Query 030804
Match_columns 171
No_of_seqs 142 out of 1123
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 04:49:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030804.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030804hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05593 rplR 50S ribosomal pr 100.0 2.9E-46 6.3E-51 287.1 15.3 116 53-171 2-117 (117)
2 TIGR00060 L18_bact ribosomal p 100.0 4.5E-46 9.8E-51 285.2 15.0 111 55-171 2-114 (114)
3 CHL00139 rpl18 ribosomal prote 100.0 4.1E-45 8.9E-50 277.8 11.5 109 61-171 1-109 (109)
4 COG0256 RplR Ribosomal protein 100.0 2.3E-43 5E-48 273.9 14.2 120 51-171 5-125 (125)
5 PF00861 Ribosomal_L18p: Ribos 100.0 2.1E-40 4.5E-45 254.2 14.7 118 54-171 2-119 (119)
6 PTZ00032 60S ribosomal protein 100.0 5.7E-39 1.2E-43 266.0 12.5 99 73-171 103-211 (211)
7 cd00432 Ribosomal_L18_L5e Ribo 100.0 3.1E-36 6.6E-41 224.6 12.6 102 66-169 2-103 (103)
8 PRK08569 rpl18p 50S ribosomal 100.0 3.5E-34 7.6E-39 236.3 12.9 114 53-171 13-130 (193)
9 KOG3333 Mitochondrial/chloropl 99.5 1.1E-13 2.4E-18 112.0 8.1 93 76-171 61-154 (188)
10 PTZ00069 60S ribosomal protein 99.5 1.9E-13 4.2E-18 119.2 9.0 96 74-171 47-174 (300)
11 PTZ00090 40S ribosomal protein 97.8 0.00041 8.9E-09 59.2 11.6 89 75-171 118-208 (233)
12 TIGR03632 bact_S11 30S ribosom 97.7 0.0006 1.3E-08 51.7 10.6 86 78-171 3-89 (108)
13 PF00411 Ribosomal_S11: Riboso 97.6 0.0011 2.4E-08 50.2 10.4 86 78-171 3-89 (110)
14 CHL00041 rps11 ribosomal prote 97.6 0.0014 3E-08 50.4 10.7 88 76-171 14-102 (116)
15 PRK05309 30S ribosomal protein 97.5 0.0025 5.4E-08 49.9 10.9 89 75-171 17-106 (128)
16 TIGR03628 arch_S11P archaeal r 97.1 0.011 2.3E-07 45.8 10.4 89 78-171 5-100 (114)
17 PRK09607 rps11p 30S ribosomal 96.8 0.01 2.2E-07 47.0 8.9 91 76-171 10-107 (132)
18 KOG0875 60S ribosomal protein 96.8 0.0022 4.8E-08 55.7 5.0 120 50-171 23-173 (264)
19 PTZ00129 40S ribosomal protein 96.5 0.043 9.2E-07 44.4 10.3 92 75-171 28-126 (149)
20 COG0100 RpsK Ribosomal protein 94.4 0.6 1.3E-05 37.0 9.7 84 78-170 21-106 (129)
21 KOG0408 Mitochondrial/chloropl 92.7 1.3 2.8E-05 36.8 9.3 89 74-170 78-167 (190)
22 KOG0407 40S ribosomal protein 87.3 10 0.00022 29.9 9.7 90 77-170 18-113 (139)
23 TIGR00725 conserved hypothetic 72.0 8.7 0.00019 30.6 4.9 40 121-169 16-55 (159)
24 cd06280 PBP1_LacI_like_4 Ligan 71.5 16 0.00035 29.3 6.4 45 127-171 101-147 (263)
25 cd06285 PBP1_LacI_like_7 Ligan 69.6 16 0.00035 29.2 6.0 48 120-171 97-147 (265)
26 cd06286 PBP1_CcpB_like Ligand- 69.3 17 0.00037 28.9 6.1 46 121-170 98-146 (260)
27 cd06276 PBP1_FucR_like Ligand- 69.2 15 0.00033 29.8 5.9 46 126-171 100-149 (247)
28 PRK10423 transcriptional repre 66.2 21 0.00045 29.7 6.2 44 128-171 161-207 (327)
29 cd06288 PBP1_sucrose_transcrip 66.1 21 0.00045 28.4 6.0 42 129-170 104-148 (269)
30 cd06274 PBP1_FruR Ligand bindi 64.9 23 0.00051 28.2 6.1 46 121-170 100-148 (264)
31 PRK10703 DNA-binding transcrip 64.2 22 0.00048 29.8 6.1 45 127-171 164-211 (341)
32 PF03646 FlaG: FlaG protein; 64.0 40 0.00086 24.7 6.7 45 56-100 37-81 (107)
33 cd06267 PBP1_LacI_sugar_bindin 63.9 27 0.00059 27.1 6.1 43 128-170 103-148 (264)
34 cd06275 PBP1_PurR Ligand-bindi 63.7 28 0.0006 27.7 6.3 45 127-171 103-150 (269)
35 PRK09492 treR trehalose repres 62.4 29 0.00062 28.7 6.4 48 120-171 158-209 (315)
36 cd06293 PBP1_LacI_like_11 Liga 62.2 30 0.00064 27.7 6.2 47 120-170 99-148 (269)
37 TIGR01917 gly_red_sel_B glycin 61.9 31 0.00067 32.4 7.0 53 118-170 314-366 (431)
38 cd06296 PBP1_CatR_like Ligand- 61.6 31 0.00068 27.4 6.2 43 128-170 104-149 (270)
39 PF00875 DNA_photolyase: DNA p 61.4 14 0.0003 28.7 4.0 44 128-171 76-120 (165)
40 cd06270 PBP1_GalS_like Ligand 61.0 32 0.00069 27.5 6.2 43 129-171 104-149 (268)
41 cd01543 PBP1_XylR Ligand-bindi 61.0 35 0.00076 27.4 6.5 43 128-170 96-140 (265)
42 PRK10727 DNA-binding transcrip 60.0 30 0.00064 29.3 6.1 44 128-171 163-209 (343)
43 smart00481 POLIIIAc DNA polyme 59.6 26 0.00055 23.2 4.6 40 129-171 17-57 (67)
44 TIGR00612 ispG_gcpE 1-hydroxy- 59.5 33 0.00071 31.4 6.5 52 119-170 55-123 (346)
45 PF14419 SPOUT_MTase_2: AF2226 59.0 32 0.00069 28.6 5.8 49 119-167 10-58 (173)
46 PF00070 Pyr_redox: Pyridine n 58.2 33 0.00071 23.3 5.1 45 127-171 9-57 (80)
47 PF00532 Peripla_BP_1: Peripla 57.9 23 0.0005 29.9 5.1 44 127-170 104-151 (279)
48 PRK10014 DNA-binding transcrip 57.7 39 0.00085 28.3 6.4 44 128-171 169-215 (342)
49 cd06271 PBP1_AglR_RafR_like Li 57.3 35 0.00077 26.9 5.8 44 127-170 106-152 (268)
50 TIGR01918 various_sel_PB selen 57.1 41 0.00089 31.6 6.9 53 118-170 314-366 (431)
51 cd06282 PBP1_GntR_like_2 Ligan 56.9 35 0.00077 26.9 5.8 45 126-170 101-149 (266)
52 cd06319 PBP1_ABC_sugar_binding 56.9 43 0.00093 26.8 6.3 52 119-170 101-157 (277)
53 cd01545 PBP1_SalR Ligand-bindi 55.6 48 0.001 26.3 6.4 46 126-171 103-151 (270)
54 cd01540 PBP1_arabinose_binding 54.9 42 0.00092 27.1 6.0 53 118-170 104-162 (289)
55 TIGR01481 ccpA catabolite cont 53.8 47 0.001 27.7 6.3 44 128-171 163-210 (329)
56 cd06295 PBP1_CelR Ligand bindi 53.8 54 0.0012 26.3 6.5 44 127-170 111-157 (275)
57 PRK11303 DNA-binding transcrip 53.0 50 0.0011 27.5 6.3 43 128-170 166-211 (328)
58 cd06287 PBP1_LacI_like_8 Ligan 53.0 45 0.00098 27.4 6.0 44 127-170 104-150 (269)
59 COG1611 Predicted Rossmann fol 52.8 21 0.00045 29.8 3.9 40 122-170 33-72 (205)
60 COG1609 PurR Transcriptional r 52.5 47 0.001 29.0 6.3 44 128-171 162-208 (333)
61 PF13380 CoA_binding_2: CoA bi 52.1 19 0.00041 26.9 3.3 42 125-171 64-105 (116)
62 cd06278 PBP1_LacI_like_2 Ligan 52.0 56 0.0012 25.8 6.2 47 120-170 98-147 (266)
63 cd01575 PBP1_GntR Ligand-bindi 51.4 55 0.0012 25.8 6.1 44 127-170 102-148 (268)
64 cd06294 PBP1_ycjW_transcriptio 51.4 58 0.0013 25.8 6.2 45 126-170 107-154 (270)
65 cd06292 PBP1_LacI_like_10 Liga 50.9 62 0.0013 25.8 6.3 47 120-170 105-154 (273)
66 COG1908 FrhD Coenzyme F420-red 50.4 35 0.00077 27.1 4.6 40 131-170 44-93 (132)
67 cd06283 PBP1_RegR_EndR_KdgR_li 49.9 59 0.0013 25.7 6.0 44 127-170 102-149 (267)
68 cd06273 PBP1_GntR_like_1 This 49.8 57 0.0012 25.9 5.9 45 126-170 101-149 (268)
69 cd01541 PBP1_AraR Ligand-bindi 49.3 57 0.0012 26.1 5.9 47 120-170 104-152 (273)
70 cd06277 PBP1_LacI_like_1 Ligan 48.9 60 0.0013 25.9 6.0 44 128-171 105-151 (268)
71 cd06290 PBP1_LacI_like_9 Ligan 48.7 69 0.0015 25.5 6.3 47 120-170 98-147 (265)
72 PRK14987 gluconate operon tran 48.2 60 0.0013 27.2 6.1 46 120-169 163-210 (331)
73 cd01574 PBP1_LacI Ligand-bindi 47.9 73 0.0016 25.2 6.3 43 128-170 103-148 (264)
74 COG0299 PurN Folate-dependent 47.8 35 0.00076 29.0 4.5 38 133-170 43-81 (200)
75 TIGR02417 fruct_sucro_rep D-fr 47.4 64 0.0014 26.9 6.1 42 129-170 166-210 (327)
76 PRK11041 DNA-binding transcrip 46.9 73 0.0016 26.1 6.3 48 120-171 135-185 (309)
77 PRK07523 gluconate 5-dehydroge 46.6 48 0.001 26.6 5.1 40 125-168 19-58 (255)
78 PRK12744 short chain dehydroge 46.0 60 0.0013 26.2 5.6 41 127-167 19-59 (257)
79 cd06281 PBP1_LacI_like_5 Ligan 45.7 83 0.0018 25.2 6.4 42 129-170 104-148 (269)
80 cd06284 PBP1_LacI_like_6 Ligan 45.3 83 0.0018 24.8 6.2 44 127-170 101-147 (267)
81 cd06272 PBP1_hexuronate_repres 45.0 66 0.0014 25.5 5.6 44 127-170 97-143 (261)
82 cd06326 PBP1_STKc_like Type I 44.8 61 0.0013 26.9 5.6 46 125-170 120-166 (336)
83 cd06298 PBP1_CcpA_like Ligand- 44.8 88 0.0019 24.7 6.3 47 120-170 99-149 (268)
84 PRK12827 short chain dehydroge 44.7 63 0.0014 25.4 5.4 41 126-166 16-56 (249)
85 cd04906 ACT_ThrD-I_1 First of 44.7 59 0.0013 22.7 4.7 34 138-171 24-69 (85)
86 PRK07738 flagellar protein Fla 44.6 90 0.002 24.2 6.1 43 58-100 48-90 (117)
87 PF02065 Melibiase: Melibiase; 44.6 35 0.00075 31.3 4.4 41 131-171 62-120 (394)
88 PRK00366 ispG 4-hydroxy-3-meth 44.3 51 0.0011 30.3 5.3 52 119-170 63-132 (360)
89 COG3345 GalA Alpha-galactosida 44.1 33 0.00072 33.7 4.3 86 53-171 266-371 (687)
90 PRK09526 lacI lac repressor; R 43.7 84 0.0018 26.3 6.3 42 129-170 169-213 (342)
91 cd06291 PBP1_Qymf_like Ligand 43.6 95 0.0021 24.6 6.3 44 127-170 98-145 (265)
92 cd01391 Periplasmic_Binding_Pr 43.2 77 0.0017 24.0 5.5 44 127-170 110-155 (269)
93 smart00812 Alpha_L_fucos Alpha 43.0 45 0.00098 30.3 4.8 42 130-171 84-144 (384)
94 cd06339 PBP1_YraM_LppC_lipopro 42.7 59 0.0013 27.8 5.3 44 128-171 111-155 (336)
95 cd06310 PBP1_ABC_sugar_binding 42.5 72 0.0016 25.5 5.5 49 120-170 104-156 (273)
96 PF02826 2-Hacid_dh_C: D-isome 41.9 34 0.00074 27.1 3.5 25 127-151 46-70 (178)
97 PF14488 DUF4434: Domain of un 41.3 52 0.0011 26.4 4.4 41 131-171 24-81 (166)
98 PRK10401 DNA-binding transcrip 41.2 96 0.0021 26.2 6.3 47 120-170 159-208 (346)
99 PF08032 SpoU_sub_bind: RNA 2' 41.2 22 0.00048 23.8 2.0 40 129-170 4-45 (76)
100 cd06299 PBP1_LacI_like_13 Liga 41.0 1E+02 0.0022 24.4 6.1 42 129-170 104-148 (265)
101 PF04273 DUF442: Putative phos 40.1 35 0.00077 25.7 3.1 37 135-171 22-60 (110)
102 TIGR02766 crypt_chrom_pln cryp 39.2 57 0.0012 29.9 4.9 43 129-171 76-119 (475)
103 cd06333 PBP1_ABC-type_HAAT_lik 38.6 88 0.0019 25.9 5.6 45 127-171 119-164 (312)
104 TIGR03581 EF_0839 conserved hy 38.2 85 0.0018 27.3 5.5 71 90-170 108-179 (236)
105 PRK08085 gluconate 5-dehydroge 37.9 79 0.0017 25.3 5.1 39 125-167 18-56 (254)
106 PF01120 Alpha_L_fucos: Alpha- 37.8 49 0.0011 29.3 4.1 43 129-171 93-154 (346)
107 PF13727 CoA_binding_3: CoA-bi 37.7 50 0.0011 24.7 3.7 41 130-171 131-171 (175)
108 cd06297 PBP1_LacI_like_12 Liga 37.5 90 0.002 25.2 5.4 48 119-171 96-152 (269)
109 PF07071 DUF1341: Protein of u 37.2 81 0.0018 27.1 5.1 37 134-170 142-179 (218)
110 cd06308 PBP1_sensor_kinase_lik 37.1 93 0.002 24.9 5.4 49 120-170 103-155 (270)
111 PF00933 Glyco_hydro_3: Glycos 36.9 71 0.0015 27.5 4.9 51 119-169 81-149 (299)
112 TIGR02405 trehalos_R_Ecol treh 36.6 1.1E+02 0.0024 25.4 5.9 47 120-170 155-205 (311)
113 TIGR02765 crypto_DASH cryptoch 36.2 68 0.0015 28.9 4.8 42 130-171 86-128 (429)
114 TIGR03556 photolyase_8HDF deox 36.1 67 0.0015 29.7 4.9 42 130-171 80-122 (471)
115 PF03928 DUF336: Domain of unk 36.0 68 0.0015 24.3 4.2 32 121-152 4-37 (132)
116 PF02789 Peptidase_M17_N: Cyto 36.0 1.7E+02 0.0036 21.1 6.6 51 120-170 66-118 (126)
117 TIGR02571 ComEB ComE operon pr 35.8 58 0.0012 25.9 3.9 35 133-171 101-135 (151)
118 PF12683 DUF3798: Protein of u 35.7 56 0.0012 29.0 4.1 48 124-171 114-166 (275)
119 PRK12548 shikimate 5-dehydroge 35.4 1E+02 0.0022 26.5 5.6 40 127-167 136-176 (289)
120 COG1052 LdhA Lactate dehydroge 35.2 56 0.0012 29.1 4.1 24 127-150 156-179 (324)
121 cd06320 PBP1_allose_binding Pe 35.2 1.1E+02 0.0023 24.6 5.4 49 120-170 103-155 (275)
122 COG0041 PurE Phosphoribosylcar 35.0 1.1E+02 0.0025 25.1 5.5 42 130-171 19-60 (162)
123 PRK06114 short chain dehydroge 34.6 1E+02 0.0022 24.8 5.3 38 126-166 18-55 (254)
124 PRK07791 short chain dehydroge 34.6 1E+02 0.0022 25.8 5.4 44 125-168 15-63 (286)
125 PRK12457 2-dehydro-3-deoxyphos 34.3 1.1E+02 0.0023 27.3 5.6 51 121-171 28-90 (281)
126 PF02811 PHP: PHP domain; Int 34.1 77 0.0017 23.7 4.2 37 131-170 20-57 (175)
127 PRK06124 gluconate 5-dehydroge 34.0 1E+02 0.0022 24.7 5.1 40 125-168 20-59 (256)
128 PRK10339 DNA-binding transcrip 33.4 1.4E+02 0.003 25.0 6.0 44 126-169 159-205 (327)
129 PHA02588 cd deoxycytidylate de 33.3 67 0.0015 25.9 3.9 36 133-171 115-150 (168)
130 PRK04302 triosephosphate isome 33.3 1.1E+02 0.0023 25.2 5.2 44 127-170 72-116 (223)
131 PRK14719 bifunctional RNAse/5- 33.1 47 0.001 30.1 3.3 37 132-171 58-98 (360)
132 cd06303 PBP1_LuxPQ_Quorum_Sens 32.7 1.4E+02 0.003 24.3 5.8 49 120-170 112-163 (280)
133 PRK05867 short chain dehydroge 32.6 1.1E+02 0.0024 24.5 5.2 38 126-167 19-56 (253)
134 PF07355 GRDB: Glycine/sarcosi 32.6 76 0.0016 29.1 4.5 29 118-146 318-346 (349)
135 cd06317 PBP1_ABC_sugar_binding 32.5 1.5E+02 0.0033 23.4 5.9 47 121-169 107-156 (275)
136 PRK08278 short chain dehydroge 32.5 1.2E+02 0.0026 24.9 5.5 44 125-168 15-61 (273)
137 PF06370 DUF1069: Protein of u 32.2 25 0.00054 28.8 1.3 19 138-156 164-182 (206)
138 PLN00125 Succinyl-CoA ligase [ 31.6 88 0.0019 27.7 4.7 40 132-171 85-124 (300)
139 PF02254 TrkA_N: TrkA-N domain 30.8 1.3E+02 0.0028 21.3 4.8 35 127-169 8-42 (116)
140 TIGR02867 spore_II_P stage II 30.6 1.1E+02 0.0023 25.6 4.8 26 123-149 30-55 (196)
141 cd06289 PBP1_MalI_like Ligand- 30.6 1.8E+02 0.0039 22.8 6.0 43 128-170 104-149 (268)
142 PRK08703 short chain dehydroge 30.6 1.2E+02 0.0027 24.0 5.1 37 126-166 16-52 (239)
143 PF14540 NTF-like: Nucleotidyl 30.6 27 0.00058 27.2 1.1 25 142-166 93-119 (119)
144 PRK07109 short chain dehydroge 30.5 1.2E+02 0.0027 26.1 5.4 39 126-168 18-56 (334)
145 cd06279 PBP1_LacI_like_3 Ligan 30.4 1.7E+02 0.0038 23.7 6.0 47 120-170 99-165 (283)
146 cd01537 PBP1_Repressors_Sugar_ 30.0 1.7E+02 0.0038 22.5 5.7 42 127-168 104-148 (264)
147 PF04551 GcpE: GcpE protein; 29.8 2E+02 0.0043 26.6 6.7 50 120-170 53-133 (359)
148 cd06300 PBP1_ABC_sugar_binding 29.7 1.5E+02 0.0033 23.6 5.5 49 120-170 106-158 (272)
149 TIGR02801 tolR TolR protein. T 29.1 2.4E+02 0.0053 20.9 6.2 29 142-170 94-122 (129)
150 PRK07792 fabG 3-ketoacyl-(acyl 29.0 1.3E+02 0.0028 25.5 5.2 40 126-168 22-61 (306)
151 cd06322 PBP1_ABC_sugar_binding 28.9 1.8E+02 0.0039 23.0 5.8 49 120-170 102-153 (267)
152 PRK13397 3-deoxy-7-phosphohept 28.9 82 0.0018 27.3 4.0 50 122-171 24-82 (250)
153 PRK08277 D-mannonate oxidoredu 28.9 1.4E+02 0.003 24.4 5.2 26 125-150 19-44 (278)
154 cd06325 PBP1_ABC_uncharacteriz 28.7 1.3E+02 0.0028 24.0 4.9 44 127-170 115-162 (281)
155 PRK05866 short chain dehydroge 28.4 1.4E+02 0.0031 25.1 5.3 36 126-165 50-85 (293)
156 cd06350 PBP1_GPCR_family_C_lik 28.4 1.5E+02 0.0033 24.7 5.5 47 124-171 143-191 (348)
157 PF02006 DUF137: Protein of un 28.3 1.2E+02 0.0025 25.5 4.5 46 121-170 12-59 (178)
158 cd00175 SNc Staphylococcal nuc 28.3 2.4E+02 0.0051 20.5 7.3 55 94-169 69-124 (129)
159 PRK07097 gluconate 5-dehydroge 28.2 1.6E+02 0.0035 23.8 5.4 25 126-150 20-44 (265)
160 PRK15395 methyl-galactoside AB 28.0 2E+02 0.0044 24.5 6.2 52 119-170 132-194 (330)
161 PF03446 NAD_binding_2: NAD bi 28.0 80 0.0017 24.5 3.5 27 127-153 11-37 (163)
162 cd01544 PBP1_GalR Ligand-bindi 28.0 2.1E+02 0.0044 23.0 6.0 41 129-169 100-148 (270)
163 PRK12826 3-ketoacyl-(acyl-carr 27.9 1.4E+02 0.003 23.5 4.9 40 125-168 15-54 (251)
164 cd06311 PBP1_ABC_sugar_binding 27.8 1.6E+02 0.0035 23.6 5.3 50 119-170 107-158 (274)
165 PRK08452 flagellar protein Fla 27.8 2.1E+02 0.0046 22.3 5.7 28 73-100 70-97 (124)
166 PRK06139 short chain dehydroge 27.7 1.5E+02 0.0032 25.9 5.4 39 126-168 17-55 (330)
167 PRK12549 shikimate 5-dehydroge 27.4 1.4E+02 0.0031 25.6 5.3 38 125-166 135-173 (284)
168 COG0007 CysG Uroporphyrinogen- 27.3 1.2E+02 0.0025 26.4 4.6 44 126-171 68-112 (244)
169 PF01488 Shikimate_DH: Shikima 27.3 1.4E+02 0.003 22.5 4.6 34 127-164 22-56 (135)
170 COG1472 BglX Beta-glucosidase- 27.3 1.2E+02 0.0026 27.8 4.9 52 118-169 91-161 (397)
171 PTZ00445 p36-lilke protein; Pr 27.0 1.6E+02 0.0035 25.3 5.4 45 127-171 29-94 (219)
172 PRK11702 hypothetical protein; 26.8 26 0.00057 27.0 0.5 13 59-71 3-15 (108)
173 PRK06194 hypothetical protein; 26.7 1.6E+02 0.0034 24.1 5.2 26 125-150 15-40 (287)
174 PF02878 PGM_PMM_I: Phosphoglu 26.7 2.7E+02 0.0059 20.8 6.2 49 120-171 18-71 (137)
175 PRK07478 short chain dehydroge 26.6 1.7E+02 0.0037 23.4 5.3 38 126-167 16-53 (254)
176 PRK05876 short chain dehydroge 26.3 1.6E+02 0.0034 24.5 5.1 39 126-168 16-54 (275)
177 PRK08868 flagellar protein Fla 26.3 2.4E+02 0.0052 22.7 5.9 39 62-100 77-115 (144)
178 PRK08303 short chain dehydroge 26.3 1.6E+02 0.0034 25.2 5.3 43 126-168 18-66 (305)
179 cd04885 ACT_ThrD-I Tandem C-te 26.3 1.2E+02 0.0026 20.1 3.7 34 138-171 22-66 (68)
180 COG0821 gcpE 1-hydroxy-2-methy 26.2 1.4E+02 0.0029 27.6 5.0 52 119-170 57-125 (361)
181 PRK07814 short chain dehydroge 26.2 1.7E+02 0.0037 23.7 5.3 35 127-165 21-55 (263)
182 TIGR02717 AcCoA-syn-alpha acet 25.8 1.3E+02 0.0028 27.7 4.9 42 130-171 78-124 (447)
183 PF01408 GFO_IDH_MocA: Oxidore 25.5 1.9E+02 0.0042 20.3 4.9 40 130-170 76-115 (120)
184 PRK13111 trpA tryptophan synth 25.1 1.6E+02 0.0036 25.2 5.1 37 131-170 108-144 (258)
185 PRK12823 benD 1,6-dihydroxycyc 25.0 1.7E+02 0.0036 23.5 4.9 25 125-149 17-41 (260)
186 PRK08945 putative oxoacyl-(acy 24.8 2E+02 0.0044 22.8 5.4 25 126-150 22-46 (247)
187 cd06306 PBP1_TorT-like TorT-li 24.4 1.7E+02 0.0038 23.5 5.0 51 120-170 103-157 (268)
188 PRK13398 3-deoxy-7-phosphohept 24.3 2E+02 0.0044 24.8 5.6 43 129-171 43-94 (266)
189 cd07940 DRE_TIM_IPMS 2-isoprop 24.3 1.6E+02 0.0034 24.9 4.9 48 121-169 108-157 (268)
190 PRK12738 kbaY tagatose-bisphos 24.2 1.7E+02 0.0036 25.8 5.1 41 130-170 87-130 (286)
191 cd06323 PBP1_ribose_binding Pe 24.1 2.1E+02 0.0046 22.4 5.3 49 120-170 102-154 (268)
192 PRK06487 glycerate dehydrogena 24.1 92 0.002 27.3 3.5 25 126-150 157-181 (317)
193 COG2179 Predicted hydrolase of 24.0 1.5E+02 0.0033 24.7 4.5 44 127-170 14-64 (175)
194 PRK10653 D-ribose transporter 23.8 1.9E+02 0.0041 23.8 5.1 44 127-170 132-180 (295)
195 PRK13125 trpA tryptophan synth 23.6 2.1E+02 0.0045 23.9 5.4 39 132-170 93-131 (244)
196 PRK07454 short chain dehydroge 23.4 1.8E+02 0.004 22.9 4.9 25 126-150 16-40 (241)
197 cd06312 PBP1_ABC_sugar_binding 23.0 2.7E+02 0.0058 22.3 5.8 48 120-170 107-157 (271)
198 PRK07326 short chain dehydroge 23.0 1.9E+02 0.0041 22.6 4.8 26 125-150 15-40 (237)
199 cd04509 PBP1_ABC_transporter_G 22.8 2.3E+02 0.0049 22.2 5.2 44 126-170 121-166 (299)
200 PHA03003 palmytilated EEV memb 22.5 95 0.0021 27.8 3.3 40 125-171 62-102 (369)
201 PRK08628 short chain dehydroge 22.3 1.8E+02 0.0039 23.2 4.7 26 126-151 17-42 (258)
202 PRK07806 short chain dehydroge 22.3 2.3E+02 0.0051 22.3 5.3 25 126-150 16-40 (248)
203 TIGR02955 TMAO_TorT TMAO reduc 22.3 1.9E+02 0.004 23.9 4.8 52 119-170 102-157 (295)
204 PRK06125 short chain dehydroge 22.2 2.3E+02 0.005 22.8 5.2 37 126-166 17-53 (259)
205 cd07041 STAS_RsbR_RsbS_like Su 22.1 2.9E+02 0.0063 19.4 6.7 50 121-170 21-75 (109)
206 PLN02591 tryptophan synthase 22.0 1.8E+02 0.004 24.9 4.8 38 130-170 96-133 (250)
207 PRK12828 short chain dehydroge 21.8 2.1E+02 0.0045 22.2 4.8 24 127-150 18-41 (239)
208 cd06314 PBP1_tmGBP Periplasmic 21.7 2.6E+02 0.0057 22.3 5.5 49 120-170 101-152 (271)
209 cd06360 PBP1_alkylbenzenes_lik 21.6 2.1E+02 0.0046 23.7 5.0 45 127-171 120-165 (336)
210 PF13671 AAA_33: AAA domain; P 21.6 2.9E+02 0.0064 19.9 5.3 45 124-170 54-98 (143)
211 PF07137 VDE: Violaxanthin de- 21.5 99 0.0021 26.3 3.0 29 143-171 150-178 (198)
212 PF03900 Porphobil_deamC: Porp 21.3 69 0.0015 22.0 1.7 59 67-138 12-74 (74)
213 PRK08339 short chain dehydroge 21.3 2.3E+02 0.005 23.1 5.2 24 126-149 18-41 (263)
214 PRK13761 hypothetical protein; 20.9 2.1E+02 0.0045 25.2 4.9 46 121-170 75-122 (248)
215 PRK06935 2-deoxy-D-gluconate 3 20.7 2.3E+02 0.0051 22.7 5.0 26 124-149 23-48 (258)
216 PRK11024 colicin uptake protei 20.7 3.9E+02 0.0085 20.4 6.3 40 131-170 93-132 (141)
217 PRK05855 short chain dehydroge 20.6 2E+02 0.0042 25.9 4.9 41 124-168 323-363 (582)
218 cd01536 PBP1_ABC_sugar_binding 20.5 2.9E+02 0.0063 21.4 5.4 41 128-168 106-151 (267)
219 PF06414 Zeta_toxin: Zeta toxi 20.4 2.5E+02 0.0054 22.3 5.0 48 121-170 74-121 (199)
220 PRK07370 enoyl-(acyl carrier p 20.3 2.3E+02 0.0051 23.1 5.0 23 127-149 19-41 (258)
221 cd01538 PBP1_ABC_xylose_bindin 20.3 2.7E+02 0.0058 22.8 5.4 49 120-168 102-155 (288)
222 PF03447 NAD_binding_3: Homose 20.3 70 0.0015 23.2 1.7 42 130-171 73-114 (117)
223 cd07939 DRE_TIM_NifV Streptomy 20.2 2.5E+02 0.0053 23.6 5.2 47 122-169 105-153 (259)
224 COG2131 ComEB Deoxycytidylate 20.1 1.7E+02 0.0037 24.0 4.1 39 132-171 110-148 (164)
225 PRK07666 fabG 3-ketoacyl-(acyl 20.1 2.4E+02 0.0053 22.2 4.9 25 126-150 17-41 (239)
226 PRK06949 short chain dehydroge 20.0 2.8E+02 0.006 22.0 5.3 26 125-150 18-43 (258)
No 1
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=100.00 E-value=2.9e-46 Score=287.14 Aligned_cols=116 Identities=62% Similarity=0.963 Sum_probs=111.6
Q ss_pred CcHHHHHHHHHHhhhhhcCCCCCceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHH
Q 030804 53 TKREDRTARHSRIRKKIDGTPERPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMI 132 (171)
Q Consensus 53 ~r~~~r~~R~~RirkKi~gt~~rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~L 132 (171)
++++.|++||+|+|+||.||+++|||+||+||+|||||||||.+++||+||||+|++++..|+ ++|++||+.||++|
T Consensus 2 ~~~~~r~~r~~r~r~ki~g~~~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~~---~~n~~aa~~vG~~l 78 (117)
T PRK05593 2 DKKEARLRRHRRVRKKISGTAERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGLK---GGNKEAAKKVGKLI 78 (117)
T ss_pred chHHHHHHHHHHHHHHhcCCCCCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhcccc---CCCHHHHHHHHHHH
Confidence 466788999999999999999999999999999999999999999999999999999988763 78999999999999
Q ss_pred HHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 133 AKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 133 Akra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
|++|+++||++|+||||+|+|||||+||+|++||+||+|
T Consensus 79 a~ra~~~gi~~vvfDrg~~~yhGrV~a~a~~are~Gl~f 117 (117)
T PRK05593 79 AERAKAKGIKQVVFDRGGYKYHGRVKALADAAREAGLKF 117 (117)
T ss_pred HHHHHHCCCCEEEEcCCCCcccHHHHHHHHHHHHhCCCC
Confidence 999999999999999999999999999999999999998
No 2
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=100.00 E-value=4.5e-46 Score=285.23 Aligned_cols=111 Identities=56% Similarity=0.895 Sum_probs=106.0
Q ss_pred HHHHHHHHHHhhhhhcCCC--CCceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHH
Q 030804 55 REDRTARHSRIRKKIDGTP--ERPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMI 132 (171)
Q Consensus 55 ~~~r~~R~~RirkKi~gt~--~rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~L 132 (171)
++.|++||+|+|+||.||+ ++|||+||+||+|||||||||.+++||+|+||+|++++ .++|+++|++||++|
T Consensus 2 ~~~r~~r~~r~r~ki~gt~~~~rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~------~~~n~~aA~~vG~~l 75 (114)
T TIGR00060 2 KSARIRRHKRIRRKLRETGEANRPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK------YTGNKDAAKKVGKLV 75 (114)
T ss_pred cHHHHHHHHHHHHHhcCCCCCCCcEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc------CCCCHHHHHHHHHHH
Confidence 3567799999999999998 89999999999999999999999999999999999875 367999999999999
Q ss_pred HHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 133 AKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 133 Akra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
|++|+++||++|+||||||+|||||+||+|++||+||+|
T Consensus 76 a~ra~~~gi~~vvfDrgg~~YhGrv~A~a~~aRe~Gl~F 114 (114)
T TIGR00060 76 AERLKEKGIKDVVFDRGGYKYHGRVAALAEAAREAGLNF 114 (114)
T ss_pred HHHHHHCCCCEEEEeCCCCcchHHHHHHHHHHHHhCCCC
Confidence 999999999999999999999999999999999999998
No 3
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=100.00 E-value=4.1e-45 Score=277.84 Aligned_cols=109 Identities=61% Similarity=0.923 Sum_probs=104.4
Q ss_pred HHHHhhhhhcCCCCCceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcC
Q 030804 61 RHSRIRKKIDGTPERPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKG 140 (171)
Q Consensus 61 R~~RirkKi~gt~~rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~G 140 (171)
+++|+|+||.||+++|||+||+||+|||||||||.+|+||+||||+||+++..+ .+++|+++|+.||++||+||+++|
T Consensus 1 ~~~r~r~ki~g~~~rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~--~~~~n~~aA~~vG~lla~ra~~~g 78 (109)
T CHL00139 1 KRERVRKKIKGTAERPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSL--SSTSTCDASKLVGQKLAKKSLKKG 78 (109)
T ss_pred CCeeeeeeecCCCCCCEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccc--cCCCCHHHHHHHHHHHHHHHHHCC
Confidence 367999999999999999999999999999999999999999999999998765 468899999999999999999999
Q ss_pred CCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 141 ITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 141 I~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
|++|+||||+|+|||||+||+|++||+||+|
T Consensus 79 i~~vvfDrgg~~yhGrV~a~a~~are~GL~f 109 (109)
T CHL00139 79 ITKVVFDRGGKLYHGRIKALAEAAREAGLQF 109 (109)
T ss_pred CCEEEEcCCCCccchHHHHHHHHHHHhCCCC
Confidence 9999999999999999999999999999998
No 4
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-43 Score=273.92 Aligned_cols=120 Identities=53% Similarity=0.805 Sum_probs=112.6
Q ss_pred CCCcHHHHHHHHHHhhhhhcCCCCCceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCccccc-ccCCCCCCcHHHHHHHH
Q 030804 51 PRTKREDRTARHSRIRKKIDGTPERPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISE-ELDYSSGPTIEVSKKVG 129 (171)
Q Consensus 51 ~~~r~~~r~~R~~RirkKi~gt~~rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~-~l~~~~~~n~~AA~~VG 129 (171)
...|++++.+|+.|+|+||.|++++|||+||+||+|||||||||..+.||+++||++++++. .|. ..++|+++|++||
T Consensus 5 ~~~rr~~~~kr~~r~R~kl~g~~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~-~~~~N~~aA~~vG 83 (125)
T COG0256 5 VKFRRRRRGKRAYRIRKKLLGTSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKK-GGGGNTEAAYLVG 83 (125)
T ss_pred hhhHHHHHHhHHHHHHHhhccCCCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhccc-CCCCCHHHHHHHH
Confidence 35678899999999999999999999999999999999999999999999999999999974 342 3567999999999
Q ss_pred HHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 130 EMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
+++|++++++||++|+|||+||+|||||+||+|++||+||+|
T Consensus 84 ~lia~ra~~kgi~~vVfdr~g~~yhgRV~Ala~~AreaGL~f 125 (125)
T COG0256 84 KLIAERALAKGIEEVVFDRGGYKYHGRVAALADGAREAGLEF 125 (125)
T ss_pred HHHHHHHHHcCCcEEEEcCCCCCcchHHHHHHHHHHHcCcCC
Confidence 999999999999999999999999999999999999999998
No 5
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=100.00 E-value=2.1e-40 Score=254.19 Aligned_cols=118 Identities=59% Similarity=0.875 Sum_probs=109.8
Q ss_pred cHHHHHHHHHHhhhhhcCCCCCceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHH
Q 030804 54 KREDRTARHSRIRKKIDGTPERPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIA 133 (171)
Q Consensus 54 r~~~r~~R~~RirkKi~gt~~rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LA 133 (171)
+++.+.+|+.++|+++.++.++|||+||+||+|||||||||.++++|++|||++++++......+++|++||+.||++||
T Consensus 2 k~~~~~~r~~~~r~~~~~~~~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~~vG~lla 81 (119)
T PF00861_consen 2 KKRRRRRRKLRIRRKIKGTAERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAYLVGELLA 81 (119)
T ss_dssp SCHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHhcCCCCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHHHHHHHHH
Confidence 45688899999999999999999999999999999999999999999999999999997421246789999999999999
Q ss_pred HHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 134 KSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 134 kra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
+||+++||..|+|||++++|||||+||+|++||+||+|
T Consensus 82 ~ra~~~gi~~v~fdr~~~~y~grv~a~~~~~re~Gl~f 119 (119)
T PF00861_consen 82 KRALEKGIAKVVFDRGGYKYHGRVKALADGAREGGLEF 119 (119)
T ss_dssp HHHHHTTSSEEEECTSTSSSSSHHHHHHHHHHHTTCB-
T ss_pred HHHHHcCCcEEEEcCCCCcccHHHHHHHHHHHHcCCCC
Confidence 99999999999999999999999999999999999998
No 6
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=100.00 E-value=5.7e-39 Score=266.03 Aligned_cols=99 Identities=39% Similarity=0.678 Sum_probs=92.7
Q ss_pred CCCceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCC----------CCCCcHHHHHHHHHHHHHHHHHcCCC
Q 030804 73 PERPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDY----------SSGPTIEVSKKVGEMIAKSCLEKGIT 142 (171)
Q Consensus 73 ~~rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~----------~~~~n~~AA~~VG~~LAkra~e~GI~ 142 (171)
..+|||+||+||+|||||||||.+++||+++||++++++..+.. ..++|+++|+.||++||++|+++||+
T Consensus 103 krrPRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAerAl~kGI~ 182 (211)
T PTZ00032 103 KRRPRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGIS 182 (211)
T ss_pred CCcceEEEEecCCeEEEEEEECCCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHHHHHHHHHCCCC
Confidence 46899999999999999999999999999999999999875421 14789999999999999999999999
Q ss_pred EEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 143 KVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 143 ~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
+|+||||||+|||||+||||++||+||+|
T Consensus 183 kVvFDRgGy~YHGRVkALAdaARe~GLkF 211 (211)
T PTZ00032 183 KVRFDRAHYKYAGKVEALAEGARAVGLQF 211 (211)
T ss_pred EEEEeCCCCeehhHHHHHHHHHHHcCCCC
Confidence 99999999999999999999999999998
No 7
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=100.00 E-value=3.1e-36 Score=224.58 Aligned_cols=102 Identities=58% Similarity=0.861 Sum_probs=96.3
Q ss_pred hhhhcCCCCCceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEE
Q 030804 66 RKKIDGTPERPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVA 145 (171)
Q Consensus 66 rkKi~gt~~rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~Vv 145 (171)
++++.|+..+|||+||+||+|||||||||.+++||++|||+|++++..+ .+++|++||+.||++||+||+|+||++|+
T Consensus 2 ~~~~~~~~~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~--~~~~n~~aA~~vG~~la~r~~~~gi~~vv 79 (103)
T cd00432 2 RRKRLGTQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVL--GSGNNVEAAYLVGRLLAKRALEKGIKKVV 79 (103)
T ss_pred ceEecCcCCCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccc--cCCCcHHHHHHHHHHHHHHHHHCCCCEEE
Confidence 3456677789999999999999999999999999999999999998876 47899999999999999999999999999
Q ss_pred EecCCCchhhHHHHHHHHHHHcCC
Q 030804 146 FDRGGYPYHGRIQALADAAREYGL 169 (171)
Q Consensus 146 fDRgg~~YhGrVkAlad~aRe~GL 169 (171)
||||+++|||||+||+|++||+||
T Consensus 80 ~D~~~~~~~grv~a~~~~~r~~Gl 103 (103)
T cd00432 80 FDRGGYRYHGRVKALAKGAREGGL 103 (103)
T ss_pred EeCCCcccccHHHHHHHHHHHcCC
Confidence 999999999999999999999997
No 8
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=100.00 E-value=3.5e-34 Score=236.34 Aligned_cols=114 Identities=25% Similarity=0.350 Sum_probs=101.0
Q ss_pred CcHHHHHHHHHHhhhhhcCCCCCceEEEEeeCCcEEEEEE--eCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHH
Q 030804 53 TKREDRTARHSRIRKKIDGTPERPRLCVFRSNKHLYVQVI--DDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGE 130 (171)
Q Consensus 53 ~r~~~r~~R~~RirkKi~gt~~rPRL~V~rSnkhiyAQvI--dd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~ 130 (171)
.|+|-+...+.|.|... +++|||+||+||+||||||| ||.+++||+||||+|+++.+ |. ..++|++||+.||.
