~~D~~IL~~L~~--d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 6 LDDIDRRILRLLQE--DARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred ccHHHHHHHHHHHH--hCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeE
Confidence 33455678888885 445999999999999999999999999999999876
No 87
>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=71.72 E-value=7.7 Score=23.16 Aligned_cols=33 Identities=12% Similarity=0.320 Sum_probs=23.1
Q ss_pred HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHH
Q psy8797 66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
....++++.+. +.+.++|+.++|++.=||=+.|
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 44556666543 8999999999999999997764
No 88
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=71.46 E-value=7.5 Score=29.67 Aligned_cols=40 Identities=13% Similarity=0.095 Sum_probs=35.9
Q ss_pred CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 76 sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
.|+..+.-.++|+.|||+|==+=+.+..|+..|||+....
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~ 69 (221)
T PRK11414 30 KPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPA 69 (221)
T ss_pred CCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCC
Confidence 4788888899999999999999999999999999987643
No 89
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=71.15 E-value=8.2 Score=25.50 Aligned_cols=47 Identities=15% Similarity=0.229 Sum_probs=33.8
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
..+..+. .+.....+++...++.-.++..++|-|+.-|+|++ ..+.|
T Consensus 10 ~IL~~l~---~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~-~~~~Y 56 (77)
T PF14947_consen 10 DILKILS---KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK-KDGKY 56 (77)
T ss_dssp HHHHHH----TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE-ETTEE
T ss_pred HHHHHHH---cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC-CCCEE
Confidence 3444444 56678899999999999999999999999999977 45544
No 90
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=71.07 E-value=6.5 Score=23.23 Aligned_cols=36 Identities=17% Similarity=0.317 Sum_probs=22.2
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIG 108 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ig 108 (122)
.+.++.+ -....++|+.|||+++-+|.|++=.+.-|
T Consensus 10 ii~l~~~----G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 10 IIRLLRE----GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp HHHHHHH----T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred HHHHHHC----CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 4455554 36889999999999999999998775444
No 91
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=71.06 E-value=1.3 Score=36.90 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=21.4
Q ss_pred ccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797 81 VDLNVASESLDVQKRRIYDITNVLEGI 107 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NVLE~i 107 (122)
+-|..+=-.||.++|-+||.+||+|+=
T Consensus 41 iGLRNLDlimGlE~RiVYd~vdVi~g~ 67 (272)
T COG2894 41 IGLRNLDLIMGLENRIVYDLVDVIEGE 67 (272)
T ss_pred cCchhhhhhhcccceeeeeehhhhcCc
Confidence 344555557899999999999999974
No 92
>PRK11569 transcriptional repressor IclR; Provisional
Probab=71.03 E-value=29 Score=27.70 Aligned_cols=47 Identities=13% Similarity=0.254 Sum_probs=39.6
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
-..+++|... +..+.+.++|+.+|..|=-+|=+++-|+..|++++..
T Consensus 31 l~IL~~l~~~-~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~ 77 (274)
T PRK11569 31 LKLLEWIAES-NGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVG 77 (274)
T ss_pred HHHHHHHHhC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence 3456666654 5568999999999999999999999999999999864
No 93
>KOG2747|consensus
Probab=70.46 E-value=11 Score=33.10 Aligned_cols=56 Identities=20% Similarity=0.353 Sum_probs=43.8
Q ss_pred CcHHHHHHH------HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797 60 TSLGLLTKK------FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC 120 (122)
Q Consensus 60 kSLg~Lt~k------Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W 120 (122)
.-||+|+-+ .+++|....+..|+|+++|+.-++. --||++.|+.+++|.-. |. |.|
T Consensus 303 SDLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~---~~DIisTL~~L~m~~y~-k~-~~~ 364 (396)
T KOG2747|consen 303 SDLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIR---PDDIISTLQSLNMIKYY-KG-YII 364 (396)
T ss_pred chhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCC---HHHHHHHHHhhCCcccc-CC-eeE
Confidence 347777643 7788877666669999999999985 47999999999999766 33 555
No 94
>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=70.28 E-value=15 Score=28.11 Aligned_cols=45 Identities=18% Similarity=0.276 Sum_probs=38.0
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.+.+.++... +.++..++|+.|++.+=-+.-.++.|+.-|+|++.
T Consensus 4 ~~IL~~L~~~--~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQ--GQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 4566677654 33899999999999999999999999999999876
No 95
>PRK13503 transcriptional activator RhaS; Provisional
Probab=69.99 E-value=8.6 Score=29.72 Aligned_cols=41 Identities=7% Similarity=0.084 Sum_probs=35.0
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhh
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVL 104 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVL 104 (122)
....++++++.+++...++|+++|+.+++.++.|..+..=.
T Consensus 171 ~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~ 211 (278)
T PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQ 211 (278)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34788999999999999999999999999999888776533
No 96
>PF12728 HTH_17: Helix-turn-helix domain
Probab=69.88 E-value=4.6 Score=24.12 Aligned_cols=23 Identities=17% Similarity=0.352 Sum_probs=20.7
Q ss_pred ccHHHHHhHhccchhhhhhHHHh
Q psy8797 81 VDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NV 103 (122)
+++.++|+.|+|.+.-+|.+++-
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 57899999999999999999863
No 97
>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=68.94 E-value=24 Score=23.14 Aligned_cols=57 Identities=18% Similarity=0.192 Sum_probs=46.3
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceeec
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCK 121 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W~ 121 (122)
+-++.++++....+....--..+..|+++++.+==+..=|+.=|.|.|.+-+--.|.
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 456778888777666667778888999989999999999999999999988888883
No 98
>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=68.72 E-value=4.6 Score=29.10 Aligned_cols=39 Identities=23% Similarity=0.337 Sum_probs=25.3
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHh
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NV 103 (122)
||.+=-+++.-.-..-++|.++|+.++|+|=-+||.++-
T Consensus 18 LT~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 18 LTEKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp S-HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 555544444444456689999999999999999998864
No 99
>PF13551 HTH_29: Winged helix-turn helix
Probab=68.67 E-value=6.3 Score=26.27 Aligned_cols=27 Identities=15% Similarity=0.294 Sum_probs=25.5
Q ss_pred cHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797 82 DLNVASESLDVQKRRIYDITNVLEGIG 108 (122)
Q Consensus 82 dL~~aa~~L~v~kRRiYDI~NVLE~ig 108 (122)
.+.++|..||+.++-+|.+++-++.=|
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 699999999999999999999998877
No 100
>PRK10870 transcriptional repressor MprA; Provisional
Probab=68.67 E-value=11 Score=28.53 Aligned_cols=40 Identities=20% Similarity=0.255 Sum_probs=35.5
Q ss_pred hhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 74 QSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 74 ~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
...+++.+...++|+.+++.+=-+-=+++-||.-|+|+|.
T Consensus 65 ~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~ 104 (176)
T PRK10870 65 ESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERR 104 (176)
T ss_pred hcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 3345677899999999999999999999999999999997
No 101
>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=68.51 E-value=9 Score=21.50 Aligned_cols=23 Identities=17% Similarity=0.131 Sum_probs=19.4
Q ss_pred ccHHHHHhHhccchhhhhhHHHh
Q psy8797 81 VDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NV 103 (122)
+++.++|+.|+|.++-||..+.-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 46789999999999999988764
No 102
>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=68.13 E-value=16 Score=25.24 Aligned_cols=46 Identities=24% Similarity=0.296 Sum_probs=37.2
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
+-.|+.+.+. +.+|.=.++|+.|++.-=-|..+.-.||.+|||+++
T Consensus 11 ~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 11 KALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 3455555554 777888889999999888888999999999999875
No 103
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=67.96 E-value=16 Score=26.41 Aligned_cols=49 Identities=18% Similarity=0.213 Sum_probs=40.5
Q ss_pred HHHHHHHHHhhCCCC--cccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 65 LTKKFVKLLQSSPQG--VVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~--~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
+-..|..++...++. .+.|+++|+.|.+++|-.==|++-|+..|.|.=+
T Consensus 2 l~~~y~~L~~~~~~~~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~ 52 (115)
T PF12793_consen 2 LLEQYQRLWQHYGGQPVEVTLDELAELLFCSRRNARTLLKKMQEEGWITWQ 52 (115)
T ss_pred HHHHHHHHHHHcCCCCcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeee
Confidence 345677777766644 5799999999999999999999999999988643
No 104
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=67.90 E-value=10 Score=28.88 Aligned_cols=40 Identities=5% Similarity=0.117 Sum_probs=36.0
Q ss_pred CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 76 sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
.|+..+...++|+.|||+|==+=+.+..|+.-|||+-...
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~ 65 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQ 65 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCC
Confidence 4788889999999999999999999999999999986643
No 105
>PRK03837 transcriptional regulator NanR; Provisional
Probab=67.73 E-value=7.7 Score=29.72 Aligned_cols=49 Identities=10% Similarity=0.247 Sum_probs=39.6
Q ss_pred HHHHHHHHHhh---CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 65 LTKKFVKLLQS---SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 65 Lt~kFi~ll~~---sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
+...+.+.+.. .|+..+ ...++|+.|||+|==+=|.+..|+.-|+|+..
T Consensus 18 v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 18 VEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS 70 (241)
T ss_pred HHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 33444444433 367788 89999999999999999999999999999875
No 106
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=67.10 E-value=9.1 Score=29.77 Aligned_cols=54 Identities=17% Similarity=0.281 Sum_probs=41.9
Q ss_pred CcHHH-HHHHHHHHHhh---CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 60 TSLGL-LTKKFVKLLQS---SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 60 kSLg~-Lt~kFi~ll~~---sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.++.. +...+.+.+.. .|+..+ .-.++|+.|||+|=-+-+.+..|++.|||+..
T Consensus 9 ~~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~ 67 (254)
T PRK09464 9 PKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR 67 (254)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 34543 34555555543 467777 89999999999999999999999999999855
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=66.58 E-value=5.7 Score=24.29 Aligned_cols=24 Identities=21% Similarity=0.434 Sum_probs=19.6
Q ss_pred CcccHHHHHhHhccchhhhhhHHH
Q psy8797 79 GVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 79 ~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
..+++.++++.+++++.-||..++
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 457899999999999999999887
No 108
>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=66.50 E-value=12 Score=28.23 Aligned_cols=39 Identities=15% Similarity=0.298 Sum_probs=35.5
Q ss_pred CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 76 sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.|+..+.-.++|+.|||+|==+=+.+..|++-|+|+...
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~ 68 (212)
T TIGR03338 30 PPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEK 68 (212)
T ss_pred CCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEec
Confidence 478888999999999999999999999999999998663
No 109
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=66.25 E-value=12 Score=29.95 Aligned_cols=43 Identities=9% Similarity=0.165 Sum_probs=35.7
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGI 107 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~i 107 (122)
...+.+.++.++..+.++|+++|+.+++++|-|.=+..-.-|+
T Consensus 6 ~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~ 48 (289)
T PRK15121 6 IIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGH 48 (289)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCc
Confidence 5678889999999999999999999999988887776655443
No 110
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=65.75 E-value=7.9 Score=27.84 Aligned_cols=36 Identities=14% Similarity=0.113 Sum_probs=33.6
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.+.+...++|+.+++.+=-+--+++-||.-|+|+|.
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~ 87 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL 87 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 445899999999999999999999999999999987
No 111
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=65.70 E-value=11 Score=25.24 Aligned_cols=37 Identities=19% Similarity=0.350 Sum_probs=33.0
Q ss_pred CCcccHHHHHhHh-ccchhhhhhHHHhhhhccceeecc
Q psy8797 78 QGVVDLNVASESL-DVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 78 ~~~idL~~aa~~L-~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.+....+++.+.+ +++.+=|.+=...|+..|||+|..
T Consensus 16 ~g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 16 QGPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp TSSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred hCCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhccc
Confidence 3778999999999 999999999999999999999973
No 112
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=65.66 E-value=11 Score=24.77 Aligned_cols=32 Identities=22% Similarity=0.303 Sum_probs=29.8
Q ss_pred HHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 83 LNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 83 L~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+.++|+.|++.+=-++.++..|+.-|+|.+..
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence 56899999999999999999999999999975
No 113
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=65.65 E-value=19 Score=24.83 Aligned_cols=59 Identities=24% Similarity=0.434 Sum_probs=44.2
Q ss_pred CcHHHHHHHHHHHHhhC-CCCcccHHHHHhHhccchhhhhhHHH-hhhhccceeeccCCce
Q psy8797 60 TSLGLLTKKFVKLLQSS-PQGVVDLNVASESLDVQKRRIYDITN-VLEGIGILEKKSKNNI 118 (122)
Q Consensus 60 kSLg~Lt~kFi~ll~~s-p~~~idL~~aa~~L~v~kRRiYDI~N-VLE~igLI~K~~Kn~~ 118 (122)
..|..+=++++..+.+. .++++.|+.+|..|+..+.-|=|++- -|--.|+|+|+.+...
T Consensus 4 ~GLd~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT~rGR~ 64 (76)
T PF05491_consen 4 LGLDELDRRYLKTLIENFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRTPRGRV 64 (76)
T ss_dssp TS-BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEETTEEE
T ss_pred ccCCHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhCccHHH
Confidence 34556678888887665 68899999999999999998888765 5778999999977653
No 114
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=65.15 E-value=29 Score=25.00 Aligned_cols=46 Identities=15% Similarity=0.235 Sum_probs=36.9
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+.|..+.. .++.+.+.++|+.|+|.+=-+-..++-|+.-|+|.+..