T Consensus 13 RrRegkTdY~~R~rl~~---~~kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g-~~-~~~~N~~AAy~vG~ 87 (193)
T PRK08569 13 RRREGKTDYRKRLKLLL---SGKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYG-WK-GDTGNTPAAYLTGL 87 (193)
T ss_pred ccccccccHHHHHHHHh---cCCCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhcc-cc-CCCCCHHHHHHHHH
Confidence 45555666666665443 57999999999999999999 89999999999999998744 32 46889999999999
Q ss_pred HHHHHHHHcCCCEEEEecCCCchh--hHHHHHHHHHHHcCCcC
Q 030804 131 MIAKSCLEKGITKVAFDRGGYPYH--GRIQALADAAREYGLQF 171 (171)
Q Consensus 131 ~LAkra~e~GI~~VvfDRgg~~Yh--GrVkAlad~aRe~GL~f 171 (171)
+||+||+++||++|+||||+++|| |||+||+|++||+||+|
T Consensus 88 llA~ral~kGi~~vvfDrGg~~yh~gGRV~A~akgArd~GL~f 130 (193)
T PRK08569 88 LAGKKALKAGVEEAVLDIGLHRPTKGSRVFAALKGAIDAGLEI 130 (193)
T ss_pred HHHHHHHHCCCCEEEEecCCccccCCccHHHHHHHHHHcCCcC
Confidence 999999999999999999999999 99999999999999997
No 9
>KOG3333 consensus Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=99.48 E-value=1.1e-13 Score=112.02 Aligned_cols=93 Identities=26% Similarity=0.345 Sum_probs=83.3
Q ss_pred ceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEEEecCC-Cchh
Q 030804 76 PRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVAFDRGG-YPYH 154 (171)
Q Consensus 76 PRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg-~~Yh 154 (171)
++|.|-++..|+-+-|.|.++| +++||||.||.|+.+| +++.|+.|+..+|++||+||++.||..+++.-.. ..-.
T Consensus 61 h~lev~~~~~hveg~v~H~~~g-vvvSAST~EwaIk~qL--Yst~dtsA~~niGRVLAqRCLqsGI~fm~~~~t~ea~~~ 137 (188)
T KOG3333|consen 61 HRLEVIRTQHHVEGLVEHQNGG-VVVSASTREWAIKKQL--YSTRDTSACENIGRVLAQRCLQSGINFMVYQPTPEAAAS 137 (188)
T ss_pred eEEEEeecccceeeeeeEecCC-EEEEecccchHHHHHH--hhccchHHHHHHHHHHHHHHHHhCcceeccCCChhhccc
Confidence 4999999999999999986665 6799999999999998 6899999999999999999999999999998543 3447
Q ss_pred hHHHHHHHHHHHcCCcC
Q 030804 155 GRIQALADAAREYGLQF 171 (171)
Q Consensus 155 GrVkAlad~aRe~GL~f 171 (171)
..++-|..+|.|+|+.|
T Consensus 138 s~~q~l~~a~~e~Gv~l 154 (188)
T KOG3333|consen 138 SSMQRLQSAMTEGGVVL 154 (188)
T ss_pred hHHHHHHHHHHhCCeee
Confidence 88999999999999865
No 10
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=99.47 E-value=1.9e-13 Score=119.22 Aligned_cols=96 Identities=23% Similarity=0.252 Sum_probs=86.1
Q ss_pred CCceEEEEeeCCcEEEEEEe--CCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHc--------CCC-
Q 030804 74 ERPRLCVFRSNKHLYVQVID--DTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEK--------GIT- 142 (171)
Q Consensus 74 ~rPRL~V~rSnkhiyAQvId--d~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~--------GI~- 142 (171)
.+|||+|.+||++|.|||+. ..+++||++|.+.|+. +.+|+ .+.+|.+|||.+|.++|.|++++ |++
T Consensus 47 pK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~-kyG~k-~gl~N~~AAY~TGlL~arR~L~kl~ld~~y~G~~e 124 (300)
T PTZ00069 47 PKYRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELP-RFGIP-VGLTNYAAAYATGLLLARRLLKKLGLDKQFEGVKE 124 (300)
T ss_pred CCceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHh-hcCcC-CCCccHHHHHHHHHHHHHHHHHhhcccccccCccc
Confidence 48999999999999999997 6799999999999987 67886 57889999999999999999998 773
Q ss_pred -------------------EEEEecCCCc--hhhHHHHHHHHHHHcCCcC
Q 030804 143 -------------------KVAFDRGGYP--YHGRIQALADAAREYGLQF 171 (171)
Q Consensus 143 -------------------~VvfDRgg~~--YhGrVkAlad~aRe~GL~f 171 (171)
++++|.|..+ .++||.|.+.|+.|+||++
T Consensus 125 ~~g~~y~v~e~~~~~~rpf~a~LDiGL~rtt~G~RVFaalKGa~DgGl~I 174 (300)
T PTZ00069 125 ADGEYYHVDEEDDEERRPFKAILDVGLARTTTGNRVFGALKGAVDGGLHI 174 (300)
T ss_pred ccCcccccccccccCCCCceEEEeeccccCCCCceeeeehhcccccCccc
Confidence 7789998655 4899999999999999975
No 11
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=97.79 E-value=0.00041 Score=59.17 Aligned_cols=89 Identities=24% Similarity=0.234 Sum_probs=72.7
Q ss_pred CceEEEEeeCCcEEEEEEeCCCCc-EEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEE-EEecCCCc
Q 030804 75 RPRLCVFRSNKHLYVQVIDDTKMH-TLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKV-AFDRGGYP 152 (171)
Q Consensus 75 rPRL~V~rSnkhiyAQvIdd~~~k-tLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~V-vfDRgg~~ 152 (171)
+.+|+|+-|-++..++|.|..+.. ||+-+|.-...+++. ...+-=||+.+++.+++.|++.||.+| ++=+|.
T Consensus 118 ~f~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~GFKGs----KKsTpfAAQ~aae~aakka~~~GIk~V~V~vKGp-- 191 (233)
T PTZ00090 118 RFMLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKK----LQQSERCAYRIGENIAKKCRRLGIFAVDIKFRRI-- 191 (233)
T ss_pred cEEEEEEeccCcEEEEEEeCCCCEEEEEEEcccccCcccC----ccCCHHHHHHHHHHHHHHHHHcCCeEEEEEEeCC--
Confidence 348999999999999999877664 677777777777653 345677999999999999999999999 555664
Q ss_pred hhhHHHHHHHHHHHcCCcC
Q 030804 153 YHGRIQALADAAREYGLQF 171 (171)
Q Consensus 153 YhGrVkAlad~aRe~GL~f 171 (171)
+| .++.+.++...||++
T Consensus 192 -Gg-REtALRaL~~~GLkI 208 (233)
T PTZ00090 192 -MR-VETVLQAFYANGLQV 208 (233)
T ss_pred -Ch-HHHHHHHHHHCCCEE
Confidence 24 899999999999974
No 12
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=97.73 E-value=0.0006 Score=51.74 Aligned_cols=86 Identities=21% Similarity=0.202 Sum_probs=67.3
Q ss_pred EEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEE-EecCCCchhhH
Q 030804 78 LCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVA-FDRGGYPYHGR 156 (171)
Q Consensus 78 L~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~Vv-fDRgg~~YhGr 156 (171)
+.|+.|.++..+.|.|. +|.+++.+|.-...++.. ...+.-||..+++.++++|++.||+.|. +=|| .-+ ||
T Consensus 3 ~hI~~s~NNT~itlTd~-~g~~~~~~S~G~~gfkg~----rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~kG-~G~-gr 75 (108)
T TIGR03632 3 AHIHATFNNTIVTITDP-QGNVLSWASAGAVGFKGS----KKSTPYAAQLAAEDAAKKAKEFGMKTVDVYVKG-PGA-GR 75 (108)
T ss_pred EEEEccCCCEEEEEEcC-CCCEEEEEecCceeeCCC----ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEC-CCC-cH
Confidence 67999999999999976 556888888877777764 4567889999999999999999999984 4455 322 44
Q ss_pred HHHHHHHHHHcCCcC
Q 030804 157 IQALADAAREYGLQF 171 (171)
Q Consensus 157 VkAlad~aRe~GL~f 171 (171)
+++..++...||++
T Consensus 76 -~~~ir~l~~~glkI 89 (108)
T TIGR03632 76 -ESAIRALQAAGLEV 89 (108)
T ss_pred -HHHHHHHHHCCCEE
Confidence 56677777788863
No 13
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=97.59 E-value=0.0011 Score=50.21 Aligned_cols=86 Identities=26% Similarity=0.208 Sum_probs=66.8
Q ss_pred EEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEEE-ecCCCchhhH
Q 030804 78 LCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVAF-DRGGYPYHGR 156 (171)
Q Consensus 78 L~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~Vvf-DRgg~~YhGr 156 (171)
+.|+.|.++..+.|.| ..|.++++.|+-...++.. ...+..||+.+++.++++|++.||+.|.. =+| .--||
T Consensus 3 ihI~~s~NNt~vtlTd-~~G~~~~~~S~G~~gfK~~----rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG--~g~gr 75 (110)
T PF00411_consen 3 IHIKSSFNNTIVTLTD-LKGNVLFWSSAGSLGFKGA----RKSTPYAAQQAAEKIAKKAKELGIKTVRVKIKG--FGPGR 75 (110)
T ss_dssp EEEEEESSEEEEEEEE-TTSEEEEEEETTTSSTTTT----CGSSHHHHHHHHHHHHHHHHCTTEEEEEEEEES--SSTTH
T ss_pred EEEEecCCCEEEEEEC-CCCCEEEEEeccccccccc----cccCHHHHHHHHHHHHHHHHHcCCeEEEEEEcC--CCccH
Confidence 6799999999999986 5577888888888877764 45678999999999999999999998843 344 22355
Q ss_pred HHHHHHHHHHcCCcC
Q 030804 157 IQALADAAREYGLQF 171 (171)
Q Consensus 157 VkAlad~aRe~GL~f 171 (171)
- ++..++...||++
T Consensus 76 ~-~~lk~l~~~gl~I 89 (110)
T PF00411_consen 76 E-AALKALKKSGLKI 89 (110)
T ss_dssp H-HHHHHHHHTTSEE
T ss_pred H-HHHHHHHhcCCEE
Confidence 4 3446777788753
No 14
>CHL00041 rps11 ribosomal protein S11
Probab=97.57 E-value=0.0014 Score=50.43 Aligned_cols=88 Identities=17% Similarity=0.193 Sum_probs=70.5
Q ss_pred ceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEE-EecCCCchh
Q 030804 76 PRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVA-FDRGGYPYH 154 (171)
Q Consensus 76 PRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~Vv-fDRgg~~Yh 154 (171)
--+.|+.|.++....|.|. .|++|+.+|.-...++.. ...+.-||..+++.++++|++.||+.|. +=|| +- .
T Consensus 14 gi~hI~~t~NNTiiTlTd~-~G~~l~~~S~G~~gfKg~----rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I~ikG-~G-~ 86 (116)
T CHL00041 14 GVIHIQASFNNTIVTVTDV-RGRVISWSSAGACGFKGA----RKGTPFAAQTAAENAIRTVIDQGMKRAEVMIKG-PG-L 86 (116)
T ss_pred EEEEEEcccCCEEEEEEcC-CCCEEEEEecCceeeCCC----ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEC-CC-C
Confidence 3789999999999999876 467899999887777764 3457789999999999999999999984 4455 22 3
Q ss_pred hHHHHHHHHHHHcCCcC
Q 030804 155 GRIQALADAAREYGLQF 171 (171)
Q Consensus 155 GrVkAlad~aRe~GL~f 171 (171)
|| +++..++...||++
T Consensus 87 Gr-~~~ir~l~~~glkI 102 (116)
T CHL00041 87 GR-DTALRAIRRSGLKL 102 (116)
T ss_pred cH-HHHHHHHHHCCCEE
Confidence 66 56678888888863
No 15
>PRK05309 30S ribosomal protein S11; Validated
Probab=97.45 E-value=0.0025 Score=49.90 Aligned_cols=89 Identities=19% Similarity=0.172 Sum_probs=69.2
Q ss_pred CceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEEE-ecCCCch
Q 030804 75 RPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVAF-DRGGYPY 153 (171)
Q Consensus 75 rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~Vvf-DRgg~~Y 153 (171)
.-.+.|+.|.++..+.|.|. .|.+++..|.-...+++. ...+..||..+++.+++.|++.||+.|.. =+| +-+
T Consensus 17 ~gi~hI~~t~NNTiitlTd~-~G~~~~~~S~G~~gfKg~----rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG-~G~ 90 (128)
T PRK05309 17 SGVAHIHATFNNTIVTITDR-QGNVISWASAGGLGFKGS----RKSTPYAAQVAAEDAAKKAKEHGMKTVEVFVKG-PGS 90 (128)
T ss_pred eeEEEEEccCCCEEEEEEcC-CCCEEEEEecCccEeCCC----ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEC-CCC
Confidence 45899999999999999975 667888888776667653 35677899999999999999999998844 455 322
Q ss_pred hhHHHHHHHHHHHcCCcC
Q 030804 154 HGRIQALADAAREYGLQF 171 (171)
Q Consensus 154 hGrVkAlad~aRe~GL~f 171 (171)
|| +++..++...||++
T Consensus 91 -Gr-~~air~L~~~glkI 106 (128)
T PRK05309 91 -GR-ESAIRALQAAGLEV 106 (128)
T ss_pred -cH-HHHHHHHHHCCCEE
Confidence 44 56666777788863
No 16
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=97.05 E-value=0.011 Score=45.78 Aligned_cols=89 Identities=21% Similarity=0.194 Sum_probs=65.9
Q ss_pred EEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEE-EecC--CCc--
Q 030804 78 LCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVA-FDRG--GYP-- 152 (171)
Q Consensus 78 L~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~Vv-fDRg--g~~-- 152 (171)
+.|+-|-++....|.|..+..+|+-+|.-...++.. ..++-=||....+.++++|+|.||+.|. +=|| |.+
T Consensus 5 ~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~kg~----kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~ 80 (114)
T TIGR03628 5 AHIYSSFNNTIITITDITGAETIARSSGGMVVKADR----DESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQK 80 (114)
T ss_pred EEEEccCCCeEEEEEcCCCCEEEEEecCcceEeCCC----ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCC
Confidence 578889999999999877768888888877766542 2345668999999999999999999994 4454 333
Q ss_pred -h-hhHHHHHHHHHHHcCCcC
Q 030804 153 -Y-HGRIQALADAAREYGLQF 171 (171)
Q Consensus 153 -Y-hGrVkAlad~aRe~GL~f 171 (171)
+ -|| ++.+.++...||++
T Consensus 81 ~~G~Gr-~~air~l~~~glkI 100 (114)
T TIGR03628 81 SPGPGA-QAAIRALARAGLRI 100 (114)
T ss_pred CCCCcH-HHHHHHHHHCCCEE
Confidence 2 244 44556777788763
No 17
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=96.85 E-value=0.01 Score=46.98 Aligned_cols=91 Identities=24% Similarity=0.216 Sum_probs=66.4
Q ss_pred ceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEEE-ecC--CCc
Q 030804 76 PRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVAF-DRG--GYP 152 (171)
Q Consensus 76 PRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~Vvf-DRg--g~~ 152 (171)
--+.|+-|-++.+..|.|..+..||+.+|.-...++.. ...+-=||...++.++++|++.||+.|.. =+| |..
T Consensus 10 gi~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~kg~----kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~Ggn~ 85 (132)
T PRK09607 10 GIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADR----DESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNG 85 (132)
T ss_pred eEEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeCCC----ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCC
Confidence 37889999999999999866657888887776655542 23455699999999999999999999954 454 222
Q ss_pred ---h-hhHHHHHHHHHHHcCCcC
Q 030804 153 ---Y-HGRIQALADAAREYGLQF 171 (171)
Q Consensus 153 ---Y-hGrVkAlad~aRe~GL~f 171 (171)
+ -|| ++.+.++...||++
T Consensus 86 ~~~~G~Gr-~~airal~~~glkI 107 (132)
T PRK09607 86 QKSPGPGA-QAAIRALARAGLRI 107 (132)
T ss_pred CcCCCCcH-HHHHHHHHHCCCEE
Confidence 2 244 34456777778763
No 18
>KOG0875 consensus 60S ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=96.77 E-value=0.0022 Score=55.65 Aligned_cols=120 Identities=17% Similarity=0.122 Sum_probs=81.1
Q ss_pred CCCCcHHHHHHHHHHhhhhhcCCCCCceEEEEeeCCcEEEEEEe--CCCCcEEEEEecCCcccccccCCCCCCcHHHHHH
Q 030804 50 RPRTKREDRTARHSRIRKKIDGTPERPRLCVFRSNKHLYVQVID--DTKMHTLASASTMQKPISEELDYSSGPTIEVSKK 127 (171)
Q Consensus 50 ~~~~r~~~r~~R~~RirkKi~gt~~rPRL~V~rSnkhiyAQvId--d~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~ 127 (171)
|..-+..-..++|.-+.-|-+-...+.||.|..+|+.|.+||+- -+.+.+++++-+.|.. +..+. ..-.|-.||+.
T Consensus 23 rreGkTdy~arkrl~~qdknk~nt~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s~elp-kyg~~-~GLtNyaAay~ 100 (264)
T KOG0875|consen 23 RREGKTDYYARKRLVVQDKNKYNTPKYRMIVRVINKDIICQIAYATIEGDVIVRAAYAHELP-KYGVK-VGLTNYAAAYC 100 (264)
T ss_pred ecCCCccHHHHHHHHhhcccccCCCceEEEEEEechhhHHHHHhheecceEEEEeecccccc-ccccc-cccchhHHHHh
Confidence 44455555555565555554443468899999999999999986 3456667777777775 33332 23468899999
Q ss_pred HHHHHHHHHHH-cCCCE--------------------------EEEecCCCc--hhhHHHHHHHHHHHcCCcC
Q 030804 128 VGEMIAKSCLE-KGITK--------------------------VAFDRGGYP--YHGRIQALADAAREYGLQF 171 (171)
Q Consensus 128 VG~~LAkra~e-~GI~~--------------------------VvfDRgg~~--YhGrVkAlad~aRe~GL~f 171 (171)
.|-+||.|.++ .|.++ +.+|-|.-+ -+-||...++++.++||.+
T Consensus 101 TglLLarR~l~~~gmD~~yeg~~e~~gde~~~e~idgq~~aFt~~Ld~GLaRtttg~kvFGAlkga~dGGL~I 173 (264)
T KOG0875|consen 101 TGLLLACRLLKRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSI 173 (264)
T ss_pred hHHHHHHHHHHHhCcccccccceeecCcccccccccCCCCCeEEEecccccccCCCceeeeeeehhcccceec
Confidence 99999999986 45322 233333222 2567777788888888753
No 19
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=96.49 E-value=0.043 Score=44.37 Aligned_cols=92 Identities=20% Similarity=0.170 Sum_probs=65.9
Q ss_pred CceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEE-EEecC--CC
Q 030804 75 RPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKV-AFDRG--GY 151 (171)
Q Consensus 75 rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~V-vfDRg--g~ 151 (171)
.--+.|+-|-++....|.|.. |.+++..|+-...++..- ..++-=||....+.++++|++.||+.| ++=|+ |.
T Consensus 28 ~Gi~hI~as~NNTiItiTD~~-G~~~~w~SsG~~gfKg~r---~KsTpyAAq~aa~~~a~k~~~~Gi~~v~V~vr~~gg~ 103 (149)
T PTZ00129 28 FGVAHIFASFNDTFIHVTDLS-GRETLVRVTGGMKVKADR---DESSPYAAMMAAQDVAARCKELGINALHIKLRATGGV 103 (149)
T ss_pred EEEEEEEcccCCeEEEEEccc-CCEEEEEecCcceecccc---cCCCHHHHHHHHHHHHHHHHHcCCeEEEEEEEecCCC
Confidence 347899999999999998655 556677777666666542 133456899999999999999999999 45542 32
Q ss_pred ch----hhHHHHHHHHHHHcCCcC
Q 030804 152 PY----HGRIQALADAAREYGLQF 171 (171)
Q Consensus 152 ~Y----hGrVkAlad~aRe~GL~f 171 (171)
.- .|+ ++.+.+|...||++
T Consensus 104 ~~kg~GpGr-~~airaL~~~glkI 126 (149)
T PTZ00129 104 RTKTPGPGA-QAALRALARAGLKI 126 (149)
T ss_pred CCCCCCCCH-HHHHHHHHHCCCEE
Confidence 22 233 45567777788763
No 20
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=94.39 E-value=0.6 Score=36.98 Aligned_cols=84 Identities=25% Similarity=0.216 Sum_probs=60.4
Q ss_pred EEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEE-EEecC-CCchhh
Q 030804 78 LCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKV-AFDRG-GYPYHG 155 (171)
Q Consensus 78 L~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~V-vfDRg-g~~YhG 155 (171)
..|+.|-++-...+- |..|..++.+|+=..-++.. ..++--||...++..++.++|.||+.| ++=+| |. |
T Consensus 21 ahI~asfNNTivtit-D~~Gn~i~wassG~~gfk~~----rk~tpyAA~~aa~~aa~~a~e~Gi~~v~v~vkgpG~---G 92 (129)
T COG0100 21 AHIHASFNNTIVTIT-DLTGNVIIWASSGGMGFKGS----RKSTPYAAQLAAEDAAKKAKEHGIKSVEVKVKGPGP---G 92 (129)
T ss_pred EEEEcccCCcEEEec-CCCCCEEEEEecCCceEcCC----CCCCHHHHHHHHHHHHHHHHHhCccEEEEEEECCCC---c
Confidence 566677666666665 67788889999988888764 245667888999999999999999998 44455 22 3
Q ss_pred HHHHHHHHHHHcCCc
Q 030804 156 RIQALADAAREYGLQ 170 (171)
Q Consensus 156 rVkAlad~aRe~GL~ 170 (171)
| ++...+|..+||+
T Consensus 93 r-eaAiraL~~ag~~ 106 (129)
T COG0100 93 R-EAAIRALAAAGLK 106 (129)
T ss_pred H-HHHHHHHHHccce
Confidence 3 3444445566765
No 21
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=92.70 E-value=1.3 Score=36.82 Aligned_cols=89 Identities=21% Similarity=0.236 Sum_probs=69.0
Q ss_pred CCceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEEEe-cCCCc
Q 030804 74 ERPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVAFD-RGGYP 152 (171)
Q Consensus 74 ~rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~VvfD-Rgg~~ 152 (171)
+-|-..|.-|.++...+|.| ..|.++...|--...||.. ..++--||...|-..+.++++.|+..|--- +| .
T Consensus 78 eiPi~hIraS~NNTivtVtd-~kg~vi~~~ScgteGFrnt----rkgT~iAaQtaavaa~~r~v~~G~~~vrV~VkG--l 150 (190)
T KOG0408|consen 78 EIPIIHIRASFNNTIVTVTD-VKGEVISWSSCGTEGFRNT----RKGTPIAAQTAAVAAIRRAVDQGMQTVRVRVKG--L 150 (190)
T ss_pred ccceEEEEecCCCeEEEEEc-cCCcEEEEeeccccccccc----ccCCchhHHHHHHHHHHHHHHhcceEEEEEEec--C
Confidence 67899999999999999985 6677777777766667653 344566889999999999999999988443 44 3
Q ss_pred hhhHHHHHHHHHHHcCCc
Q 030804 153 YHGRIQALADAAREYGLQ 170 (171)
Q Consensus 153 YhGrVkAlad~aRe~GL~ 170 (171)
--||+.|+ .+|+-+||.
T Consensus 151 GpGRmsa~-kgl~m~Gl~ 167 (190)
T KOG0408|consen 151 GPGRMSAL-KGLRMGGLL 167 (190)
T ss_pred CccHHHHH-hhhhhcceE
Confidence 45888764 688888875
No 22
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=87.33 E-value=10 Score=29.87 Aligned_cols=90 Identities=21% Similarity=0.258 Sum_probs=61.2
Q ss_pred eEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEEEe-c--CCCch
Q 030804 77 RLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVAFD-R--GGYPY 153 (171)
Q Consensus 77 RL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~VvfD-R--gg~~Y 153 (171)
...||-|-+..++.|.|-.+..||+-...--+ +|.+- ..++--||-+-..-.|.+|++.||+.+.|. | ||.+-
T Consensus 18 vahi~asfndtfvhitdlsg~eti~rvtggmk-vkadr---desspyaamlaaqdva~kck~~gi~alh~klratgg~kt 93 (139)
T KOG0407|consen 18 VAHIFASFNDTFVHVTDLSGKETIVRVTGGMK-VKADR---DESSPYAAMLAAQDVAAKCKELGITALHIKLRATGGTKT 93 (139)
T ss_pred EEEEEeecccceEEEeccCCceEEEEecCCeE-Eeccc---ccCChHHHHHHHHHHHHHHHhcCeeEEEEEEEecCCccc
Confidence 45678888888889988888899988765544 34332 234566888888999999999999999876 2 44332
Q ss_pred ---hhHHHHHHHHHHHcCCc
Q 030804 154 ---HGRIQALADAAREYGLQ 170 (171)
Q Consensus 154 ---hGrVkAlad~aRe~GL~ 170 (171)
+---++.+.+|-..|+.
T Consensus 94 ktpgpgaqsalralar~gmr 113 (139)
T KOG0407|consen 94 KTPGPGAQSALRALARSGMR 113 (139)
T ss_pred CCCCccHHHHHHHHHHhcce
Confidence 22234444455555554
No 23
>TIGR00725 conserved hypothetical protein, DprA/Smf-related, family 1. This model represents one branch of a subfamily of uncharacterized proteins. Both PSI-BLAST and weak hits by this model show a low level of similarity and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting the branches may have distinct functions. This family is one of several families within the scope of PFAM model pfam03641, several members of which are annotated as lysine decarboxylases. That larger family, and the branch described by this model, have a well-conserved motif PGGXGTXXE.
Probab=71.98 E-value=8.7 Score=30.61 Aligned_cols=40 Identities=35% Similarity=0.523 Sum_probs=31.1
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCC
Q 030804 121 TIEVSKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGL 169 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL 169 (171)
-.++|+.+|+.||+ .|+ .+++ ||. .|-+.++++++.++|-
T Consensus 16 ~~~~A~~lg~~La~----~g~-~lv~--Gg~--~GlM~a~a~ga~~~gg 55 (159)
T TIGR00725 16 LYEIAYRLGKELAK----KGH-ILIN--GGR--TGVMEAVSKGAREAGG 55 (159)
T ss_pred HHHHHHHHHHHHHH----CCC-EEEc--CCc--hhHHHHHHHHHHHCCC
Confidence 45788888888877 487 5666 653 3999999999999884
No 24
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=71.53 E-value=16 Score=29.26 Aligned_cols=45 Identities=16% Similarity=0.186 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHcCCCEEEE--ecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 127 KVGEMIAKSCLEKGITKVAF--DRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~Vvf--DRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
..|+.+++.+.+.|..++.| +........|+..|.+.+.++|+.+
T Consensus 101 ~~g~~a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~~~~~~~ 147 (263)
T cd06280 101 AAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAP 147 (263)
T ss_pred HHHHHHHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHHHcCCCC
Confidence 35556666667789988865 3322334689999999999999863
No 25
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=69.57 E-value=16 Score=29.18 Aligned_cols=48 Identities=17% Similarity=0.212 Sum_probs=32.4
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCcC
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRGG---YPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~f 171 (171)
.|.++++.+++. +.+.|..++.|=-+. .....|++.|.+.++++|+++
T Consensus 97 d~~~ag~~a~~~----L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 147 (265)
T cd06285 97 DDVLGGRLATRH----LLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEAGIEV 147 (265)
T ss_pred CcHHHHHHHHHH----HHHCCCccEEEEeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 345555555544 455688888764332 234689999999999999863
No 26
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=69.33 E-value=17 Score=28.91 Aligned_cols=46 Identities=30% Similarity=0.347 Sum_probs=32.1
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCEEEEec---CCCchhhHHHHHHHHHHHcCCc
Q 030804 121 TIEVSKKVGEMIAKSCLEKGITKVAFDR---GGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI~~VvfDR---gg~~YhGrVkAlad~aRe~GL~ 170 (171)
|.++++ .+++...+.|..++.|=- +......|...|.+.+.++|++
T Consensus 98 ~~~~~~----~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~ 146 (260)
T cd06286 98 HYEAFY----EALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLT 146 (260)
T ss_pred ChHHHH----HHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCC
Confidence 445555 455555667999997632 2233468999999999999975
No 27
>cd06276 PBP1_FucR_like Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. FcuR acts as an inducer of fucRRIAK and as a corepressor of another locus that regulates production of fucosylated glycans. FcuR and its close homologs in this group are a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes t
Probab=69.20 E-value=15 Score=29.84 Aligned_cols=46 Identities=13% Similarity=0.064 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHH--cCCCEEEEe--cCCCchhhHHHHHHHHHHHcCCcC
Q 030804 126 KKVGEMIAKSCLE--KGITKVAFD--RGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 126 ~~VG~~LAkra~e--~GI~~VvfD--Rgg~~YhGrVkAlad~aRe~GL~f 171 (171)
+..|+.+++.+.+ .|.+++.|= ........|...|.++++++|++|
T Consensus 100 ~~~~~~a~~~L~~~~~G~~~Ia~i~~~~~~~~~~R~~gf~~~l~~~g~~~ 149 (247)
T cd06276 100 EKAIYNALQEGLEKLKKYKKLILVFPNKTAIPKEIKRGFERFCKDYNIET 149 (247)
T ss_pred HHHHHHHHHHHHHHhcCCCEEEEEecCccHhHHHHHHHHHHHHHHcCCCc
Confidence 3445667777777 899999653 322334689999999999999864
No 28
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=66.16 E-value=21 Score=29.66 Aligned_cols=44 Identities=25% Similarity=0.426 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHcCCCEEEEecC---CCchhhHHHHHHHHHHHcCCcC
Q 030804 128 VGEMIAKSCLEKGITKVAFDRG---GYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRg---g~~YhGrVkAlad~aRe~GL~f 171 (171)
-|+.+++.+.+.|..++.|=-+ ......|...|.+++.++|+.+
T Consensus 161 ~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~ 207 (327)
T PRK10423 161 GGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNI 207 (327)
T ss_pred HHHHHHHHHHHcCCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCC
Confidence 3566666777789999976322 1233679999999999999863
No 29
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=66.11 E-value=21 Score=28.39 Aligned_cols=42 Identities=21% Similarity=0.314 Sum_probs=29.0
Q ss_pred HHHHHHHHHHcCCCEEEE--ecCC-CchhhHHHHHHHHHHHcCCc
Q 030804 129 GEMIAKSCLEKGITKVAF--DRGG-YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 129 G~~LAkra~e~GI~~Vvf--DRgg-~~YhGrVkAlad~aRe~GL~ 170 (171)
|+.+++.+.+.|..++.| +..+ ..-..|.+.|.+.+.++|++
T Consensus 104 ~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~~ 148 (269)
T cd06288 104 GYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQALAEAGIP 148 (269)
T ss_pred HHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHHHHcCCC
Confidence 445555555669888866 2222 22357999999999999974
No 30
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=64.87 E-value=23 Score=28.25 Aligned_cols=46 Identities=17% Similarity=0.206 Sum_probs=31.0
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCc
Q 030804 121 TIEVSKKVGEMIAKSCLEKGITKVAFDRGG---YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~ 170 (171)
|.++++.+++.|. +.|..++.|=.+. ..-+.|+++|.+.+.++|++
T Consensus 100 ~~~~g~~~~~~l~----~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 148 (264)
T cd06274 100 NRDGAAELTRELL----AAPPEEVLFLGGLPELSPSRERLAGFRQALADAGLP 148 (264)
T ss_pred cHHHHHHHHHHHH----HCCCCcEEEEeCCCcccchHHHHHHHHHHHHHcCCC
Confidence 4555555555544 5788888664332 23367999999999999874
No 31
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=64.18 E-value=22 Score=29.84 Aligned_cols=45 Identities=18% Similarity=0.301 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHcCCCEEEEecC---CCchhhHHHHHHHHHHHcCCcC
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRG---GYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRg---g~~YhGrVkAlad~aRe~GL~f 171 (171)
..|+.+++.+.+.|..++.|=-+ ....+.|+..|.+++.++|+++
T Consensus 164 ~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~~ 211 (341)
T PRK10703 164 EGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKV 211 (341)
T ss_pred HHHHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHHHHHHHcCCCC
Confidence 34666667777789888876322 2334689999999999999864
No 32
>PF03646 FlaG: FlaG protein; InterPro: IPR005186 Although these proteins are known to be important for flagellar their exact function is unknown.; PDB: 2HC5_A.
Probab=64.04 E-value=40 Score=24.70 Aligned_cols=45 Identities=16% Similarity=0.219 Sum_probs=32.5
Q ss_pred HHHHHHHHHhhhhhcCCCCCceEEEEeeCCcEEEEEEeCCCCcEE
Q 030804 56 EDRTARHSRIRKKIDGTPERPRLCVFRSNKHLYVQVIDDTKMHTL 100 (171)
Q Consensus 56 ~~r~~R~~RirkKi~gt~~rPRL~V~rSnkhiyAQvIdd~~~ktL 100 (171)
+....--.++...+......-+..|+.....++++|||..+|++|
T Consensus 37 e~l~~~v~~ln~~~~~~~~~l~F~vde~~~~~vVkViD~~T~eVI 81 (107)
T PF03646_consen 37 EELEEAVEKLNEFLQALNTSLRFSVDEESGRVVVKVIDKETGEVI 81 (107)
T ss_dssp HHHHHHHHHHHHHHTTSS--EEEEEEEETTEEEEEEEETTT-SEE
T ss_pred HHHHHHHHHHHHHHHhcCCceEEEEecCCCcEEEEEEECCCCcEE
Confidence 344445556666666555577999999999999999999999985
No 33
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=63.87 E-value=27 Score=27.13 Aligned_cols=43 Identities=19% Similarity=0.308 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHcCCCEEEE--ecCCCc-hhhHHHHHHHHHHHcCCc
Q 030804 128 VGEMIAKSCLEKGITKVAF--DRGGYP-YHGRIQALADAAREYGLQ 170 (171)
Q Consensus 128 VG~~LAkra~e~GI~~Vvf--DRgg~~-YhGrVkAlad~aRe~GL~ 170 (171)
.|+.+++.+.+.|..+|.| +..+.. ...|.+.|.+.+.++|++
T Consensus 103 ~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~~ 148 (264)
T cd06267 103 GAYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAGIP 148 (264)
T ss_pred HHHHHHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHHHcCCC
Confidence 3555556666678888865 233333 368999999999999853
No 34
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a
Probab=63.69 E-value=28 Score=27.74 Aligned_cols=45 Identities=20% Similarity=0.284 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHcCCCEEEEe--c-CCCchhhHHHHHHHHHHHcCCcC
Q 030804 127 KVGEMIAKSCLEKGITKVAFD--R-GGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfD--R-gg~~YhGrVkAlad~aRe~GL~f 171 (171)
..|+.+++.+.+.|..++.|= . +.....-|.+.|.+++.++|+++
T Consensus 103 ~~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~ 150 (269)
T cd06275 103 EGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPV 150 (269)
T ss_pred HHHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCCC
Confidence 445555566667798888652 2 22334679999999999999763
No 35
>PRK09492 treR trehalose repressor; Provisional
Probab=62.45 E-value=29 Score=28.75 Aligned_cols=48 Identities=13% Similarity=0.076 Sum_probs=33.0
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecCC--C--chhhHHHHHHHHHHHcCCcC
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRGG--Y--PYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg--~--~YhGrVkAlad~aRe~GL~f 171 (171)
.|..+++ .+++.+.+.|..++.|=.++ . ....|...|.+++.++|+++
T Consensus 158 D~~~~~~----~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~ 209 (315)
T PRK09492 158 DDEGAIK----LLMQRLYDQGHRHISYLGVDHSDVTTGKRRHQAYLAFCKQHKLTP 209 (315)
T ss_pred CcHHHHH----HHHHHHHHcCCCeEEEEcCCcccchhHHHHHHHHHHHHHHcCCCc
Confidence 3455554 45555567899999774321 1 12589999999999999863
No 36
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=62.24 E-value=30 Score=27.73 Aligned_cols=47 Identities=15% Similarity=0.195 Sum_probs=31.3
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecC--CC-chhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRG--GY-PYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRg--g~-~YhGrVkAlad~aRe~GL~ 170 (171)
.+.++++.+ ++.+.++|..++.|=.+ .. .-..|.+.|.+++.++|+.
T Consensus 99 d~~~~~~~~----~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~ 148 (269)
T cd06293 99 DNEQGGRLA----TRHLARAGHRRIAFVGGPDALISARERYAGYREALAEAHIP 148 (269)
T ss_pred CCHHHHHHH----HHHHHHCCCceEEEEecCcccccHHHHHHHHHHHHHHcCCC
Confidence 345555554 45555679999876432 21 2247899999999999975
No 37
>TIGR01917 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon.
Probab=61.93 E-value=31 Score=32.42 Aligned_cols=53 Identities=15% Similarity=0.206 Sum_probs=41.5
Q ss_pred CCCcHHHHHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 118 SGPTIEVSKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 118 ~~~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.+.+...++..|+.||+++++.|++.|++--.=-.-|=-....+..+-++||.
T Consensus 314 ~gt~~~~a~~~g~eIa~~Lk~dgVDAvILtstCgtCtrcga~m~keiE~~GIP 366 (431)
T TIGR01917 314 NGTAVANSKQFAKEFSKELLAAGVDAVILTSTUGTCTRCGATMVKEIERAGIP 366 (431)
T ss_pred CCccHHHHHHHHHHHHHHHHHcCCCEEEEcCCCCcchhHHHHHHHHHHHcCCC
Confidence 45678889999999999999999999999854224454556667777778874
No 38
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=61.56 E-value=31 Score=27.44 Aligned_cols=43 Identities=23% Similarity=0.319 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHcCCCEEEEecC--CCc-hhhHHHHHHHHHHHcCCc
Q 030804 128 VGEMIAKSCLEKGITKVAFDRG--GYP-YHGRIQALADAAREYGLQ 170 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRg--g~~-YhGrVkAlad~aRe~GL~ 170 (171)
.|+.+++.+.++|..++.|=.+ +.. ...|...|.+.+.+.|++
T Consensus 104 ~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~ 149 (270)
T cd06296 104 GGLAATEHLLELGHRRIGFITGPPDLLCSRARLDGYRAALAEAGIP 149 (270)
T ss_pred HHHHHHHHHHHcCCCcEEEEcCCCcchhHHHHHHHHHHHHHHcCCC
Confidence 4555566666679999976332 222 368999999999998875
No 39
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=61.35 E-value=14 Score=28.69 Aligned_cols=44 Identities=25% Similarity=0.375 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHcCCCEEEEecCCCch-hhHHHHHHHHHHHcCCcC
Q 030804 128 VGEMIAKSCLEKGITKVAFDRGGYPY-HGRIQALADAAREYGLQF 171 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRgg~~Y-hGrVkAlad~aRe~GL~f 171 (171)
.-+.|.+-|.+.||+.|++++..-.| ..+.+.+.+.+.+.|+.|
T Consensus 76 ~~~~l~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~ 120 (165)
T PF00875_consen 76 PEEVLPELAKEYGATAVYFNEEYTPYERRRDERVRKALKKHGIKV 120 (165)
T ss_dssp HHHHHHHHHHHHTESEEEEE---SHHHHHHHHHHHHHHHHTTSEE
T ss_pred hHHHHHHHHHhcCcCeeEeccccCHHHHHHHHHHHHHHHhcceEE
Confidence 34566677788999999999974444 477889999999999864
No 40
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=61.03 E-value=32 Score=27.53 Aligned_cols=43 Identities=26% Similarity=0.241 Sum_probs=29.5
Q ss_pred HHHHHHHHHHcCCCEEEEe--cCC-CchhhHHHHHHHHHHHcCCcC
Q 030804 129 GEMIAKSCLEKGITKVAFD--RGG-YPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 129 G~~LAkra~e~GI~~VvfD--Rgg-~~YhGrVkAlad~aRe~GL~f 171 (171)
|+.+++.+.+.|..++.|= ..+ ..-.-|.+.|.+.++++|+++
T Consensus 104 ~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 149 (268)
T cd06270 104 GYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEAGIAL 149 (268)
T ss_pred HHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 4555555566788888652 222 233578999999999999753
No 41
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=61.00 E-value=35 Score=27.39 Aligned_cols=43 Identities=28% Similarity=0.320 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHcCCCEEEEecCC-C-chhhHHHHHHHHHHHcCCc
Q 030804 128 VGEMIAKSCLEKGITKVAFDRGG-Y-PYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRgg-~-~YhGrVkAlad~aRe~GL~ 170 (171)
.|+.+++.+.+.|.+++.|=.+. . ....|.+.|.++++++|++
T Consensus 96 ~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~ 140 (265)
T cd01543 96 IGRMAAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEAGYE 140 (265)
T ss_pred HHHHHHHHHHHCCCcEEEEEcCCCCHHHHHHHHHHHHHHHHcCCc
Confidence 45556666677899999874221 2 1247899999999999975
No 42
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=59.98 E-value=30 Score=29.25 Aligned_cols=44 Identities=18% Similarity=0.256 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCcC
Q 030804 128 VGEMIAKSCLEKGITKVAFDRGG---YPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~f 171 (171)
-|+.+++.+.+.|..++.|=.+. .....|...|.+++.++|+.+
T Consensus 163 ~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~ 209 (343)
T PRK10727 163 GAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPA 209 (343)
T ss_pred HHHHHHHHHHHCCCccEEEEeCCccccchHHHHHHHHHHHHHCCCCC
Confidence 35556666777899998763322 234679999999999999853
No 43
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=59.62 E-value=26 Score=23.17 Aligned_cols=40 Identities=28% Similarity=0.462 Sum_probs=28.3
Q ss_pred HHHHHHHHHHcCCCEEEE-ecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 129 GEMIAKSCLEKGITKVAF-DRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 129 G~~LAkra~e~GI~~Vvf-DRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
-+.+.++|++.|++.+.+ |.+ .+.|-. .+.+.+++.||++
T Consensus 17 ~~~~~~~a~~~g~~~v~iTDh~--~~~~~~-~~~~~~~~~gi~~ 57 (67)
T smart00481 17 PEELVKRAKELGLKAIAITDHG--NLFGAV-EFYKAAKKAGIKP 57 (67)
T ss_pred HHHHHHHHHHcCCCEEEEeeCC--cccCHH-HHHHHHHHcCCeE
Confidence 356889999999999976 776 344433 4446667788753
No 44
>TIGR00612 ispG_gcpE 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase. Chlamydial members of the family have a long insert. The family is largely restricted to Bacteria, where it is widely but not universally distributed. No homology can be detected between the GcpE family and other proteins.
Probab=59.51 E-value=33 Score=31.39 Aligned_cols=52 Identities=23% Similarity=0.444 Sum_probs=45.7
Q ss_pred CCcHHHHHHHHHH-----------------HHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 119 GPTIEVSKKVGEM-----------------IAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 119 ~~n~~AA~~VG~~-----------------LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
..+.++|..++++ +|-.+.+.|++++=.+.|..-...+++.+++.+++.|+.
T Consensus 55 vp~~~~A~al~~I~~~~~iPlVADIHFd~~lAl~a~~~g~dkiRINPGNig~~e~v~~vv~~ak~~~ip 123 (346)
T TIGR00612 55 VPDRESAAAFEAIKEGTNVPLVADIHFDYRLAALAMAKGVAKVRINPGNIGFRERVRDVVEKARDHGKA 123 (346)
T ss_pred CCCHHHHHhHHHHHhCCCCCEEEeeCCCcHHHHHHHHhccCeEEECCCCCCCHHHHHHHHHHHHHCCCC
Confidence 3677888888864 888999999999999999888889999999999999975
No 45
>PF14419 SPOUT_MTase_2: AF2226-like SPOUT RNA Methylase fused to THUMP
Probab=59.04 E-value=32 Score=28.56 Aligned_cols=49 Identities=12% Similarity=0.116 Sum_probs=40.4
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHc
Q 030804 119 GPTIEVSKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREY 167 (171)
Q Consensus 119 ~~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~ 167 (171)
-++.++|+++|+.|+..+....+.+.+---.++.-.=-+..|+++++++
T Consensus 10 lGd~~a~r~mGerIGRaaQ~FEV~eLiiap~~~vda~eL~~Fl~gV~~G 58 (173)
T PF14419_consen 10 LGDLKACRKMGERIGRAAQAFEVKELIIAPKEKVDAYELMEFLRGVREG 58 (173)
T ss_pred cCCHHHHHHHHHHHhHHHhhcchheEEEeccCccCHHHHHHHHHHHHHh
Confidence 4588999999999999999999999987665555555678888888764
No 46
>PF00070 Pyr_redox: Pyridine nucleotide-disulphide oxidoreductase; InterPro: IPR001327 FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons (rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase [, , ]. Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently []. Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases [] and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) []. Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR. To date, 3D structures of glutathione reductase [], thioredoxin reductase [], mercuric reductase [], lipoamide dehydrogenase [], trypanothione reductase [] and NADH peroxidase [] have been solved. The enzymes share similar tertiary structures based on a doubly-wound alpha/beta fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication []. This entry describes a small NADH binding domain within a larger FAD binding domain described by IPR023753 from INTERPRO. It is found in both class I and class II oxidoreductases. ; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZKQ_A 3DGZ_A 1ZDL_A 2R9Z_B 2RAB_A 2A87_B 1M6I_A 2YVG_A 2GR1_A 2GQW_A ....
Probab=58.22 E-value=33 Score=23.25 Aligned_cols=45 Identities=18% Similarity=0.226 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCCch----hhHHHHHHHHHHHcCCcC
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRGGYPY----HGRIQALADAAREYGLQF 171 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRgg~~Y----hGrVkAlad~aRe~GL~f 171 (171)
.+|-.+|..+.+.|.+-.+++|+.... ..--+.+.+.+++.|++|
T Consensus 9 ~ig~E~A~~l~~~g~~vtli~~~~~~~~~~~~~~~~~~~~~l~~~gV~v 57 (80)
T PF00070_consen 9 FIGIELAEALAELGKEVTLIERSDRLLPGFDPDAAKILEEYLRKRGVEV 57 (80)
T ss_dssp HHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEE
T ss_pred HHHHHHHHHHHHhCcEEEEEeccchhhhhcCHHHHHHHHHHHHHCCCEE
Confidence 356677777788998777899876544 334566778899999874
No 47
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=57.94 E-value=23 Score=29.87 Aligned_cols=44 Identities=30% Similarity=0.412 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHcCCCE-EEEecCC---CchhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITK-VAFDRGG---YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~-VvfDRgg---~~YhGrVkAlad~aRe~GL~ 170 (171)
.-|+.+++.+.+.|.++ |.|=.+. .....|++.|.+++.++|+.
T Consensus 104 ~a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~ 151 (279)
T PF00532_consen 104 EAGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLP 151 (279)
T ss_dssp HHHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSC
T ss_pred HHHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCC
Confidence 34556777778899999 7653332 22368999999999999985
No 48
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=57.71 E-value=39 Score=28.30 Aligned_cols=44 Identities=16% Similarity=0.395 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHcCCCEEEEecCC--C-chhhHHHHHHHHHHHcCCcC
Q 030804 128 VGEMIAKSCLEKGITKVAFDRGG--Y-PYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRgg--~-~YhGrVkAlad~aRe~GL~f 171 (171)
.|+.+++.+.+.|..++.|=.+. . ....|+..|.+++.++|+++
T Consensus 169 ~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~ 215 (342)
T PRK10014 169 AAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPF 215 (342)
T ss_pred HHHHHHHHHHHCCCCEEEEEcCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 34445555566799999774322 2 23579999999999999853
No 49
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=57.25 E-value=35 Score=26.95 Aligned_cols=44 Identities=16% Similarity=0.139 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHcCCCEEEEe--cCCCc-hhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAFD--RGGYP-YHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfD--Rgg~~-YhGrVkAlad~aRe~GL~ 170 (171)
..|+.+++.+.+.|..++.|= ..... ...|.+.|.+++.++|+.
T Consensus 106 ~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 152 (268)
T cd06271 106 AAAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEAGLP 152 (268)
T ss_pred HHHHHHHHHHHHcCCCcEEEecCccccchHHHHHHHHHHHHHHhCCC
Confidence 445555666667799998662 22222 257899999999999874
No 50
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=57.08 E-value=41 Score=31.62 Aligned_cols=53 Identities=13% Similarity=0.150 Sum_probs=41.2
Q ss_pred CCCcHHHHHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 118 SGPTIEVSKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 118 ~~~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.+.+...++..|..||+++++.|++.|++--.=-.-|=-....+..+-++||.
T Consensus 314 ~gt~~~~a~~~g~eIa~~Lk~dgVDAVILTstCgtC~r~~a~m~keiE~~GiP 366 (431)
T TIGR01918 314 NGTTVAESKQFAKEFVVELKQGGVDAVILTSTUGTCTRCGATMVKEIERAGIP 366 (431)
T ss_pred CCchHHHHHHHHHHHHHHHHHcCCCEEEEcCCCCcchhHHHHHHHHHHHcCCC
Confidence 45678889999999999999999999999854224454556667777777774
No 51
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=56.94 E-value=35 Score=26.91 Aligned_cols=45 Identities=20% Similarity=0.244 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecC---CC-chhhHHHHHHHHHHHcCCc
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRG---GY-PYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRg---g~-~YhGrVkAlad~aRe~GL~ 170 (171)
+..|+.+++.+.+.|..+|.|=-+ .. ..+.|.+.|.+.+.++|++
T Consensus 101 ~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~ 149 (266)
T cd06282 101 RAAARDVAQALAALGHRRIAMLAGRLAASDRARQRYAGYRAAMRAAGLA 149 (266)
T ss_pred HHHHHHHHHHHHHcCcccEEEeccccccCchHHHHHHHHHHHHHHcCCC
Confidence 455556666666679999865322 12 2467999999999999975
No 52
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=56.92 E-value=43 Score=26.76 Aligned_cols=52 Identities=17% Similarity=0.165 Sum_probs=39.2
Q ss_pred CCcHHHHHHHHHHHHHHHHHc--CCCEEEEecC---CCchhhHHHHHHHHHHHcCCc
Q 030804 119 GPTIEVSKKVGEMIAKSCLEK--GITKVAFDRG---GYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 119 ~~n~~AA~~VG~~LAkra~e~--GI~~VvfDRg---g~~YhGrVkAlad~aRe~GL~ 170 (171)
..+.++++.+++.|++.+++. |..++.|=.+ .....-|.+.|.+.+.++|++
T Consensus 101 ~d~~~~g~~~~~~l~~~~~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~ 157 (277)
T cd06319 101 SDNYEGAYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCD 157 (277)
T ss_pred eccHHHHHHHHHHHHHHHHhhCCCCCcEEEEeccCCCccHHHHHHHHHHHHHhcCCc
Confidence 357788999999999998876 5667755322 223468899999999999975
No 53
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=55.64 E-value=48 Score=26.27 Aligned_cols=46 Identities=20% Similarity=0.317 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHcCCCEEEEec--CCCch-hhHHHHHHHHHHHcCCcC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDR--GGYPY-HGRIQALADAAREYGLQF 171 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDR--gg~~Y-hGrVkAlad~aRe~GL~f 171 (171)
+..|+.+++.+.+.|.+++.|=. .++.. ..|...|.+.+.+.|+++
T Consensus 103 ~~~g~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 151 (270)
T cd01545 103 RAAAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALAEAGLPL 151 (270)
T ss_pred HHHHHHHHHHHHHCCCceEEEEeCCCCchhHHHHHHHHHHHHHHcCCCC
Confidence 44556666666777989987632 23332 478899999999998763
No 54
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=54.87 E-value=42 Score=27.14 Aligned_cols=53 Identities=19% Similarity=0.232 Sum_probs=39.4
Q ss_pred CCCcHHHHHHHHHHHHHHHHHcCC--CEEEE-e---cCCCchhhHHHHHHHHHHHcCCc
Q 030804 118 SGPTIEVSKKVGEMIAKSCLEKGI--TKVAF-D---RGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 118 ~~~n~~AA~~VG~~LAkra~e~GI--~~Vvf-D---Rgg~~YhGrVkAlad~aRe~GL~ 170 (171)
...|.++++..|+.|++.+.+.|. .++.| . .....-..|+..|.+++.+.|+.
T Consensus 104 ~~d~~~~g~~~~~~l~~~~~~~g~~~~~i~~i~~~~~~~~~~~~R~~G~~~~l~~~~~~ 162 (289)
T cd01540 104 GMSATKIGEQVGEAIADEMKKRGWDPKEVGALRITYDELDTAKPRTDGALEALKAPGFP 162 (289)
T ss_pred cCCHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecCCCCcchhhHHHHHHHHHhcCCCC
Confidence 346889999999999999988887 55543 2 12122367999999999998875
No 55
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=53.82 E-value=47 Score=27.67 Aligned_cols=44 Identities=23% Similarity=0.342 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHcCCCEEEEecCC--Cc--hhhHHHHHHHHHHHcCCcC
Q 030804 128 VGEMIAKSCLEKGITKVAFDRGG--YP--YHGRIQALADAAREYGLQF 171 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRgg--~~--YhGrVkAlad~aRe~GL~f 171 (171)
-|+.+++.+.+.|..++.|=-+. .. ...|...|.+++.++|+++
T Consensus 163 ~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~~R~~Gf~~~l~~~g~~~ 210 (329)
T TIGR01481 163 ATKEAVGELIAKGHKSIAFVGGPLSDSINGEDRLEGYKEALNKAGIQF 210 (329)
T ss_pred HHHHHHHHHHHCCCCeEEEEecCcccccchHHHHHHHHHHHHHcCCCC
Confidence 35566666777899999764322 22 2679999999999999863
No 56
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=53.77 E-value=54 Score=26.27 Aligned_cols=44 Identities=27% Similarity=0.462 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHcCCCEEEEecC--CCch-hhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRG--GYPY-HGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRg--g~~Y-hGrVkAlad~aRe~GL~ 170 (171)
..|+.+++.+.+.|..++.|=.+ .... +.|...|.++++++|++
T Consensus 111 ~~g~~~a~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~ 157 (275)
T cd06295 111 GGGRLATEHLLARGRRRIAFLGGPQDMPEGEERLEGYREALAEAGLP 157 (275)
T ss_pred HHHHHHHHHHHHCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHcCCC
Confidence 45555666666789999976332 2222 47899999999999853
No 57
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=53.00 E-value=50 Score=27.47 Aligned_cols=43 Identities=19% Similarity=0.078 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCc
Q 030804 128 VGEMIAKSCLEKGITKVAFDRGG---YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~ 170 (171)
-|..+++.+.+.|..+|.|=.+. .....|.+.|.+++.++|+.
T Consensus 166 ~~~~a~~~L~~~G~r~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~ 211 (328)
T PRK11303 166 DAEMLAESLLKFPAESILLLGALPELSVSFEREQGFRQALKDDPRE 211 (328)
T ss_pred HHHHHHHHHHHCCCCeEEEEeCccccccHHHHHHHHHHHHHHcCCC
Confidence 35566677777899999764322 22357999999999999975
No 58
>cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=52.99 E-value=45 Score=27.36 Aligned_cols=44 Identities=20% Similarity=0.243 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHcCCCEEEEecC---CCchhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRG---GYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRg---g~~YhGrVkAlad~aRe~GL~ 170 (171)
..|..+++.+.++|..++.|=-+ ......|...|.++++++|+.
T Consensus 104 ~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~~ 150 (269)
T cd06287 104 ATARMLLEHLRAQGARQIALIVGSARRNSYLEAEAAYRAFAAEHGMP 150 (269)
T ss_pred HHHHHHHHHHHHcCCCcEEEEeCCcccccHHHHHHHHHHHHHHcCCC
Confidence 44777788888889999865322 123457899999999999985
No 59
>COG1611 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]
Probab=52.75 E-value=21 Score=29.83 Aligned_cols=40 Identities=28% Similarity=0.350 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 122 IEVSKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 122 ~~AA~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.+.|+.+|+.|+++. .++|-=| ..|-+.|.++++.++|-.