T Consensus 11 ~~I~~l~~--~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 11 EQIYLLIE--EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred HHHHHHHh--cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEec
Confidence 33444443 34567899999999999999999999999999998653
No 115
>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=65.03 E-value=12 Score=29.50 Aligned_cols=46 Identities=20% Similarity=0.374 Sum_probs=33.1
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceee
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEK 112 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K 112 (122)
+-..||+|+.. ..++.|+++|..+++..==.-|-|+-|+.-|.|+=
T Consensus 100 lL~~Fi~yIK~--~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltG 145 (188)
T PF09756_consen 100 LLQEFINYIKE--HKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTG 145 (188)
T ss_dssp HHHHHHHHHHH---SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-E
T ss_pred HHHHHHHHHHH--cceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCcee
Confidence 77899999997 46799999999999976666666777777776653
No 116
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=64.46 E-value=14 Score=25.76 Aligned_cols=48 Identities=21% Similarity=0.392 Sum_probs=38.0
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhc-----cchhhhhhHHHhhhhccceeeccCC
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLD-----VQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~-----v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
..++++.+++. .++.+++.+.|. +..=-+|-.++.|+..|+|.+...+
T Consensus 12 ~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 12 AILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 47788888766 789999998884 4555699999999999999997543
No 117
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=64.26 E-value=11 Score=29.60 Aligned_cols=38 Identities=21% Similarity=0.260 Sum_probs=31.5
Q ss_pred HHHHHHHHHhhCCCCc-ccHHHHHhHhccchhhhhhHHH
Q psy8797 65 LTKKFVKLLQSSPQGV-VDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~-idL~~aa~~L~v~kRRiYDI~N 102 (122)
...++++++.++-... +++.++|+.+++++|.||-+..
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 3457777887776665 8999999999999999998876
No 118
>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=64.18 E-value=13 Score=21.89 Aligned_cols=38 Identities=18% Similarity=0.347 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHH
Q psy8797 62 LGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDIT 101 (122)
Q Consensus 62 Lg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~ 101 (122)
|..+=+.+|.-.....++ ++..||+.||+.++-||.=+
T Consensus 2 l~~~E~~~i~~aL~~~~g--n~~~aA~~Lgisr~tL~~kl 39 (42)
T PF02954_consen 2 LEEFEKQLIRQALERCGG--NVSKAARLLGISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHHHHHTTT---HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCC--CHHHHHHHHCCCHHHHHHHH
Confidence 444445566554433332 56899999999999998643
No 119
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=63.99 E-value=21 Score=26.47 Aligned_cols=52 Identities=15% Similarity=0.232 Sum_probs=44.9
Q ss_pred cCcHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceee
Q psy8797 59 DTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEK 112 (122)
Q Consensus 59 ~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K 112 (122)
...|-.+=++.+..|+. ++.+...++|+++|++.--++.=++=|+.-|+|++
T Consensus 9 ~~~lD~~D~~IL~~Lq~--d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 9 GKDLDRIDRNILNELQK--DGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred hhhHHHHHHHHHHHhcc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 34477777889998885 67788999999999999999999999999999986
No 120
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=63.26 E-value=15 Score=29.66 Aligned_cols=44 Identities=5% Similarity=0.026 Sum_probs=37.0
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGI 107 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~i 107 (122)
....++++++.++....++++++|+.++++.|.|+-.++-.-|+
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~ 261 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGM 261 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCc
Confidence 34578899999999999999999999999999988877755444
No 121
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=62.97 E-value=12 Score=28.67 Aligned_cols=38 Identities=18% Similarity=0.267 Sum_probs=34.5
Q ss_pred CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 76 SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 76 sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.|+..+ .-.++|++|||+|==+-+.+..|+.-|+|+..
T Consensus 26 ~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~ 64 (239)
T PRK04984 26 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ 64 (239)
T ss_pred CCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 367778 68999999999999999999999999999865
No 122
>PF14178 YppF: YppF-like protein
Probab=62.80 E-value=21 Score=23.71 Aligned_cols=51 Identities=20% Similarity=0.307 Sum_probs=43.7
Q ss_pred cHHHHHHHHHHHHhhCCCCcccHHHHHhHh----ccchhhhhhHHHhhhhcccee
Q psy8797 61 SLGLLTKKFVKLLQSSPQGVVDLNVASESL----DVQKRRIYDITNVLEGIGILE 111 (122)
Q Consensus 61 SLg~Lt~kFi~ll~~sp~~~idL~~aa~~L----~v~kRRiYDI~NVLE~igLI~ 111 (122)
.|..|-++|++.-+-.|.....|-+-|.++ .+.-+..+|++-.||..|-+.
T Consensus 2 ~l~eLk~~F~~~k~y~p~~~NeLLDFar~~Yi~gei~i~eYR~lvreLE~~GA~~ 56 (60)
T PF14178_consen 2 NLHELKQKFMQKKKYEPEDMNELLDFARKLYIQGEISINEYRNLVRELEANGAVS 56 (60)
T ss_pred CHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhCCCC
Confidence 367888999999998898888888888887 568899999999999998654
No 123
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=62.73 E-value=19 Score=23.61 Aligned_cols=44 Identities=14% Similarity=0.227 Sum_probs=34.4
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.++++... ++++.-.++|+.+++.+--.-=+.+.||.-|.|++.
T Consensus 5 Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~ 48 (62)
T PF04703_consen 5 ILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEGKVERS 48 (62)
T ss_dssp HHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE
T ss_pred HHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45566553 556888999999999888888889999999999974
No 124
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=62.70 E-value=13 Score=29.11 Aligned_cols=41 Identities=5% Similarity=0.091 Sum_probs=34.5
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhh
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLE 105 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE 105 (122)
...++++++..+..+.++++++|+.++++++.|.-++.=--
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~ 224 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQL 224 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46778899988899999999999999999998877665433
No 125
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=62.67 E-value=14 Score=30.17 Aligned_cols=58 Identities=17% Similarity=0.383 Sum_probs=47.1
Q ss_pred CcHHHHHHHHHH-HHhhCCCCcccHHHHHhHhccchhhhhhHHH-hhhhccceeeccCCc
Q psy8797 60 TSLGLLTKKFVK-LLQSSPQGVVDLNVASESLDVQKRRIYDITN-VLEGIGILEKKSKNN 117 (122)
Q Consensus 60 kSLg~Lt~kFi~-ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N-VLE~igLI~K~~Kn~ 117 (122)
..|....++++. ++..-+++.+.++.+|..|+....-+-|++. .|-..|+|++.+...
T Consensus 255 ~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~gr 314 (328)
T PRK00080 255 LGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRGR 314 (328)
T ss_pred CCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCchH
Confidence 455566777886 5666677789999999999999999888888 888999998876543
No 126
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=62.64 E-value=15 Score=26.13 Aligned_cols=43 Identities=28% Similarity=0.488 Sum_probs=34.2
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
..|.+++.+.|+ +.+.++|+.|+|...-|+ ..|.-+|+..|+.
T Consensus 60 ~~L~~~v~~~pd--~tl~Ela~~l~Vs~~ti~---~~Lkrlg~t~KK~ 102 (119)
T PF01710_consen 60 DELKALVEENPD--ATLRELAERLGVSPSTIW---RALKRLGITRKKK 102 (119)
T ss_pred HHHHHHHHHCCC--cCHHHHHHHcCCCHHHHH---HHHHHcCchhccC
Confidence 557788888777 667899999999777766 5677888888874
No 127
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=62.47 E-value=28 Score=26.74 Aligned_cols=38 Identities=11% Similarity=0.163 Sum_probs=33.0
Q ss_pred ccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 81 VDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
++-.++|..||+.+--+.=+++-|+.-|+|+..+.+.+
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i 217 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQI 217 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceE
Confidence 45689999999999999999999999999987754444
No 128
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=62.45 E-value=10 Score=29.21 Aligned_cols=38 Identities=21% Similarity=0.316 Sum_probs=36.3
Q ss_pred CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 76 sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.|+..++.+++|+.|||+|=-+=+.+..|++-|||+..
T Consensus 35 ~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~ 72 (230)
T COG1802 35 APGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIE 72 (230)
T ss_pred CCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEec
Confidence 48999999999999999999999999999999999987
No 129
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=62.44 E-value=21 Score=30.55 Aligned_cols=43 Identities=12% Similarity=0.159 Sum_probs=37.6
Q ss_pred CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCcee
Q psy8797 77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119 (122)
Q Consensus 77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~ 119 (122)
.+..++.+++++.+++.-+.+-||.+-|+..|+|.+...+.|.
T Consensus 307 ~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~~~g~~~ 349 (412)
T PRK04214 307 HGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRGERGQWV 349 (412)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEecCCCceE
Confidence 4568899999999999999999999999999999987656543
No 130
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=61.46 E-value=13 Score=28.97 Aligned_cols=49 Identities=20% Similarity=0.256 Sum_probs=39.1
Q ss_pred HHHHHHHHHhh---CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 65 LTKKFVKLLQS---SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 65 Lt~kFi~ll~~---sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
+...+.+.+.. .|+..+ +-.++|+.|||+|==+=+.+..|++-|||+..
T Consensus 14 v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~ 66 (257)
T PRK10225 14 VGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVR 66 (257)
T ss_pred HHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 33444444433 478888 69999999999999999999999999999765
No 131
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=61.19 E-value=20 Score=26.73 Aligned_cols=44 Identities=11% Similarity=0.179 Sum_probs=35.6
Q ss_pred HHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 70 VKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 70 i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
+-++...++..+.+.++|+.+++...-+.=|+..|.--|+|+-.
T Consensus 14 L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~ 57 (153)
T PRK11920 14 LMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETV 57 (153)
T ss_pred HHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence 33444556778899999999999999999999999999988654
No 132
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=60.80 E-value=25 Score=22.02 Aligned_cols=38 Identities=13% Similarity=0.261 Sum_probs=34.6
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
++.+++.++=+.++++|+-.--+..-|...|+..+.+-
T Consensus 8 ~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~gd 45 (50)
T PF09107_consen 8 NGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVGD 45 (50)
T ss_dssp TSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred CCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeCC
Confidence 78899999999999999999999999999999999864
No 133
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=60.76 E-value=8.9 Score=33.65 Aligned_cols=35 Identities=20% Similarity=0.245 Sum_probs=29.2
Q ss_pred CCCcccHHHHHhHhccchhhhhhHHHhhhhcccee
Q psy8797 77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILE 111 (122)
Q Consensus 77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~ 111 (122)
.+|..+|.++|+++++.-.+++|+++.|...|||+
T Consensus 352 ~DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 352 SDGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp -EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred ccCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 36778999999999999999999999999999985
No 134
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=60.60 E-value=24 Score=28.74 Aligned_cols=44 Identities=18% Similarity=0.275 Sum_probs=36.6
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccc-eee
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGI-LEK 112 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igL-I~K 112 (122)
.+.+.++.+ +..+...++|+.|++++.-++-.+..|+.-|+ |..
T Consensus 7 ~~il~~L~~--~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~ 51 (319)
T PRK11886 7 LQLLSLLAD--GDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFS 51 (319)
T ss_pred HHHHHHHHc--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEE
Confidence 456677764 46678889999999999999999999999999 543
No 135
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=60.58 E-value=22 Score=26.84 Aligned_cols=40 Identities=20% Similarity=0.336 Sum_probs=36.3
Q ss_pred CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797 77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
..+.+...++|+.|+|+.--.-+.+|=|+..|+|......
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~ 60 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYG 60 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCC
Confidence 6788999999999999999999999999999999986443
No 136
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=60.01 E-value=17 Score=26.90 Aligned_cols=37 Identities=16% Similarity=0.141 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhh
Q psy8797 63 GLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYD 99 (122)
Q Consensus 63 g~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYD 99 (122)
..+-..+++++.+.+-.-+.++++|++.||.+.-||.
T Consensus 14 ~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~ 50 (213)
T PRK09975 14 QELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYW 50 (213)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHH
Confidence 4567778899988777789999999999999999994
No 137
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=59.21 E-value=20 Score=28.92 Aligned_cols=50 Identities=20% Similarity=0.171 Sum_probs=37.8
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
--.+.++++++.+ .+.+.++|+.|+|+.+=+.==++.||.-|++.+....
T Consensus 18 R~~~Il~~L~~~~--~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~GG 67 (269)
T PRK09802 18 RREQIIQRLRQQG--SVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGG 67 (269)
T ss_pred HHHHHHHHHHHcC--CEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeCC
Confidence 3455777777643 4999999999999876665445678999999987543
No 138
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=59.11 E-value=16 Score=28.37 Aligned_cols=38 Identities=21% Similarity=0.267 Sum_probs=35.1
Q ss_pred CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 76 SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 76 sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.|+..+ .-.++|+.|||+|==+-+.+..|+.-|||+..
T Consensus 26 ~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~ 64 (251)
T PRK09990 26 KVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETA 64 (251)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 478888 89999999999999999999999999999765
No 139
>PRK06474 hypothetical protein; Provisional
Probab=59.08 E-value=25 Score=26.89 Aligned_cols=47 Identities=19% Similarity=0.217 Sum_probs=38.8
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHh-ccchhhhhhHHHhhhhccceeecc
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESL-DVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L-~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.+.++++...+. .++..++++.| ++.+=-+|=.+++|+..|+|....
T Consensus 14 ~~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 14 MKICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee
Confidence 346677766544 38999999999 789999999999999999999753
No 140
>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=58.38 E-value=9.9 Score=30.73 Aligned_cols=30 Identities=30% Similarity=0.556 Sum_probs=24.4
Q ss_pred HHHhHhc---cchhhhhhHHHhhhhccceeecc
Q psy8797 85 VASESLD---VQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 85 ~aa~~L~---v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.+|+.++ +..|++||+++-||.+|||+-..
T Consensus 319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~ 351 (365)
T TIGR02928 319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAEE 351 (365)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEE
Confidence 4555555 57899999999999999998753
No 141
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=57.90 E-value=24 Score=29.10 Aligned_cols=42 Identities=12% Similarity=0.154 Sum_probs=35.9
Q ss_pred CCCcccHHHHHhHhc--cchhhhhhHHHhhhhccceeeccCCce
Q psy8797 77 PQGVVDLNVASESLD--VQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 77 p~~~idL~~aa~~L~--v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
.++.-|..++|..++ |.--.+=|.++.|+.+|||+|.+-+.|
T Consensus 134 ~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y 177 (271)
T TIGR02147 134 MPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFY 177 (271)
T ss_pred CCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcE
Confidence 456668899999998 888999999999999999999865533
No 142
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=57.51 E-value=30 Score=26.35 Aligned_cols=36 Identities=22% Similarity=0.201 Sum_probs=32.5
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
..+-.++|+.||+.++-+.=+++-|+--|+|+...+
T Consensus 169 ~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~ 204 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKR 204 (226)
T ss_pred cchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCC
Confidence 356799999999999999999999999999998743
No 143
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=56.67 E-value=16 Score=28.56 Aligned_cols=38 Identities=13% Similarity=0.121 Sum_probs=34.3
Q ss_pred CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 76 SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 76 sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.|+..+ .-.++|+.|||+|==+=+.+..||+.|||+..