T Consensus 33 ~~~a~~lg~~la~~g------~~V~tGG---~~GiMea~~~gA~~~gg~ 72 (205)
T COG1611 33 YELARELGRELAKRG------LLVITGG---GPGVMEAVARGALEAGGL 72 (205)
T ss_pred HHHHHHHHHHHHhCC------cEEEeCC---chhhhhHHHHHHHHcCCe
Confidence 478888888888876 5666654 479999999999998854
No 60
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=52.53 E-value=47 Score=28.97 Aligned_cols=44 Identities=25% Similarity=0.337 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCcC
Q 030804 128 VGEMIAKSCLEKGITKVAFDRGG---YPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~f 171 (171)
-|+.+++.+.++|..++.|=-++ .....|...|.++++++|+.+
T Consensus 162 ~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~ 208 (333)
T COG1609 162 GAYLATEHLIELGHRRIAFIGGPLDSSASRERLEGYRAALREAGLPI 208 (333)
T ss_pred HHHHHHHHHHHCCCceEEEEeCCCccccHhHHHHHHHHHHHHCCCCC
Confidence 45667777888999999875544 445899999999999999863
No 61
>PF13380 CoA_binding_2: CoA binding domain; PDB: 3FF4_A 2D5A_A 2D59_A 2E6U_X 1IUL_A 1IUK_A 1Y81_A 2DUW_A.
Probab=52.07 E-value=19 Score=26.95 Aligned_cols=42 Identities=24% Similarity=0.329 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
.......+.+.|.++|+..|+|--| ..-..+.+.++++||.+
T Consensus 64 ~~~~~~~~v~~~~~~g~~~v~~~~g-----~~~~~~~~~a~~~gi~v 105 (116)
T PF13380_consen 64 PPDKVPEIVDEAAALGVKAVWLQPG-----AESEELIEAAREAGIRV 105 (116)
T ss_dssp -HHHHHHHHHHHHHHT-SEEEE-TT-----S--HHHHHHHHHTT-EE
T ss_pred CHHHHHHHHHHHHHcCCCEEEEEcc-----hHHHHHHHHHHHcCCEE
Confidence 3344455677888899999999887 56678888999999864
No 62
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=51.98 E-value=56 Score=25.76 Aligned_cols=47 Identities=26% Similarity=0.398 Sum_probs=30.5
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecC--CC-chhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRG--GY-PYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRg--g~-~YhGrVkAlad~aRe~GL~ 170 (171)
.|..+++.+++.| .+.|..+|.|=.+ +. .-..|...|.+.+.+.|++
T Consensus 98 d~~~~g~~~~~~l----~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 147 (266)
T cd06278 98 DNYEAGRLAAELL----LAKGCRRIAFIGGPADTSTSRERERGFRDALAAAGVP 147 (266)
T ss_pred ChHHHHHHHHHHH----HHCCCceEEEEcCCCcccchHHHHHHHHHHHHHcCCC
Confidence 3455555555544 4568888866322 22 2246899999999999875
No 63
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=51.41 E-value=55 Score=25.82 Aligned_cols=44 Identities=25% Similarity=0.466 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHcCCCEEEE--ecCC-CchhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAF--DRGG-YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~Vvf--DRgg-~~YhGrVkAlad~aRe~GL~ 170 (171)
..|+.+++.+.+.|..++.| +... ..-..|...|.++++++|++
T Consensus 102 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~ 148 (268)
T cd01575 102 EAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLD 148 (268)
T ss_pred HHHHHHHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCC
Confidence 44555566666778888865 3222 23367899999999999874
No 64
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=51.39 E-value=58 Score=25.82 Aligned_cols=45 Identities=20% Similarity=0.254 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHcCCCEEEEe--cCCCc-hhhHHHHHHHHHHHcCCc
Q 030804 126 KKVGEMIAKSCLEKGITKVAFD--RGGYP-YHGRIQALADAAREYGLQ 170 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfD--Rgg~~-YhGrVkAlad~aRe~GL~ 170 (171)
+..|+.+++.+.+.|..++.|= ..++. .+-|.+.|.+.+++.|+.
T Consensus 107 ~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~ 154 (270)
T cd06294 107 IQAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALEDHGIP 154 (270)
T ss_pred HHHHHHHHHHHHHcCCccEEEecCCcccHHHHHHHHHHHHHHHHcCCC
Confidence 3455555666666688888542 33322 356999999999999863
No 65
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=50.86 E-value=62 Score=25.83 Aligned_cols=47 Identities=17% Similarity=0.235 Sum_probs=31.7
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecCC--Cc-hhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRGG--YP-YHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg--~~-YhGrVkAlad~aRe~GL~ 170 (171)
.|..+++.+++.| .++|..++.|=-+. .. -+.|.+.|.+.+.++|++
T Consensus 105 d~~~~~~~~~~~l----~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 154 (273)
T cd06292 105 DDALAMRLAVRHL----VALGHRRIGFASGPGRTVPRRRKIAGFRAALEEAGLE 154 (273)
T ss_pred CcHHHHHHHHHHH----HHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCC
Confidence 4555655555555 45699999763322 22 257899999999999974
No 66
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=50.41 E-value=35 Score=27.14 Aligned_cols=40 Identities=25% Similarity=0.453 Sum_probs=33.1
Q ss_pred HHHHHHHHcCCCEE----------EEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 131 MIAKSCLEKGITKV----------AFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 131 ~LAkra~e~GI~~V----------vfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.++-+|+..|++-| .|++|.|+-.-|+..+.+.|-|-||+
T Consensus 44 ~fvl~Al~~GaDGV~v~GC~~geCHy~~GN~ka~rR~~~lke~l~elgie 93 (132)
T COG1908 44 EFVLKALRKGADGVLVAGCKIGECHYISGNYKAKRRMELLKELLKELGIE 93 (132)
T ss_pred HHHHHHHHcCCCeEEEecccccceeeeccchHHHHHHHHHHHHHHHhCCC
Confidence 45667888887644 58899999999999999999999985
No 67
>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=49.94 E-value=59 Score=25.66 Aligned_cols=44 Identities=18% Similarity=0.264 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHcCCCEEEEe--cCC-Cc-hhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAFD--RGG-YP-YHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfD--Rgg-~~-YhGrVkAlad~aRe~GL~ 170 (171)
..|+.+++.+.+.|..++.|= ... .. -+.|...|.+.+.++|+.
T Consensus 102 ~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~~~~~~~ 149 (267)
T cd06283 102 EAAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEALAEHGIG 149 (267)
T ss_pred HHHHHHHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHHHHcCCC
Confidence 346777777778899888643 222 22 258999999999999864
No 68
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=49.76 E-value=57 Score=25.91 Aligned_cols=45 Identities=22% Similarity=0.309 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCC--C-ch-hhHHHHHHHHHHHcCCc
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGG--Y-PY-HGRIQALADAAREYGLQ 170 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg--~-~Y-hGrVkAlad~aRe~GL~ 170 (171)
+..|+.+++.+.+.|..+|.|=-+. . .+ ..|...|.+.+.++|+.
T Consensus 101 ~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~ 149 (268)
T cd06273 101 REAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAALAEAGLE 149 (268)
T ss_pred HHHHHHHHHHHHHCCCCeEEEEeccccCCccHHHHHHHHHHHHHHcCCC
Confidence 3445555555566799998653221 1 12 36899999999999864
No 69
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=49.30 E-value=57 Score=26.12 Aligned_cols=47 Identities=23% Similarity=0.201 Sum_probs=30.4
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEe--cCCCchhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFD--RGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfD--Rgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.|..+++.+++.| .++|..++.|- ......+-|+..|.+++.++|++
T Consensus 104 D~~~~g~~~~~~l----~~~G~~~i~~l~~~~~~~~~~r~~g~~~~l~~~~~~ 152 (273)
T cd01541 104 DDEKGGYKATEYL----IELGHRKIAGIFKADDLQGVKRMKGFIKAYREHGIP 152 (273)
T ss_pred CcHHHHHHHHHHH----HHcCCcCEEEecCCCcccHHHHHHHHHHHHHHcCCC
Confidence 3445555555544 55788888653 22223467899999999999874
No 70
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=48.92 E-value=60 Score=25.91 Aligned_cols=44 Identities=20% Similarity=0.286 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCcC
Q 030804 128 VGEMIAKSCLEKGITKVAFDRGG---YPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~f 171 (171)
.|+.+++.+.+.|..++.|=.+. ....-|.+.|.+.+.++|+++
T Consensus 105 ~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 151 (268)
T cd06277 105 GAYAATEYLIEKGHRKIGFVGDPLYSPSFEERYEGYKKALLDHGIPF 151 (268)
T ss_pred HHHHHHHHHHHCCCCcEEEECCCCCCcchHHHHHHHHHHHHHcCCCC
Confidence 45556666677798888653322 223468999999999999863
No 71
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=48.74 E-value=69 Score=25.46 Aligned_cols=47 Identities=17% Similarity=0.205 Sum_probs=31.3
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecCC--C-chhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRGG--Y-PYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg--~-~YhGrVkAlad~aRe~GL~ 170 (171)
.|.++++.+++. +.++|..++.|=.+. . .-..|.+.|.+.+.+.|++
T Consensus 98 d~~~a~~~~~~~----l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~ 147 (265)
T cd06290 98 DNFQGGYLATQH----LIDLGHRRIAHITGPRGHIDARDRLAGYRKALEEAGLE 147 (265)
T ss_pred CcHHHHHHHHHH----HHHCCCCeEEEEeCccccchhhHHHHHHHHHHHHcCCC
Confidence 355665555554 555688888764322 1 2247899999999999875
No 72
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=48.23 E-value=60 Score=27.19 Aligned_cols=46 Identities=13% Similarity=0.196 Sum_probs=31.8
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecC--CCchhhHHHHHHHHHHHcCC
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRG--GYPYHGRIQALADAAREYGL 169 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRg--g~~YhGrVkAlad~aRe~GL 169 (171)
.|.+++ +.+++.+.+.|..++.|=.+ ......|...|.+++.++|+
T Consensus 163 Dn~~~~----~~a~~~L~~~Gh~~I~~i~~~~~~~~~~R~~Gf~~al~~~g~ 210 (331)
T PRK14987 163 DNFEAA----RQMTTAIIARGHRHIAYLGARLDERTIIKQKGYEQAMLDAGL 210 (331)
T ss_pred CcHHHH----HHHHHHHHHCCCceEEEEcCCCcccHHHHHHHHHHHHHHcCC
Confidence 355554 44555556789999977422 22345699999999999997
No 73
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=47.87 E-value=73 Score=25.22 Aligned_cols=43 Identities=19% Similarity=0.255 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHcCCCEEEEecC--CCc-hhhHHHHHHHHHHHcCCc
Q 030804 128 VGEMIAKSCLEKGITKVAFDRG--GYP-YHGRIQALADAAREYGLQ 170 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRg--g~~-YhGrVkAlad~aRe~GL~ 170 (171)
.|+.+++...+.|..+|.|=.+ ... ...|...|.+++++.|+.
T Consensus 103 ~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~ 148 (264)
T cd01574 103 GARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALEAAGIA 148 (264)
T ss_pred HHHHHHHHHHHCCCCEEEEEecCCccchHHHHHHHHHHHHHHCCCC
Confidence 3444445555578888865322 222 347899999999999875
No 74
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=47.82 E-value=35 Score=28.96 Aligned_cols=38 Identities=32% Similarity=0.497 Sum_probs=28.7
Q ss_pred HHHHHHcCCCEEEEecCCCch-hhHHHHHHHHHHHcCCc
Q 030804 133 AKSCLEKGITKVAFDRGGYPY-HGRIQALADAAREYGLQ 170 (171)
Q Consensus 133 Akra~e~GI~~VvfDRgg~~Y-hGrVkAlad~aRe~GL~ 170 (171)
.+||++.||..++||+..|.- .--=.++++.+++.+.+
T Consensus 43 lerA~~~gIpt~~~~~k~~~~r~~~d~~l~~~l~~~~~d 81 (200)
T COG0299 43 LERAAKAGIPTVVLDRKEFPSREAFDRALVEALDEYGPD 81 (200)
T ss_pred HHHHHHcCCCEEEeccccCCCHHHHHHHHHHHHHhcCCC
Confidence 478999999999999986652 12346778888887765
No 75
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=47.38 E-value=64 Score=26.87 Aligned_cols=42 Identities=10% Similarity=0.113 Sum_probs=32.3
Q ss_pred HHHHHHHHHHcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCc
Q 030804 129 GEMIAKSCLEKGITKVAFDRGG---YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 129 G~~LAkra~e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~ 170 (171)
|+.+++.+.+.|..++.|=.+. .....|...|.+++.++|++
T Consensus 166 ~~~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~ 210 (327)
T TIGR02417 166 AAELIERLLSQHADEFWYLGAQPELSVSRDRLAGFRQALKQATLE 210 (327)
T ss_pred HHHHHHHHHHCCCCeEEEEeCcccchhHHHHHHHHHHHHHHcCCC
Confidence 6667778888999999764332 22467999999999999974
No 76
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=46.86 E-value=73 Score=26.10 Aligned_cols=48 Identities=21% Similarity=0.300 Sum_probs=31.8
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEe--cCCCc-hhhHHHHHHHHHHHcCCcC
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFD--RGGYP-YHGRIQALADAAREYGLQF 171 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfD--Rgg~~-YhGrVkAlad~aRe~GL~f 171 (171)
.|..+.+..++.| .+.|..++.|= ..... -..|.+.|.++++++|+++
T Consensus 135 Dn~~~g~~a~~~l----~~~G~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 185 (309)
T PRK11041 135 DNLTAAFEAVNYL----HELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGITV 185 (309)
T ss_pred CcHHHHHHHHHHH----HHcCCceEEEEeCCccccchHHHHHHHHHHHHHcCCCC
Confidence 3555555555544 45688888753 22222 2579999999999999853
No 77
>PRK07523 gluconate 5-dehydrogenase; Provisional
Probab=46.58 E-value=48 Score=26.62 Aligned_cols=40 Identities=20% Similarity=0.328 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYG 168 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~G 168 (171)
..-+|..+++++.+.|.+-+.+||+. .+.+++.+.+++.|
T Consensus 19 ~g~iG~~ia~~l~~~G~~V~~~~r~~----~~~~~~~~~i~~~~ 58 (255)
T PRK07523 19 SQGIGYALAEGLAQAGAEVILNGRDP----AKLAAAAESLKGQG 58 (255)
T ss_pred cchHHHHHHHHHHHcCCEEEEEeCCH----HHHHHHHHHHHhcC
Confidence 45689999999999998766788863 24445555555443
No 78
>PRK12744 short chain dehydrogenase; Provisional
Probab=45.97 E-value=60 Score=26.16 Aligned_cols=41 Identities=17% Similarity=0.251 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHc
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREY 167 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~ 167 (171)
-+|..+|+...+.|..-++.++.........+.+++.+...
T Consensus 19 gIG~~~a~~l~~~G~~vv~i~~~~~~~~~~~~~~~~~l~~~ 59 (257)
T PRK12744 19 NLGGLIARDLAAQGAKAVAIHYNSAASKADAEETVAAVKAA 59 (257)
T ss_pred hHHHHHHHHHHHCCCcEEEEecCCccchHHHHHHHHHHHHh
Confidence 48999999999999887777664444445555555555443
No 79
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=45.69 E-value=83 Score=25.17 Aligned_cols=42 Identities=21% Similarity=0.286 Sum_probs=29.6
Q ss_pred HHHHHHHHHHcCCCEEEEecCCC---chhhHHHHHHHHHHHcCCc
Q 030804 129 GEMIAKSCLEKGITKVAFDRGGY---PYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 129 G~~LAkra~e~GI~~VvfDRgg~---~YhGrVkAlad~aRe~GL~ 170 (171)
|+.+++.+.+.|..++.|=.+.. ....|+..|.+++.++|++
T Consensus 104 g~~a~~~l~~~G~~~i~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~ 148 (269)
T cd06281 104 MRQAVEYLISLGHRRIALVGGGSNTRPGRERLEGYKAAFAAAGLP 148 (269)
T ss_pred HHHHHHHHHHCCCcEEEEecCccccccHHHHHHHHHHHHHHcCCC
Confidence 45555666667999997643322 2246899999999999975
No 80
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=45.28 E-value=83 Score=24.79 Aligned_cols=44 Identities=18% Similarity=0.292 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHcCCCEEEEe--cCCCc-hhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAFD--RGGYP-YHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfD--Rgg~~-YhGrVkAlad~aRe~GL~ 170 (171)
..|+.+++.+.+.|..++.|= ..... ...|+..|.+.+.+.|++
T Consensus 101 ~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~~~~~~~~ 147 (267)
T cd06284 101 AAARLAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAEAGLP 147 (267)
T ss_pred HHHHHHHHHHHHcCCceEEEEcCCccchhHHHHHHHHHHHHHHcCCC
Confidence 344555555566788888652 22222 367999999999999964
No 81
>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor
Probab=45.03 E-value=66 Score=25.55 Aligned_cols=44 Identities=23% Similarity=0.250 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHcCCCEEEEe--cCC-CchhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAFD--RGG-YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfD--Rgg-~~YhGrVkAlad~aRe~GL~ 170 (171)
..|+.+++.+.+.|..++.|= ... ....-|...|.+.+++.|+.
T Consensus 97 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 143 (261)
T cd06272 97 KAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDENGIS 143 (261)
T ss_pred HHHHHHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHHHcCCC
Confidence 345566666667799888653 222 23467899999999999863
No 82
>cd06326 PBP1_STKc_like Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins. The type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins, some of which contain a conserved catalytic serine/threonine protein kinase (STKc) domain in the N-terminal region. Members of this group are sequence-similar to the branched-chain amino acid ABC transporter leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=44.83 E-value=61 Score=26.90 Aligned_cols=46 Identities=13% Similarity=0.183 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCCCch-hhHHHHHHHHHHHcCCc
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGGYPY-HGRIQALADAAREYGLQ 170 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg~~Y-hGrVkAlad~aRe~GL~ 170 (171)
....+..+++.+++.|.++|.+=...+.| ..+.++|.+.+.+.|++
T Consensus 120 ~~~~~~~~~~~l~~~g~~~v~~l~~~~~~~~~~~~~~~~~~~~~G~~ 166 (336)
T cd06326 120 YADEIAAIVRHLVTLGLKRIAVFYQDDAFGKDGLAGVEKALAARGLK 166 (336)
T ss_pred hHHHHHHHHHHHHHhCCceEEEEEecCcchHHHHHHHHHHHHHcCCC
Confidence 33456777888888899998653323334 57899999999999975
No 83
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=44.79 E-value=88 Score=24.74 Aligned_cols=47 Identities=17% Similarity=0.221 Sum_probs=31.0
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecC--C-C-chhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRG--G-Y-PYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRg--g-~-~YhGrVkAlad~aRe~GL~ 170 (171)
.|.++++.+ ++.+.+.|..++.|=.+ . . --+.|.+.|.+.+.++|++
T Consensus 99 d~~~~~~~~----~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~gf~~~~~~~~~~ 149 (268)
T cd06298 99 DYKKAAFEA----TELLIKNGHKKIAFISGPLEDSINGDERLAGYKEALSEANIE 149 (268)
T ss_pred CcHHHHHHH----HHHHHHcCCceEEEEeCCcccccchhHHHHHHHHHHHHcCCC
Confidence 345555544 55555578888865322 2 2 2368999999999999975
No 84
>PRK12827 short chain dehydrogenase; Provisional
Probab=44.71 E-value=63 Score=25.41 Aligned_cols=41 Identities=17% Similarity=0.162 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHH
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAARE 166 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe 166 (171)
.-+|..|++.+.+.|.+-+..||....-......+.+.+.+
T Consensus 16 g~iG~~la~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~ 56 (249)
T PRK12827 16 GGLGRAIAVRLAADGADVIVLDIHPMRGRAEADAVAAGIEA 56 (249)
T ss_pred ChHHHHHHHHHHHCCCeEEEEcCcccccHHHHHHHHHHHHh
Confidence 45899999999999988778787543334455555555443
No 85
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=44.69 E-value=59 Score=22.74 Aligned_cols=34 Identities=12% Similarity=0.218 Sum_probs=26.0
Q ss_pred HcCCCEEEEecCCCch------------hhHHHHHHHHHHHcCCcC
Q 030804 138 EKGITKVAFDRGGYPY------------HGRIQALADAAREYGLQF 171 (171)
Q Consensus 138 e~GI~~VvfDRgg~~Y------------hGrVkAlad~aRe~GL~f 171 (171)
..+|.++.|+|....+ ..-+..+.+.|++.|++|
T Consensus 24 ~anI~~~~y~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~ 69 (85)
T cd04906 24 PRNITEFNYRYADEKDAHIFVGVSVANGAEELAELLEDLKSAGYEV 69 (85)
T ss_pred CCceeEEEEEccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCe
Confidence 6899999999843222 345889999999999875
No 86
>PRK07738 flagellar protein FlaG; Provisional
Probab=44.64 E-value=90 Score=24.21 Aligned_cols=43 Identities=12% Similarity=0.223 Sum_probs=33.2
Q ss_pred HHHHHHHhhhhhcCCCCCceEEEEeeCCcEEEEEEeCCCCcEE
Q 030804 58 RTARHSRIRKKIDGTPERPRLCVFRSNKHLYVQVIDDTKMHTL 100 (171)
Q Consensus 58 r~~R~~RirkKi~gt~~rPRL~V~rSnkhiyAQvIdd~~~ktL 100 (171)
...--.++-..+......-+..|+.....++++|||..+|++|
T Consensus 48 l~~aveklN~~l~~~~~~L~F~vdeet~~~vVkVvD~~T~EVI 90 (117)
T PRK07738 48 LEEVVDGMNELLEPSQTSLKFELHEKLNEYYVQVVDERTNEVI 90 (117)
T ss_pred HHHHHHHHHHHHHhcCCceEEEEecCCCcEEEEEEECCCCeee
Confidence 3344455556666555677999999999999999999999885
No 87
>PF02065 Melibiase: Melibiase; InterPro: IPR000111 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycosyl hydrolase family 27, family 31 and family 36 alpha-galactosidases form the glycosyl hydrolase clan GH-D (acc_GH from CAZY), a superfamily of alpha-galactosidases, alpha-N-acetylgalactosaminidases, and isomaltodextranases which are likely to share a common catalytic mechanism and structural topology. Alpha-galactosidase (3.2.1.22 from EC) (melibiase) [] catalyzes the hydrolysis of melibiose into galactose and glucose. In man, the deficiency of this enzyme is the cause of Fabry's disease (X-linked sphingolipidosis). Alpha-galactosidase is present in a variety of organisms. There is a considerable degree of similarity in the sequence of alpha-galactosidase from various eukaryotic species. Escherichia coli alpha-galactosidase (gene melA), which requires NAD and magnesium as cofactors, is not structurally related to the eukaryotic enzymes; by contrast, an Escherichia coli plasmid encoded alpha-galactosidase (gene rafA P16551 from SWISSPROT) [] contains a region of about 50 amino acids which is similar to a domain of the eukaryotic alpha-galactosidases. Alpha-N-acetylgalactosaminidase (3.2.1.49 from EC) [] catalyzes the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D- galactosaminides. In man, the deficiency of this enzyme is the cause of Schindler and Kanzaki diseases. The sequence of this enzyme is highly related to that of the eukaryotic alpha-galactosidases.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1KTC_A 1KTB_A 1UAS_A 3H55_A 3H53_A 3IGU_B 3H54_A 3LRM_A 3LRL_A 3LRK_A ....
Probab=44.63 E-value=35 Score=31.31 Aligned_cols=41 Identities=24% Similarity=0.404 Sum_probs=29.5
Q ss_pred HHHHHHHHcCCCEEEEecCC------------------CchhhHHHHHHHHHHHcCCcC
Q 030804 131 MIAKSCLEKGITKVAFDRGG------------------YPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 131 ~LAkra~e~GI~~VvfDRgg------------------~~YhGrVkAlad~aRe~GL~f 171 (171)
.+++.+++.|++-++.|=|= .++-+-+++|++.+++.|++|
T Consensus 62 ~~a~~~~~~G~e~fviDDGW~~~r~~d~~~~GdW~~~~~kFP~Gl~~l~~~i~~~Gmk~ 120 (394)
T PF02065_consen 62 ELADAAAELGYEYFVIDDGWFGGRDDDNAGLGDWEPDPKKFPNGLKPLADYIHSLGMKF 120 (394)
T ss_dssp HHHHHHHHHT-SEEEE-SSSBCTESTTTSTTSBECBBTTTSTTHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHhCCEEEEEcCccccccCCCcccCCceeEChhhhCCcHHHHHHHHHHCCCeE
Confidence 45677799999999998431 244445999999999999986
No 88
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=44.28 E-value=51 Score=30.34 Aligned_cols=52 Identities=23% Similarity=0.488 Sum_probs=44.5
Q ss_pred CCcHHHHHHHHHH-----------------HHHHHHHcCCCEEEEecCCCch-hhHHHHHHHHHHHcCCc
Q 030804 119 GPTIEVSKKVGEM-----------------IAKSCLEKGITKVAFDRGGYPY-HGRIQALADAAREYGLQ 170 (171)
Q Consensus 119 ~~n~~AA~~VG~~-----------------LAkra~e~GI~~VvfDRgg~~Y-hGrVkAlad~aRe~GL~ 170 (171)
..|.++|..++++ ||-.|.+.|++++=.+.|.... ..++..+++.+++.|+.
T Consensus 63 v~~~~~a~al~~I~~~~~iPlvADIHFd~~lAl~a~~~G~~~iRINPGNig~~~~~v~~vv~~ak~~~ip 132 (360)
T PRK00366 63 VPDMEAAAALPEIKKQLPVPLVADIHFDYRLALAAAEAGADALRINPGNIGKRDERVREVVEAAKDYGIP 132 (360)
T ss_pred cCCHHHHHhHHHHHHcCCCCEEEecCCCHHHHHHHHHhCCCEEEECCCCCCchHHHHHHHHHHHHHCCCC
Confidence 4678888888864 7889999999999888887766 78999999999999975
No 89
>COG3345 GalA Alpha-galactosidase [Carbohydrate transport and metabolism]
Probab=44.09 E-value=33 Score=33.69 Aligned_cols=86 Identities=21% Similarity=0.249 Sum_probs=55.8
Q ss_pred CcHHHHHHHHHHhhhhhcC--CCCCceEEEEeeCCcEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHH
Q 030804 53 TKREDRTARHSRIRKKIDG--TPERPRLCVFRSNKHLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGE 130 (171)
Q Consensus 53 ~r~~~r~~R~~RirkKi~g--t~~rPRL~V~rSnkhiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~ 130 (171)
.=...-+.-+-=+|..+.- -.++||=.-.+|=.++|..+- -.. + .
T Consensus 266 gl~~lsq~y~~~v~~~i~~~~~~~kprPi~~nsWea~Yfd~t---~e~-----------i-------------------l 312 (687)
T COG3345 266 GLNGLSQKYAELVRMEIVPRPRVKKPRPIGWNSWEAYYFDFT---EEE-----------I-------------------L 312 (687)
T ss_pred CcchHHHHHHHHHHhhcCcccccCCCCcceeeceeeeeecCC---HHH-----------H-------------------H
Confidence 3344455555556666544 245666666666555555331 000 0 2
Q ss_pred HHHHHHHHcCCCEEEEecCCC------------------chhhHHHHHHHHHHHcCCcC
Q 030804 131 MIAKSCLEKGITKVAFDRGGY------------------PYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 131 ~LAkra~e~GI~~VvfDRgg~------------------~YhGrVkAlad~aRe~GL~f 171 (171)
.+++-|++.|++-++.|-|-+ +|.+-|.-++++++|.|++|
T Consensus 313 e~vk~akk~gvE~FvlDDGwfg~rndd~~slGDWlv~seKfPsgiE~li~~I~e~Gl~f 371 (687)
T COG3345 313 ENVKEAKKFGVELFVLDDGWFGGRNDDLKSLGDWLVNSEKFPSGIEELIEAIAENGLIF 371 (687)
T ss_pred HHHHHHhhcCeEEEEEccccccccCcchhhhhceecchhhccccHHHHHHHHHHcCCcc
Confidence 356677888899999886544 57777999999999999987
No 90
>PRK09526 lacI lac repressor; Reviewed
Probab=43.66 E-value=84 Score=26.29 Aligned_cols=42 Identities=19% Similarity=0.256 Sum_probs=29.2
Q ss_pred HHHHHHHHHHcCCCEEEEecC---CCchhhHHHHHHHHHHHcCCc
Q 030804 129 GEMIAKSCLEKGITKVAFDRG---GYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 129 G~~LAkra~e~GI~~VvfDRg---g~~YhGrVkAlad~aRe~GL~ 170 (171)
|+.+++.+.+.|..++.|=.| ......|...|.+++.++|++
T Consensus 169 ~~~a~~~L~~~G~~~I~~l~g~~~~~~~~~R~~Gf~~al~~~gi~ 213 (342)
T PRK09526 169 TRLGVEHLVELGHQRIALLAGPESSVSARLRLAGWLEYLTDYQLQ 213 (342)
T ss_pred HHHHHHHHHHCCCCeEEEEeCCCccccHHHHHHHHHHHHHHcCCC
Confidence 444555555679999976332 223358999999999999985
No 91
>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription
Probab=43.60 E-value=95 Score=24.63 Aligned_cols=44 Identities=25% Similarity=0.413 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHcCCCEEEEe--cCC--CchhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAFD--RGG--YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfD--Rgg--~~YhGrVkAlad~aRe~GL~ 170 (171)
..|+.+++.+.+.|..++.|= ... .....|.+.|.+.+.++|++
T Consensus 98 ~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~ 145 (265)
T cd06291 98 EGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLE 145 (265)
T ss_pred HHHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHHHcCCC
Confidence 345555555666798888653 222 22348899999999999985
No 92
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=43.23 E-value=77 Score=24.00 Aligned_cols=44 Identities=27% Similarity=0.406 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHcCCCEEEE--ecCCCchhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAF--DRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~Vvf--DRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
..|+.+++.+.+.|..++.+ +........++.+|.+.+.+.|++
T Consensus 110 ~~~~~~~~~l~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (269)
T cd01391 110 QAGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAGIE 155 (269)
T ss_pred HHHHHHHHHHHHhCCceEEEEecCCcchhhHHHHHHHHHHHhcCcE
Confidence 45666777777777888854 333234578899999999998854
No 93
>smart00812 Alpha_L_fucos Alpha-L-fucosidase. O-Glycosyl hydrolases (EC 3.2.1.-) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site PUBMED:. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Family 29 encompasses alpha-L-fucosidases, which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Deficiency of alpha-L-fucosidase results in the lysosomal storage disease fucosidosis.
Probab=43.00 E-value=45 Score=30.34 Aligned_cols=42 Identities=31% Similarity=0.407 Sum_probs=32.5
Q ss_pred HHHHHHHHHcCCCEEEEec---CCCc----------------hhhHHHHHHHHHHHcCCcC
Q 030804 130 EMIAKSCLEKGITKVAFDR---GGYP----------------YHGRIQALADAAREYGLQF 171 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDR---gg~~----------------YhGrVkAlad~aRe~GL~f 171 (171)
+..|+.++++|.+-||+-- .||- -..-|+.|++++|+.||+|
T Consensus 84 ~~Wa~~~k~AGakY~vlTaKHHDGF~lw~S~~t~~n~~~~~pkrDiv~el~~A~rk~Glk~ 144 (384)
T smart00812 84 EEWADLFKKAGAKYVVLTAKHHDGFCLWDSKYSNWNAVDTGPKRDLVGELADAVRKRGLKF 144 (384)
T ss_pred HHHHHHHHHcCCCeEEeeeeecCCccccCCCCCCCcccCCCCCcchHHHHHHHHHHcCCeE
Confidence 6789999999999888741 1211 1356999999999999986
No 94
>cd06339 PBP1_YraM_LppC_lipoprotein_like Periplasmic binding component of lipoprotein LppC, an immunodominant antigen. This subgroup includes periplasmic binding component of lipoprotein LppC, an immunodominant antigen, whose molecular function is not characterized. Members of this subgroup are predicted to be involved in transport of lipid compounds, and they are sequence similar to the family of ABC-type hydrophobic amino acid transporters (HAAT).
Probab=42.69 E-value=59 Score=27.81 Aligned_cols=44 Identities=14% Similarity=0.060 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHcCCCEEEEecCCCch-hhHHHHHHHHHHHcCCcC
Q 030804 128 VGEMIAKSCLEKGITKVAFDRGGYPY-HGRIQALADAAREYGLQF 171 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRgg~~Y-hGrVkAlad~aRe~GL~f 171 (171)
.+..+++-+.+.|+++|.+=-..+.| .+...+|.+.+.+.|+++
T Consensus 111 ~~~~~~~~~~~~g~k~vaii~~~~~~g~~~~~~f~~~~~~~G~~v 155 (336)
T cd06339 111 EARRAAEYARSQGKRRPLVLAPDGAYGQRVADAFRQAWQQLGGTV 155 (336)
T ss_pred HHHHHHHHHHhcCccceEEEecCChHHHHHHHHHHHHHHHcCCce
Confidence 35667777777899887443223455 488899999999999864
No 95
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=42.55 E-value=72 Score=25.47 Aligned_cols=49 Identities=20% Similarity=0.186 Sum_probs=32.2
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecCCCch---hhHHHHHHHHHHHc-CCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRGGYPY---HGRIQALADAAREY-GLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg~~Y---hGrVkAlad~aRe~-GL~ 170 (171)
.+.++.+.+++.|.+++ .|..++.|=.+...+ .-|.+.|.++++++ |++
T Consensus 104 d~~~~~~~~~~~l~~~~--~g~~~i~~i~~~~~~~~~~~r~~gf~~a~~~~~~~~ 156 (273)
T cd06310 104 DNVAAGKLAAEALAELL--GKKGKVAVISFVPGSSTTDQREEGFLEGLKEYPGIE 156 (273)
T ss_pred ChHHHHHHHHHHHHHHc--CCCceEEEEeCCCCCccHHHHHHHHHHHHHhCCCcE
Confidence 34556666666666553 377888765432222 45889999999998 874
No 96
>PF02826 2-Hacid_dh_C: D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; InterPro: IPR006140 A number of NAD-dependent 2-hydroxyacid dehydrogenases which seem to be specific for the D-isomer of their substrate have been shown to be functionally and structurally related. All contain a glycine-rich region located in the central section of these enzymes, this region corresponds to the NAD-binding domain. The catalytic domain is described in IPR006139 from INTERPRO ; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0048037 cofactor binding, 0055114 oxidation-reduction process; PDB: 3JTM_A 3NAQ_B 3N7U_J 3KB6_B 3GG9_A 1QP8_B 2CUK_C 2W2L_D 2W2K_A 1WWK_A ....
Probab=41.88 E-value=34 Score=27.06 Aligned_cols=25 Identities=20% Similarity=0.470 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCC
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRGGY 151 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRgg~ 151 (171)
.+|+.+|++++..|.+-++|||...
T Consensus 46 ~IG~~vA~~l~~fG~~V~~~d~~~~ 70 (178)
T PF02826_consen 46 RIGRAVARRLKAFGMRVIGYDRSPK 70 (178)
T ss_dssp HHHHHHHHHHHHTT-EEEEEESSCH
T ss_pred CCcCeEeeeeecCCceeEEecccCC
Confidence 6899999999999998889999753
No 97
>PF14488 DUF4434: Domain of unknown function (DUF4434)
Probab=41.28 E-value=52 Score=26.42 Aligned_cols=41 Identities=24% Similarity=0.413 Sum_probs=30.3
Q ss_pred HHHHHHHHcCCCEEEEecCCC----ch--hh-----------HHHHHHHHHHHcCCcC
Q 030804 131 MIAKSCLEKGITKVAFDRGGY----PY--HG-----------RIQALADAAREYGLQF 171 (171)
Q Consensus 131 ~LAkra~e~GI~~VvfDRgg~----~Y--hG-----------rVkAlad~aRe~GL~f 171 (171)
.+-+..++.||+.|++-+.++ -| .+ -|..+++++.+.||+|
T Consensus 24 ~~~~~m~~~GidtlIlq~~~~~~~~~yps~~~~~~~~~~~~d~l~~~L~~A~~~Gmkv 81 (166)
T PF14488_consen 24 EEFRAMKAIGIDTLILQWTGYGGFAFYPSKLSPGGFYMPPVDLLEMILDAADKYGMKV 81 (166)
T ss_pred HHHHHHHHcCCcEEEEEEeecCCcccCCccccCccccCCcccHHHHHHHHHHHcCCEE
Confidence 345667889999998764322 12 22 6899999999999986
No 98
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=41.18 E-value=96 Score=26.17 Aligned_cols=47 Identities=13% Similarity=0.175 Sum_probs=31.7
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRGG---YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~ 170 (171)
.|..+.+. +++.+.+.|..++.|=.+. .....|++.|.+++.++|+.
T Consensus 159 D~~~~~~~----a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~ 208 (346)
T PRK10401 159 DNVSGARM----ATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWMSALKEQGII 208 (346)
T ss_pred CcHHHHHH----HHHHHHHCCCCeEEEEeCCCcCcchHHHHHHHHHHHHHcCCC
Confidence 34455444 4444556799998654322 22368999999999999985
No 99
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=41.15 E-value=22 Score=23.75 Aligned_cols=40 Identities=23% Similarity=0.387 Sum_probs=26.6
Q ss_pred HHHHHHHHHHcC--CCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 129 GEMIAKSCLEKG--ITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 129 G~~LAkra~e~G--I~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
|.-+...|++.| |.++.++.+ ..+.++..+.+.+.+.|++
T Consensus 4 G~~~V~eaL~~~~~i~~l~~~~~--~~~~~~~~i~~~~~~~~i~ 45 (76)
T PF08032_consen 4 GRHAVEEALKSGPRIKKLFVTEE--KADKRIKEILKLAKKKGIP 45 (76)
T ss_dssp SHHHHHHHHHCTGGEEEEEEETT-----CCTHHHHHHHHHCT-E
T ss_pred EHHHHHHHHcCCCCccEEEEEcC--ccchhHHHHHHHHHHcCCe
Confidence 556677777777 778888776 4555577788888877765
No 100
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=40.97 E-value=1e+02 Score=24.41 Aligned_cols=42 Identities=17% Similarity=0.188 Sum_probs=29.3
Q ss_pred HHHHHHHHHHcCCCEEEEe--cCC-CchhhHHHHHHHHHHHcCCc
Q 030804 129 GEMIAKSCLEKGITKVAFD--RGG-YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 129 G~~LAkra~e~GI~~VvfD--Rgg-~~YhGrVkAlad~aRe~GL~ 170 (171)
+..+++.+.+.|..+|.|= ... ..-..|+..|.+++.++|++
T Consensus 104 ~~~~~~~l~~~g~~~I~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 148 (265)
T cd06299 104 MTEAVSLLVALGHKKIGYISGPQDTSTGRERLEAFRQACASLGLE 148 (265)
T ss_pred HHHHHHHHHHcCCCcEEEEeCCCCcccHHHHHHHHHHHHHHCCCC
Confidence 4555666667788888652 222 23358999999999999964
No 101
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=40.08 E-value=35 Score=25.71 Aligned_cols=37 Identities=27% Similarity=0.236 Sum_probs=17.4
Q ss_pred HHHHcCCCEEEEecC-CCch-hhHHHHHHHHHHHcCCcC
Q 030804 135 SCLEKGITKVAFDRG-GYPY-HGRIQALADAAREYGLQF 171 (171)
Q Consensus 135 ra~e~GI~~VvfDRg-g~~Y-hGrVkAlad~aRe~GL~f 171 (171)
.+.+.|++.|+.-|. +... ..--..+.+.+.+.||.|
T Consensus 22 ~la~~GfktVInlRpd~E~~~qp~~~~~~~~a~~~Gl~y 60 (110)
T PF04273_consen 22 QLAAQGFKTVINLRPDGEEPGQPSSAEEAAAAEALGLQY 60 (110)
T ss_dssp HHHHCT--EEEE-S-TTSTTT-T-HHCHHHHHHHCT-EE
T ss_pred HHHHCCCcEEEECCCCCCCCCCCCHHHHHHHHHHcCCeE
Confidence 455677777777663 2222 234455666677777653
No 102
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=39.18 E-value=57 Score=29.94 Aligned_cols=43 Identities=14% Similarity=0.139 Sum_probs=33.8
Q ss_pred HHHHHHHHHHcCCCEEEEecCCCchh-hHHHHHHHHHHHcCCcC
Q 030804 129 GEMIAKSCLEKGITKVAFDRGGYPYH-GRIQALADAAREYGLQF 171 (171)
Q Consensus 129 G~~LAkra~e~GI~~VvfDRgg~~Yh-GrVkAlad~aRe~GL~f 171 (171)
-++|.+-+.+.||+.|.+++....|. -|-+++.+.+.+.||++
T Consensus 76 ~~~l~~l~~~~~i~~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~ 119 (475)
T TIGR02766 76 VAALLDCVRSTGATRLFFNHLYDPVSLVRDHRAKEVLTAQGISV 119 (475)
T ss_pred HHHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHcCCEE
Confidence 34567777899999999999865664 56778888899999864
No 103
>cd06333 PBP1_ABC-type_HAAT_like Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. This subgroup includes the type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. Members of this subgroup are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=38.60 E-value=88 Score=25.85 Aligned_cols=45 Identities=24% Similarity=0.394 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCCch-hhHHHHHHHHHHHcCCcC
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRGGYPY-HGRIQALADAAREYGLQF 171 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRgg~~Y-hGrVkAlad~aRe~GL~f 171 (171)
..++.+++.+.+.|.++|.+=-....| ..+...|.+.+.+.|+++
T Consensus 119 ~~~~~~~~~l~~~g~~~vail~~~~~~~~~~~~~~~~~~~~~G~~v 164 (312)
T cd06333 119 LMAEAILADMKKRGVKTVAFIGFSDAYGESGLKELKALAPKYGIEV 164 (312)
T ss_pred HHHHHHHHHHHHcCCCEEEEEecCcHHHHHHHHHHHHHHHHcCCEE
Confidence 345556666677899999654332334 478889999999999863
No 104
>TIGR03581 EF_0839 conserved hypothetical protein EF_0839/AHA_3917. Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.
Probab=38.22 E-value=85 Score=27.31 Aligned_cols=71 Identities=21% Similarity=0.168 Sum_probs=46.5
Q ss_pred EEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEE-EEecCCCchhhHHHHHHHHHHHcC
Q 030804 90 QVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKV-AFDRGGYPYHGRIQALADAAREYG 168 (171)
Q Consensus 90 QvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~V-vfDRgg~~YhGrVkAlad~aRe~G 168 (171)
-+|.+.+..=.+-.||-...-+.. ..--.++.| ..-+++.|++.+ .|.-+|-++-.-++|+++++-++|
T Consensus 108 ~LvsPTG~~G~VkISTGp~Ss~~~---~~iV~vetA-------iaml~dmG~~SiKffPM~Gl~~leE~~avA~aca~~g 177 (236)
T TIGR03581 108 GLVSPTGTPGLVNISTGPLSSQGK---EAIVPIETA-------IAMLKDMGGSSVKFFPMGGLKHLEEYAAVAKACAKHG 177 (236)
T ss_pred EeecCCCccceEEeccCcccccCC---CceeeHHHH-------HHHHHHcCCCeeeEeecCCcccHHHHHHHHHHHHHcC
Confidence 345555444445555554432211 011234444 345789999999 567899999999999999999999
Q ss_pred Cc
Q 030804 169 LQ 170 (171)
Q Consensus 169 L~ 170 (171)
+.
T Consensus 178 ~~ 179 (236)
T TIGR03581 178 FY 179 (236)
T ss_pred Cc
Confidence 74
No 105
>PRK08085 gluconate 5-dehydrogenase; Provisional
Probab=37.91 E-value=79 Score=25.33 Aligned_cols=39 Identities=18% Similarity=0.202 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHc
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREY 167 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~ 167 (171)
..-+|..+++++.+.|.+-+..||+. .+...+.+.+++.
T Consensus 18 s~giG~~ia~~L~~~G~~vvl~~r~~----~~~~~~~~~l~~~ 56 (254)
T PRK08085 18 AQGIGFLLATGLAEYGAEIIINDITA----ERAELAVAKLRQE 56 (254)
T ss_pred CChHHHHHHHHHHHcCCEEEEEcCCH----HHHHHHHHHHHhc
Confidence 34689999999999998777888862 3445555555443
No 106
>PF01120 Alpha_L_fucos: Alpha-L-fucosidase; InterPro: IPR000933 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Family 29 (GH29 from CAZY) encompasses alpha-L-fucosidases (3.2.1.51 from EC) [], which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Alpha-L-fucosidase is responsible for hydrolysing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Fucosylated glycoconjugates are involved in numerous biological events, making alpha-l-fucosidases, the enzymes responsible for their processing, critically important. Deficiency in alpha-l-fucosidase activity is associated with fucosidosis, a lysosomal storage disorder characterised by rapid neurodegeneration, resulting in severe mental and motor deterioration []. The enzyme is a hexamer and displays a two-domain fold, composed of a catalytic (beta/alpha)(8)-like domain and a C-terminal beta-sandwich domain []. Drosophila melanogaster spermatozoa contains an alpha-l-fucosidase that might be involved in fertilisation by interacting with alpha-l-fucose residues on the micropyle of the eggshell []. In human sperm, membrane-associated alpha-l-fucosidase is stable for extended periods of time, which is made possible by membrane domains and compartmentalisation. These help preserve protein integrity []. ; GO: 0004560 alpha-L-fucosidase activity, 0005975 carbohydrate metabolic process; PDB: 3EYP_B 2ZX6_A 2ZWY_B 2ZX8_B 2WSP_A 2ZXA_A 2ZWZ_B 1ODU_B 1HL9_A 2ZX5_B ....
Probab=37.79 E-value=49 Score=29.34 Aligned_cols=43 Identities=33% Similarity=0.530 Sum_probs=30.1
Q ss_pred HHHHHHHHHHcCCCEEEEe---cCCCc----------------hhhHHHHHHHHHHHcCCcC
Q 030804 129 GEMIAKSCLEKGITKVAFD---RGGYP----------------YHGRIQALADAAREYGLQF 171 (171)
Q Consensus 129 G~~LAkra~e~GI~~VvfD---Rgg~~----------------YhGrVkAlad~aRe~GL~f 171 (171)
.+..++.++++|.+-||+- ..||- ...-|+.|++++|+.||+|
T Consensus 93 ~dqW~~~ak~aGakY~VlTakHHDGF~LW~S~~t~~~v~~~~~krDiv~El~~A~rk~Glk~ 154 (346)
T PF01120_consen 93 ADQWAKLAKDAGAKYVVLTAKHHDGFCLWPSKYTDYNVVNSGPKRDIVGELADACRKYGLKF 154 (346)
T ss_dssp HHHHHHHHHHTT-SEEEEEEE-TT--BSS--TT-SSBGGGGGGTS-HHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHcCCCEEEeehhhcCccccCCCCCCcccccCCCCCCCHHHHHHHHHHHcCCeE
Confidence 3568899999999999874 12221 1345999999999999986
No 107
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=37.68 E-value=50 Score=24.65 Aligned_cols=41 Identities=12% Similarity=0.238 Sum_probs=28.3
Q ss_pred HHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 130 EMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
+.|.+.+.+.+|++|+..-. ..-++.|+.+.+.+++.|+++
T Consensus 131 ~~l~~~~~~~~id~v~ial~-~~~~~~i~~ii~~~~~~~v~v 171 (175)
T PF13727_consen 131 DDLPELVREHDIDEVIIALP-WSEEEQIKRIIEELENHGVRV 171 (175)
T ss_dssp GGHHHHHHHHT--EEEE--T-TS-HHHHHHHHHHHHTTT-EE
T ss_pred HHHHHHHHhCCCCEEEEEcC-ccCHHHHHHHHHHHHhCCCEE
Confidence 34667778899999988753 345789999999999999864
No 108
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=37.45 E-value=90 Score=25.18 Aligned_cols=48 Identities=13% Similarity=0.083 Sum_probs=32.6
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCCEEEEe---cCCC------chhhHHHHHHHHHHHcCCcC
Q 030804 119 GPTIEVSKKVGEMIAKSCLEKGITKVAFD---RGGY------PYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 119 ~~n~~AA~~VG~~LAkra~e~GI~~VvfD---Rgg~------~YhGrVkAlad~aRe~GL~f 171 (171)
..|..+++..++.|.++ ..++.|= .+.. .-+.|++.|.+++.++|+++
T Consensus 96 ~d~~~~g~~a~~~L~~~-----~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~~~~~~~g~~~ 152 (269)
T cd06297 96 LDNRLGGRLAGAYLADF-----PGRIGAITVEEEPDRAFRRTVFAERRAGFQQALKDAGRPF 152 (269)
T ss_pred ECcHHHHHHHHHHHHHh-----CCceEEEeCccccccccccccHHHHHHHHHHHHHHcCCCC
Confidence 45778888888777776 2444332 1212 23589999999999999863
No 109
>PF07071 DUF1341: Protein of unknown function (DUF1341); InterPro: IPR010763 Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.; PDB: 3NZR_D 3LM7_A 3M0Z_B 3M6Y_A 3N73_A 3MUX_A.
Probab=37.22 E-value=81 Score=27.14 Aligned_cols=37 Identities=22% Similarity=0.328 Sum_probs=27.5
Q ss_pred HHHHHcCCCEEE-EecCCCchhhHHHHHHHHHHHcCCc
Q 030804 134 KSCLEKGITKVA-FDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 134 kra~e~GI~~Vv-fDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.-+++.|+..+- |.-+|..+-.-++++++++-++|+.
T Consensus 142 aml~dmG~~SiKffPm~Gl~~leE~~avAkA~a~~g~~ 179 (218)
T PF07071_consen 142 AMLKDMGGSSIKFFPMGGLKHLEELKAVAKACARNGFT 179 (218)
T ss_dssp HHHHHTT--EEEE---TTTTTHHHHHHHHHHHHHCT-E
T ss_pred HHHHHcCCCeeeEeecCCcccHHHHHHHHHHHHHcCce
Confidence 457889999995 5679999999999999999999974
No 110
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=37.07 E-value=93 Score=24.91 Aligned_cols=49 Identities=22% Similarity=0.304 Sum_probs=33.1
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecCC--C-chhhHHHHHHHHHHHc-CCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRGG--Y-PYHGRIQALADAAREY-GLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg--~-~YhGrVkAlad~aRe~-GL~ 170 (171)
.+.++++.+++.|.+.. .|..++.|=.+. . .-+.|.+.|.+.+.++ |++
T Consensus 103 d~~~~g~~~~~~l~~~~--~g~~~i~~l~~~~~~~~~~~R~~g~~~~l~~~~~~~ 155 (270)
T cd06308 103 DNYEIGRQAGEYIANLL--PGKGNILEIWGLEGSSPAIERHDGFKEALSKYPKIK 155 (270)
T ss_pred CcHHHHHHHHHHHHHHc--CCCceEEEEECCCCCchHHHHHHHHHHHHHHCCCCE
Confidence 45566666666666544 477888664332 2 2357899999999999 874
No 111
>PF00933 Glyco_hydro_3: Glycosyl hydrolase family 3 N terminal domain; InterPro: IPR001764 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 3 GH3 from CAZY comprises enzymes with a number of known activities; beta-glucosidase (3.2.1.21 from EC); beta-xylosidase (3.2.1.37 from EC); N-acetyl beta-glucosaminidase (3.2.1.52 from EC); glucan beta-1,3-glucosidase (3.2.1.58 from EC); cellodextrinase (3.2.1.74 from EC); exo-1,3-1,4-glucanase (3.2.1 from EC). These enzymes are two-domain globular proteins that are N-glycosylated at three sites []. This domain is often N-terminal to the glycoside hydrolase family 3, C-terminal domain IPR002772 from INTERPRO.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1Y65_A 2OXN_A 3GS6_A 1TR9_A 3GSM_A 3UT0_B 3RRX_A 3USZ_A 2X42_A 2X40_A ....
Probab=36.93 E-value=71 Score=27.50 Aligned_cols=51 Identities=22% Similarity=0.262 Sum_probs=35.3
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCCEE---EEe--cCCC--c----hh------h-HHHHHHHHHHHcCC
Q 030804 119 GPTIEVSKKVGEMIAKSCLEKGITKV---AFD--RGGY--P----YH------G-RIQALADAAREYGL 169 (171)
Q Consensus 119 ~~n~~AA~~VG~~LAkra~e~GI~~V---vfD--Rgg~--~----Yh------G-rVkAlad~aRe~GL 169 (171)
+.|.+.++.+|..+|+.+.+.||+-. +.| |+.. + |+ + -..|++++++++|+
T Consensus 81 t~d~~~a~~~g~~~a~el~~~Gin~~~aPv~Dv~~~p~~~~~~rsfgeDp~~v~~~~~a~v~G~q~~gv 149 (299)
T PF00933_consen 81 TWDPELAYEVGRIIARELRALGINVNFAPVVDVNRNPRWGRGERSFGEDPDLVAEMARAFVRGLQGAGV 149 (299)
T ss_dssp HTCHHHHHHHHHHHHHHHHHTT-SEEEEEB----SSTTSTTGGGSS-SSHHHHHHHHHHHHHHHHCTTS
T ss_pred hccchHHHHHHHHHHHHHHHhhhccccccceeeeeeccccccccccchhHHHHHHHHHHHhcccccccc
Confidence 46889999999999999999999863 344 2211 1 11 1 25689999999887
No 112
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=36.57 E-value=1.1e+02 Score=25.41 Aligned_cols=47 Identities=13% Similarity=0.089 Sum_probs=32.7
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecCC---Cch-hhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRGG---YPY-HGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg---~~Y-hGrVkAlad~aRe~GL~ 170 (171)
.|..++ +.+++.+.+.|..++.|=.+. ..+ ..|.++|.++++++|++
T Consensus 155 D~~~~~----~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~~R~~gf~~a~~~~gi~ 205 (311)
T TIGR02405 155 DDYGAI----ELLMANLYQQGHRHISFLGVDPSDKTTGLMRHNAYLAYCESANLE 205 (311)
T ss_pred CcHHHH----HHHHHHHHHcCCCcEEEEccCcccchhHHHHHHHHHHHHHHcCCC
Confidence 345555 455666666899999764321 122 57999999999999985
No 113
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=36.19 E-value=68 Score=28.90 Aligned_cols=42 Identities=14% Similarity=0.177 Sum_probs=32.0
Q ss_pred HHHHHHHHHcCCCEEEEecCCCch-hhHHHHHHHHHHHcCCcC
Q 030804 130 EMIAKSCLEKGITKVAFDRGGYPY-HGRIQALADAAREYGLQF 171 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDRgg~~Y-hGrVkAlad~aRe~GL~f 171 (171)
++|.+-+.+.||+.|++|+..-.| .-+-..+++.+.+.|+.+
T Consensus 86 ~vl~~L~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~ 128 (429)
T TIGR02765 86 DVLPELIKELGVRTVFLHQEVGSEEKSVERLLQQALARLGIHV 128 (429)
T ss_pred HHHHHHHHHhCCCEEEEeccCCHHHHHHHHHHHHHHHhcCceE
Confidence 355566678899999999975444 345889999999999863
No 114
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=36.14 E-value=67 Score=29.69 Aligned_cols=42 Identities=26% Similarity=0.377 Sum_probs=32.9
Q ss_pred HHHHHHHHHcCCCEEEEecCCCchh-hHHHHHHHHHHHcCCcC
Q 030804 130 EMIAKSCLEKGITKVAFDRGGYPYH-GRIQALADAAREYGLQF 171 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDRgg~~Yh-GrVkAlad~aRe~GL~f 171 (171)
++|.+-+.+.||+.|+|++..-.|. .+-+.+.+.+.+.|+++
T Consensus 80 ~vl~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~ 122 (471)
T TIGR03556 80 QLIPQLAQQLGAKAVYWNLDVEPYGRKRDRAVAAALKEAGIAV 122 (471)
T ss_pred HHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHCCCEE
Confidence 3566667788999999998755553 66888999999999863
No 115
>PF03928 DUF336: Domain of unknown function (DUF336); InterPro: IPR005624 This entry contains uncharacterised proteins, including GlcG P45504 from SWISSPROT. The alignment contains many conserved motifs that are suggestive of cofactor binding and enzymatic activity.; PDB: 2A2L_D 3FPW_A 3FPV_E.
Probab=36.03 E-value=68 Score=24.28 Aligned_cols=32 Identities=28% Similarity=0.464 Sum_probs=25.3
Q ss_pred cHHHHHHHHHHHHHHHHHcCC--CEEEEecCCCc
Q 030804 121 TIEVSKKVGEMIAKSCLEKGI--TKVAFDRGGYP 152 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI--~~VvfDRgg~~ 152 (171)
+.+.|..++...-+.|.+.|. .-.+.|++|+.
T Consensus 4 ~~~~A~~l~~~a~~~a~~~g~~v~iaVvd~~G~~ 37 (132)
T PF03928_consen 4 TLEDAWKLGDAAVEEARERGLPVSIAVVDAGGHL 37 (132)
T ss_dssp -HHHHHHHHHHHHHHHHHTT---EEEEEETTS-E
T ss_pred CHHHHHHHHHHHHHHHHHhCCCeEEEEEECCCCE
Confidence 568999999999999999994 45578988754
No 116
>PF02789 Peptidase_M17_N: Cytosol aminopeptidase family, N-terminal domain; InterPro: IPR008283 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The two zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3PEI_A 1GYT_C 3JRU_A 3H8F_D 3H8G_F 3H8E_A 3KZW_L 1LAP_A 1LAN_A 1LCP_B ....
Probab=35.96 E-value=1.7e+02 Score=21.11 Aligned_cols=51 Identities=24% Similarity=0.170 Sum_probs=38.3
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecC--CCchhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRG--GYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRg--g~~YhGrVkAlad~aRe~GL~ 170 (171)
-+.+..+..+-.+++.+++.++.++.++-. +...-.-+.++++++..+.-.
T Consensus 66 ~~~~~~r~a~~~~~~~l~~~~~~~v~i~l~~~~~~~~~~~~~~~~g~~l~~Y~ 118 (126)
T PF02789_consen 66 LTAESLRKAGAAAARALKKLKVKSVAIDLPIDGENSDEAAEAAAEGALLGSYR 118 (126)
T ss_dssp BCHHHHHHHHHHHHHHHHHTT-SEEEEEGCSSBTTCHHHHHHHHHHHHHHT--
T ss_pred CCHHHHHHHHHHHHHHHhhCCceEEEEeCcccccCcHHHHHHHHHHHHHcCcc
Confidence 367899999999999999999999987654 222238899999998766543
No 117
>TIGR02571 ComEB ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.
Probab=35.81 E-value=58 Score=25.92 Aligned_cols=35 Identities=23% Similarity=0.448 Sum_probs=23.6
Q ss_pred HHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 133 AKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 133 Akra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
+......||++|+|-.. |...+ +-.+-+++.||++
T Consensus 101 a~ai~~agI~~Vvy~~~-~~~~~---~~~~~l~~~gi~v 135 (151)
T TIGR02571 101 TKSIIQAGIKKIYYAQD-YHNHP---YAIELFEQAGVEL 135 (151)
T ss_pred HHHHHHhCCCEEEEccC-CCCcH---HHHHHHHHCCCEE
Confidence 44456789999999632 32222 3468899999874
No 118
>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria. They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.
Probab=35.68 E-value=56 Score=29.04 Aligned_cols=48 Identities=21% Similarity=0.344 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHcCCCEE---EEecCC-Cc-hhhHHHHHHHHHHHcCCcC
Q 030804 124 VSKKVGEMIAKSCLEKGITKV---AFDRGG-YP-YHGRIQALADAAREYGLQF 171 (171)
Q Consensus 124 AA~~VG~~LAkra~e~GI~~V---vfDRgg-~~-YhGrVkAlad~aRe~GL~f 171 (171)
.-..-|+.|+..|++.|-+.. +|.|-- |. ..-|..-+-+.+.+.||+|
T Consensus 114 D~~~~G~~i~~~Ak~mGAktFVh~sfprhms~~~l~~Rr~~M~~~C~~lGi~f 166 (275)
T PF12683_consen 114 DEISRGYTIVWAAKKMGAKTFVHYSFPRHMSYELLARRRDIMEEACKDLGIKF 166 (275)
T ss_dssp -HHHHHHHHHHHHHHTT-S-EEEEEETTGGGSHHHHHHHHHHHHHHHHCT--E
T ss_pred chhhccHHHHHHHHHcCCceEEEEechhhcchHHHHHHHHHHHHHHHHcCCeE
Confidence 345679999999999998865 478842 22 2567888889999999987
No 119
>PRK12548 shikimate 5-dehydrogenase; Provisional
Probab=35.42 E-value=1e+02 Score=26.54 Aligned_cols=40 Identities=15% Similarity=0.296 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHcCCCEE-EEecCCCchhhHHHHHHHHHHHc
Q 030804 127 KVGEMIAKSCLEKGITKV-AFDRGGYPYHGRIQALADAAREY 167 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~V-vfDRgg~~YhGrVkAlad~aRe~ 167 (171)
-+|+.++..+.+.|+++| ++||.. .+..+.+.+++.+.+.
T Consensus 136 GagrAia~~La~~G~~~V~I~~R~~-~~~~~a~~l~~~l~~~ 176 (289)
T PRK12548 136 GAATAIQVQCALDGAKEITIFNIKD-DFYERAEQTAEKIKQE 176 (289)
T ss_pred HHHHHHHHHHHHCCCCEEEEEeCCc-hHHHHHHHHHHHHhhc
Confidence 566778888889999966 789973 2345677777776554
No 120
>COG1052 LdhA Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]
Probab=35.25 E-value=56 Score=29.12 Aligned_cols=24 Identities=21% Similarity=0.475 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCC
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
.+|+.+|++++..|.+-++|||..
T Consensus 156 rIG~avA~r~~~Fgm~v~y~~~~~ 179 (324)
T COG1052 156 RIGQAVARRLKGFGMKVLYYDRSP 179 (324)
T ss_pred HHHHHHHHHHhcCCCEEEEECCCC
Confidence 689999999999999999999875
No 121
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=35.24 E-value=1.1e+02 Score=24.58 Aligned_cols=49 Identities=18% Similarity=0.236 Sum_probs=31.6
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEec---CCCchhhHHHHHHHHHHHc-CCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDR---GGYPYHGRIQALADAAREY-GLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDR---gg~~YhGrVkAlad~aRe~-GL~ 170 (171)
.+.++.+.+++.|.++. .|..++.|=. ....-..|.++|.+.++++ |++
T Consensus 103 d~~~~g~~~~~~l~~~~--~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~ 155 (275)
T cd06320 103 DNKANGVRGAEWIIDKL--AEGGKVAIIEGKAGAFAAEQRTEGFTEAIKKASGIE 155 (275)
T ss_pred CcHHHHHHHHHHHHHHh--CCCceEEEEeCCCCCccHHHHHHHHHHHHhhCCCcE
Confidence 45566666666666553 2666775422 2222367899999999998 875
No 122
>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
Probab=35.05 E-value=1.1e+02 Score=25.15 Aligned_cols=42 Identities=17% Similarity=0.089 Sum_probs=32.3
Q ss_pred HHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 130 EMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
+..++-+.|.||+--+.=-..++-..++..+++.+++.|+++
T Consensus 19 k~Aa~~L~~fgi~ye~~VvSAHRTPe~m~~ya~~a~~~g~~v 60 (162)
T COG0041 19 KKAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVKV 60 (162)
T ss_pred HHHHHHHHHcCCCeEEEEEeccCCHHHHHHHHHHHHHCCCeE
Confidence 344566677898765555566778899999999999999963
No 123
>PRK06114 short chain dehydrogenase; Provisional
Probab=34.63 E-value=1e+02 Score=24.81 Aligned_cols=38 Identities=18% Similarity=0.212 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHH
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAARE 166 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe 166 (171)
.-+|..|++++.+.|.+-++.||+.. .....+++.+++
T Consensus 18 ~gIG~~ia~~l~~~G~~v~~~~r~~~---~~~~~~~~~l~~ 55 (254)
T PRK06114 18 SGIGQRIAIGLAQAGADVALFDLRTD---DGLAETAEHIEA 55 (254)
T ss_pred chHHHHHHHHHHHCCCEEEEEeCCcc---hHHHHHHHHHHh
Confidence 35899999999999998788898642 233444444444
No 124
>PRK07791 short chain dehydrogenase; Provisional
Probab=34.62 E-value=1e+02 Score=25.77 Aligned_cols=44 Identities=23% Similarity=0.148 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCCC-----chhhHHHHHHHHHHHcC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGGY-----PYHGRIQALADAAREYG 168 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg~-----~YhGrVkAlad~aRe~G 168 (171)
+.-+|..+|+++.+.|..-++.||+.. .-..+...+++.+++.|
T Consensus 15 s~GIG~aia~~la~~G~~vii~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 63 (286)
T PRK07791 15 GGGIGRAHALAFAAEGARVVVNDIGVGLDGSASGGSAAQAVVDEIVAAG 63 (286)
T ss_pred CchHHHHHHHHHHHCCCEEEEeeCCccccccccchhHHHHHHHHHHhcC
Confidence 346899999999999998888887531 11245666666666544
No 125
>PRK12457 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=34.26 E-value=1.1e+02 Score=27.30 Aligned_cols=51 Identities=20% Similarity=0.408 Sum_probs=38.7
Q ss_pred cHHHHHHHHHHHHHHHHHcCCC---EEEEe---c-CCCchh--h---HHHHHHHHHHHcCCcC
Q 030804 121 TIEVSKKVGEMIAKSCLEKGIT---KVAFD---R-GGYPYH--G---RIQALADAAREYGLQF 171 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI~---~VvfD---R-gg~~Yh--G---rVkAlad~aRe~GL~f 171 (171)
+.+-...+++.|.+.+.+.||. +-.|| | ..|.|. | -++-|.+.-.+.||.+
T Consensus 28 s~e~~~~iA~~lk~i~~~~g~~~~fK~sf~KapRTSp~sFqG~G~eeGL~iL~~vk~~~Glpv 90 (281)
T PRK12457 28 SLDFTLDVCGEYVEVTRKLGIPFVFKASFDKANRSSIHSYRGVGLDEGLRIFEEVKARFGVPV 90 (281)
T ss_pred CHHHHHHHHHHHHHHHHHCCCcEEeeeccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCce
Confidence 4567788888888888999984 55788 5 456664 3 4888889889998863
No 126
>PF02811 PHP: PHP domain; InterPro: IPR004013 The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. This family is often associated with an N-terminal region IPR003141 from INTERPRO.; GO: 0003824 catalytic activity; PDB: 2WJE_A 3QY8_A 2WJD_A 2WJF_A 1PB0_B 1M68_A 1M65_A 3E38_B 2W9M_A 3E0F_A ....