T Consensus 21 ~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~ 59 (253)
T PRK10421 21 EAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSR 59 (253)
T ss_pred CCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 467788 68999999999999999999999999999754
No 144
>smart00351 PAX Paired Box domain.
Probab=56.14 E-value=23 Score=25.47 Aligned_cols=44 Identities=20% Similarity=0.150 Sum_probs=35.5
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceee
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEK 112 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K 112 (122)
+=.+||.++.+. ....++|+.|+|.+.-+|.|++=...-|.++-
T Consensus 22 ~R~riv~~~~~G----~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~p 65 (125)
T smart00351 22 ERQRIVELAQNG----VRPCDISRQLCVSHGCVSKILGRYYETGSIRP 65 (125)
T ss_pred HHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 335788877632 47789999999999999999998888877654
No 145
>PRK09462 fur ferric uptake regulator; Provisional
Probab=56.05 E-value=33 Score=24.97 Aligned_cols=46 Identities=17% Similarity=0.359 Sum_probs=37.5
Q ss_pred HHHHHhhCCCCcccHHHHHhHh-----ccchhhhhhHHHhhhhccceeecc
Q psy8797 69 FVKLLQSSPQGVVDLNVASESL-----DVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L-----~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.++++.++++..++.+++-+.| .+.+=-+|-+++.|+..|+|.+..
T Consensus 22 Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 22 ILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 5667776666778888888877 357788999999999999998863
No 146
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=56.03 E-value=20 Score=26.33 Aligned_cols=37 Identities=22% Similarity=0.337 Sum_probs=30.1
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhcc----chhhhhhHHHhhhh
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDV----QKRRIYDITNVLEG 106 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v----~kRRiYDI~NVLE~ 106 (122)
..||..|-.+.+ +|.+++..||| .|-||.||+..|.-
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 458888876655 78999999998 79999999877654
No 147
>PRK15185 transcriptional regulator HilD; Provisional
Probab=55.55 E-value=22 Score=30.13 Aligned_cols=40 Identities=13% Similarity=0.167 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHh
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NV 103 (122)
.++.++.+++.+++...++++++|+.++++.|.|+-...-
T Consensus 206 ~~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~ 245 (309)
T PRK15185 206 TLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAE 245 (309)
T ss_pred HHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3667888899999999999999999999999999888763
No 148
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=55.16 E-value=26 Score=30.74 Aligned_cols=50 Identities=24% Similarity=0.375 Sum_probs=42.2
Q ss_pred HHHHHHHHHHhhCC--CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 64 LLTKKFVKLLQSSP--QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp--~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.|-+.|+.|++... +..+.|+++|+.|.+++|-.==|+|-|+..|.|.=+
T Consensus 5 ~~~~~~~~L~~~~~~~~~~~~l~~la~~l~cs~R~~~~~l~~~~~~gwl~w~ 56 (552)
T PRK13626 5 RLQQQFIRLWQCCEGKSQETTLNELAELLNCSRRHMRTLLNTMQQRGWLTWQ 56 (552)
T ss_pred HHHHHHHHHHHhcCCCcceeeHHHHHHHhcCChhHHHHHHHHHHHCCCeeee
Confidence 46678888887653 457899999999999999999999999999998643
No 149
>PRK13502 transcriptional activator RhaR; Provisional
Probab=55.15 E-value=21 Score=27.78 Aligned_cols=40 Identities=15% Similarity=0.150 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHh
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NV 103 (122)
.+..++++++.++....+.++++|+.++++.+.|.-++--
T Consensus 176 ~~~~~~~~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~ 215 (282)
T PRK13502 176 TLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRA 215 (282)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3567888999888888899999999999999988877654
No 150
>PRK11642 exoribonuclease R; Provisional
Probab=55.14 E-value=28 Score=32.98 Aligned_cols=50 Identities=10% Similarity=0.063 Sum_probs=40.5
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccc----hhhhhhHHHhhhhccceeeccCCce
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQ----KRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~----kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
..+++|.+. +..+.+.+++..|++. +..|..+++-|+..|.|.+...+.|
T Consensus 23 ~Il~~l~~~-~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~~~~~ 76 (813)
T PRK11642 23 FILEHLTKR-EKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCY 76 (813)
T ss_pred HHHHHHHhc-CCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceE
Confidence 356666653 4889999999999985 4569999999999999998766655
No 151
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=54.92 E-value=22 Score=28.77 Aligned_cols=43 Identities=7% Similarity=0.162 Sum_probs=35.7
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGI 107 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~i 107 (122)
..++.+.++.++....+++.++|+.+++++|.++-+..--.|+
T Consensus 192 ~i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~ 234 (302)
T PRK10371 192 YVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQL 234 (302)
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHHhCC
Confidence 5678888888888889999999999999999888777654443
No 152
>PLN03239 histone acetyltransferase; Provisional
Probab=54.60 E-value=49 Score=28.80 Aligned_cols=59 Identities=17% Similarity=0.218 Sum_probs=43.4
Q ss_pred CCCCCCcCcHHHHH------HHHHHHHhhCC--CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 53 EKGTRYDTSLGLLT------KKFVKLLQSSP--QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 53 ~~~~R~~kSLg~Lt------~kFi~ll~~sp--~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+...|-=.-||.++ ...++++.... +..++|+++|...++. .-||+..|+.+|++....
T Consensus 249 G~PEkPLSdlG~~sY~~YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~---~~DIi~tL~~l~~l~~~~ 315 (351)
T PLN03239 249 GSPEKPMSDLGQQAYIPYWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIM---AEDIVFALNQLGILKFIN 315 (351)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHhCCC---HHHHHHHHHHCCcEEEEC
Confidence 33455556677775 33666665543 3579999999999995 579999999999997653
No 153
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=54.59 E-value=24 Score=30.16 Aligned_cols=50 Identities=20% Similarity=0.202 Sum_probs=45.6
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHh-ccchhhhhhHHHhhhhccceeec
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESL-DVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L-~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.+.++++.++..+.+..++.+.+|..+ ++.++-++.-++.||..-++-..
T Consensus 220 ~~~k~i~~~l~~~~g~~~s~~~la~~l~~is~~Ti~~Yl~~le~~fll~~~ 270 (398)
T COG1373 220 DLMKRILRFLASNIGSPISYSSLARELKGISKDTIRKYLSYLEDAFLLFLV 270 (398)
T ss_pred HHHHHHHHHHHhhcCCccCHHHHHHHHhccchHHHHHHHHHHHHhhheEEe
Confidence 577889999999999999999999999 79999999999999999988743
No 154
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=54.52 E-value=12 Score=30.70 Aligned_cols=35 Identities=26% Similarity=0.423 Sum_probs=26.3
Q ss_pred CcccHHHHH-------hHhcc---chhhhhhHHHhhhhccceeec
Q psy8797 79 GVVDLNVAS-------ESLDV---QKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 79 ~~idL~~aa-------~~L~v---~kRRiYDI~NVLE~igLI~K~ 113 (122)
+.+...++. +.+++ ..|+++|+.|-|+..|||+-.
T Consensus 314 ~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~~~glI~~~ 358 (394)
T PRK00411 314 DEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIINTR 358 (394)
T ss_pred CcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHHhcCCeEEE
Confidence 345555555 44677 459999999999999999743
No 155
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=54.29 E-value=15 Score=22.53 Aligned_cols=27 Identities=19% Similarity=0.281 Sum_probs=21.0
Q ss_pred ccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797 81 VDLNVASESLDVQKRRIYDITNVLEGI 107 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NVLE~i 107 (122)
++|+++|+.+++..+.|+.+.+-.-++
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~ 28 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGT 28 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCc
Confidence 578888888888888888888765444
No 156
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=53.50 E-value=48 Score=24.36 Aligned_cols=36 Identities=11% Similarity=0.231 Sum_probs=32.6
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
.+.-.++|+.||+.+..+.=+.+-|+.-|+|+...+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~ 203 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGK 203 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 566799999999999999999999999999987744
No 157
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=52.84 E-value=23 Score=29.26 Aligned_cols=39 Identities=5% Similarity=0.005 Sum_probs=34.8
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHH
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
....++++++.++....++++++|..+++++|-|+-.+.
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 356789999999999999999999999999999888775
No 158
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=52.48 E-value=23 Score=20.92 Aligned_cols=38 Identities=13% Similarity=0.163 Sum_probs=24.0
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHH
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
+|.+|.+++...-....++.++|..+++.--.+..|+|
T Consensus 12 ~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 12 ITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 45555555433222237999999999996665555554
No 159
>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=52.16 E-value=12 Score=23.28 Aligned_cols=30 Identities=13% Similarity=0.212 Sum_probs=21.2
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHH
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
.|+.+... . ...++|..+||.+--|+||.+
T Consensus 15 iI~~~e~g---~-s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 15 IIKRLEEG---E-SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp HHHHHHCT---T--HHHHHHHHT--CCHHHHHHH
T ss_pred HHHHHHcC---C-CHHHHHHHhCCCHHHHHHHHH
Confidence 55555543 3 789999999999999999986
No 160
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=51.42 E-value=34 Score=22.48 Aligned_cols=42 Identities=10% Similarity=0.172 Sum_probs=33.9
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccc
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGI 109 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igL 109 (122)
++++++.......++++++|..+++.++-|.-.+.-..|+..
T Consensus 24 ~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~ 65 (127)
T COG2207 24 RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSP 65 (127)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
Confidence 777777777777799999999999999988888876665544
No 161
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=51.22 E-value=27 Score=27.57 Aligned_cols=56 Identities=23% Similarity=0.394 Sum_probs=41.4
Q ss_pred HHHHHHHHHH-HHhhCCCCcccHHHHHhHhccchhhhhhHHH-hhhhccceeeccCCc
Q psy8797 62 LGLLTKKFVK-LLQSSPQGVVDLNVASESLDVQKRRIYDITN-VLEGIGILEKKSKNN 117 (122)
Q Consensus 62 Lg~Lt~kFi~-ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N-VLE~igLI~K~~Kn~ 117 (122)
|...-+.++. ++..-.+..+.+.++|..||+....+.+++- .|-..|+|++.+...
T Consensus 236 l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~~g~ 293 (305)
T TIGR00635 236 LDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGR 293 (305)
T ss_pred CCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCCchh
Confidence 3334445665 4454455568899999999999999999777 788899998776544
No 162
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=51.07 E-value=38 Score=24.77 Aligned_cols=50 Identities=12% Similarity=0.157 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 62 LGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 62 Lg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
|-.+=++.+++|+. ++.....++|+.||++.--+..=++=|+.-|+|++.
T Consensus 7 lD~~D~~Il~~Lq~--d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 7 IDNLDRGILEALME--NARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred cCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 44566788999986 477899999999999988888889999999999864
No 163
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=50.81 E-value=37 Score=31.14 Aligned_cols=53 Identities=15% Similarity=0.288 Sum_probs=44.1
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccc----hhhhhhHHHhhhhccceeeccCCcee
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQ----KRRIYDITNVLEGIGILEKKSKNNIQ 119 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~----kRRiYDI~NVLE~igLI~K~~Kn~~~ 119 (122)
.+.++++...+...+...+++..|++. +.-|+.+++-|+.-|.|.+..++.|.
T Consensus 5 ~~il~~l~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~~~~~~~ 61 (709)
T TIGR02063 5 ELILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYA 61 (709)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEe
Confidence 357788888788899999999999984 45599999999999999987666554
No 164
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=50.61 E-value=17 Score=23.87 Aligned_cols=22 Identities=23% Similarity=0.439 Sum_probs=16.9
Q ss_pred HHHhhCCCCcccHHHHHhHhccc
Q psy8797 71 KLLQSSPQGVVDLNVASESLDVQ 93 (122)
Q Consensus 71 ~ll~~sp~~~idL~~aa~~L~v~ 93 (122)
+++.+ .++.+.+.++|++|+|+
T Consensus 14 e~y~~-~~g~i~lkdIA~~Lgvs 35 (60)
T PF10668_consen 14 EIYKE-SNGKIKLKDIAEKLGVS 35 (60)
T ss_pred HHHHH-hCCCccHHHHHHHHCCC
Confidence 34444 36778999999999984
No 165
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=50.58 E-value=26 Score=27.32 Aligned_cols=47 Identities=11% Similarity=0.145 Sum_probs=37.7
Q ss_pred HHHHHHHhh---CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 67 KKFVKLLQS---SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 67 ~kFi~ll~~---sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
..+.+.+.. .|+..+ .-.++|+.|||+|==+=+.+..|+..|||+..
T Consensus 15 ~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~ 65 (253)
T PRK11523 15 AELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVR 65 (253)
T ss_pred HHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 444444433 467788 48899999999999999999999999999755
No 166
>PRK13501 transcriptional activator RhaR; Provisional
Probab=50.47 E-value=28 Score=27.42 Aligned_cols=40 Identities=13% Similarity=0.071 Sum_probs=34.1
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhh
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVL 104 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVL 104 (122)
...++++++.+...+.++|.++|+.++++.+-|..++.-.
T Consensus 177 ~~~~i~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~ 216 (290)
T PRK13501 177 QLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQ 216 (290)
T ss_pred HHHHHHHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4567888998888899999999999999999888877643
No 167
>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=49.72 E-value=24 Score=27.07 Aligned_cols=38 Identities=18% Similarity=0.267 Sum_probs=34.9
Q ss_pred CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 76 SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 76 sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.|+..+ +-.++|+.|||+|==+=+.+..|+.-|||+..
T Consensus 25 ~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~ 63 (235)
T TIGR02812 25 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ 63 (235)
T ss_pred CCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 478888 89999999999999999999999999999865
No 168
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=49.02 E-value=27 Score=28.97 Aligned_cols=39 Identities=21% Similarity=0.393 Sum_probs=31.9
Q ss_pred HHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797 70 VKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGIL 110 (122)
Q Consensus 70 i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI 110 (122)
+.++...+. +...++|+.++|++|-||==+|-|+..|+=
T Consensus 14 i~~L~~~~~--vta~~lA~~~~VS~RTi~RDi~~L~~~gvP 52 (311)
T COG2378 14 IQILRAKET--VTAAELADEFEVSVRTIYRDIATLRAAGVP 52 (311)
T ss_pred HHHHHhCcc--chHHHHHHhcCCCHHHHHHHHHHHHHCCCC
Confidence 344555443 999999999999999999889999988873
No 169
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=48.80 E-value=31 Score=28.40 Aligned_cols=39 Identities=15% Similarity=0.088 Sum_probs=33.5
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHh
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NV 103 (122)
+..++.+++.+.+...++++++|+.+++++|.|+-...-
T Consensus 182 ~~~~i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~ 220 (291)
T PRK15186 182 LAENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQ 220 (291)
T ss_pred HHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 556777888899999999999999999999988877654
No 170
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=48.54 E-value=73 Score=27.04 Aligned_cols=57 Identities=18% Similarity=0.253 Sum_probs=42.4
Q ss_pred CCCCCCcCcHHHHH------HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 53 EKGTRYDTSLGLLT------KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 53 ~~~~R~~kSLg~Lt------~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
+...|-=.-||.++ ...++++.+ ....++|+++|...++. ..||+..|+.+|++...
T Consensus 191 G~PEkPLSdlG~~sY~~YW~~~il~~L~~-~~~~isi~~is~~T~i~---~~Dii~tL~~l~~l~~~ 253 (290)
T PLN03238 191 GTPERPLSDLGKVSFRSYWTRVLLEQLRD-VKGDVSIKDLSLATGIR---GEDIVSTLQSLNLIKYW 253 (290)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHh-cCCCccHHHHHHHhCCC---HHHHHHHHHHCCcEEEE
Confidence 33455556677765 335666654 35689999999999995 47999999999999654
No 171
>PRK13500 transcriptional activator RhaR; Provisional
Probab=48.12 E-value=27 Score=28.23 Aligned_cols=39 Identities=15% Similarity=0.169 Sum_probs=32.8
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHH
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
.+..++++++.++....++++++|+.++++.|-|--++.
T Consensus 206 ~~l~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK 244 (312)
T PRK13500 206 TLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFR 244 (312)
T ss_pred HHHHHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 356889999999888889999999999998888765554
No 172
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=47.98 E-value=28 Score=26.80 Aligned_cols=38 Identities=32% Similarity=0.420 Sum_probs=30.2
Q ss_pred CCcccHHHHHhHhccchhh--------------hhhHHHhhhhccceeeccC
Q psy8797 78 QGVVDLNVASESLDVQKRR--------------IYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRR--------------iYDI~NVLE~igLI~K~~K 115 (122)
.+.+-+..++..+|..+|| +=-++..||.+|+|++...
T Consensus 65 ~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~~ 116 (150)
T PRK09333 65 DGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTKK 116 (150)
T ss_pred cCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCCC
Confidence 3457778888899886554 7789999999999998753
No 173
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=46.54 E-value=37 Score=27.13 Aligned_cols=45 Identities=20% Similarity=0.234 Sum_probs=36.3
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.+.++++.+ .+.+.+.++|+.|+|+.-=|+==+..||.-|++.|.
T Consensus 8 ~~Il~~l~~--~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 8 DAIIELVKQ--QGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHH--cCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 446677764 557999999999999876666568899999999986
No 174
>PRK15044 transcriptional regulator SirC; Provisional
Probab=46.06 E-value=34 Score=28.94 Aligned_cols=38 Identities=8% Similarity=-0.030 Sum_probs=32.2
Q ss_pred HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHh
Q psy8797 66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NV 103 (122)
..+.++++.+++...++++++|+.+++.+|.|+-..+-
T Consensus 194 ~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 194 KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 35577788888899999999999999999999887663
No 175
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=45.43 E-value=65 Score=23.21 Aligned_cols=36 Identities=11% Similarity=0.142 Sum_probs=32.8
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
.+.-.++|+.+|+.+--+.-+++-|+.-|+|+...+
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~ 178 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHKK 178 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCC
Confidence 467899999999999999999999999999988743
No 176
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=44.98 E-value=28 Score=21.02 Aligned_cols=24 Identities=8% Similarity=0.088 Sum_probs=18.6
Q ss_pred cccHHHHHhHhccchhhhhhHHHh
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NV 103 (122)
.+++..||..+||.+-=|||-++-
T Consensus 16 ~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 16 KMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp SS-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHcC
Confidence 389999999999999999988764
No 177
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=44.72 E-value=21 Score=21.12 Aligned_cols=23 Identities=22% Similarity=0.278 Sum_probs=18.6
Q ss_pred ccHHHHHhHhccchhhhhhHHHh
Q psy8797 81 VDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NV 103 (122)
++..++|+.+|+.+.-++++.|=
T Consensus 10 ls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 10 LSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCHHHHHHHhCCCcchhHHHhcC
Confidence 67899999999999999998873
No 178
>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=44.60 E-value=29 Score=20.48 Aligned_cols=29 Identities=17% Similarity=0.266 Sum_probs=23.6
Q ss_pred HHHHhhCCCCcccHHHHHhHhccchhhhh
Q psy8797 70 VKLLQSSPQGVVDLNVASESLDVQKRRIY 98 (122)
Q Consensus 70 i~ll~~sp~~~idL~~aa~~L~v~kRRiY 98 (122)
++++.+.+-..+.++++|++.++.+.-||
T Consensus 6 ~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y 34 (47)
T PF00440_consen 6 LELFAEKGYEAVSIRDIARRAGVSKGSFY 34 (47)
T ss_dssp HHHHHHHHTTTSSHHHHHHHHTSCHHHHH
T ss_pred HHHHHHhCHHhCCHHHHHHHHccchhhHH
Confidence 45555555667899999999999999888
No 179
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=44.46 E-value=22 Score=28.14 Aligned_cols=49 Identities=18% Similarity=0.304 Sum_probs=37.7
Q ss_pred HHHHHHHHHhhC---CCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 65 LTKKFVKLLQSS---PQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 65 Lt~kFi~ll~~s---p~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
+..++.+++.+. |+..+ .=.++|++|||+|=-+=+.+-+|+..|+|+-.
T Consensus 15 v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~r 67 (241)
T COG2186 15 VAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEIR 67 (241)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeec
Confidence 445555555543 34433 47899999999999999999999999999754
No 180
>PF14830 Haemocyan_bet_s: Haemocyanin beta-sandwich; PDB: 1JS8_B 3QJO_A 1LNL_A.
Probab=44.34 E-value=8.4 Score=27.96 Aligned_cols=14 Identities=43% Similarity=0.800 Sum_probs=10.0
Q ss_pred hhhHHHhhhhccce
Q psy8797 97 IYDITNVLEGIGIL 110 (122)
Q Consensus 97 iYDI~NVLE~igLI 110 (122)
-||||.+|+.+||=
T Consensus 57 kydIT~~l~~l~l~ 70 (103)
T PF14830_consen 57 KYDITDALKKLGLH 70 (103)
T ss_dssp EEE-HHHHHHCT--
T ss_pred hhhHHHHHHHcCCC
Confidence 48999999999985
No 181
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=44.17 E-value=84 Score=20.06 Aligned_cols=49 Identities=16% Similarity=0.234 Sum_probs=39.7
Q ss_pred cHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcccee
Q psy8797 61 SLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILE 111 (122)
Q Consensus 61 SLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~ 111 (122)
.+|.++.+..+.+.. .+...+.+++...+...+.+-...-+|.-.|++.
T Consensus 10 ~fG~~~~~V~~~Ll~--~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 10 HFGEIVAKVGEVLLS--RGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HHHHHHHHHHHHHHH--C-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred HcChHHHHHHHHHHH--cCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 478899998888876 4567899999999999999999999999888875
No 182
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=42.62 E-value=47 Score=26.54 Aligned_cols=45 Identities=20% Similarity=0.254 Sum_probs=32.3
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+.++++++ .+.+.+.++|+.|+|+.=-|.==++.||.-|+|.|..
T Consensus 9 ~Il~~L~~--~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 9 AILEYLQK--QGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHH--cCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 45666665 5669999999999995322222267799999998863
No 183
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=42.19 E-value=75 Score=21.76 Aligned_cols=44 Identities=16% Similarity=0.199 Sum_probs=36.6
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGIL 110 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI 110 (122)
.....++....+..++-+++|+.||++|=-|.--|+-|+..|+=
T Consensus 6 ~~~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~ 49 (79)
T COG1654 6 QMLLLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVD 49 (79)
T ss_pred HHHHHHHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCc
Confidence 34455667777888999999999999999999999999888874
No 184
>PRK00118 putative DNA-binding protein; Validated
Probab=42.03 E-value=20 Score=25.79 Aligned_cols=34 Identities=24% Similarity=0.333 Sum_probs=28.0
Q ss_pred cccHHHHHhHhccchhhhhhHHH--------hhhhccceeec
Q psy8797 80 VVDLNVASESLDVQKRRIYDITN--------VLEGIGILEKK 113 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~N--------VLE~igLI~K~ 113 (122)
-.+..++|+.+|+++..+|..+. +++.+|++++.
T Consensus 33 g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~ 74 (104)
T PRK00118 33 DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKF 74 (104)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHH
Confidence 47899999999998888887754 78888888765
No 185
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=41.91 E-value=23 Score=21.68 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=17.4
Q ss_pred ccHHHHHhHhccchhhhhhHHH
Q psy8797 81 VDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~N 102 (122)
+...++|+.+++.+..||.|.|
T Consensus 13 lt~~~~a~~~~i~~~~i~~~e~ 34 (64)
T PF12844_consen 13 LTQKDLAEKLGISRSTISKIEN 34 (64)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHC
Confidence 6899999999999999998875
No 186
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=41.90 E-value=56 Score=22.25 Aligned_cols=32 Identities=22% Similarity=0.308 Sum_probs=23.1
Q ss_pred HHHHhhCCCCcccHHHHHhHhccchhhhhhHH
Q psy8797 70 VKLLQSSPQGVVDLNVASESLDVQKRRIYDIT 101 (122)
Q Consensus 70 i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~ 101 (122)
..+|.++|+..+.|+..|+.+++-|=-|-|=+
T Consensus 10 t~~L~~~P~~lisL~~Fae~f~~AKSsISEDl 41 (70)
T PF09182_consen 10 TKYLLENPNKLISLTYFAERFGAAKSSISEDL 41 (70)
T ss_dssp HHHHHTSTT--EEHHHHHHHHT--HHHHHHHH
T ss_pred HHHHHcCCcceEcHHHHHHHhcccccchHHHH
Confidence 35667899999999999999999888887633
No 187
>PRK12423 LexA repressor; Provisional
Probab=41.89 E-value=56 Score=25.09 Aligned_cols=37 Identities=11% Similarity=0.132 Sum_probs=31.3
Q ss_pred CCcccHHHHHhHhcc-chhhhhhHHHhhhhccceeecc
Q psy8797 78 QGVVDLNVASESLDV-QKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 78 ~~~idL~~aa~~L~v-~kRRiYDI~NVLE~igLI~K~~ 114 (122)
+..-.+.++|+.||+ ++=-++.-+.+|+.-|+|++..
T Consensus 23 g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~ 60 (202)
T PRK12423 23 GQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVP 60 (202)
T ss_pred CCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecC
Confidence 334699999999996 6667899999999999999863
No 188
>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.
Probab=41.72 E-value=31 Score=23.03 Aligned_cols=24 Identities=8% Similarity=0.329 Sum_probs=19.7
Q ss_pred CcccHHHHHhHhccchhhhhhHHH
Q psy8797 79 GVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 79 ~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
..+.+++||+-.|+-+++|++++.
T Consensus 12 ~~LTi~EAa~Y~gIG~~klr~l~~ 35 (67)
T PF09035_consen 12 YTLTIEEAAEYFGIGEKKLRELAE 35 (67)
T ss_dssp SEEEHHHHHHHT-S-HHHHHHHHH
T ss_pred hccCHHHHHHHhCccHHHHHHHHH
Confidence 468899999999999999999993
No 189
>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=41.66 E-value=26 Score=23.35 Aligned_cols=35 Identities=17% Similarity=0.317 Sum_probs=27.0
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.+--..+|++.|+.|.-|-.-+-=||+.|+|+-.+
T Consensus 4 ~lvas~iAd~~GiTRSvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 4 RLVASKIADRVGITRSVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp EE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred eehHHHHHHHhCccHHHHHHHHHHHHhcCceeecc
Confidence 44556899999999999888888899999998654
No 190
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=41.36 E-value=66 Score=24.76 Aligned_cols=46 Identities=17% Similarity=0.278 Sum_probs=36.8
Q ss_pred HHHHHHhhCCCCcc--cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 68 KFVKLLQSSPQGVV--DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 68 kFi~ll~~sp~~~i--dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
++..++...+...+ .+..+|..|++.++-|-=+++|+.-+|.|+-.
T Consensus 102 ~~Y~~l~~~~~~~l~~~~~~La~~l~i~~~~l~fml~VF~EL~FVti~ 149 (195)
T PF10141_consen 102 KLYKFLKQHPNFDLKEQLQALAKYLGISPDTLKFMLKVFFELGFVTIE 149 (195)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCcEEEe
Confidence 35555566655432 57899999999999999999999999999865
No 191
>PRK05638 threonine synthase; Validated
Probab=41.05 E-value=48 Score=28.51 Aligned_cols=58 Identities=19% Similarity=0.304 Sum_probs=45.4
Q ss_pred CCCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHhc--cchhhhhhHHHhhhhccceeec
Q psy8797 53 EKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLD--VQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 53 ~~~~R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~--v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.+..|.+-.++.+-...+.++.+.+ ....++++.|+ +.+--+|-.++.||.-|||+..
T Consensus 360 ~~~~~~~~~~~~~r~~IL~~L~~~~---~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~ 419 (442)
T PRK05638 360 GEGGREKFTIGGTKLEILKILSERE---MYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEA 419 (442)
T ss_pred CCCchhhhcccchHHHHHHHHhhCC---ccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEe
Confidence 4556656666666666777777543 67888899998 8999999999999999999753
No 192
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=40.53 E-value=51 Score=26.39 Aligned_cols=46 Identities=28% Similarity=0.370 Sum_probs=35.5
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
++.++++.+ .+.+.++++|+.|+|+.==|.==+|.||.-|++.|..