Probab=34.05 E-value=77 Score=23.71 Aligned_cols=37 Identities=22% Similarity=0.446 Sum_probs=25.8
Q ss_pred HHHHHHHHcCCCEEEE-ecCCCchhhHHHHHHHHHHHcCCc
Q 030804 131 MIAKSCLEKGITKVAF-DRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 131 ~LAkra~e~GI~~Vvf-DRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.+.++|++.|++.+.+ |.+ .+.| +..+-+.+++.||+
T Consensus 20 e~v~~A~~~Gl~~i~iTDH~--~~~~-~~~~~~~~~~~~i~ 57 (175)
T PF02811_consen 20 EYVEQAKEKGLDAIAITDHN--NFAG-YPDFYKEAKKKGIK 57 (175)
T ss_dssp HHHHHHHHTTESEEEEEEET--TTTT-HHHHHHHHHHTTSE
T ss_pred HHHHHHHHcCCCEEEEcCCc--cccc-chHHHHHHHhcCCc
Confidence 4559999999999976 884 3333 55566666667765
No 127
>PRK06124 gluconate 5-dehydrogenase; Provisional
Probab=34.03 E-value=1e+02 Score=24.66 Aligned_cols=40 Identities=23% Similarity=0.301 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYG 168 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~G 168 (171)
..-+|..+++.+.+.|..-+.+||.. ....++++.+++.|
T Consensus 20 s~~IG~~la~~l~~~G~~v~~~~r~~----~~~~~~~~~~~~~~ 59 (256)
T PRK06124 20 ARGLGFEIARALAGAGAHVLVNGRNA----ATLEAAVAALRAAG 59 (256)
T ss_pred CchHHHHHHHHHHHcCCeEEEEeCCH----HHHHHHHHHHHhcC
Confidence 45689999999999998777888863 33445555554433
No 128
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=33.39 E-value=1.4e+02 Score=25.03 Aligned_cols=44 Identities=18% Similarity=0.252 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecC--C-CchhhHHHHHHHHHHHcCC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRG--G-YPYHGRIQALADAAREYGL 169 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRg--g-~~YhGrVkAlad~aRe~GL 169 (171)
+..|+.+++.+.++|..++.|=-+ . .....|..+|.+.+.++|+
T Consensus 159 ~~~~~~a~~~l~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~g~ 205 (327)
T PRK10339 159 ARISKEIIDFYINQGVNRIGFIGGEDEPGKADIREVAFAEYGRLKQV 205 (327)
T ss_pred HHHHHHHHHHHHHCCCCeEEEeCCccccchhhHHHHHHHHHHHHcCC
Confidence 566788888889999999976422 1 1235789999999999886
No 129
>PHA02588 cd deoxycytidylate deaminase; Provisional
Probab=33.32 E-value=67 Score=25.93 Aligned_cols=36 Identities=22% Similarity=0.252 Sum_probs=23.4
Q ss_pred HHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 133 AKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 133 Akra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
+......||++|+|.-...+..+. -.+-|+++|+++
T Consensus 115 a~aI~~~gI~rVvy~~~~~~~~~~---~~~~L~~~Gi~v 150 (168)
T PHA02588 115 AKAIAQSGIKKLVYCEKYDRNGPG---WDDILRKSGIEV 150 (168)
T ss_pred HHHHHHhCCCEEEEeeccCCCcHH---HHHHHHHCCCEE
Confidence 455667899999986431122221 377888999864
No 130
>PRK04302 triosephosphate isomerase; Provisional
Probab=33.28 E-value=1.1e+02 Score=25.22 Aligned_cols=44 Identities=16% Similarity=0.336 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHcCCCEEEEec-CCCchhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAFDR-GGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDR-gg~~YhGrVkAlad~aRe~GL~ 170 (171)
-.|+..++.+++.|++-|..+- ....+++.+..+.+.+.+.||.
T Consensus 72 ~tg~~~~~~l~~~G~~~vii~~ser~~~~~e~~~~v~~a~~~Gl~ 116 (223)
T PRK04302 72 HTGHILPEAVKDAGAVGTLINHSERRLTLADIEAVVERAKKLGLE 116 (223)
T ss_pred chhhhHHHHHHHcCCCEEEEeccccccCHHHHHHHHHHHHHCCCe
Confidence 4577789999999999998864 2346777899999999999984
No 131
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=33.10 E-value=47 Score=30.08 Aligned_cols=37 Identities=22% Similarity=0.455 Sum_probs=26.8
Q ss_pred HHHHHHHcCCCEEEE--ecCCCchhhHH--HHHHHHHHHcCCcC
Q 030804 132 IAKSCLEKGITKVAF--DRGGYPYHGRI--QALADAAREYGLQF 171 (171)
Q Consensus 132 LAkra~e~GI~~Vvf--DRgg~~YhGrV--kAlad~aRe~GL~f 171 (171)
.++...++||.+|++ |-+. +|+. +.+.+-|+++|+++
T Consensus 58 cad~ii~~gi~rVVi~~D~d~---~G~~~~~~~~~~L~~aGi~V 98 (360)
T PRK14719 58 IADDLIAENISEVILLTDFDR---AGRVYAKNIMEEFQSRGIKV 98 (360)
T ss_pred HHHHHHHcCCCEEEEEECCCC---CCCccchHHHHHHHHCCCEE
Confidence 778888999999974 5442 5554 34677889999864
No 132
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=32.70 E-value=1.4e+02 Score=24.27 Aligned_cols=49 Identities=12% Similarity=0.095 Sum_probs=31.8
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecC--CCchhhHHHHHHHHHHHc-CCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRG--GYPYHGRIQALADAAREY-GLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRg--g~~YhGrVkAlad~aRe~-GL~ 170 (171)
.|.++++.+++.|.+.. .|..++.|=.+ .+..+.|+..|.++++++ |++
T Consensus 112 d~~~~g~~~~~~L~~~~--~g~~~i~~l~~~~~~~~~~R~~gf~~al~~~~~~~ 163 (280)
T cd06303 112 DHAAGARLLADYFIKRY--PNHARYAMLYFSPGYISTARGDTFIDCVHARNNWT 163 (280)
T ss_pred CHHHHHHHHHHHHHHhc--CCCcEEEEEECCCCcchhHHHHHHHHHHHhCCCce
Confidence 45556555555554432 67777755322 244578999999999998 764
No 133
>PRK05867 short chain dehydrogenase; Provisional
Probab=32.63 E-value=1.1e+02 Score=24.50 Aligned_cols=38 Identities=21% Similarity=0.246 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHc
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREY 167 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~ 167 (171)
.-+|..+++++.+.|.+-+..||+. .+.+.+++.+.+.
T Consensus 19 ~gIG~~ia~~l~~~G~~V~~~~r~~----~~~~~~~~~l~~~ 56 (253)
T PRK05867 19 TGIGKRVALAYVEAGAQVAIAARHL----DALEKLADEIGTS 56 (253)
T ss_pred chHHHHHHHHHHHCCCEEEEEcCCH----HHHHHHHHHHHhc
Confidence 4689999999999998766778752 3455555555443
No 134
>PF07355 GRDB: Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); InterPro: IPR022787 This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon. ; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=32.55 E-value=76 Score=29.09 Aligned_cols=29 Identities=31% Similarity=0.512 Sum_probs=25.9
Q ss_pred CCCcHHHHHHHHHHHHHHHHHcCCCEEEE
Q 030804 118 SGPTIEVSKKVGEMIAKSCLEKGITKVAF 146 (171)
Q Consensus 118 ~~~n~~AA~~VG~~LAkra~e~GI~~Vvf 146 (171)
.+.+.+.++..|..||+.+++.|++-|++
T Consensus 318 ~gt~~~~~~~~g~eIa~~Lk~dgVDAVIL 346 (349)
T PF07355_consen 318 NGTAVANAKRFGPEIAKELKEDGVDAVIL 346 (349)
T ss_pred CCccHHHHHHHHHHHHHHHHHcCCCEEEE
Confidence 44678889999999999999999999986
No 135
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=32.48 E-value=1.5e+02 Score=23.42 Aligned_cols=47 Identities=17% Similarity=0.179 Sum_probs=30.4
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCEEEEecCC--C-chhhHHHHHHHHHHHcCC
Q 030804 121 TIEVSKKVGEMIAKSCLEKGITKVAFDRGG--Y-PYHGRIQALADAAREYGL 169 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI~~VvfDRgg--~-~YhGrVkAlad~aRe~GL 169 (171)
|..+++.+++.|++.. .|..+|.+-.+. + ....|+++|.+.+.++|.
T Consensus 107 ~~~~g~~~~~~l~~~~--~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~ 156 (275)
T cd06317 107 DISQGERSAEAMCKAL--GGKGQIVVIAGQPGNGTAIERQKGFEDELAEVCP 156 (275)
T ss_pred HHHHHHHHHHHHHHHc--CCCceEEEEecCCCCchHHHHHHHHHHHHHhhCC
Confidence 4556666666666543 266677654332 2 235789999999999974
No 136
>PRK08278 short chain dehydrogenase; Provisional
Probab=32.46 E-value=1.2e+02 Score=24.93 Aligned_cols=44 Identities=25% Similarity=0.339 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCCCc---hhhHHHHHHHHHHHcC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGGYP---YHGRIQALADAAREYG 168 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg~~---YhGrVkAlad~aRe~G 168 (171)
..-+|..|++.+.+.|.+-+++||.... --+.++.+++.+++.|
T Consensus 15 s~gIG~~ia~~l~~~G~~V~~~~r~~~~~~~~~~~l~~~~~~~~~~~ 61 (273)
T PRK08278 15 SRGIGLAIALRAARDGANIVIAAKTAEPHPKLPGTIHTAAEEIEAAG 61 (273)
T ss_pred CchHHHHHHHHHHHCCCEEEEEecccccccchhhHHHHHHHHHHhcC
Confidence 3468999999999999987788986432 1234556666665544
No 137
>PF06370 DUF1069: Protein of unknown function (DUF1069); InterPro: IPR009421 This family consists of several Maize streak virus 21.7 kDa proteins. The function of this family is unknown.
Probab=32.19 E-value=25 Score=28.83 Aligned_cols=19 Identities=37% Similarity=0.798 Sum_probs=16.4
Q ss_pred HcCCCEEEEecCCCchhhH
Q 030804 138 EKGITKVAFDRGGYPYHGR 156 (171)
Q Consensus 138 e~GI~~VvfDRgg~~YhGr 156 (171)
.-|+++|.|.-||.+|||-
T Consensus 164 gigvdevtyasggdryhgg 182 (206)
T PF06370_consen 164 GIGVDEVTYASGGDRYHGG 182 (206)
T ss_pred CccceeEEeccCCccccCC
Confidence 3578999999999999974
No 138
>PLN00125 Succinyl-CoA ligase [GDP-forming] subunit alpha
Probab=31.64 E-value=88 Score=27.73 Aligned_cols=40 Identities=18% Similarity=0.217 Sum_probs=31.1
Q ss_pred HHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 132 IAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 132 LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
..+.|.++||..++.=-.||.-.|..+.+.+.+|++|+.+
T Consensus 85 al~e~~~~Gvk~~vIisaGf~e~g~~~~~~~~ar~~girv 124 (300)
T PLN00125 85 AILEAMEAELDLVVCITEGIPQHDMVRVKAALNRQSKTRL 124 (300)
T ss_pred HHHHHHHcCCCEEEEECCCCCcccHHHHHHHHHhhcCCEE
Confidence 4566889999988776777888886666677789999853
No 139
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....
Probab=30.79 E-value=1.3e+02 Score=21.29 Aligned_cols=35 Identities=34% Similarity=0.498 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCC
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGL 169 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL 169 (171)
.+|..|++.+.+.+++-++.|+.. ...+.+++.|+
T Consensus 8 ~~~~~i~~~L~~~~~~vvvid~d~--------~~~~~~~~~~~ 42 (116)
T PF02254_consen 8 RIGREIAEQLKEGGIDVVVIDRDP--------ERVEELREEGV 42 (116)
T ss_dssp HHHHHHHHHHHHTTSEEEEEESSH--------HHHHHHHHTTS
T ss_pred HHHHHHHHHHHhCCCEEEEEECCc--------HHHHHHHhccc
Confidence 589999999999777788889873 22555555554
No 140
>TIGR02867 spore_II_P stage II sporulation protein P. Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members.
Probab=30.64 E-value=1.1e+02 Score=25.57 Aligned_cols=26 Identities=42% Similarity=0.500 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHcCCCEEEEecC
Q 030804 123 EVSKKVGEMIAKSCLEKGITKVAFDRG 149 (171)
Q Consensus 123 ~AA~~VG~~LAkra~e~GI~~VvfDRg 149 (171)
-.-..||+.|++.+.++||. |++|+.
T Consensus 30 ~~V~~VG~~L~~~Le~~Gi~-vihd~t 55 (196)
T TIGR02867 30 GNITKVGDRLAKELEEKGIG-VIHDKT 55 (196)
T ss_pred CcHHHHHHHHHHHHHHCCCe-EEEeCC
Confidence 35678999999999999986 566765
No 141
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=30.62 E-value=1.8e+02 Score=22.84 Aligned_cols=43 Identities=21% Similarity=0.294 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHcCCCEEEEecC--CCc-hhhHHHHHHHHHHHcCCc
Q 030804 128 VGEMIAKSCLEKGITKVAFDRG--GYP-YHGRIQALADAAREYGLQ 170 (171)
Q Consensus 128 VG~~LAkra~e~GI~~VvfDRg--g~~-YhGrVkAlad~aRe~GL~ 170 (171)
.|+.+++...++|..+|.|=.+ ... ...|+..|.+.+.++|++
T Consensus 104 ~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~l~~~~~~ 149 (268)
T cd06289 104 GARLATEHLISLGHRRIAFIGGLEDSSTRRERLAGYRAALAEAGLP 149 (268)
T ss_pred HHHHHHHHHHHCCCCCEEEecCCccccchHHHHHHHHHHHHHcCCC
Confidence 4666666777788888865322 222 257899999999999864
No 142
>PRK08703 short chain dehydrogenase; Provisional
Probab=30.57 E-value=1.2e+02 Score=23.96 Aligned_cols=37 Identities=27% Similarity=0.388 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHH
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAARE 166 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe 166 (171)
.-+|..|++.+.+.|..-+++||+. .+...+.+.+++
T Consensus 16 ggiG~~la~~l~~~g~~V~~~~r~~----~~~~~~~~~l~~ 52 (239)
T PRK08703 16 QGLGEQVAKAYAAAGATVILVARHQ----KKLEKVYDAIVE 52 (239)
T ss_pred CcHHHHHHHHHHHcCCEEEEEeCCh----HHHHHHHHHHHH
Confidence 3689999999999999877889874 234445454443
No 143
>PF14540 NTF-like: Nucleotidyltransferase-like; PDB: 3C18_A.
Probab=30.55 E-value=27 Score=27.18 Aligned_cols=25 Identities=32% Similarity=0.562 Sum_probs=15.7
Q ss_pred CEEEEecCCCch--hhHHHHHHHHHHH
Q 030804 142 TKVAFDRGGYPY--HGRIQALADAARE 166 (171)
Q Consensus 142 ~~VvfDRgg~~Y--hGrVkAlad~aRe 166 (171)
.+|+|||+.|.. .-++..|-+..|+
T Consensus 93 G~IlfDRneyl~~Lr~~l~~FP~~~R~ 119 (119)
T PF14540_consen 93 GKILFDRNEYLHNLRQRLLEFPEEERE 119 (119)
T ss_dssp SEEEEESTTHHHHHHHHTT---HHHH-
T ss_pred CEEEEehhHHHHHHHHHHHHcChhhcC
Confidence 689999998765 5666666666654
No 144
>PRK07109 short chain dehydrogenase; Provisional
Probab=30.50 E-value=1.2e+02 Score=26.12 Aligned_cols=39 Identities=31% Similarity=0.454 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYG 168 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~G 168 (171)
.-||..+++++.+.|.+-+..+|+. .++..+.+.+++.|
T Consensus 18 ~gIG~~la~~la~~G~~Vvl~~R~~----~~l~~~~~~l~~~g 56 (334)
T PRK07109 18 AGVGRATARAFARRGAKVVLLARGE----EGLEALAAEIRAAG 56 (334)
T ss_pred CHHHHHHHHHHHHCCCEEEEEECCH----HHHHHHHHHHHHcC
Confidence 4689999999999998767788863 34555555555544
No 145
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=30.40 E-value=1.7e+02 Score=23.69 Aligned_cols=47 Identities=13% Similarity=0.175 Sum_probs=29.6
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecC--------------------CCchhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRG--------------------GYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRg--------------------g~~YhGrVkAlad~aRe~GL~ 170 (171)
.|.++.+..++.| .++|..++.|=-+ ...-..|+..|.+++.++|++
T Consensus 99 d~~~~g~~~~~~L----~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~ 165 (283)
T cd06279 99 DDRAAAREAARHL----LDLGHRRIGILGLRLGRDRNTGRVTDERLASATFSVARERLEGYLEALEEAGID 165 (283)
T ss_pred CcHHHHHHHHHHH----HHcCCCcEEEecCcccccccccccccccccccccccHHHHHHHHHHHHHHcCCC
Confidence 3455555555555 5578888754211 111257899999999999864
No 146
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=29.95 E-value=1.7e+02 Score=22.46 Aligned_cols=42 Identities=26% Similarity=0.411 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHcCCCEEEE--ecCCCch-hhHHHHHHHHHHHcC
Q 030804 127 KVGEMIAKSCLEKGITKVAF--DRGGYPY-HGRIQALADAAREYG 168 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~Vvf--DRgg~~Y-hGrVkAlad~aRe~G 168 (171)
..|..+++.+.+.|..+|.| +...+.+ ..+...|.+.+.+.|
T Consensus 104 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~ 148 (264)
T cd01537 104 QAGYLAGEHLAEKGHRRIALLAGPLGSSTARERVAGFKDALKEAG 148 (264)
T ss_pred HHHHHHHHHHHHhcCCcEEEEECCCCCCcHHHHHHHHHHHHHHcC
Confidence 57778888888888888854 3333233 578999999999887
No 147
>PF04551 GcpE: GcpE protein; InterPro: IPR004588 This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is largely restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.; GO: 0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity, 0016114 terpenoid biosynthetic process, 0055114 oxidation-reduction process; PDB: 2Y0F_C 3NOY_A.
Probab=29.78 E-value=2e+02 Score=26.58 Aligned_cols=50 Identities=20% Similarity=0.491 Sum_probs=36.7
Q ss_pred CcHHHHHHHHHHHHH----------------------HHHHcCCCEEEEecCCC--------ch-hhHHHHHHHHHHHcC
Q 030804 120 PTIEVSKKVGEMIAK----------------------SCLEKGITKVAFDRGGY--------PY-HGRIQALADAAREYG 168 (171)
Q Consensus 120 ~n~~AA~~VG~~LAk----------------------ra~e~GI~~VvfDRgg~--------~Y-hGrVkAlad~aRe~G 168 (171)
.+.++|..++++-.+ .|.+. ++++=.+.|.. .. ..+++.+++.++|.|
T Consensus 53 p~~~~a~al~~I~~~l~~~g~~iPlVADIHFd~~lAl~a~~~-v~kiRINPGNi~~~~~~~~g~~~~~~~~vv~~ake~~ 131 (359)
T PF04551_consen 53 PDMEAAEALKEIKKRLRALGSPIPLVADIHFDYRLALEAIEA-VDKIRINPGNIVDEFQEELGSIREKVKEVVEAAKERG 131 (359)
T ss_dssp -SHHHHHHHHHHHHHHHCTT-SS-EEEEESTTCHHHHHHHHC--SEEEE-TTTSS----SS-SS-HHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHhhccCCCCCCeeeecCCCHHHHHHHHHH-hCeEEECCCcccccccccccchHHHHHHHHHHHHHCC
Confidence 567888888776444 67777 88888888877 44 789999999999999
Q ss_pred Cc
Q 030804 169 LQ 170 (171)
Q Consensus 169 L~ 170 (171)
+.
T Consensus 132 ip 133 (359)
T PF04551_consen 132 IP 133 (359)
T ss_dssp -E
T ss_pred CC
Confidence 74
No 148
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=29.73 E-value=1.5e+02 Score=23.59 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=30.7
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecC--C-CchhhHHHHHHHHHHHcC-Cc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRG--G-YPYHGRIQALADAAREYG-LQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRg--g-~~YhGrVkAlad~aRe~G-L~ 170 (171)
.|..+++..++.|.+++ .|..++.|=.+ . .....|.+.|.+++.++| ++
T Consensus 106 d~~~~g~~~~~~l~~~~--~g~~~i~~i~~~~~~~~~~~R~~g~~~a~~~~~~~~ 158 (272)
T cd06300 106 DQAEFGKQGAEWLVKEL--GGKGNVLVVRGLAGHPVDEDRYAGAKEVLKEYPGIK 158 (272)
T ss_pred CHHHHHHHHHHHHHHHc--CCCceEEEEECCCCCcchHHHHHHHHHHHHHCCCcE
Confidence 35556666666555543 26777754332 2 223578999999999988 64
No 149
>TIGR02801 tolR TolR protein. The model describes the inner membrane protein TolR, part of the TolR/TolQ complex that transduces energy from the proton-motive force, through TolA, to an outer membrane complex made up of TolB and Pal (peptidoglycan-associated lipoprotein). The complex is required to maintain outer membrane integrity, and defects may cause a defect in the import of some organic compounds in addition to the resulting morphologic. While several gene pairs homologous to talR and tolQ may be found in a single genome, but the scope of this model is set to favor finding only bone fide TolR, supported by operon structure as well as by score.
Probab=29.05 E-value=2.4e+02 Score=20.95 Aligned_cols=29 Identities=14% Similarity=0.159 Sum_probs=22.8
Q ss_pred CEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 142 TKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 142 ~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
..|+..-.....+|.+-.+.|.+|++|++
T Consensus 94 ~~v~i~aD~~~~~~~vv~vmd~~~~~G~~ 122 (129)
T TIGR02801 94 TPVLIRADKTVPYGEVIKVMALLKQAGIE 122 (129)
T ss_pred ceEEEEcCCCCCHHHHHHHHHHHHHcCCC
Confidence 34655444468899999999999999984
No 150
>PRK07792 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=29.02 E-value=1.3e+02 Score=25.47 Aligned_cols=40 Identities=23% Similarity=0.152 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYG 168 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~G 168 (171)
.-||..+|+.+.+.|..-++.|++. ....+.+++.+++.|
T Consensus 22 ~gIG~~ia~~L~~~Ga~Vv~~~~~~---~~~~~~~~~~i~~~g 61 (306)
T PRK07792 22 AGLGRAEALGLARLGATVVVNDVAS---ALDASDVLDEIRAAG 61 (306)
T ss_pred ChHHHHHHHHHHHCCCEEEEecCCc---hhHHHHHHHHHHhcC
Confidence 4689999999999999877788752 234555666665544
No 151
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=28.91 E-value=1.8e+02 Score=23.04 Aligned_cols=49 Identities=20% Similarity=0.236 Sum_probs=31.4
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecC--CCchhhHHHHHHHHHHHc-CCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRG--GYPYHGRIQALADAAREY-GLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRg--g~~YhGrVkAlad~aRe~-GL~ 170 (171)
.+.++++..++.|.++. .|..++.|=-+ ...-..|.+.|.+++.++ |++
T Consensus 102 d~~~~g~~~~~~l~~~~--~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~~ 153 (267)
T cd06322 102 DNYAGGVLAGELAAKVL--NGKGQVAIIDYPTVQSVVDRVRGFKEALADYPNIK 153 (267)
T ss_pred ChHHHHHHHHHHHHHHh--CCCceEEEEecCCCccHHHHHHHHHHHHHhCCCcE
Confidence 34566666666666653 36667754322 222346899999999998 875
No 152
>PRK13397 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=28.91 E-value=82 Score=27.35 Aligned_cols=50 Identities=24% Similarity=0.312 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHcCCCEE---EEe-c-CCCchhh----HHHHHHHHHHHcCCcC
Q 030804 122 IEVSKKVGEMIAKSCLEKGITKV---AFD-R-GGYPYHG----RIQALADAAREYGLQF 171 (171)
Q Consensus 122 ~~AA~~VG~~LAkra~e~GI~~V---vfD-R-gg~~YhG----rVkAlad~aRe~GL~f 171 (171)
.--.+..-..+|+.+++.|+.-+ +|| | ..|.|.| -++.|.+..++.||.|
T Consensus 24 ~vEs~e~~~~~a~~~~~~g~~~~r~g~~kpRts~~sf~G~G~~gl~~L~~~~~~~Gl~~ 82 (250)
T PRK13397 24 SIESYDHIRLAASSAKKLGYNYFRGGAYKPRTSAASFQGLGLQGIRYLHEVCQEFGLLS 82 (250)
T ss_pred ccCCHHHHHHHHHHHHHcCCCEEEecccCCCCCCcccCCCCHHHHHHHHHHHHHcCCCE
Confidence 33345556677888999998755 788 3 3455543 3888999999999975
No 153
>PRK08277 D-mannonate oxidoreductase; Provisional
Probab=28.86 E-value=1.4e+02 Score=24.37 Aligned_cols=26 Identities=23% Similarity=0.314 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
+.-+|..|++++.+.|..-++.||+.
T Consensus 19 s~giG~~ia~~l~~~G~~V~~~~r~~ 44 (278)
T PRK08277 19 GGVLGGAMAKELARAGAKVAILDRNQ 44 (278)
T ss_pred CchHHHHHHHHHHHCCCEEEEEeCCH
Confidence 34689999999999999777788863
No 154
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=28.68 E-value=1.3e+02 Score=23.98 Aligned_cols=44 Identities=14% Similarity=0.067 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHc--CCCEEEE--ecCCCchhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEK--GITKVAF--DRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~--GI~~Vvf--DRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
..|+.+++.+.+. |.+++.| +.....-..|.+.|.+.+.+.|++
T Consensus 115 ~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~r~~g~~~~~~~~g~~ 162 (281)
T cd06325 115 VPVETQLELLKKLLPDAKTVGVLYNPSEANSVVQVKELKKAAAKLGIE 162 (281)
T ss_pred cchHHHHHHHHHHCCCCcEEEEEeCCCCccHHHHHHHHHHHHHhCCCE
Confidence 3356666777776 8999865 433211247889999999999985
No 155
>PRK05866 short chain dehydrogenase; Provisional
Probab=28.40 E-value=1.4e+02 Score=25.05 Aligned_cols=36 Identities=31% Similarity=0.391 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHH
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAR 165 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aR 165 (171)
.-+|..|++.+.+.|.+-+..||+. .+.+.+.+.+.
T Consensus 50 ggIG~~la~~La~~G~~Vi~~~R~~----~~l~~~~~~l~ 85 (293)
T PRK05866 50 SGIGEAAAEQFARRGATVVAVARRE----DLLDAVADRIT 85 (293)
T ss_pred cHHHHHHHHHHHHCCCEEEEEECCH----HHHHHHHHHHH
Confidence 4689999999999998777889863 33444444443
No 156
>cd06350 PBP1_GPCR_family_C_like Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). The metabotropic glutamate receptors (mGluR) are key receptors in the modulation of excitatory synaptic transmission in the central nervous system. The mGluRs are coupled to G proteins and are thus distinct from the iGluRs which internally contain ligand-gated ion channels. The mGluR structure is divided into three regions: the extracellular region, the seven-spanning transmembrane region and the cytoplasmic region. The extr
Probab=28.40 E-value=1.5e+02 Score=24.71 Aligned_cols=47 Identities=15% Similarity=0.170 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHcCCCEEE--EecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 124 VSKKVGEMIAKSCLEKGITKVA--FDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 124 AA~~VG~~LAkra~e~GI~~Vv--fDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
.....+..+++-++..|.++|. ++...| ..+-++.|.+.+++.|+++
T Consensus 143 ~~~~~~~a~~~~~~~~~~~~v~~l~~~~~~-g~~~~~~~~~~~~~~gi~v 191 (348)
T cd06350 143 SDTSQALAIVALLKHFGWTWVGLVYSDDDY-GRSGLSDLEEELEKNGICI 191 (348)
T ss_pred CcHHHHHHHHHHHHHCCCeEEEEEEecchh-HHHHHHHHHHHHHHCCCcE
Confidence 3445666677777778998874 444322 3678999999999999864
No 157
>PF02006 DUF137: Protein of unknown function DUF137; InterPro: IPR002855 The archaeal proteins in this family have no known function.
Probab=28.33 E-value=1.2e+02 Score=25.46 Aligned_cols=46 Identities=26% Similarity=0.328 Sum_probs=36.6
Q ss_pred cHHHHHHHHHHHHHHHHHcCCC-EE-EEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 121 TIEVSKKVGEMIAKSCLEKGIT-KV-AFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI~-~V-vfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
|=..|.++-+.+++-+++.|.+ +| .|.|. ..|+++.++-++++|-+
T Consensus 12 NGN~AAL~p~eiveLa~~~~A~iEVNLFyRT----~eR~~~I~~~L~~~Ga~ 59 (178)
T PF02006_consen 12 NGNTAALVPEEIVELAKATGAKIEVNLFYRT----EERVEKIAELLREHGAE 59 (178)
T ss_pred cccHHHhChHHHHHHHHHhCCCEEEEcccCC----HHHHHHHHHHHHHcCCC
Confidence 3357889999999999998855 44 56554 68999999999999963
No 158
>cd00175 SNc Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.
Probab=28.33 E-value=2.4e+02 Score=20.54 Aligned_cols=55 Identities=22% Similarity=0.206 Sum_probs=39.9
Q ss_pred CCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHHcCCCEEEEecCCC-chhhHHHHHHHHHHHcCC
Q 030804 94 DTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLEKGITKVAFDRGGY-PYHGRIQALADAAREYGL 169 (171)
Q Consensus 94 d~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg~-~YhGrVkAlad~aRe~GL 169 (171)
|..|..|+.+-... |.-|++.+++.|.-.+....... .|+..+.++.+.+++.++
T Consensus 69 d~~gr~la~v~~~~---------------------~~~v~~~Lv~~G~A~~~~~~~~~~~~~~~l~~ae~~Ak~~k~ 124 (129)
T cd00175 69 DRYGRTLGTVYLNG---------------------GENIAEELVKEGLARVYRYYPDDSEYYDELLEAEEAAKKARK 124 (129)
T ss_pred CCCCCEEEEEEeCC---------------------CCcHHHHHHhcCCEEEEEECCCCcHHHHHHHHHHHHHHHhCc
Confidence 66788887764321 33467778888988777665443 789999999999998765
No 159
>PRK07097 gluconate 5-dehydrogenase; Provisional
Probab=28.19 E-value=1.6e+02 Score=23.85 Aligned_cols=25 Identities=32% Similarity=0.236 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
.-+|..+++++.+.|.+-++.||..