T Consensus 8 ~~Il~~l~~--~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 8 QKILELLKE--KGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred HHHHHHHHH--cCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEe
Confidence 456777775 6789999999999995433333368999999999963
No 193
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=39.61 E-value=68 Score=26.33 Aligned_cols=59 Identities=22% Similarity=0.313 Sum_probs=47.2
Q ss_pred cHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797 61 SLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC 120 (122)
Q Consensus 61 SLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W 120 (122)
.|-.-=+..+.++..+ +|.+.-.++...||.+|=-++=++-=||-.|+|++..++.=.|
T Consensus 192 ~L~~~e~~il~~i~~~-GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~ 250 (258)
T COG2512 192 DLNEDEKEILDLIRER-GGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNI 250 (258)
T ss_pred CCCHHHHHHHHHHHHh-CCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeE
Confidence 3333445677777764 7888999999999999999999999999999999987765554
No 194
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=39.49 E-value=72 Score=26.62 Aligned_cols=37 Identities=19% Similarity=0.408 Sum_probs=34.7
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
++.+.-.++|+++||+|=-+-.-+-.||.-|+|+-.+
T Consensus 196 egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 196 EGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred cccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 6889999999999999999999999999999999876
No 195
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=39.45 E-value=99 Score=21.11 Aligned_cols=46 Identities=24% Similarity=0.348 Sum_probs=39.7
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
++++++..+... ...|+++-+..++.|=-+-=..+=|..-|+|.+.
T Consensus 6 ~~~~IL~~ls~~---c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 6 VTQKILIILSKR---CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHHHHhc---cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 456777777654 6899999999999999999999999999999887
No 196
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=39.26 E-value=44 Score=19.11 Aligned_cols=29 Identities=10% Similarity=0.062 Sum_probs=19.0
Q ss_pred hhCCCCcccHHHHHhHhccchhhhhhHHH
Q psy8797 74 QSSPQGVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 74 ~~sp~~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
.++....+.|+++|+.+|++.+-+.-+..
T Consensus 2 ~~~~~~~~~l~~iA~~~g~S~~~f~r~Fk 30 (42)
T PF00165_consen 2 EENLQQKLTLEDIAEQAGFSPSYFSRLFK 30 (42)
T ss_dssp HTTT-SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred CccccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34556679999999999998877765543
No 197
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=39.09 E-value=41 Score=21.44 Aligned_cols=39 Identities=8% Similarity=0.005 Sum_probs=26.4
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGI 107 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~i 107 (122)
....|.+.-+..-+..++|+.||+....++++.+.....
T Consensus 9 a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~ 47 (78)
T PF04539_consen 9 ARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRP 47 (78)
T ss_dssp HHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCC
T ss_pred HHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCC
Confidence 334444444556789999999999999999998865544
No 198
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=39.04 E-value=1.3e+02 Score=27.09 Aligned_cols=56 Identities=18% Similarity=0.417 Sum_probs=42.4
Q ss_pred CCCCCcCcHHHHH------HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 54 KGTRYDTSLGLLT------KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 54 ~~~R~~kSLg~Lt------~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
...|--.-||.++ ...+++|..+ .+.++|++++...++. .-||+..|+.+|++...
T Consensus 343 ~PEkPLSdlG~~sY~~YW~~~i~~~L~~~-~~~~si~~is~~T~i~---~~Dii~tL~~l~~l~~~ 404 (450)
T PLN00104 343 TPERPLSDLGLVSYRGYWTRVLLEILKKH-KGNISIKELSDMTAIK---AEDIVSTLQSLNLIQYR 404 (450)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHhc-CCCccHHHHHHHhCCC---HHHHHHHHHHCCCEEec
Confidence 3345555677775 3366666654 4579999999999995 47999999999999865
No 199
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=38.30 E-value=83 Score=27.02 Aligned_cols=58 Identities=19% Similarity=0.276 Sum_probs=50.0
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec---cCCceeec
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK---SKNNIQCK 121 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~---~Kn~~~W~ 121 (122)
.+..+.+..+..+...-+|=.++.+-+|++|=++-+...-||..|+|.+. +|+.=.|.
T Consensus 4 ~~reklir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~RrkvsGKs~rVwL 64 (321)
T COG3888 4 SLREKLIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRKVSGKSKRVWL 64 (321)
T ss_pred cHHHHHHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeeeecCcceEEee
Confidence 45678888998887777899999999999999999999999999999876 66666663
No 200
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=37.33 E-value=50 Score=18.18 Aligned_cols=23 Identities=9% Similarity=0.158 Sum_probs=19.9
Q ss_pred ccHHHHHhHhccchhhhhhHHHh
Q psy8797 81 VDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NV 103 (122)
.+..++|+.+++....+|-+++-
T Consensus 27 ~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 27 LSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 68899999999999999887653
No 201
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=36.94 E-value=24 Score=20.90 Aligned_cols=24 Identities=17% Similarity=0.213 Sum_probs=17.7
Q ss_pred CCcccHHHHHhHhccchhhhhhHH
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDIT 101 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~ 101 (122)
....++.++|+.||+++-++..+.
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~ 41 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRIL 41 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHH
Confidence 445789999999999776665554
No 202
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=36.81 E-value=1.2e+02 Score=22.45 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=34.3
Q ss_pred HHHhhCCC-CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 71 KLLQSSPQ-GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 71 ~ll~~sp~-~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
-++-..++ +.+++.++|+..++.+-=+.-|+.-|.--|||+=.
T Consensus 15 ~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~ 58 (150)
T COG1959 15 LYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSV 58 (150)
T ss_pred HHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEee
Confidence 33443444 48999999999999999999999999999998654
No 203
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=36.02 E-value=32 Score=27.09 Aligned_cols=28 Identities=14% Similarity=0.338 Sum_probs=24.6
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGI 107 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~i 107 (122)
.+..+.+|+.+||.||-.|+.+|-.|+=
T Consensus 41 EI~~t~iAka~gVdRrvV~~Ti~~I~sd 68 (167)
T COG2150 41 EIPITKIAKATGVDRRVVYATIELIESD 68 (167)
T ss_pred EechHHHHHHhCcchHhHHHHHHHHhcC
Confidence 5789999999999999999999877653
No 204
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=35.82 E-value=58 Score=15.78 Aligned_cols=20 Identities=15% Similarity=0.306 Sum_probs=17.2
Q ss_pred ccHHHHHhHhccchhhhhhH
Q psy8797 81 VDLNVASESLDVQKRRIYDI 100 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI 100 (122)
..+.++|+.+++.+.-+|-+
T Consensus 22 ~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 22 ESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHCCCHHHHHHh
Confidence 38899999999999888865
No 205
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=35.49 E-value=74 Score=19.58 Aligned_cols=44 Identities=18% Similarity=0.443 Sum_probs=32.5
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhh---hccceeeccCC
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLE---GIGILEKKSKN 116 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE---~igLI~K~~Kn 116 (122)
-|+.+.... ++..||+.|++..--+..-++-|| +.-|+.+.+++
T Consensus 6 ~f~~v~~~g-----s~~~AA~~l~is~~~vs~~i~~LE~~lg~~Lf~r~~~~ 52 (60)
T PF00126_consen 6 YFLAVAETG-----SISAAAEELGISQSAVSRQIKQLEEELGVPLFERSGRG 52 (60)
T ss_dssp HHHHHHHHS-----SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-SEEECSSS
T ss_pred HHHHHHHhC-----CHHHHHHHhhccchHHHHHHHHHHHHhCCeEEEECCCC
Confidence 355555543 899999999999999999888888 45667766543
No 206
>PRK10736 hypothetical protein; Provisional
Probab=35.05 E-value=87 Score=27.21 Aligned_cols=43 Identities=14% Similarity=0.103 Sum_probs=38.8
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC 120 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W 120 (122)
...+.+++++.+++..-..++-+.=-||--|+|+....+.|..
T Consensus 319 ~~~~~iD~L~~~~~l~~~~v~~~L~~LEl~G~v~~~~g~~~~~ 361 (374)
T PRK10736 319 DEVTPVDVVAERAGQPVPEVVTQLLELELAGWIAAVPGGYVRL 361 (374)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEcCCcEEEE
Confidence 4567899999999999999999999999999999998887754
No 207
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=34.35 E-value=68 Score=24.17 Aligned_cols=36 Identities=17% Similarity=0.193 Sum_probs=32.4
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
.+...++|+.||+.+--+.=+.+-|+.=|+|+...+
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~ 219 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGK 219 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCC
Confidence 356789999999999999999999999999998754
No 208
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=34.08 E-value=79 Score=23.79 Aligned_cols=34 Identities=15% Similarity=0.172 Sum_probs=31.5
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhcccee
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILE 111 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~ 111 (122)
.+.+.-+++|..||++.+-+=-++|.|...|||.
T Consensus 26 ~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 26 KGEFTDEEISLELGIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 5578999999999999999999999999999994
No 209
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=33.61 E-value=1.2e+02 Score=23.71 Aligned_cols=51 Identities=22% Similarity=0.244 Sum_probs=41.4
Q ss_pred CcHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797 60 TSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGIL 110 (122)
Q Consensus 60 kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI 110 (122)
..+.....+.++++.....+.++..++|+.++...=|.-+.++.+|.-|++
T Consensus 170 ~e~~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l 220 (223)
T PF04157_consen 170 SELSKDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLL 220 (223)
T ss_dssp CHH-HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSE
T ss_pred hhhhHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCE
Confidence 345677888899885556788999999999999999999999999999876
No 210
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=33.53 E-value=36 Score=23.80 Aligned_cols=26 Identities=15% Similarity=0.371 Sum_probs=19.8
Q ss_pred ccHHHHHhHhccchhhhhhHHHhhhh
Q psy8797 81 VDLNVASESLDVQKRRIYDITNVLEG 106 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NVLE~ 106 (122)
.++.++|.+++++-|+||-|++-...
T Consensus 73 ~n~~eLA~kyglS~r~I~~Ii~~~~~ 98 (108)
T PF08765_consen 73 MNVRELARKYGLSERQIYRIIKRVRR 98 (108)
T ss_dssp S-HHHHHHHHT--HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 47899999999999999999876543
No 211
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=33.44 E-value=91 Score=27.39 Aligned_cols=48 Identities=21% Similarity=0.286 Sum_probs=39.3
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
.+.+..+.. .+.++..++|+.+++.+--+--+++-|+.-|+|++....
T Consensus 9 ~~vL~~L~~--~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~~~ 56 (489)
T PRK04172 9 KKVLKALKE--LKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEERV 56 (489)
T ss_pred HHHHHHHHh--CCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEeee
Confidence 445555543 346899999999999999999999999999999987543
No 212
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=33.26 E-value=1e+02 Score=23.82 Aligned_cols=42 Identities=17% Similarity=0.182 Sum_probs=33.9
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcccee
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILE 111 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~ 111 (122)
.++..+.. .+.+.-+++|..||++.--+=-+.+-|+.-|||.
T Consensus 26 ~Vl~~L~~--~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 26 EVLKALIK--KGEVTDEEIAEQTGIKLNTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHHHH--cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 34444442 3568999999999998888888999999999998
No 213
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=33.17 E-value=45 Score=28.49 Aligned_cols=37 Identities=8% Similarity=0.221 Sum_probs=31.4
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHH
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDIT 101 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~ 101 (122)
...+.|++|+++..+.+++.++|+.+++++|-|--..
T Consensus 221 ~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF 257 (328)
T COG4977 221 RLLRAIELMEANLEEPLSLEELADRAGLSRRQLERLF 257 (328)
T ss_pred HHHHHHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHH
Confidence 3457789999999999999999999999999765543
No 214
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=32.68 E-value=69 Score=23.40 Aligned_cols=37 Identities=11% Similarity=0.001 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhH
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDI 100 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI 100 (122)
.+-..-++++.+..-.-++++++|++.||.+.-||--
T Consensus 12 ~Il~aA~~lf~e~G~~~~s~~~IA~~agvs~~~lY~h 48 (202)
T TIGR03613 12 AILSAALDTFSRFGFHGTSLEQIAELAGVSKTNLLYY 48 (202)
T ss_pred HHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHH
Confidence 3455567777777777899999999999999999853
No 215
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=32.67 E-value=47 Score=18.96 Aligned_cols=21 Identities=5% Similarity=-0.029 Sum_probs=17.1
Q ss_pred ccHHHHHhHhccchhhhhhHH
Q psy8797 81 VDLNVASESLDVQKRRIYDIT 101 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~ 101 (122)
+.+.++|+.+||..+.|....
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHH
Confidence 367899999999998887663
No 216
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=32.29 E-value=53 Score=26.86 Aligned_cols=36 Identities=8% Similarity=0.031 Sum_probs=29.8
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHH
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
.++.+++.+...+.++++++|+.+++.+|.|.-...
T Consensus 137 ~kv~~~I~~~~~~~~tl~~LA~~~gmS~s~l~R~FK 172 (253)
T PRK09940 137 GKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLK 172 (253)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 567777788888889999999999998887766654
No 217
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=32.27 E-value=87 Score=24.20 Aligned_cols=36 Identities=14% Similarity=0.195 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhh
Q psy8797 63 GLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIY 98 (122)
Q Consensus 63 g~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiY 98 (122)
..+..--++++.+..-.-+++..+|++|||.+.-||
T Consensus 7 e~Il~aA~~l~~e~G~~~lsmr~lA~~lgv~~~slY 42 (205)
T PRK13756 7 EKVIDSALELLNEVGIEGLTTRKLAQKLGVEQPTLY 42 (205)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchHHH
Confidence 345666788888877778999999999999888888
No 218
>PHA00738 putative HTH transcription regulator
Probab=32.23 E-value=1.5e+02 Score=21.70 Aligned_cols=48 Identities=15% Similarity=0.269 Sum_probs=37.5
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
++.++++... +.....++++.+++.+=.+-==+.||+..|||+.....
T Consensus 15 r~IL~lL~~~--e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~G 62 (108)
T PHA00738 15 RKILELIAEN--YILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEG 62 (108)
T ss_pred HHHHHHHHHc--CCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEEC
Confidence 3456666553 34788899999999999999999999999999766433
No 219
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=32.03 E-value=1.1e+02 Score=22.97 Aligned_cols=45 Identities=16% Similarity=0.277 Sum_probs=35.9
Q ss_pred HHHHHhhCCCCcccHHHHHhHh-----ccchhhhhhHHHhhhhccceeecc
Q psy8797 69 FVKLLQSSPQGVVDLNVASESL-----DVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L-----~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.++++... ++.++.+++.+.| ++.+=-+|-.++.|+..|||.+..
T Consensus 31 IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 31 VLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred HHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEe
Confidence 45555554 5678888888888 467788999999999999999873
No 220
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=32.02 E-value=1e+02 Score=25.29 Aligned_cols=50 Identities=28% Similarity=0.396 Sum_probs=36.6
Q ss_pred CcCcHHHHH-HHHHHHHhhCCCCcccHHHHHhHhccch---hhhhhHHHhhhhcccee
Q psy8797 58 YDTSLGLLT-KKFVKLLQSSPQGVVDLNVASESLDVQK---RRIYDITNVLEGIGILE 111 (122)
Q Consensus 58 ~~kSLg~Lt-~kFi~ll~~sp~~~idL~~aa~~L~v~k---RRiYDI~NVLE~igLI~ 111 (122)
-.|.|..+| ++..+.++ .++..+.-+++|+.+|++| ||- .+-|++.|+++
T Consensus 151 LPkGi~~~Tl~~i~~~~~-~~~~~~Taeela~~~giSRvTaRRY---Leyl~~~~~l~ 204 (224)
T COG4565 151 LPKGLDELTLQKVREALK-EPDQELTAEELAQALGISRVTARRY---LEYLVSNGILE 204 (224)
T ss_pred CCCCcCHHHHHHHHHHHh-CcCCccCHHHHHHHhCccHHHHHHH---HHHHHhcCeee
Confidence 346777788 55666667 8899999999999999843 332 45677777765
No 221
>PRK09480 slmA division inhibitor protein; Provisional
Probab=31.38 E-value=89 Score=22.44 Aligned_cols=35 Identities=14% Similarity=0.336 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhh
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIY 98 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiY 98 (122)
.+...+++++...++.-++++++|++.||.|--||
T Consensus 14 ~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y 48 (194)
T PRK09480 14 QILQALAQMLESPPGERITTAKLAARVGVSEAALY 48 (194)
T ss_pred HHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHH
Confidence 46667778876653478899999999999888877
No 222
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=30.99 E-value=49 Score=21.13 Aligned_cols=22 Identities=18% Similarity=0.383 Sum_probs=19.7
Q ss_pred ccHHHHHhHhccchhhhhhHHH
Q psy8797 81 VDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~N 102 (122)
..+.++|+.||+..+-+|-...
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH
Confidence 6899999999999999998764
No 223
>KOG0416|consensus
Probab=30.58 E-value=25 Score=28.08 Aligned_cols=44 Identities=27% Similarity=0.522 Sum_probs=23.0
Q ss_pred cCcHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797 59 DTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGI 107 (122)
Q Consensus 59 ~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~i 107 (122)
--|.|.+++-|=--+..+ .|.|.|+.+-+. ==-+||.+||+|..
T Consensus 63 SPSIGFvnKIfHPNIDe~-SGsVCLDViNQt----WSp~yDL~NIfetf 106 (189)
T KOG0416|consen 63 SPSIGFVNKIFHPNIDEA-SGSVCLDVINQT----WSPLYDLVNIFETF 106 (189)
T ss_pred CCcccceeeccCCCchhc-cCccHHHHHhhh----hhHHHHHHHHHHHH
Confidence 345555555442222221 244555443322 33589999999964
No 224
>PF08020 DUF1706: Protein of unknown function (DUF1706) ; InterPro: IPR012550 This family contains many hypothetical proteins from bacteria and yeast.
Probab=30.41 E-value=69 Score=24.61 Aligned_cols=56 Identities=16% Similarity=0.235 Sum_probs=46.8
Q ss_pred CcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceeec
Q psy8797 58 YDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCK 121 (122)
Q Consensus 58 ~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W~ 121 (122)
+=+-||.|.+.|.+-+++ .+|.++-+.|.-...+|.+.|+-+.-=.|-++. .|.|-
T Consensus 81 kWn~lg~Ln~~f~~~y~~-----~sl~e~~~~l~~s~~~v~~lI~~~sdeeLf~~~---~~~W~ 136 (166)
T PF08020_consen 81 KWNQLGELNQSFYEKYQD-----TSLEELKALLKESHQKVIALIESFSDEELFEKG---QFKWT 136 (166)
T ss_pred ChhhhhHHHHHHHHHHcC-----CCHHHHHHHHHHHHHHHHHHHHhCcchhhcccc---ccCCc
Confidence 457899999999987765 599999999999999999999999888887764 45554
No 225
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=29.31 E-value=1.1e+02 Score=27.18 Aligned_cols=54 Identities=28% Similarity=0.405 Sum_probs=42.1
Q ss_pred CcHHHHHH------HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797 60 TSLGLLTK------KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 60 kSLg~Lt~------kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
.-||+++- ..+.++........||+++|..-+. +.-||+.-||.++++.--..+
T Consensus 305 SdlGLlsYr~YW~~~v~~~L~k~~~~~~~I~~Is~~TgM---~~dDVI~tLe~L~il~~~~~~ 364 (395)
T COG5027 305 SDLGLLSYRAYWSEIVAKLLLKMDKEITDINEISKETGM---STDDVIHTLEALNILREYKGQ 364 (395)
T ss_pred chhhHHHHHHHHHHHHHHHHHhcCcccccHHHHHhhhCC---chhhHHHHHHHhccchhhCce
Confidence 34777763 3667777777778889999999987 468999999999998766333
No 226
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=29.28 E-value=1.4e+02 Score=25.15 Aligned_cols=60 Identities=15% Similarity=0.163 Sum_probs=43.7
Q ss_pred cHHHHHHHHHHHHhhC-CCCcccHHHHHhH-hccchhhhhhHHHhhhhccceeec-cCCceee
Q psy8797 61 SLGLLTKKFVKLLQSS-PQGVVDLNVASES-LDVQKRRIYDITNVLEGIGILEKK-SKNNIQC 120 (122)
Q Consensus 61 SLg~Lt~kFi~ll~~s-p~~~idL~~aa~~-L~v~kRRiYDI~NVLE~igLI~K~-~Kn~~~W 120 (122)
.|..+.++++++|..+ ++..+..+++.+. .+....-+-+++|-|..-|+++=. ..+.+.|
T Consensus 6 ~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~~~~~l~~ 68 (327)
T PF05158_consen 6 KLSELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLKKGGGLSY 68 (327)
T ss_dssp -HHHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE-SSSEEE
T ss_pred hHHHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEEcCCEEEE
Confidence 6788999999999988 5667888888887 577889999999999999887532 3344554
No 227
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=29.25 E-value=1.1e+02 Score=22.66 Aligned_cols=35 Identities=14% Similarity=0.240 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhh
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIY 98 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiY 98 (122)
.+...-++++.+..-.-+.+.++|+..||.+.-||
T Consensus 15 ~Il~AA~~lf~e~G~~~~t~~~Ia~~agvs~~tlY 49 (215)
T PRK10668 15 HILDAALRLFSQQGVSATSLADIAKAAGVTRGAIY 49 (215)
T ss_pred HHHHHHHHHHHHcCcccCCHHHHHHHhCCChHHHH
Confidence 45666778888777777899999999999998888
No 228
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=29.11 E-value=1.5e+02 Score=19.12 Aligned_cols=47 Identities=19% Similarity=0.406 Sum_probs=34.5
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCcee
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~ 119 (122)
.+++++.+.| +++...+++.|++..+---. .++.+|+-|-++...|.
T Consensus 3 ~Lidll~~~P--~Vsa~mva~~L~vT~~~A~~---li~eLg~rEiTGr~R~R 49 (54)
T PF11972_consen 3 RLIDLLLSRP--LVSAPMVAKELGVTPQAAQR---LIAELGLREITGRGRYR 49 (54)
T ss_pred HHHHHHHhCc--cccHHHHHHHhCCCHHHHHH---HHHHhhceeecCCcccc
Confidence 4778888766 48899999999998876544 35777776666666553
No 229
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=29.03 E-value=96 Score=24.02 Aligned_cols=54 Identities=11% Similarity=0.171 Sum_probs=40.8
Q ss_pred HHHHHHHHHhh---CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec-cCCce
Q psy8797 65 LTKKFVKLLQS---SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK-SKNNI 118 (122)
Q Consensus 65 Lt~kFi~ll~~---sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~-~Kn~~ 118 (122)
+...+.+.+.+ .|+..+ +=.++|+.++|+|==+-..++.|+.-|+|.+. ++..|
T Consensus 10 i~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G~Gtf 68 (240)
T PRK09764 10 IADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTY 68 (240)
T ss_pred HHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCceeE
Confidence 34455555544 245555 67999999999999999999999999999865 45444
No 230
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=28.99 E-value=89 Score=22.79 Aligned_cols=39 Identities=10% Similarity=0.154 Sum_probs=33.3
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCcee
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~ 119 (122)
.+.-.++|+.||+.+--+-=+.+-|+.-|+|+.. .+.+.
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~-~~~i~ 187 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIRSG-YGKIQ 187 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcC-CCEEE
Confidence 4568899999999999999999999999999854 44454
No 231
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=28.86 E-value=1.1e+02 Score=20.14 Aligned_cols=35 Identities=14% Similarity=0.231 Sum_probs=26.4
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHH
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
+.|++.....+..=+...+|.+++|.++.|-++.-
T Consensus 13 ~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 13 KVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp HHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred HHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHH
Confidence 67888877766666889999999999999887753
No 232
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=28.58 E-value=97 Score=21.93 Aligned_cols=39 Identities=10% Similarity=0.136 Sum_probs=34.9
Q ss_pred CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 76 sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
.+...|.....|+..++++..+.+..|.|...|+|.+.+
T Consensus 50 Kk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~~g 88 (100)
T PF04492_consen 50 KKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIRDG 88 (100)
T ss_pred CccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC
Confidence 345678999999999999999999999999999997765
No 233
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=28.29 E-value=1.3e+02 Score=22.51 Aligned_cols=37 Identities=11% Similarity=-0.006 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhh
Q psy8797 63 GLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYD 99 (122)
Q Consensus 63 g~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYD 99 (122)
..+-..-++++.+..-.-+.++++|+..||.+.-||-
T Consensus 21 ~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gtiY~ 57 (212)
T PRK15008 21 KAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLY 57 (212)
T ss_pred HHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHH
Confidence 3455666677777666678999999999999999884
No 234
>PRK14999 histidine utilization repressor; Provisional
Probab=28.14 E-value=1.9e+02 Score=22.37 Aligned_cols=54 Identities=11% Similarity=0.137 Sum_probs=41.3
Q ss_pred HHHHHHHHHhh---CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec-cCCce
Q psy8797 65 LTKKFVKLLQS---SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK-SKNNI 118 (122)
Q Consensus 65 Lt~kFi~ll~~---sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~-~Kn~~ 118 (122)
+.....+.+.+ .|+..+ +=.++|++++|+|=-+-..++.|+.=|+|.+. ++..|
T Consensus 17 i~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~GkGTf 75 (241)
T PRK14999 17 VKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTF 75 (241)
T ss_pred HHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCcEEE
Confidence 44555555554 345555 78999999999999999999999999999875 45544
No 235
>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.03 E-value=34 Score=22.86 Aligned_cols=17 Identities=18% Similarity=0.346 Sum_probs=14.2
Q ss_pred hhhHHHhhhhccceeec
Q psy8797 97 IYDITNVLEGIGILEKK 113 (122)
Q Consensus 97 iYDI~NVLE~igLI~K~ 113 (122)
||||.++|..+||--..
T Consensus 15 L~~i~~~l~~~gl~I~~ 31 (72)
T cd04895 15 LLEAVQVLTDLDLCITK 31 (72)
T ss_pred HHHHHHHHHHCCcEEEE
Confidence 79999999999986443
No 236
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=28.00 E-value=51 Score=20.00 Aligned_cols=22 Identities=9% Similarity=0.173 Sum_probs=16.7
Q ss_pred ccHHHHHhHhccchhhhhhHHH
Q psy8797 81 VDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~N 102 (122)
++..++|+..|+.+-.||.+.|
T Consensus 11 it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 11 ITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp --HHHHHHHHT--HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHh
Confidence 5889999999999999999887
No 237
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=27.67 E-value=66 Score=18.15 Aligned_cols=23 Identities=9% Similarity=0.128 Sum_probs=20.2
Q ss_pred ccHHHHHhHhccchhhhhhHHHh
Q psy8797 81 VDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NV 103 (122)
.+..++|+.|++.+..+|..++-
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 58999999999999998887764
No 238
>KOG2255|consensus
Probab=27.60 E-value=30 Score=28.31 Aligned_cols=30 Identities=27% Similarity=0.452 Sum_probs=26.3
Q ss_pred cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 82 DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 82 dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
=|+.+|++|+|+.+++-| |.+++|++|.-.
T Consensus 63 Ml~~larrlgv~~nt~s~--~a~~~l~~v~d~ 92 (224)
T KOG2255|consen 63 MLDMLARRLGVPMNTISS--KALEGLGLVGDV 92 (224)
T ss_pred HHHHHHHHhCCcccccCc--ccccceeeecce
Confidence 467899999999999999 999999998643
No 239
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=27.55 E-value=1.1e+02 Score=22.06 Aligned_cols=37 Identities=19% Similarity=0.229 Sum_probs=25.8
Q ss_pred HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHh
Q psy8797 66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NV 103 (122)
.+++|++.--.+. ..+..++|..|+++++.+|-+-|.
T Consensus 87 er~II~~rY~~~~-~~t~~~Ia~~l~iS~~t~~r~r~~ 123 (134)
T TIGR01636 87 TRVIIQELYMKKR-PLTLVGLAQQLFISKSTAYRLRNH 123 (134)
T ss_pred HHHHHHHHHccCC-CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3445555322222 268999999999999999988664
No 240
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=27.55 E-value=1e+02 Score=22.51 Aligned_cols=35 Identities=3% Similarity=0.092 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhh
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIY 98 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiY 98 (122)
.+...-++++.+..=.-++++++|+..||+|.-||
T Consensus 12 ~Il~aA~~lf~e~G~~~tSi~~Ia~~aGvsk~~lY 46 (192)
T PRK14996 12 VILQAAMRVALAEGFAAMTVRRIASEAQVAAGQVH 46 (192)
T ss_pred HHHHHHHHHHHhcChhhccHHHHHHHhCCCcHHHH
Confidence 35556677777766667899999999999888888
No 241
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=27.24 E-value=1.9e+02 Score=22.06 Aligned_cols=48 Identities=13% Similarity=0.255 Sum_probs=37.6
Q ss_pred HHHHHHHHhh---CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 66 TKKFVKLLQS---SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 66 t~kFi~ll~~---sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
...+.+.+.+ .|+..+ +-.++|+.++|+|==+-..++.|+.=|+|.+.