T Consensus 20 ~~iG~~ia~~l~~~G~~vv~~~~~~ 44 (265)
T PRK07097 20 YGIGFAIAKAYAKAGATIVFNDINQ 44 (265)
T ss_pred chHHHHHHHHHHHCCCeEEEEeCCH
Confidence 4689999999999999877888864
No 160
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=28.05 E-value=2e+02 Score=24.49 Aligned_cols=52 Identities=19% Similarity=0.286 Sum_probs=36.4
Q ss_pred CCcHHHHHHHHHHHHHHHH--------HcCCCEEEE--ecCCCch-hhHHHHHHHHHHHcCCc
Q 030804 119 GPTIEVSKKVGEMIAKSCL--------EKGITKVAF--DRGGYPY-HGRIQALADAAREYGLQ 170 (171)
Q Consensus 119 ~~n~~AA~~VG~~LAkra~--------e~GI~~Vvf--DRgg~~Y-hGrVkAlad~aRe~GL~ 170 (171)
..|..+.+..|+.|++.+. +.|.-.+.| -...... ..|...|.++++++|++
T Consensus 132 ~D~~~ag~~a~~~l~~~~~~~~~~~~~~~g~~~i~~i~g~~~~~~~~~R~~G~~~al~~~g~~ 194 (330)
T PRK15395 132 TDSKESGIIQGDLIAKHWKANPAWDLNKDGKIQYVLLKGEPGHPDAEARTTYVIKELNDKGIK 194 (330)
T ss_pred cChHHHHHHHHHHHHHHHhhccccccCCCCceEEEEEecCCCCchHHHHHHHHHHHHHhcCCC
Confidence 4678888988999998876 345444443 2222233 46999999999999985
No 161
>PF03446 NAD_binding_2: NAD binding domain of 6-phosphogluconate dehydrogenase; InterPro: IPR006115 6-Phosphogluconate dehydrogenase (1.1.1.44 from EC) (6PGD) is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP. This reaction is a component of the hexose mono-phosphate shunt and pentose phosphate pathways (PPP) [, ]. Prokaryotic and eukaryotic 6PGD are proteins of about 470 amino acids whose sequence are highly conserved []. The protein is a homodimer in which the monomers act independently []: each contains a large, mainly alpha-helical domain and a smaller beta-alpha-beta domain, containing a mixed parallel and anti-parallel 6-stranded beta sheet []. NADP is bound in a cleft in the small domain, the substrate binding in an adjacent pocket []. This family represents the NADP binding domain of 6-phosphogluconate dehydrogenase which adopts a Rossman fold. The C-terminal domain is described in IPR006114 from INTERPRO.; GO: 0004616 phosphogluconate dehydrogenase (decarboxylating) activity, 0006098 pentose-phosphate shunt, 0055114 oxidation-reduction process; PDB: 3AX6_D 3PDU_G 3Q3C_A 3OBB_A 4DLL_B 1PGP_A 1PGN_A 2PGD_A 1PGQ_A 1PGO_A ....
Probab=27.98 E-value=80 Score=24.46 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCCch
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRGGYPY 153 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRgg~~Y 153 (171)
..|.-||+++.++|++-.+|||...+.
T Consensus 11 ~mG~~~a~~L~~~g~~v~~~d~~~~~~ 37 (163)
T PF03446_consen 11 NMGSAMARNLAKAGYEVTVYDRSPEKA 37 (163)
T ss_dssp HHHHHHHHHHHHTTTEEEEEESSHHHH
T ss_pred HHHHHHHHHHHhcCCeEEeeccchhhh
Confidence 579999999999999988999985444
No 162
>cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar bindi
Probab=27.96 E-value=2.1e+02 Score=23.02 Aligned_cols=41 Identities=32% Similarity=0.346 Sum_probs=28.6
Q ss_pred HHHHHHHHHHcCCCEEEEecCC--------CchhhHHHHHHHHHHHcCC
Q 030804 129 GEMIAKSCLEKGITKVAFDRGG--------YPYHGRIQALADAAREYGL 169 (171)
Q Consensus 129 G~~LAkra~e~GI~~VvfDRgg--------~~YhGrVkAlad~aRe~GL 169 (171)
|..+++...+.|..++.|=-+. +..+.|...|.+.+.++|+
T Consensus 100 ~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~ 148 (270)
T cd01544 100 VEKALDYLLELGHTRIGFIGGEEKTTDGHEYIEDPRETAFREYMKEKGL 148 (270)
T ss_pred HHHHHHHHHHcCCCcEEEECCCcccccccchhhhHHHHHHHHHHHHcCC
Confidence 5555566666899988653221 1346789999999999984
No 163
>PRK12826 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed
Probab=27.93 E-value=1.4e+02 Score=23.49 Aligned_cols=40 Identities=23% Similarity=0.312 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYG 168 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~G 168 (171)
.-.+|..|++.+.+.|.+-+.++|+. .+...+++.+++.|
T Consensus 15 sg~iG~~l~~~l~~~g~~V~~~~r~~----~~~~~~~~~l~~~~ 54 (251)
T PRK12826 15 ARGIGRAIAVRLAADGAEVIVVDICG----DDAAATAELVEAAG 54 (251)
T ss_pred CCcHHHHHHHHHHHCCCEEEEEeCCH----HHHHHHHHHHHhcC
Confidence 35689999999999998777889873 34555555555443
No 164
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=27.80 E-value=1.6e+02 Score=23.56 Aligned_cols=50 Identities=24% Similarity=0.327 Sum_probs=32.5
Q ss_pred CCcHHHHHHHHHHHHHHHHHcCCCEEEEecC--CCchhhHHHHHHHHHHHcCCc
Q 030804 119 GPTIEVSKKVGEMIAKSCLEKGITKVAFDRG--GYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 119 ~~n~~AA~~VG~~LAkra~e~GI~~VvfDRg--g~~YhGrVkAlad~aRe~GL~ 170 (171)
..|.++.+..++.|.+++. |-.+|.+=.+ ...-+.|++.|.+.+.+.|++
T Consensus 107 ~d~~~~g~~aa~~l~~~~~--g~~~i~~~~g~~~~~~~~R~~gf~~~l~~~~~~ 158 (274)
T cd06311 107 GDNYGMGRVAGEYIATKLG--GNGNIVVLRGIPTPIDNERVDAFDAAIAKYPIK 158 (274)
T ss_pred CCcHHHHHHHHHHHHHHhC--CCCeEEEEECCCCcchhHHHHHHHHHHhhCCcE
Confidence 3456677777777766542 5556643221 133467999999999999864
No 165
>PRK08452 flagellar protein FlaG; Provisional
Probab=27.79 E-value=2.1e+02 Score=22.34 Aligned_cols=28 Identities=18% Similarity=0.070 Sum_probs=24.0
Q ss_pred CCCceEEEEeeCCcEEEEEEeCCCCcEE
Q 030804 73 PERPRLCVFRSNKHLYVQVIDDTKMHTL 100 (171)
Q Consensus 73 ~~rPRL~V~rSnkhiyAQvIdd~~~ktL 100 (171)
...-+..++..-..+|++|+|..+|++|
T Consensus 70 ~~~L~F~~de~~~~~vVkVvD~~T~eVI 97 (124)
T PRK08452 70 DTNIRFGYNDKIKGLVVSVKEANGGKVI 97 (124)
T ss_pred CCceEEEEcCCCCcEEEEEEECCCCcee
Confidence 3466888888889999999999999885
No 166
>PRK06139 short chain dehydrogenase; Provisional
Probab=27.69 E-value=1.5e+02 Score=25.86 Aligned_cols=39 Identities=26% Similarity=0.405 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYG 168 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~G 168 (171)
.-+|..+++++.+.|.+-+..+|+. .+.+.+++.+++.|
T Consensus 17 ~GIG~aia~~la~~G~~Vvl~~R~~----~~l~~~~~~~~~~g 55 (330)
T PRK06139 17 SGIGQATAEAFARRGARLVLAARDE----EALQAVAEECRALG 55 (330)
T ss_pred CHHHHHHHHHHHHCCCEEEEEECCH----HHHHHHHHHHHhcC
Confidence 4689999999999998877788863 34555555555544
No 167
>PRK12549 shikimate 5-dehydrogenase; Reviewed
Probab=27.44 E-value=1.4e+02 Score=25.62 Aligned_cols=38 Identities=29% Similarity=0.450 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHcCCCEE-EEecCCCchhhHHHHHHHHHHH
Q 030804 125 SKKVGEMIAKSCLEKGITKV-AFDRGGYPYHGRIQALADAARE 166 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~V-vfDRgg~~YhGrVkAlad~aRe 166 (171)
|--+|+.++..+.+.|+.+| ++||. .+|.++|++.+.+
T Consensus 135 aGGaaraia~aL~~~G~~~I~I~nR~----~~ka~~la~~l~~ 173 (284)
T PRK12549 135 AGGAGAAVAHALLTLGVERLTIFDVD----PARAAALADELNA 173 (284)
T ss_pred CcHHHHHHHHHHHHcCCCEEEEECCC----HHHHHHHHHHHHh
Confidence 33466777777788999877 78997 3678888877654
No 168
>COG0007 CysG Uroporphyrinogen-III methylase [Coenzyme metabolism]
Probab=27.34 E-value=1.2e+02 Score=26.44 Aligned_cols=44 Identities=30% Similarity=0.539 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCch-hhHHHHHHHHHHHcCCcC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPY-HGRIQALADAAREYGLQF 171 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~Y-hGrVkAlad~aRe~GL~f 171 (171)
..+-++|.+.|.+ | +.|+==.||..| +||...=++.+.++||+|
T Consensus 68 ~eIn~~lv~~a~~-G-~~VVRLKgGDP~iFGRggEE~~~l~~~gI~~ 112 (244)
T COG0007 68 DEINALLVELARE-G-KRVVRLKGGDPYIFGRGGEEIEALAEAGIEF 112 (244)
T ss_pred HHHHHHHHHHHhc-C-CeEEEecCCCCCeecCcHHHHHHHHHcCCce
Confidence 3666778888887 6 666655677887 899999999999999987
No 169
>PF01488 Shikimate_DH: Shikimate / quinate 5-dehydrogenase; InterPro: IPR006151 This entry represents a domain found in shikimate and quinate dehydrogenases, as well as glutamyl-tRNA reductases. Shikimate 5-dehydrogenase (1.1.1.25 from EC) catalyses the conversion of shikimate to 5-dehydroshikimate [, ]. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids []. Quinate 5-dehydrogenase catalyses the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites, 3-dehydroquinate and dehydroshikimate. Glutamyl-tRNA reductase (1.2.1.70 from EC) catalyzes the first step of tetrapyrrole biosynthesis in plants, archaea and most bacteria. The dimeric enzyme has an unusual V-shaped architecture where each monomer consists of three domains linked by a long 'spinal' alpha-helix. The central catalytic domain specifically recognises the glutamate moiety of the substrate []. ; PDB: 2EV9_B 2CY0_B 1WXD_A 2D5C_A 1NVT_B 2EGG_A 3PWZ_A 3DOO_A 3DON_A 3FBT_C ....
Probab=27.33 E-value=1.4e+02 Score=22.53 Aligned_cols=34 Identities=21% Similarity=0.284 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHcCCCEE-EEecCCCchhhHHHHHHHHH
Q 030804 127 KVGEMIAKSCLEKGITKV-AFDRGGYPYHGRIQALADAA 164 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~V-vfDRgg~~YhGrVkAlad~a 164 (171)
-.|+.++..+.+.|+++| +++|. ..|.+.|++.+
T Consensus 22 g~ar~v~~~L~~~g~~~i~i~nRt----~~ra~~l~~~~ 56 (135)
T PF01488_consen 22 GAARAVAAALAALGAKEITIVNRT----PERAEALAEEF 56 (135)
T ss_dssp HHHHHHHHHHHHTTSSEEEEEESS----HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCEEEEEECC----HHHHHHHHHHc
Confidence 467778888888999987 68986 46788888877
No 170
>COG1472 BglX Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]
Probab=27.27 E-value=1.2e+02 Score=27.80 Aligned_cols=52 Identities=27% Similarity=0.302 Sum_probs=37.2
Q ss_pred CCCcHHHHHHHHHHHHHHHHHcCCCEE---EEe--------cCCCc-hhh-------HHHHHHHHHHHcCC
Q 030804 118 SGPTIEVSKKVGEMIAKSCLEKGITKV---AFD--------RGGYP-YHG-------RIQALADAAREYGL 169 (171)
Q Consensus 118 ~~~n~~AA~~VG~~LAkra~e~GI~~V---vfD--------Rgg~~-YhG-------rVkAlad~aRe~GL 169 (171)
..-|.+.++.+|+++|+.+.+.||+-. +.| |.+.. |+. =..|++++++..|+
T Consensus 91 a~~~~~la~~~g~~~A~Elra~Gin~~fAPvlDv~~~p~~~ri~ersfgeDP~lv~~l~~a~i~Glq~~gv 161 (397)
T COG1472 91 ATWDPELARKVGRVIAKELRALGINLDFAPVLDVARDPRWGRIGERSFGEDPELVALLAAAFIKGLQGAGV 161 (397)
T ss_pred hcCCHHHHHHHHHHHHHHHHHcCCCccccceeecccCCCcCccccccCCCCHHHHHHHHHHHHHHHhhCCc
Confidence 445789999999999999999999732 233 22233 432 25688888888876
No 171
>PTZ00445 p36-lilke protein; Provisional
Probab=27.01 E-value=1.6e+02 Score=25.30 Aligned_cols=45 Identities=20% Similarity=0.290 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHcCCCEEEEe---------cCCCchh------------hHHHHHHHHHHHcCCcC
Q 030804 127 KVGEMIAKSCLEKGITKVAFD---------RGGYPYH------------GRIQALADAAREYGLQF 171 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfD---------Rgg~~Yh------------GrVkAlad~aRe~GL~f 171 (171)
.-...+.+.+++.||+-|.+| -|||.-. --.+.+++.|.+.||.+
T Consensus 29 ~~~~~~v~~L~~~GIk~Va~D~DnTlI~~HsgG~~~~~~~~~~~~~~~tpefk~~~~~l~~~~I~v 94 (219)
T PTZ00445 29 ESADKFVDLLNECGIKVIASDFDLTMITKHSGGYIDPDNDDIRVLTSVTPDFKILGKRLKNSNIKI 94 (219)
T ss_pred HHHHHHHHHHHHcCCeEEEecchhhhhhhhcccccCCCcchhhhhccCCHHHHHHHHHHHHCCCeE
Confidence 344667888999999999887 2343222 23889999999999864
No 172
>PRK11702 hypothetical protein; Provisional
Probab=26.77 E-value=26 Score=26.99 Aligned_cols=13 Identities=38% Similarity=0.542 Sum_probs=10.0
Q ss_pred HHHHHHhhhhhcC
Q 030804 59 TARHSRIRKKIDG 71 (171)
Q Consensus 59 ~~R~~RirkKi~g 71 (171)
+.|++|+|||+.-
T Consensus 3 ~~RsRRlRKKL~v 15 (108)
T PRK11702 3 KNRSRRLRKKMHI 15 (108)
T ss_pred cchhHHHHhhhhh
Confidence 3578999999853
No 173
>PRK06194 hypothetical protein; Provisional
Probab=26.72 E-value=1.6e+02 Score=24.08 Aligned_cols=26 Identities=19% Similarity=0.130 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
+.-+|..|++++.+.|..-++.||..
T Consensus 15 sggIG~~la~~l~~~G~~V~~~~r~~ 40 (287)
T PRK06194 15 ASGFGLAFARIGAALGMKLVLADVQQ 40 (287)
T ss_pred ccHHHHHHHHHHHHCCCEEEEEeCCh
Confidence 45689999999999998777788853
No 174
>PF02878 PGM_PMM_I: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I; InterPro: IPR005844 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 3I3W_B 1WQA_C 1KFQ_B 1KFI_A 2Z0F_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=26.67 E-value=2.7e+02 Score=20.85 Aligned_cols=49 Identities=24% Similarity=0.234 Sum_probs=36.6
Q ss_pred CcHHHHHHHHHHHHHHHHHc-CCCEEE--EecCCCchhhH--HHHHHHHHHHcCCcC
Q 030804 120 PTIEVSKKVGEMIAKSCLEK-GITKVA--FDRGGYPYHGR--IQALADAAREYGLQF 171 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~-GI~~Vv--fDRgg~~YhGr--VkAlad~aRe~GL~f 171 (171)
-|.+.+..+|..++.-..+. +-..|+ +|. +.+++ .++++++++..|+++
T Consensus 18 lt~~~~~~~~~a~~~~~~~~~~~~~VvVg~D~---R~~s~~~~~~~~~~l~~~G~~V 71 (137)
T PF02878_consen 18 LTPEFAARLAQAFASYLKEKGNGSRVVVGRDT---RPSSPMLAKALAAGLRANGVDV 71 (137)
T ss_dssp BSHHHHHHHHHHHHHHHHHTTTSSEEEEEE-S---STTHHHHHHHHHHHHHHTTEEE
T ss_pred CCHHHHHHHHHHHHHhhcccCCCCeEEEEEcc---cCCHHHHHHHHHHHHhhccccc
Confidence 58899999999999999985 344554 564 34444 678999999999863
No 175
>PRK07478 short chain dehydrogenase; Provisional
Probab=26.63 E-value=1.7e+02 Score=23.35 Aligned_cols=38 Identities=21% Similarity=0.221 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHc
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREY 167 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~ 167 (171)
.-+|..+++...+.|.+-+..+|+. .+...+.+.+++.
T Consensus 16 ~giG~~ia~~l~~~G~~v~~~~r~~----~~~~~~~~~~~~~ 53 (254)
T PRK07478 16 SGIGRAAAKLFAREGAKVVVGARRQ----AELDQLVAEIRAE 53 (254)
T ss_pred ChHHHHHHHHHHHCCCEEEEEeCCH----HHHHHHHHHHHhc
Confidence 4588999999999998766778863 2444444444443
No 176
>PRK05876 short chain dehydrogenase; Provisional
Probab=26.33 E-value=1.6e+02 Score=24.48 Aligned_cols=39 Identities=15% Similarity=0.159 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYG 168 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~G 168 (171)
--||..|++++.+.|.+-++.||+. ..+..+++.+++.|
T Consensus 16 ~gIG~ala~~La~~G~~Vv~~~r~~----~~l~~~~~~l~~~~ 54 (275)
T PRK05876 16 SGIGLATGTEFARRGARVVLGDVDK----PGLRQAVNHLRAEG 54 (275)
T ss_pred chHHHHHHHHHHHCCCEEEEEeCCH----HHHHHHHHHHHhcC
Confidence 4589999999999998777788863 23444555554443
No 177
>PRK08868 flagellar protein FlaG; Provisional
Probab=26.32 E-value=2.4e+02 Score=22.73 Aligned_cols=39 Identities=5% Similarity=0.037 Sum_probs=30.0
Q ss_pred HHHhhhhhcCCCCCceEEEEeeCCcEEEEEEeCCCCcEE
Q 030804 62 HSRIRKKIDGTPERPRLCVFRSNKHLYVQVIDDTKMHTL 100 (171)
Q Consensus 62 ~~RirkKi~gt~~rPRL~V~rSnkhiyAQvIdd~~~ktL 100 (171)
-.++.+.+.......+..|+.....++++|||..+|.+|
T Consensus 77 VeklNe~~~~~n~~L~F~vdeetgr~VVkViD~~T~EVI 115 (144)
T PRK08868 77 VEQMNEFVKSINKGLSFRVDEESGRDVVTIYEASTGDII 115 (144)
T ss_pred HHHHHHHHHhhcCceEEEEecCCCCEEEEEEECCCCcee
Confidence 344444454445567999999999999999999999884
No 178
>PRK08303 short chain dehydrogenase; Provisional
Probab=26.30 E-value=1.6e+02 Score=25.18 Aligned_cols=43 Identities=21% Similarity=0.146 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCch------hhHHHHHHHHHHHcC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPY------HGRIQALADAAREYG 168 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~Y------hGrVkAlad~aRe~G 168 (171)
.-+|..+|+++.+.|.+-+..||+...+ ..++..+++.+.+.|
T Consensus 18 ~GIG~aia~~la~~G~~Vv~~~r~~~~~~~~~~~~~~~~~~~~~l~~~~ 66 (305)
T PRK08303 18 RGAGRGIAVELGAAGATVYVTGRSTRARRSEYDRPETIEETAELVTAAG 66 (305)
T ss_pred chHHHHHHHHHHHCCCEEEEEecccccccccccccchHHHHHHHHHhcC
Confidence 4689999999999998767778864222 345666666655444
No 179
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.30 E-value=1.2e+02 Score=20.08 Aligned_cols=34 Identities=15% Similarity=0.309 Sum_probs=26.2
Q ss_pred HcCCCEEEEecCCCch-----------hhHHHHHHHHHHHcCCcC
Q 030804 138 EKGITKVAFDRGGYPY-----------HGRIQALADAAREYGLQF 171 (171)
Q Consensus 138 e~GI~~VvfDRgg~~Y-----------hGrVkAlad~aRe~GL~f 171 (171)
..+|.++.|||.+..+ .+-+..+.+.|+++|.+|
T Consensus 22 ~~nI~~~~~~~~~~~~~~v~v~ie~~~~~~~~~i~~~L~~~G~~~ 66 (68)
T cd04885 22 PRNITEFHYRNQGGDEARVLVGIQVPDREDLAELKERLEALGYPY 66 (68)
T ss_pred CCcEEEEEEEcCCCCceEEEEEEEeCCHHHHHHHHHHHHHcCCCc
Confidence 4789999999843211 367999999999999875
No 180
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=26.22 E-value=1.4e+02 Score=27.64 Aligned_cols=52 Identities=25% Similarity=0.502 Sum_probs=42.0
Q ss_pred CCcHHHHHHHHH-----------------HHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 119 GPTIEVSKKVGE-----------------MIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 119 ~~n~~AA~~VG~-----------------~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
..+.++|..+-+ .||-.+.|.|+.++=-+.|..-...+++.+++.+++.|+.
T Consensus 57 v~~~e~A~A~~~Ik~~~~vPLVaDiHf~~rla~~~~~~g~~k~RINPGNig~~~~v~~vVe~Ak~~g~p 125 (361)
T COG0821 57 VPDMEAAEALKEIKQRLNVPLVADIHFDYRLALEAAECGVDKVRINPGNIGFKDRVREVVEAAKDKGIP 125 (361)
T ss_pred cCCHHHHHHHHHHHHhCCCCEEEEeeccHHHHHHhhhcCcceEEECCcccCcHHHHHHHHHHHHHcCCC
Confidence 356666666654 3677888899999988888888888999999999999975
No 181
>PRK07814 short chain dehydrogenase; Provisional
Probab=26.20 E-value=1.7e+02 Score=23.69 Aligned_cols=35 Identities=23% Similarity=0.332 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHH
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAR 165 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aR 165 (171)
-||..+++.+.+.|.+-+..||.. .+...+.+.+.
T Consensus 21 gIG~~~a~~l~~~G~~Vi~~~r~~----~~~~~~~~~l~ 55 (263)
T PRK07814 21 GLGAAIALAFAEAGADVLIAARTE----SQLDEVAEQIR 55 (263)
T ss_pred hHHHHHHHHHHHCCCEEEEEeCCH----HHHHHHHHHHH
Confidence 589999999999999666789863 23444444443
No 182
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=25.82 E-value=1.3e+02 Score=27.66 Aligned_cols=42 Identities=29% Similarity=0.555 Sum_probs=31.2
Q ss_pred HHHHHHHHHcCCCEEEEecCCCchhh---H--HHHHHHHHHHcCCcC
Q 030804 130 EMIAKSCLEKGITKVAFDRGGYPYHG---R--IQALADAAREYGLQF 171 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDRgg~~YhG---r--VkAlad~aRe~GL~f 171 (171)
..+.+.|.++||..+++=-+||.-.| . -..+.+.+|++|+.+
T Consensus 78 ~~~l~e~~~~gv~~~vi~s~gf~e~g~~g~~~~~~l~~~a~~~girv 124 (447)
T TIGR02717 78 PQVVEECGEKGVKGAVVITAGFKEVGEEGAELEQELVEIARKYGMRL 124 (447)
T ss_pred HHHHHHHHhcCCCEEEEECCCccccCcchHHHHHHHHHHHHHcCCEE
Confidence 34556788899999987666666544 2 378999999999853
No 183
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=25.54 E-value=1.9e+02 Score=20.35 Aligned_cols=40 Identities=30% Similarity=0.336 Sum_probs=29.9
Q ss_pred HHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 130 EMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
..+++.|+++|+ .|..+.=.-.--.-.+.+.+.+++.|+.
T Consensus 76 ~~~~~~~l~~g~-~v~~EKP~~~~~~~~~~l~~~a~~~~~~ 115 (120)
T PF01408_consen 76 AEIAKKALEAGK-HVLVEKPLALTLEEAEELVEAAKEKGVK 115 (120)
T ss_dssp HHHHHHHHHTTS-EEEEESSSSSSHHHHHHHHHHHHHHTSC
T ss_pred HHHHHHHHHcCC-EEEEEcCCcCCHHHHHHHHHHHHHhCCE
Confidence 457889999999 6777764334456678888888888875
No 184
>PRK13111 trpA tryptophan synthase subunit alpha; Provisional
Probab=25.06 E-value=1.6e+02 Score=25.24 Aligned_cols=37 Identities=22% Similarity=0.263 Sum_probs=27.1
Q ss_pred HHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 131 MIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 131 ~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.+.+.|+++|++-+.... ...+-+..+.+.++++||+
T Consensus 108 ~f~~~~~~aGvdGviipD---Lp~ee~~~~~~~~~~~gl~ 144 (258)
T PRK13111 108 RFAADAAEAGVDGLIIPD---LPPEEAEELRAAAKKHGLD 144 (258)
T ss_pred HHHHHHHHcCCcEEEECC---CCHHHHHHHHHHHHHcCCc
Confidence 467888888888887742 2336777888888888875
No 185
>PRK12823 benD 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional
Probab=24.98 E-value=1.7e+02 Score=23.46 Aligned_cols=25 Identities=24% Similarity=0.372 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRG 149 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRg 149 (171)
+.-+|..|++++.+.|.+-+.+||.
T Consensus 17 s~gIG~~la~~l~~~G~~v~~~~r~ 41 (260)
T PRK12823 17 AQGIGRGVALRAAAEGARVVLVDRS 41 (260)
T ss_pred CchHHHHHHHHHHHCCCEEEEEeCc
Confidence 3468999999999999877788986
No 186
>PRK08945 putative oxoacyl-(acyl carrier protein) reductase; Provisional
Probab=24.77 E-value=2e+02 Score=22.82 Aligned_cols=25 Identities=20% Similarity=0.284 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
.-+|..+++.+.+.|..-+..||..
T Consensus 22 g~iG~~la~~l~~~G~~Vi~~~r~~ 46 (247)
T PRK08945 22 DGIGREAALTYARHGATVILLGRTE 46 (247)
T ss_pred chHHHHHHHHHHHCCCcEEEEeCCH
Confidence 4688999999999998777888863
No 187
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=24.39 E-value=1.7e+02 Score=23.54 Aligned_cols=51 Identities=20% Similarity=0.132 Sum_probs=32.8
Q ss_pred CcHHHHHHHHHHHHHHHH-HcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCL-EKGITKVAFDRGG---YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~-e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~ 170 (171)
.|..+.+.+++.|+++.. ..+-.+|.|=.+. ..-.-|.+.|.+++.+.|++
T Consensus 103 d~~~~g~~~~~~l~~~g~~~~~~~~i~~l~g~~~~~~~~~R~~g~~~~~~~~~~~ 157 (268)
T cd06306 103 SWYEMGYQAGEYLAQRHPKGSKPAKVAWFPGPKGAGWVKAVEKGFRDALAGSAIE 157 (268)
T ss_pred ChHHHHHHHHHHHHHHhhcCCCCceEEEEeCCCCCchHHHHHHHHHHHHhhcCcE
Confidence 456677777777777664 2223666553232 22357899999999998875
No 188
>PRK13398 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=24.33 E-value=2e+02 Score=24.84 Aligned_cols=43 Identities=26% Similarity=0.502 Sum_probs=29.1
Q ss_pred HHHHHHHHHHcCCCEE---EEe-c-CCCchhh----HHHHHHHHHHHcCCcC
Q 030804 129 GEMIAKSCLEKGITKV---AFD-R-GGYPYHG----RIQALADAAREYGLQF 171 (171)
Q Consensus 129 G~~LAkra~e~GI~~V---vfD-R-gg~~YhG----rVkAlad~aRe~GL~f 171 (171)
....|+++++.|+.-+ .|| | .++.|.| -++.+.+.+++.||.|
T Consensus 43 ~~~~A~~lk~~g~~~~r~~~~kpRTs~~s~~G~g~~gl~~l~~~~~~~Gl~~ 94 (266)
T PRK13398 43 MVKVAEKLKELGVHMLRGGAFKPRTSPYSFQGLGEEGLKILKEVGDKYNLPV 94 (266)
T ss_pred HHHHHHHHHHcCCCEEEEeeecCCCCCCccCCcHHHHHHHHHHHHHHcCCCE
Confidence 4556777777888744 455 3 2355543 4778888899999875
No 189
>cd07940 DRE_TIM_IPMS 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain. 2-isopropylmalate synthase (IPMS) catalyzes an aldol-type condensation of acetyl-CoA and 2-oxoisovalerate yielding 2-isopropylmalate and CoA, the first committed step in leucine biosynthesis. This family includes the Arabidopsis thaliana IPMS1 and IPMS2 proteins, the Glycine max GmN56 protein, and the Brassica insularis BatIMS protein. This family also includes a group of archeal IPMS-like proteins represented by the Methanocaldococcus jannaschii AksA protein. AksA catalyzes the condensation of alpha-ketoglutarate and acetyl-CoA to form trans-homoaconitate, one of 13 steps in the conversion of alpha-ketoglutarate and acetylCoA to alpha-ketosuberate, a precursor to coenzyme B and biotin. AksA also catalyzes the condensation of alpha-ketoadipate or alpha-ketopimelate with acetylCoA to form, respectively, the (R)-homocitrate homologs (R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and (R)-2-h
Probab=24.27 E-value=1.6e+02 Score=24.86 Aligned_cols=48 Identities=19% Similarity=0.117 Sum_probs=21.8
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCEEEEec--CCCchhhHHHHHHHHHHHcCC
Q 030804 121 TIEVSKKVGEMIAKSCLEKGITKVAFDR--GGYPYHGRIQALADAAREYGL 169 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI~~VvfDR--gg~~YhGrVkAlad~aRe~GL 169 (171)
+.+........+++.+++.|+. |.|.- .+.---..+..+++.+.+.|.
T Consensus 108 ~~~~~~~~~~~~i~~a~~~G~~-v~~~~~~~~~~~~~~~~~~~~~~~~~G~ 157 (268)
T cd07940 108 TREEVLERAVEAVEYAKSHGLD-VEFSAEDATRTDLDFLIEVVEAAIEAGA 157 (268)
T ss_pred CHHHHHHHHHHHHHHHHHcCCe-EEEeeecCCCCCHHHHHHHHHHHHHcCC
Confidence 3444444445555566666642 43421 111113445555555555554
No 190
>PRK12738 kbaY tagatose-bisphosphate aldolase; Reviewed
Probab=24.20 E-value=1.7e+02 Score=25.83 Aligned_cols=41 Identities=10% Similarity=0.235 Sum_probs=31.7
Q ss_pred HHHHHHHHHcCCCEEEEecCCCchhhHH---HHHHHHHHHcCCc
Q 030804 130 EMIAKSCLEKGITKVAFDRGGYPYHGRI---QALADAAREYGLQ 170 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDRgg~~YhGrV---kAlad~aRe~GL~ 170 (171)
....++|++.|.+.|-||-....|..-| +.+++-+...|+.
T Consensus 87 ~e~i~~ai~~GFtSVM~DgS~lp~eeNi~~T~evv~~Ah~~gv~ 130 (286)
T PRK12738 87 LDDIRRKVHAGVRSAMIDGSHFPFAENVKLVKSVVDFCHSQDCS 130 (286)
T ss_pred HHHHHHHHHcCCCeEeecCCCCCHHHHHHHHHHHHHHHHHcCCe
Confidence 4567889999999999999888887554 5566677776653
No 191
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=24.11 E-value=2.1e+02 Score=22.43 Aligned_cols=49 Identities=22% Similarity=0.266 Sum_probs=29.4
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEE--ecCCC-chhhHHHHHHHHHHHc-CCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAF--DRGGY-PYHGRIQALADAAREY-GLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~Vvf--DRgg~-~YhGrVkAlad~aRe~-GL~ 170 (171)
.|.++++.+++.|.++. .|..++.| ..... -...|...|.++++++ |++
T Consensus 102 d~~~~~~~~~~~l~~~~--~g~~~i~~l~~~~~~~~~~~r~~g~~~~l~~~~~~~ 154 (268)
T cd06323 102 DNVAGGKMAAEYLVKLL--GGKGKVVELQGIPGASAARERGKGFHEVVDKYPGLK 154 (268)
T ss_pred CcHHHHHHHHHHHHHHh--CCCceEEEEeCCCCCccHHHHHHHHHHHHHhCCCcE
Confidence 34455555555555442 26677754 22222 3358899999999994 775
No 192
>PRK06487 glycerate dehydrogenase; Provisional
Probab=24.06 E-value=92 Score=27.27 Aligned_cols=25 Identities=16% Similarity=0.191 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
-.+|+.+|++++..|.+-+.|||.+
T Consensus 157 G~IG~~vA~~l~~fgm~V~~~~~~~ 181 (317)
T PRK06487 157 GELGGAVARLAEAFGMRVLIGQLPG 181 (317)
T ss_pred CHHHHHHHHHHhhCCCEEEEECCCC
Confidence 3689999999999999888899853
No 193
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=24.02 E-value=1.5e+02 Score=24.71 Aligned_cols=44 Identities=18% Similarity=0.206 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHcCCCEEEEecC-------CCchhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRG-------GYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRg-------g~~YhGrVkAlad~aRe~GL~ 170 (171)
.|-.+=.+.+++.||+-+++|-- ...-.-.+.+..+.++++|+.