T Consensus 7 ~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~ 58 (230)
T TIGR02018 7 KQDILERIRSGEWPPGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERR 58 (230)
T ss_pred HHHHHHHHHhCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3444455544 245545 88999999999999999999999999999876
No 242
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=27.08 E-value=79 Score=24.41 Aligned_cols=54 Identities=15% Similarity=0.190 Sum_probs=40.0
Q ss_pred HHHHHHHHHhhC---C-CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec-cCCce
Q psy8797 65 LTKKFVKLLQSS---P-QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK-SKNNI 118 (122)
Q Consensus 65 Lt~kFi~ll~~s---p-~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~-~Kn~~ 118 (122)
+...+.+.+.+. | +..-.-.++|+.++|+|==+-..++.|+.=|+|.+. ++.+|
T Consensus 14 I~~~i~~~I~~G~~~~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~GTf 72 (241)
T PRK11402 14 VRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTF 72 (241)
T ss_pred HHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCceeE
Confidence 344455555432 2 345678999999999999999999999999999877 34443
No 243
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=27.02 E-value=79 Score=24.22 Aligned_cols=52 Identities=12% Similarity=0.203 Sum_probs=38.5
Q ss_pred HHHHHHHhh---CCCC-cccHHHHHhHhccchhhhhhHHHhhhhccceeec-cCCce
Q psy8797 67 KKFVKLLQS---SPQG-VVDLNVASESLDVQKRRIYDITNVLEGIGILEKK-SKNNI 118 (122)
Q Consensus 67 ~kFi~ll~~---sp~~-~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~-~Kn~~ 118 (122)
..+.+.+.+ .|+. .-+-.++|+++||+|==+-..++.|+.=|+|.+. ++.+|
T Consensus 7 ~~l~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G~GTf 63 (233)
T TIGR02404 7 QDLEQKITHGQYKEGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKIQGKGSI 63 (233)
T ss_pred HHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCceEE
Confidence 444444543 2344 4478999999999999999999999999999876 34443
No 244
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=27.02 E-value=1.8e+02 Score=21.41 Aligned_cols=46 Identities=17% Similarity=0.284 Sum_probs=36.4
Q ss_pred HHHHHhhCCCCcccHHHHHhHhc-----cchhhhhhHHHhhhhccceeeccC
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLD-----VQKRRIYDITNVLEGIGILEKKSK 115 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~-----v~kRRiYDI~NVLE~igLI~K~~K 115 (122)
.++++.++++. ++..++=+.|. +..=-+|-..+.|+..|+|.+..-
T Consensus 26 vl~~L~~~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~ 76 (145)
T COG0735 26 VLELLLEADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEF 76 (145)
T ss_pred HHHHHHhcCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEe
Confidence 67778877666 77777776663 566778999999999999998754
No 245
>PTZ00064 histone acetyltransferase; Provisional
Probab=26.90 E-value=2.5e+02 Score=25.97 Aligned_cols=35 Identities=17% Similarity=0.245 Sum_probs=29.6
Q ss_pred ccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797 81 VDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI 118 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~ 118 (122)
++|+++++..++. ..||+..|+.+|++......++
T Consensus 472 iSI~dIS~~TgI~---~eDII~TLq~L~llky~kgq~~ 506 (552)
T PTZ00064 472 KFIDNVVRSTGIR---REDVIRILEENGIMRNIKDQHY 506 (552)
T ss_pred ccHHHHHHHhCCC---HHHHHHHHHHCCcEEEeCCCEE
Confidence 8999999999995 5799999999999987644433
No 246
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=26.86 E-value=2.2e+02 Score=21.44 Aligned_cols=36 Identities=11% Similarity=0.125 Sum_probs=29.4
Q ss_pred HHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797 83 LNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC 120 (122)
Q Consensus 83 L~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W 120 (122)
-.++|+.||+.+.-+.-+++-|+.-|++ . ..+.+..
T Consensus 176 ~~~iA~~lG~tretvsR~l~~L~~~gl~-~-~~~~i~I 211 (236)
T PRK09392 176 KRVLASYLGMTPENLSRAFAALASHGVH-V-DGSAVTI 211 (236)
T ss_pred HHHHHHHhCCChhHHHHHHHHHHhCCeE-e-eCCEEEE
Confidence 4689999999999999999999999974 3 3355543
No 247
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=26.70 E-value=66 Score=18.85 Aligned_cols=33 Identities=21% Similarity=0.195 Sum_probs=23.5
Q ss_pred cHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceeec
Q psy8797 82 DLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCK 121 (122)
Q Consensus 82 dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W~ 121 (122)
++.+||+.|++.+.-|-+.++ + .+.-++.|.|.
T Consensus 19 S~~eAa~~lg~~~~~I~~~~~---~----~~~~~ggy~~~ 51 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLN---T----GKKFKGGYYFS 51 (53)
T ss_pred CHHHHHHHhCCCHHHHHHHHh---C----CCccCCeEEEE
Confidence 689999999999988776654 2 23335567773
No 248
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=26.44 E-value=1.3e+02 Score=19.96 Aligned_cols=36 Identities=17% Similarity=0.199 Sum_probs=31.3
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.+.++..++.+.|++..=.++=-++.||.-|+|+..
T Consensus 12 ~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~ 47 (80)
T PF13601_consen 12 NEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVE 47 (80)
T ss_dssp HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEE
Confidence 556899999999999999999999999999999875
No 249
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=26.08 E-value=1e+02 Score=21.28 Aligned_cols=37 Identities=19% Similarity=0.293 Sum_probs=34.4
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS 114 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~ 114 (122)
++..++.++|..|+..-==+-+....|+..|-|+|..
T Consensus 14 ~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 14 RGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred cCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 5678999999999999999999999999999999984
No 250
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=26.04 E-value=98 Score=20.15 Aligned_cols=32 Identities=22% Similarity=0.334 Sum_probs=20.0
Q ss_pred CCcccHHHHHhHhccchhhhhhHH----Hhhhhccc
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDIT----NVLEGIGI 109 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~----NVLE~igL 109 (122)
+..+++.++|+.+.|++--+|-.+ +.|+.-||
T Consensus 28 ~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~~~l 63 (87)
T PF05043_consen 28 NEYVSIEDLAEELFISRSTIYRDIKKLNKYLKKYGL 63 (87)
T ss_dssp -SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHCCT-
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCe
Confidence 556899999999999766665544 45555444
No 251
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=25.79 E-value=1.3e+02 Score=21.19 Aligned_cols=27 Identities=19% Similarity=0.042 Sum_probs=21.8
Q ss_pred HHHHHHHHhhCCCCcccHHHHHhHhcc
Q psy8797 66 TKKFVKLLQSSPQGVVDLNVASESLDV 92 (122)
Q Consensus 66 t~kFi~ll~~sp~~~idL~~aa~~L~v 92 (122)
=++.+.++.+.......+.++|...++
T Consensus 11 R~~vl~~L~~~yp~~~~~~eIar~v~~ 37 (90)
T PF07381_consen 11 RKKVLEYLCSIYPEPAYPSEIARSVGS 37 (90)
T ss_pred HHHHHHHHHHcCCCcCCHHHHHHHHCC
Confidence 356778888887888899999998875
No 252
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=25.45 E-value=70 Score=22.26 Aligned_cols=25 Identities=24% Similarity=0.332 Sum_probs=20.2
Q ss_pred HHHHHhHhccchhhhhhHHHhhhhc
Q psy8797 83 LNVASESLDVQKRRIYDITNVLEGI 107 (122)
Q Consensus 83 L~~aa~~L~v~kRRiYDI~NVLE~i 107 (122)
-.+.|..-|+...||-||.|.|---
T Consensus 54 Q~EMA~eAgi~~~rID~IA~fLNqW 78 (81)
T PF10820_consen 54 QQEMASEAGIDEQRIDDIANFLNQW 78 (81)
T ss_pred HHHHHHHcCCcHHHHHHHHHHHHHh
Confidence 3466777899999999999998643
No 253
>PF02616 ScpA_ScpB: ScpA/B protein; InterPro: IPR003768 This family represents ScpA, which along with ScpB (IPR005234 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes [].
Probab=25.45 E-value=85 Score=24.45 Aligned_cols=31 Identities=32% Similarity=0.567 Sum_probs=25.3
Q ss_pred CcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHh
Q psy8797 58 YDTSLGLLTKKFVKLLQSSPQGVVDLNVASESL 90 (122)
Q Consensus 58 ~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L 90 (122)
.+-++..+|.+|++++... ..+||+.+|+-|
T Consensus 10 ~dI~I~~ItdqYl~~i~~~--~~~dL~~asefl 40 (242)
T PF02616_consen 10 YDIDISEITDQYLEYIEEM--KELDLEVASEFL 40 (242)
T ss_pred HhCCHHHHHHHHHHHHHHh--hhcCHHHHHHHH
Confidence 5778999999999999976 457888777755
No 254
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=25.30 E-value=64 Score=21.83 Aligned_cols=28 Identities=11% Similarity=0.237 Sum_probs=24.2
Q ss_pred CCCCcccHHHHHhHhccchhhhhhHHHh
Q psy8797 76 SPQGVVDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 76 sp~~~idL~~aa~~L~v~kRRiYDI~NV 103 (122)
..+..+.+.++++.+|+.|=-||+-+|=
T Consensus 9 ~~~r~lrl~ev~~~~GlSrstiYr~i~~ 36 (70)
T COG3311 9 HTDRLLRLPEVAQLTGLSRSTIYRLIKD 36 (70)
T ss_pred ccchhhhHHHHHHHHCccHHHHHHHHcc
Confidence 3466789999999999999999998873
No 255
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=25.06 E-value=1.4e+02 Score=21.30 Aligned_cols=36 Identities=11% Similarity=0.006 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhh
Q psy8797 64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYD 99 (122)
Q Consensus 64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYD 99 (122)
.+..-..+++....-.-+.++++|+..||.+.-||-
T Consensus 12 ~Il~aA~~lf~~~G~~~~s~~~IA~~agvsk~~ly~ 47 (189)
T TIGR03384 12 ELIDATIESIGERGSLDVTIAQIARRAGVSSGIISH 47 (189)
T ss_pred HHHHHHHHHHHhcCcccCCHHHHHHHhCCCHHHHHH
Confidence 355667788887777789999999999999988884
No 256
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=24.56 E-value=2.4e+02 Score=20.36 Aligned_cols=47 Identities=21% Similarity=0.282 Sum_probs=36.6
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
+.+.++.. .+...+.++|+.|++.+=-+-==+++|+..|||......
T Consensus 20 ~IL~~L~~--~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~G 66 (117)
T PRK10141 20 GIVLLLRE--SGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQG 66 (117)
T ss_pred HHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEc
Confidence 45555653 235789999999999999998899999999999755433
No 257
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=24.41 E-value=67 Score=20.20 Aligned_cols=22 Identities=18% Similarity=0.397 Sum_probs=19.5
Q ss_pred ccHHHHHhHhccchhhhhhHHH
Q psy8797 81 VDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~N 102 (122)
+...++|+.+|+.+-.|.++.|
T Consensus 19 ~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 19 LSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 6789999999999999888876
No 258
>PRK01905 DNA-binding protein Fis; Provisional
Probab=24.36 E-value=1.3e+02 Score=19.75 Aligned_cols=38 Identities=13% Similarity=0.232 Sum_probs=25.3
Q ss_pred HHHHHHHH-HHHHhhCCCCcccHHHHHhHhccchhhhhhHHH
Q psy8797 62 LGLLTKKF-VKLLQSSPQGVVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 62 Lg~Lt~kF-i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N 102 (122)
+..+-+.+ .+.+.... -+...+|+.||+.++.||-.+.
T Consensus 34 l~~~E~~~i~~aL~~~~---gn~s~aAr~LGIsrstL~rklk 72 (77)
T PRK01905 34 LSCVEKPLLEVVMEQAG---GNQSLAAEYLGINRNTLRKKLQ 72 (77)
T ss_pred HHHHHHHHHHHHHHHcC---CCHHHHHHHHCCCHHHHHHHHH
Confidence 34444443 34455443 2588999999999999987654
No 259
>PF14502 HTH_41: Helix-turn-helix domain
Probab=24.18 E-value=1.5e+02 Score=18.76 Aligned_cols=40 Identities=20% Similarity=0.307 Sum_probs=33.0
Q ss_pred CCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCc
Q psy8797 78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNN 117 (122)
Q Consensus 78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~ 117 (122)
+..-.+.+.++++++.+=-|=--+..||..|.|.=.++.+
T Consensus 4 dRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~rGh 43 (48)
T PF14502_consen 4 DRIPTISEYSEKFGVSRGTIQNALKFLEENGAIKLESRGH 43 (48)
T ss_pred cccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeecCc
Confidence 3455789999999999999999999999999987665543
No 260
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=23.96 E-value=1.4e+02 Score=20.73 Aligned_cols=32 Identities=9% Similarity=0.292 Sum_probs=26.9
Q ss_pred cHHHHHhHhccchhhhhhHHHhhhh---ccceeec
Q psy8797 82 DLNVASESLDVQKRRIYDITNVLEG---IGILEKK 113 (122)
Q Consensus 82 dL~~aa~~L~v~kRRiYDI~NVLE~---igLI~K~ 113 (122)
++..||+.|++....+..-+.-||. .-|+.+.
T Consensus 18 Sis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~ 52 (99)
T TIGR00637 18 SISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERA 52 (99)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEec
Confidence 7899999999999999999998884 4456665
No 261
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=23.51 E-value=1.5e+02 Score=19.61 Aligned_cols=30 Identities=13% Similarity=0.284 Sum_probs=22.7
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhh
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIY 98 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiY 98 (122)
-++++...+=.-+.+.++|+++||.+.-||
T Consensus 21 a~~l~~~~G~~~~t~~~Ia~~agvs~~~~Y 50 (201)
T COG1309 21 ALRLFAEKGYAATTVDEIAKAAGVSKGTLY 50 (201)
T ss_pred HHHHHHHcCcCCCCHHHHHHHhCCCcchhH
Confidence 334444444456899999999999999998
No 262
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=23.05 E-value=1.6e+02 Score=16.69 Aligned_cols=23 Identities=4% Similarity=0.033 Sum_probs=20.2
Q ss_pred ccHHHHHhHhccchhhhhhHHHh
Q psy8797 81 VDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NV 103 (122)
.+..++|+.+++..+-+|..++-
T Consensus 16 ~s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 16 KTNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 68999999999999888887765
No 263
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=22.50 E-value=88 Score=16.74 Aligned_cols=23 Identities=26% Similarity=0.277 Sum_probs=18.4
Q ss_pred cccHHHHHhHhccchhhhhhHHH
Q psy8797 80 VVDLNVASESLDVQKRRIYDITN 102 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~N 102 (122)
-++..++|..+++....++.+.|
T Consensus 12 ~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 12 GLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHc
Confidence 36788999999998888877654
No 264
>PF10298 WhiA_N: WhiA N-terminal LAGLIDADG-like domain; InterPro: IPR018478 This entry represents the N-terminal domain of sporulation factor WhiA []. This domain is related to the LAGLIDADG homing endonuclease domain while the C-terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain [].; PDB: 3HYI_A 3HYJ_D.
Probab=22.48 E-value=17 Score=24.33 Aligned_cols=47 Identities=19% Similarity=0.412 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHH------Hhhhhccce
Q psy8797 63 GLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDIT------NVLEGIGIL 110 (122)
Q Consensus 63 g~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~------NVLE~igLI 110 (122)
..++++|+.++++--+-..++. +...-..+|.++|-|. .+|+.+|++
T Consensus 34 ~~vARri~~llk~~f~i~~ei~-v~~~~~l~k~~~Y~i~i~~~~~~iL~~lgll 86 (86)
T PF10298_consen 34 AAVARRIYSLLKKLFDIDPEIS-VRRSRNLKKNNVYTIRIEDSAKEILRDLGLL 86 (86)
T ss_dssp HHHHHHHHHHHHHTT--EEEEE-EEE-SSSBEEE--------------------
T ss_pred HHHHHHHHHHHHHHhCCCeEEE-EecCCCCCCCCccccccccccccccccccCC
Confidence 4578889998887654433331 1112245666788776 777777764
No 265
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=22.14 E-value=90 Score=20.98 Aligned_cols=23 Identities=22% Similarity=0.556 Sum_probs=18.9
Q ss_pred HHHHHHHhhCCCCcccHHHHHhHhccc
Q psy8797 67 KKFVKLLQSSPQGVVDLNVASESLDVQ 93 (122)
Q Consensus 67 ~kFi~ll~~sp~~~idL~~aa~~L~v~ 93 (122)
..||.++... +.+.+||+.||+.
T Consensus 4 ~~fIrlLs~~----~s~~~Aa~~lG~~ 26 (65)
T PF05344_consen 4 RAFIRLLSQQ----ISVAQAADRLGTD 26 (65)
T ss_pred HHHHHHhccc----ccHHHHHHHHCcC
Confidence 4688888765 8999999999983
No 266
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=21.95 E-value=1.1e+02 Score=23.88 Aligned_cols=38 Identities=13% Similarity=0.222 Sum_probs=31.5
Q ss_pred cccHHHHHhHhccchhhhhhHHHhhhhccceeec-cCCc
Q psy8797 80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKK-SKNN 117 (122)
Q Consensus 80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~-~Kn~ 117 (122)
.-+=.++|+.++|+|==+-=-++.|+.-|+|.+. ++.+
T Consensus 31 LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~Gt 69 (236)
T COG2188 31 LPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQGKGT 69 (236)
T ss_pred CCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecCee
Confidence 4567899999999988888899999999999876 4443
No 267
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=21.93 E-value=1.6e+02 Score=22.10 Aligned_cols=34 Identities=18% Similarity=0.221 Sum_probs=26.6
Q ss_pred HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHH
Q psy8797 68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDIT 101 (122)
Q Consensus 68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~ 101 (122)
+.-+|+..+|+...++.++|+.++|+-.=|...|
T Consensus 34 kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~I 67 (137)
T TIGR03826 34 KVYKFLRKHENRQATVSEIVEETGVSEKLILKFI 67 (137)
T ss_pred HHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445667888888999999999999877666544
No 268
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=21.91 E-value=1.8e+02 Score=21.04 Aligned_cols=61 Identities=18% Similarity=0.229 Sum_probs=44.9
Q ss_pred CCCcCcHHHHHHHHHHH-HhhCCCCcccHHHHHhHhc-cchhhhhhHHHhhhhccceeeccCC
Q psy8797 56 TRYDTSLGLLTKKFVKL-LQSSPQGVVDLNVASESLD-VQKRRIYDITNVLEGIGILEKKSKN 116 (122)
Q Consensus 56 ~R~~kSLg~Lt~kFi~l-l~~sp~~~idL~~aa~~L~-v~kRRiYDI~NVLE~igLI~K~~Kn 116 (122)
+-.+..|..+..|---+ +..--++..-.+++-..++ +..+-|-+-.+-||..|+|.|...+
T Consensus 11 c~~~~~l~~ig~kW~~lIl~~L~~g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~~~~ 73 (120)
T COG1733 11 CPVEEALEVIGGKWTLLILRDLFDGPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERVVYP 73 (120)
T ss_pred CCHHHHHHHHcCccHHHHHHHHhcCCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEEeeecC
Confidence 33556666666552211 1222238889999999998 9999999999999999999998654
No 269
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=21.87 E-value=72 Score=17.93 Aligned_cols=18 Identities=17% Similarity=0.259 Sum_probs=15.2
Q ss_pred cHHHHHhHhccchhhhhh
Q psy8797 82 DLNVASESLDVQKRRIYD 99 (122)
Q Consensus 82 dL~~aa~~L~v~kRRiYD 99 (122)
++.+||+.|++.+.-|..
T Consensus 18 Si~eAa~~l~i~~~~I~~ 35 (37)
T PF07453_consen 18 SIREAARYLGISHSTISK 35 (37)
T ss_pred CHHHHHHHhCCCHHHHHH
Confidence 689999999998887654
No 270
>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=21.50 E-value=1.9e+02 Score=20.39 Aligned_cols=41 Identities=15% Similarity=0.328 Sum_probs=32.2
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGIL 110 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI 110 (122)
|=++.|.++.+. ..+.+||..++|.++-+|-+.+ -...|-+
T Consensus 7 lR~rVl~~~~~g----~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~ 47 (119)
T PF01710_consen 7 LRQRVLAYIEKG----KSIREAAKRFGVSRNTVYRWLK-RKETGDL 47 (119)
T ss_pred HHHHHHHHHHcc----chHHHHHHHhCcHHHHHHHHHH-hcccccc
Confidence 557788877763 3899999999999999999999 4445544
No 271
>PRK15340 transcriptional regulator InvF; Provisional
Probab=21.40 E-value=1.8e+02 Score=23.34 Aligned_cols=40 Identities=13% Similarity=0.089 Sum_probs=30.9
Q ss_pred HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797 69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIG 108 (122)
Q Consensus 69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ig 108 (122)
.+.++.+......+++++|+.+|++.|.|.=+..-.-|+.
T Consensus 114 l~~~Ll~~~~~~~sleeLA~~~gvS~r~f~RlFk~~~G~t 153 (216)
T PRK15340 114 LVGYLLAQSTSGNTMRMLGEDYGVSYTHFRRLCSRALGGK 153 (216)
T ss_pred HHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 4566677778889999999999999888877666554444
No 272
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=21.29 E-value=1e+02 Score=23.73 Aligned_cols=34 Identities=6% Similarity=-0.138 Sum_probs=25.5
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhh
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYD 99 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYD 99 (122)
|...=+++|.+..-. .+++++|+.-||.++-||-
T Consensus 18 Il~aA~~lF~~~Gy~-~s~~~IA~~AGvsk~tiy~ 51 (225)
T PRK11552 18 LIAAALAQFGEYGLH-ATTRDIAAQAGQNIAAITY 51 (225)
T ss_pred HHHHHHHHHHHhCcc-CCHHHHHHHhCCCHHHHHH
Confidence 334445666665556 8999999999999888884
No 273
>PHA00542 putative Cro-like protein
Probab=21.16 E-value=82 Score=20.99 Aligned_cols=23 Identities=17% Similarity=0.148 Sum_probs=20.8
Q ss_pred ccHHHHHhHhccchhhhhhHHHh
Q psy8797 81 VDLNVASESLDVQKRRIYDITNV 103 (122)
Q Consensus 81 idL~~aa~~L~v~kRRiYDI~NV 103 (122)
+...++|+.+||.+-.|+.|.|-
T Consensus 32 lTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 32 WSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred CCHHHHHHHHCcCHHHHHHHHcC
Confidence 79999999999999999999863
No 274
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=21.13 E-value=1.5e+02 Score=24.81 Aligned_cols=38 Identities=13% Similarity=0.234 Sum_probs=33.5
Q ss_pred CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797 76 SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 76 sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~ 113 (122)
.++..+ +..++|+.|+|+|=-+.+..+.|+.-|+|...
T Consensus 24 ~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~ 62 (431)
T PRK15481 24 RPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQ 62 (431)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 356666 89999999999999999999999999999865
No 275
>PLN02913 dihydrofolate synthetase
Probab=20.98 E-value=20 Score=31.65 Aligned_cols=28 Identities=14% Similarity=0.264 Sum_probs=23.8
Q ss_pred hhhhhHHHhhhh----ccceeeccCCceeecC
Q psy8797 95 RRIYDITNVLEG----IGILEKKSKNNIQCKR 122 (122)
Q Consensus 95 RRiYDI~NVLE~----igLI~K~~Kn~~~W~G 122 (122)
--.+|++||+.. +.+|+-.+-++..|.|
T Consensus 184 GGrlDaTNvi~~~~p~vsVITnIg~DH~~~LG 215 (510)
T PLN02913 184 GGARDATNVIDSSGLAASVITTIGEEHLAALG 215 (510)
T ss_pred CCCcccccccCCCCCcEEEEccccHHHHhhhc
Confidence 345799999985 8999999999988876
No 276
>cd04898 ACT_ACR-like_4 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.94 E-value=38 Score=23.58 Aligned_cols=16 Identities=50% Similarity=0.746 Sum_probs=14.3
Q ss_pred hhhhhHHHhhhhccce
Q psy8797 95 RRIYDITNVLEGIGIL 110 (122)
Q Consensus 95 RRiYDI~NVLE~igLI 110 (122)
|=+||||=.|..+|+|
T Consensus 12 rVfyDvTlALK~L~i~ 27 (77)
T cd04898 12 RVFYDITLALKKLGIC 27 (77)
T ss_pred ceeeehHHHHHHhccE
Confidence 5599999999999987
No 277
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=20.47 E-value=1.1e+02 Score=20.78 Aligned_cols=46 Identities=15% Similarity=0.083 Sum_probs=32.5
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceee
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEK 112 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K 112 (122)
.++.-+.++.. ..-++..++|+.|+++..-+.-.++-++.-|.+-|
T Consensus 19 ~~r~af~L~R~--~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~~ 64 (73)
T TIGR03879 19 LAEAAAALARE--EAGKTASEIAEELGRTEQTVRNHLKGETKAGGLVK 64 (73)
T ss_pred HHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHhcCcccchHHH
Confidence 45444444422 23368999999999999988888888777776544
No 278
>TIGR03693 ocin_ThiF_like putative thiazole-containing bacteriocin maturation protein. Members of this protein family are found in a three-gene operon in Bacillus anthracis and related Bacillus species, where the other two genes are clearly identified with maturation of a putative thiazole-containing bacteriocin precursor. While there is no detectable pairwise sequence similarity between members of this family and the proposed cyclodehydratases such as SagC of Streptococcus pyogenes (see family TIGR03603), both families show similarity through PSI-BLAST to ThiF, a protein involved in biosynthesis of the thiazole moiety for thiamine biosynthesis. This family, therefore, may contribute to cyclodehydratase function in heterocycle-containing bacteriocin biosyntheses. In Bacillus licheniformis ATCC 14580, the bacteriocin precursor gene is adjacent to the gene for this protein.
Probab=20.21 E-value=1.4e+02 Score=28.04 Aligned_cols=49 Identities=16% Similarity=0.252 Sum_probs=40.4
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhHhc-cchhhhhhHHHhhhhccceeec
Q psy8797 65 LTKKFVKLLQSSPQGVVDLNVASESLD-VQKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 65 Lt~kFi~ll~~sp~~~idL~~aa~~L~-v~kRRiYDI~NVLE~igLI~K~ 113 (122)
-..+||+.+-.-=||...|+++...|. -.+.++++++..|..-|+|+-.
T Consensus 41 ~iy~~ie~Lip~LDG~~tl~EI~~~L~~~y~~~V~Eli~~L~~nGFVrDv 90 (637)
T TIGR03693 41 GIANWFEKLLPMFNGEHSLADITDGLPAPYQKRVFEIGEILYKNGFVRDV 90 (637)
T ss_pred hHHHHHHHHHHhcCCCccHHHHHhhcCHHHHHHHHHHHHHHHhCCceeec
Confidence 345677766655688899999999994 4788999999999999999875
No 279
>KOG2729|consensus
Probab=20.05 E-value=26 Score=26.75 Aligned_cols=21 Identities=19% Similarity=0.463 Sum_probs=17.9
Q ss_pred chhhhhhHHHhhhhccceeec
Q psy8797 93 QKRRIYDITNVLEGIGILEKK 113 (122)
Q Consensus 93 ~kRRiYDI~NVLE~igLI~K~ 113 (122)
+|+.+||.|-|+..++-.+|.
T Consensus 91 ~r~~l~D~TeI~n~L~~~~k~ 111 (137)
T KOG2729|consen 91 KRPHLYDPTEIFNTLSSEKKE 111 (137)
T ss_pred cCCcccCHHHHHHHhHHHHHH
Confidence 788899999999988877765
Done!