T Consensus 14 tv~~i~~~~L~~~Gikgvi~DlDNTLv~wd~~~~tpe~~~W~~e~k~~gi~ 64 (175)
T COG2179 14 TVFDITPDILKAHGIKGVILDLDNTLVPWDNPDATPELRAWLAELKEAGIK 64 (175)
T ss_pred hHhhCCHHHHHHcCCcEEEEeccCceecccCCCCCHHHHHHHHHHHhcCCE
Confidence 56667788899999999999842 123367899999999999986
No 194
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=23.77 E-value=1.9e+02 Score=23.77 Aligned_cols=44 Identities=20% Similarity=0.126 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHc-CC-CEEEEecCC--C-chhhHHHHHHHHHHHcCCc
Q 030804 127 KVGEMIAKSCLEK-GI-TKVAFDRGG--Y-PYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 127 ~VG~~LAkra~e~-GI-~~VvfDRgg--~-~YhGrVkAlad~aRe~GL~ 170 (171)
..|+.+++.+.+. |- .++.+--+. . .-..|.+.|.+++.++|++
T Consensus 132 ~~g~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~R~~gf~~al~~~g~~ 180 (295)
T PRK10653 132 AGGKMAGDFIAKKLGEGAKVIQLEGIAGTSAARERGEGFKQAVAAHKFN 180 (295)
T ss_pred HHHHHHHHHHHHHhCCCceEEEEEccCCCccHHHHHHHHHHHHhhCCCE
Confidence 3455555555554 32 244432222 2 2248899999999999974
No 195
>PRK13125 trpA tryptophan synthase subunit alpha; Provisional
Probab=23.56 E-value=2.1e+02 Score=23.93 Aligned_cols=39 Identities=15% Similarity=0.229 Sum_probs=25.6
Q ss_pred HHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 132 IAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 132 LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
+++.+.+.|++-+.+.=-.+........+.+.++++|++
T Consensus 93 ~i~~~~~~Gadgvii~dlp~e~~~~~~~~~~~~~~~Gl~ 131 (244)
T PRK13125 93 FLNMARDVGADGVLFPDLLIDYPDDLEKYVEIIKNKGLK 131 (244)
T ss_pred HHHHHHHcCCCEEEECCCCCCcHHHHHHHHHHHHHcCCC
Confidence 466777888888877321222345677788888888875
No 196
>PRK07454 short chain dehydrogenase; Provisional
Probab=23.40 E-value=1.8e+02 Score=22.92 Aligned_cols=25 Identities=16% Similarity=0.193 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
.-+|..|++++.+.|.+-+++||+.
T Consensus 16 g~iG~~la~~l~~~G~~V~~~~r~~ 40 (241)
T PRK07454 16 SGIGKATALAFAKAGWDLALVARSQ 40 (241)
T ss_pred chHHHHHHHHHHHCCCEEEEEeCCH
Confidence 4689999999999998766789864
No 197
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=23.03 E-value=2.7e+02 Score=22.30 Aligned_cols=48 Identities=21% Similarity=0.210 Sum_probs=30.9
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRGG---YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~ 170 (171)
.|.++++.+++.|.+. .|..++.|=-+. ..-.-|+..|.+++.++|++
T Consensus 107 d~~~~g~~~~~~l~~~---~g~~~i~~i~g~~~~~~~~~r~~g~~~~~~~~~~~ 157 (271)
T cd06312 107 DEYAAGEAAGERLAEL---KGGKNVLCVIHEPGNVTLEDRCAGFADGLGGAGIT 157 (271)
T ss_pred ChHHHHHHHHHHHHHh---cCCCeEEEEecCCCCccHHHHHHHHHHHHHhcCce
Confidence 4556666666666553 677787553221 22246899999999998874
No 198
>PRK07326 short chain dehydrogenase; Provisional
Probab=23.01 E-value=1.9e+02 Score=22.63 Aligned_cols=26 Identities=31% Similarity=0.344 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
.--+|..|++++.+.|.+-+.+||+.
T Consensus 15 tg~iG~~la~~l~~~g~~V~~~~r~~ 40 (237)
T PRK07326 15 SKGIGFAIAEALLAEGYKVAITARDQ 40 (237)
T ss_pred CCcHHHHHHHHHHHCCCEEEEeeCCH
Confidence 34689999999999999877889864
No 199
>cd04509 PBP1_ABC_transporter_GCPR_C_like Family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. This CD includes members of the family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. The family C GPCR includes glutamate/glycine-gated ion channels such as the NMDA receptor, G-protein-coupled receptors, metabotropic glutamate, GABA-B, calcium sensing, phermone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. The glutamate receptors that form cation-selective ion channels, iGluR, can be classified into three different subgroups according to their binding-affinity for the agonists NMDA (N-methyl-D-asparate), AMPA (alpha-amino-3-dihydro-5-methyl-3-oxo-4-isoxazolepropionic acid), and kainate. L-glutamate is a major neurotransmitter in the brain of vertebrates and acts th
Probab=22.81 E-value=2.3e+02 Score=22.21 Aligned_cols=44 Identities=25% Similarity=0.264 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHcCCCEEE--EecCCCchhhHHHHHHHHHHHcCCc
Q 030804 126 KKVGEMIAKSCLEKGITKVA--FDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~Vv--fDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
...++.+++-+.+.|.++|. ++... -...+..++.+.+++.|++
T Consensus 121 ~~~~~~~~~~l~~~~~~~v~iv~~~~~-~~~~~~~~~~~~~~~~g~~ 166 (299)
T cd04509 121 EQQAEALADYIKEYNWKKVAILYDDDS-YGRGLLEAFKAAFKKKGGT 166 (299)
T ss_pred HHHHHHHHHHHHHcCCcEEEEEecCch-HHHHHHHHHHHHHHHcCCE
Confidence 34556666677777888885 34433 2245788999999999875
No 200
>PHA03003 palmytilated EEV membrane glycoprotein; Provisional
Probab=22.46 E-value=95 Score=27.79 Aligned_cols=40 Identities=5% Similarity=0.191 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHcCCC-EEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 125 SKKVGEMIAKSCLEKGIT-KVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~-~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
...+-+.|.+++. .||+ .+.+|-.+. ....+.|+++|+++
T Consensus 62 g~~i~~aL~~aa~-rGV~Vril~D~~~~------~~~~~~L~~~Gv~v 102 (369)
T PHA03003 62 GRLILDKLKEAAE-SGVKVTILVDEQSG------DKDEEELQSSNINY 102 (369)
T ss_pred HHHHHHHHHHhcc-CCCeEEEEecCCCC------CccHHHHHHcCCEE
Confidence 3344455555553 5887 678995331 55667889999864
No 201
>PRK08628 short chain dehydrogenase; Provisional
Probab=22.35 E-value=1.8e+02 Score=23.23 Aligned_cols=26 Identities=27% Similarity=0.382 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGY 151 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~ 151 (171)
.-+|..+++...+.|..-++.+|...
T Consensus 17 ggiG~~la~~l~~~G~~v~~~~r~~~ 42 (258)
T PRK08628 17 SGIGAAISLRLAEEGAIPVIFGRSAP 42 (258)
T ss_pred ChHHHHHHHHHHHcCCcEEEEcCChh
Confidence 45899999999999988888888643
No 202
>PRK07806 short chain dehydrogenase; Provisional
Probab=22.35 E-value=2.3e+02 Score=22.34 Aligned_cols=25 Identities=24% Similarity=0.157 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
.-+|..|++++.+.|.+-+.++|+.
T Consensus 16 ggiG~~l~~~l~~~G~~V~~~~r~~ 40 (248)
T PRK07806 16 RGIGADTAKILAGAGAHVVVNYRQK 40 (248)
T ss_pred CcHHHHHHHHHHHCCCEEEEEeCCc
Confidence 3588899999988887656677753
No 203
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT. Members of this family are the periplasmic protein TorT which, together with the the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase, and shows homology to a periplasmic D-ribose binding protein.
Probab=22.25 E-value=1.9e+02 Score=23.92 Aligned_cols=52 Identities=17% Similarity=0.127 Sum_probs=35.3
Q ss_pred CCcHHHHHHHHHHHHHHHHH-cCCCEEEEecCC---CchhhHHHHHHHHHHHcCCc
Q 030804 119 GPTIEVSKKVGEMIAKSCLE-KGITKVAFDRGG---YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 119 ~~n~~AA~~VG~~LAkra~e-~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~ 170 (171)
..|..+++.+++.|++.... .|..++.|=.+. ..-..|.+.|.+++.++|++
T Consensus 102 ~D~~~~g~~~~~~L~~~~~~~~g~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~ 157 (295)
T TIGR02955 102 VDWYQMGYQAGEYLAQRHPKGSGPTTLAWLPGPKNRGGTKPVTQGFRAALEGSDVE 157 (295)
T ss_pred ecHHHHHHHHHHHHHHhcccCCCCeeEEEEeCCCcCCchhHHHHHHHHHHhcCCcE
Confidence 45677888888888874332 345567654332 22357999999999999875
No 204
>PRK06125 short chain dehydrogenase; Provisional
Probab=22.17 E-value=2.3e+02 Score=22.77 Aligned_cols=37 Identities=24% Similarity=0.316 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHH
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAARE 166 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe 166 (171)
.-+|..|++++.+.|.+-+.+||+. .+.+.+.+.+++
T Consensus 17 ~giG~~ia~~l~~~G~~V~~~~r~~----~~~~~~~~~l~~ 53 (259)
T PRK06125 17 KGIGAAAAEAFAAEGCHLHLVARDA----DALEALAADLRA 53 (259)
T ss_pred chHHHHHHHHHHHcCCEEEEEeCCH----HHHHHHHHHHHh
Confidence 4589999999999999666788863 344555554443
No 205
>cd07041 STAS_RsbR_RsbS_like Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain of proteins related to RsbS and RsbR which are part of the "stressosome" complex that plays an important role in the regulation of the bacterial stress activated alternative sigma factor sigma-B. During stress conditions RsbS and RsbR are phosphorylated which leads to the release of RsbT, an activator of of the RsbU phosphatase, which in turn activates RsbV which leads to the release and activation of sigma factor B. RsbS is a single domain protein (STAS domain), while RsbR-like proteins have a well-conserved C-terminal STATS domain and a variable N-terminal domain. The STAS domain is also found in the C- terminal region of sulphate transporters and anti-anti-sigma factors.
Probab=22.14 E-value=2.9e+02 Score=19.41 Aligned_cols=50 Identities=22% Similarity=0.252 Sum_probs=36.7
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCEEEEecCCCch-----hhHHHHHHHHHHHcCCc
Q 030804 121 TIEVSKKVGEMIAKSCLEKGITKVAFDRGGYPY-----HGRIQALADAAREYGLQ 170 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI~~VvfDRgg~~Y-----hGrVkAlad~aRe~GL~ 170 (171)
+..++..+-+.+.+...+.+.+.+++|=.+-.| =+-+..+.+.+++.|.+
T Consensus 21 ~~~~a~~~~~~l~~~~~~~~~~~vvlDls~v~~iDssg~~~l~~~~~~~~~~g~~ 75 (109)
T cd07041 21 DDERAEQLQERLLEAISRRRARGVIIDLTGVPVIDSAVARHLLRLARALRLLGAR 75 (109)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCEEEEECCCCchhcHHHHHHHHHHHHHHHHcCCe
Confidence 566788888877777766789999999877666 24566666777777764
No 206
>PLN02591 tryptophan synthase
Probab=22.04 E-value=1.8e+02 Score=24.94 Aligned_cols=38 Identities=16% Similarity=0.209 Sum_probs=28.5
Q ss_pred HHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 130 EMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
+.+.++|+++|++-++.-. ....-..-+.+.++++||+
T Consensus 96 ~~F~~~~~~aGv~GviipD---LP~ee~~~~~~~~~~~gl~ 133 (250)
T PLN02591 96 DKFMATIKEAGVHGLVVPD---LPLEETEALRAEAAKNGIE 133 (250)
T ss_pred HHHHHHHHHcCCCEEEeCC---CCHHHHHHHHHHHHHcCCe
Confidence 3567888899998887753 2347777888888888876
No 207
>PRK12828 short chain dehydrogenase; Provisional
Probab=21.76 E-value=2.1e+02 Score=22.20 Aligned_cols=24 Identities=21% Similarity=0.290 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCC
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
-+|..|++.+.+.|.+-+.+||+.
T Consensus 18 ~iG~~la~~l~~~G~~v~~~~r~~ 41 (239)
T PRK12828 18 GLGRATAAWLAARGARVALIGRGA 41 (239)
T ss_pred cHhHHHHHHHHHCCCeEEEEeCCh
Confidence 578999999999998877888864
No 208
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=21.69 E-value=2.6e+02 Score=22.32 Aligned_cols=49 Identities=22% Similarity=0.335 Sum_probs=30.4
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCCEEEEecCC---CchhhHHHHHHHHHHHcCCc
Q 030804 120 PTIEVSKKVGEMIAKSCLEKGITKVAFDRGG---YPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~e~GI~~VvfDRgg---~~YhGrVkAlad~aRe~GL~ 170 (171)
.|..+.+..++.|.++.. .|.+.+.|- +. ....-|+++|.+++.++|++
T Consensus 101 D~~~~g~~a~~~l~~~~~-~g~~~~~~~-~~~~~~~~~~R~~gf~~~~~~~~~~ 152 (271)
T cd06314 101 DNYAAGRTAGEIMKKALP-GGGKVAIFV-GSLGADNAKERIQGIKDAIKDSKIE 152 (271)
T ss_pred ChHHHHHHHHHHHHHHcC-CCCEEEEEe-cCCCCCCHHHHHHHHHHHHhcCCcE
Confidence 355555555555555432 355555553 32 22368999999999999874
No 209
>cd06360 PBP1_alkylbenzenes_like Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene. This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.
Probab=21.61 E-value=2.1e+02 Score=23.67 Aligned_cols=45 Identities=18% Similarity=0.229 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHcCCCEEEEecCCCch-hhHHHHHHHHHHHcCCcC
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRGGYPY-HGRIQALADAAREYGLQF 171 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRgg~~Y-hGrVkAlad~aRe~GL~f 171 (171)
.-+..+++.+.+.|.++|.+--..+.| ..+...+.+.+.+.|+++
T Consensus 120 ~~~~~~~~~l~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~~G~~v 165 (336)
T cd06360 120 QWAAPMGKYAADDGYKKVVTVAWDYAFGYEVVEGFKEAFTEAGGKI 165 (336)
T ss_pred HHHHHHHHHHHHcCCCeEEEEeccchhhHHHHHHHHHHHHHcCCEE
Confidence 445566666777889988664333445 356788999999999763
No 210
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=21.56 E-value=2.9e+02 Score=19.88 Aligned_cols=45 Identities=18% Similarity=0.223 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 124 VSKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 124 AA~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.+...-..+++..++.|.. +++|...+.- .....+.+.+++.|.+
T Consensus 54 ~~~~~~~~~~~~~l~~g~~-~vvd~~~~~~-~~r~~~~~~~~~~~~~ 98 (143)
T PF13671_consen 54 RAYQILNAAIRKALRNGNS-VVVDNTNLSR-EERARLRELARKHGYP 98 (143)
T ss_dssp HHHHHHHHHHHHHHHTT-E-EEEESS--SH-HHHHHHHHHHHHCTEE
T ss_pred HHHHHHHHHHHHHHHcCCC-ceeccCcCCH-HHHHHHHHHHHHcCCe
Confidence 3444444556677788987 7778664444 4457888888888854
No 211
>PF07137 VDE: Violaxanthin de-epoxidase (VDE); InterPro: IPR010788 This family represents a conserved region approximately 350 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage [].; GO: 0046422 violaxanthin de-epoxidase activity, 0055114 oxidation-reduction process, 0009507 chloroplast; PDB: 3CQN_B 3CQR_A.
Probab=21.52 E-value=99 Score=26.28 Aligned_cols=29 Identities=24% Similarity=0.376 Sum_probs=21.3
Q ss_pred EEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 143 KVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 143 ~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
.++|-|.+.....-+..|..++.++||+|
T Consensus 150 AvVYtrs~~lP~s~~p~l~~aa~k~G~d~ 178 (198)
T PF07137_consen 150 AVVYTRSPTLPESIVPELRRAAKKAGIDF 178 (198)
T ss_dssp EEEEESSSS--GGGHHHHHHHHHHTT--G
T ss_pred eEEEeCCCCCChHHhHHHHHHHHHhCCCH
Confidence 46788888888888999999999999986
No 212
>PF03900 Porphobil_deamC: Porphobilinogen deaminase, C-terminal domain; InterPro: IPR022418 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the C-terminal domain of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this alpha/beta domain consists of alpha-beta(3)-alpha in two layers []. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 3EQ1_B 3ECR_A 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A.
Probab=21.29 E-value=69 Score=21.98 Aligned_cols=59 Identities=17% Similarity=0.247 Sum_probs=31.4
Q ss_pred hhhcCCCCCc--eEEEEeeCC--cEEEEEEeCCCCcEEEEEecCCcccccccCCCCCCcHHHHHHHHHHHHHHHHH
Q 030804 67 KKIDGTPERP--RLCVFRSNK--HLYVQVIDDTKMHTLASASTMQKPISEELDYSSGPTIEVSKKVGEMIAKSCLE 138 (171)
Q Consensus 67 kKi~gt~~rP--RL~V~rSnk--hiyAQvIdd~~~ktLasaST~ek~ik~~l~~~~~~n~~AA~~VG~~LAkra~e 138 (171)
+.+.|.=.-| -.+.+..++ ++.+.+.+.++.+.+...+- .++.+-+..+|+.||+..++
T Consensus 12 ~~l~ggC~~Piga~a~~~~~~~l~l~~~v~~~dG~~~~~~~~~-------------~~~~~~a~~lg~~la~~l~~ 74 (74)
T PF03900_consen 12 KELGGGCHSPIGAYAKIEGDERLRLRAMVGSPDGSRIIIRVEI-------------TGPIEDAEELGKKLAEELLA 74 (74)
T ss_dssp HHCT--TTSSEEEEEEEETTE-EEEEEEEE-TTSSSEEEEEEE-------------EE-GGGHCCHHHHHHHHHHH
T ss_pred HHhCCCCCCceeeEEEEcCCCEEEEEEEEECCCCCEEEEEEEE-------------EcCHHHHHHHHHHHHHHHhC
Confidence 3344432334 455555565 66666766555552222211 12556788899999988764
No 213
>PRK08339 short chain dehydrogenase; Provisional
Probab=21.26 E-value=2.3e+02 Score=23.15 Aligned_cols=24 Identities=21% Similarity=0.314 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRG 149 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRg 149 (171)
.-+|..+|+++.+.|.+-+..||+
T Consensus 18 ~gIG~aia~~l~~~G~~V~~~~r~ 41 (263)
T PRK08339 18 KGIGFGVARVLARAGADVILLSRN 41 (263)
T ss_pred CcHHHHHHHHHHHCCCEEEEEeCC
Confidence 358999999999999876677886
No 214
>PRK13761 hypothetical protein; Provisional
Probab=20.94 E-value=2.1e+02 Score=25.16 Aligned_cols=46 Identities=24% Similarity=0.271 Sum_probs=36.2
Q ss_pred cHHHHHHHHHHHHHHHHHcCCC-EE-EEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 121 TIEVSKKVGEMIAKSCLEKGIT-KV-AFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI~-~V-vfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
|=..|.++-+.+++-+++.|-+ +| .|.|. ..|+++.++-++++|.+
T Consensus 75 NGN~AAL~p~eiveLa~~~~A~iEVNLF~RT----~eR~~~I~~~l~~~Ga~ 122 (248)
T PRK13761 75 NGNTAALVPEEIVELAEALNAKLEVNLFYRT----EERVEKIAEVLREHGAK 122 (248)
T ss_pred cchHHhhChHHHHHHHHHhCCCEEEEeccCC----HHHHHHHHHHHHHcCCc
Confidence 4457788889999999987765 44 56554 68999999999999964
No 215
>PRK06935 2-deoxy-D-gluconate 3-dehydrogenase; Provisional
Probab=20.72 E-value=2.3e+02 Score=22.69 Aligned_cols=26 Identities=15% Similarity=0.174 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHcCCCEEEEecC
Q 030804 124 VSKKVGEMIAKSCLEKGITKVAFDRG 149 (171)
Q Consensus 124 AA~~VG~~LAkra~e~GI~~VvfDRg 149 (171)
++.-+|..|+++..+.|..-++.+|+
T Consensus 23 as~gIG~~ia~~l~~~G~~v~~~~~~ 48 (258)
T PRK06935 23 GNTGLGQGYAVALAKAGADIIITTHG 48 (258)
T ss_pred CCchHHHHHHHHHHHCCCEEEEEeCC
Confidence 34478999999999999988888886
No 216
>PRK11024 colicin uptake protein TolR; Provisional
Probab=20.71 E-value=3.9e+02 Score=20.41 Aligned_cols=40 Identities=8% Similarity=-0.095 Sum_probs=26.4
Q ss_pred HHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 131 MIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 131 ~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.|.+...+..=..|+..-.+...+|+|-.+.|.++++|+.
T Consensus 93 ~l~~~~~~~~~~~V~i~aD~~~~~~~vv~vmd~~k~aG~~ 132 (141)
T PRK11024 93 EAKSRFKANPKTVFLIGGAKDVPYDEIIKALNLLHSAGVK 132 (141)
T ss_pred HHHHHHhhCCCceEEEEcCCCCCHHHHHHHHHHHHHcCCC
Confidence 3444433333234554334468899999999999999984
No 217
>PRK05855 short chain dehydrogenase; Validated
Probab=20.60 E-value=2e+02 Score=25.85 Aligned_cols=41 Identities=22% Similarity=0.227 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcC
Q 030804 124 VSKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYG 168 (171)
Q Consensus 124 AA~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~G 168 (171)
+..-+|..+++++.+.|.+-+..||+. .+...+++.+++.|
T Consensus 323 ~s~giG~~~a~~l~~~G~~v~~~~r~~----~~~~~~~~~~~~~~ 363 (582)
T PRK05855 323 AGSGIGRETALAFAREGAEVVASDIDE----AAAERTAELIRAAG 363 (582)
T ss_pred CcCHHHHHHHHHHHHCCCEEEEEeCCH----HHHHHHHHHHHhcC
Confidence 346799999999999999866789863 34444555555443
No 218
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=20.49 E-value=2.9e+02 Score=21.43 Aligned_cols=41 Identities=27% Similarity=0.408 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHc--CCCEEEE--ecCCCch-hhHHHHHHHHHHHcC
Q 030804 128 VGEMIAKSCLEK--GITKVAF--DRGGYPY-HGRIQALADAAREYG 168 (171)
Q Consensus 128 VG~~LAkra~e~--GI~~Vvf--DRgg~~Y-hGrVkAlad~aRe~G 168 (171)
.|+.+++.+.+. |..++.| +...+.+ ..|...|.+.++++|
T Consensus 106 ~~~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~ 151 (267)
T cd01536 106 AGRLAGEYLAKLLGGKGKVAIIEGPPGSSNAQERVKGFRDALKEYP 151 (267)
T ss_pred HHHHHHHHHHHHhCCCceEEEEEcccccchHHHHHHHHHHHHHhCC
Confidence 344445555454 7788854 3332233 578999999999984
No 219
>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []. It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.
Probab=20.38 E-value=2.5e+02 Score=22.31 Aligned_cols=48 Identities=15% Similarity=0.284 Sum_probs=31.0
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCc
Q 030804 121 TIEVSKKVGEMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQ 170 (171)
Q Consensus 121 n~~AA~~VG~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~ 170 (171)
.-..|..+.+.+.+.|.+.|. .++||-.. .-...+..+++.++++|.+
T Consensus 74 ~~~~a~~~~~~~~~~a~~~~~-nii~E~tl-~~~~~~~~~~~~~k~~GY~ 121 (199)
T PF06414_consen 74 TQKEASRLAEKLIEYAIENRY-NIIFEGTL-SNPSKLRKLIREAKAAGYK 121 (199)
T ss_dssp HHHHHHHHHHHHHHHHHHCT---EEEE--T-TSSHHHHHHHHHHHCTT-E
T ss_pred HHHHHHHHHHHHHHHHHHcCC-CEEEecCC-CChhHHHHHHHHHHcCCce
Confidence 345567777888888999887 67888653 3335555588888888864
No 220
>PRK07370 enoyl-(acyl carrier protein) reductase; Validated
Probab=20.33 E-value=2.3e+02 Score=23.05 Aligned_cols=23 Identities=13% Similarity=-0.129 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHcCCCEEEEecC
Q 030804 127 KVGEMIAKSCLEKGITKVAFDRG 149 (171)
Q Consensus 127 ~VG~~LAkra~e~GI~~VvfDRg 149 (171)
-+|+.+|+++.+.|.+-+..+|.
T Consensus 19 GIG~aia~~la~~G~~v~~~~~~ 41 (258)
T PRK07370 19 SIAWGIAQQLHAAGAELGITYLP 41 (258)
T ss_pred chHHHHHHHHHHCCCEEEEEecC
Confidence 47888888888888765555553
No 221
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=20.31 E-value=2.7e+02 Score=22.77 Aligned_cols=49 Identities=6% Similarity=-0.083 Sum_probs=33.4
Q ss_pred CcHHHHHHHHHHHHHHHH--HcCCCEEEEe--cCC-CchhhHHHHHHHHHHHcC
Q 030804 120 PTIEVSKKVGEMIAKSCL--EKGITKVAFD--RGG-YPYHGRIQALADAAREYG 168 (171)
Q Consensus 120 ~n~~AA~~VG~~LAkra~--e~GI~~VvfD--Rgg-~~YhGrVkAlad~aRe~G 168 (171)
.|.++++.+++.|.+++. ..|..++.|= ... ..-..|..+|.+++.++|
T Consensus 102 d~~~~g~~~~~~l~~~~~~~~~g~~~i~~l~g~~~~~~~~~R~~gf~~~l~~~~ 155 (288)
T cd01538 102 DNEKVGELQGQALVDGLGAKGKPPGNIELIAGSPTDNNAKLFFNGAMSVLKPLI 155 (288)
T ss_pred ChHHHHHHHHHHHHHHHhhcCCCCceEEEEECCCCCchHHHHHHHHHHHHHhcc
Confidence 466778888888777764 2366677542 222 223578999999999987
No 222
>PF03447 NAD_binding_3: Homoserine dehydrogenase, NAD binding domain; InterPro: IPR005106 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see []. Homoserine dehydrogenase (1.1.1.3 from EC) catalyses the third step in the aspartate pathway; theNAD(P)-dependent reduction of aspartate beta-semialdehyde into homoserine [, ]. Homoserine is an intermediate in the biosynthesis of threonine, isoleucine, and methionine. The enzyme can be found in a monofunctional form, in some bacteria and yeast, or a bifunctional form consisting of an N-terminal aspartokinase domain and a C-terminal homoserine dehydrogenase domain, as found in bacteria such as Escherichia coli and in plants. Structural analysis of the yeast monofunctional enzyme (P31116 from SWISSPROT) indicates that the enzyme is a dimer composed of three distinct regions; an N-terminal nucleotide-binding domain, a short central dimerisation region, and a C-terminal catalytic domain []. The N-terminal domain forms a modified Rossman fold, while the catalytic domain forms a novel alpha-beta mixed sheet. This entry represents the NAD(P)-binding domain of aspartate and homoserine dehydrogenase. Asparate dehydrogenase (1.4.1.21 from EC) is strictly specific for L-aspartate as substrate and catalyses the first step in NAD biosynthesis from aspartate. The enzyme has a higher affinity for NAD+ than NADP+ []. Note that the C terminus of the protein contributes a helix to this domain that is not covered by this model.; GO: 0016491 oxidoreductase activity, 0050661 NADP binding, 0055114 oxidation-reduction process; PDB: 3ING_A 3MTJ_A 3DO5_A 3JSA_A 3C8M_A 1J5P_A 1H2H_A 2EJW_E 1TVE_A 1EBU_D ....
Probab=20.27 E-value=70 Score=23.18 Aligned_cols=42 Identities=24% Similarity=0.374 Sum_probs=31.0
Q ss_pred HHHHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 130 EMIAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 130 ~~LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
..+.+.+++.|+.-|....+...-...-..|.+.++++|..|
T Consensus 73 ~~~~~~~L~~G~~VVt~nk~ala~~~~~~~L~~~A~~~g~~~ 114 (117)
T PF03447_consen 73 AEYYEKALERGKHVVTANKGALADEALYEELREAARKNGVRI 114 (117)
T ss_dssp HHHHHHHHHTTCEEEES-HHHHHSHHHHHHHHHHHHHHT-EE
T ss_pred HHHHHHHHHCCCeEEEECHHHhhhHHHHHHHHHHHHHcCCEE
Confidence 357889999999999988876554466678888888888654
No 223
>cd07939 DRE_TIM_NifV Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain. FrbC (NifV) of Streptomyces rubellomurinus catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate and CoA, a reaction similar to one catalyzed by homocitrate synthase. The gene encoding FrbC is one of several genes required for the biosynthesis of FR900098, a potent antimalarial antibiotic. This protein is also required for assembly of the nitrogenase MoFe complex but its exact role is unknown. This family also includes the NifV proteins of Heliobacterium chlorum and Gluconacetobacter diazotrophicus, which appear to be orthologous to FrbC. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarbox
Probab=20.18 E-value=2.5e+02 Score=23.57 Aligned_cols=47 Identities=13% Similarity=0.080 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHHHcCCCEEEEec-CCCch-hhHHHHHHHHHHHcCC
Q 030804 122 IEVSKKVGEMIAKSCLEKGITKVAFDR-GGYPY-HGRIQALADAAREYGL 169 (171)
Q Consensus 122 ~~AA~~VG~~LAkra~e~GI~~VvfDR-gg~~Y-hGrVkAlad~aRe~GL 169 (171)
.+.+..--..+++.|++.|+ +|.|.- ...++ -..+..+++.+.+.|.
T Consensus 105 ~~~~~~~~~~~i~~a~~~G~-~v~~~~~~~~~~~~~~~~~~~~~~~~~G~ 153 (259)
T cd07939 105 RAWVLDQLRRLVGRAKDRGL-FVSVGAEDASRADPDFLIEFAEVAQEAGA 153 (259)
T ss_pred HHHHHHHHHHHHHHHHHCCC-eEEEeeccCCCCCHHHHHHHHHHHHHCCC
Confidence 44444444456666666665 343321 11112 3556666666666654
No 224
>COG2131 ComEB Deoxycytidylate deaminase [Nucleotide transport and metabolism]
Probab=20.14 E-value=1.7e+02 Score=24.03 Aligned_cols=39 Identities=23% Similarity=0.359 Sum_probs=27.1
Q ss_pred HHHHHHHcCCCEEEEecCCCchhhHHHHHHHHHHHcCCcC
Q 030804 132 IAKSCLEKGITKVAFDRGGYPYHGRIQALADAAREYGLQF 171 (171)
Q Consensus 132 LAkra~e~GI~~VvfDRgg~~YhGrVkAlad~aRe~GL~f 171 (171)
.++.....||++|+|--. |.-+-.+....+-+.++|+++
T Consensus 110 Cak~Ii~aGIk~Vvy~~~-Y~~~~~~~~s~~l~~~agv~~ 148 (164)
T COG2131 110 CAKLIIQAGIKEVVYAEP-YPTETVAPYSQELLEEAGVKV 148 (164)
T ss_pred HHHHHHHhCceEEEeecC-CCcchhhHHHHHHHHhCCceE
Confidence 466778899999999643 232335666677788888853
No 225
>PRK07666 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=20.09 E-value=2.4e+02 Score=22.17 Aligned_cols=25 Identities=16% Similarity=0.317 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHcCCCEEEEecCC
Q 030804 126 KKVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 126 ~~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
.-+|..|++++.+.|.+-+..||..
T Consensus 17 g~iG~~l~~~L~~~G~~Vi~~~r~~ 41 (239)
T PRK07666 17 RGIGRAVAIALAKEGVNVGLLARTE 41 (239)
T ss_pred chHHHHHHHHHHHCCCEEEEEeCCH
Confidence 4689999999999999766788864
No 226
>PRK06949 short chain dehydrogenase; Provisional
Probab=20.04 E-value=2.8e+02 Score=22.01 Aligned_cols=26 Identities=23% Similarity=0.199 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHcCCCEEEEecCC
Q 030804 125 SKKVGEMIAKSCLEKGITKVAFDRGG 150 (171)
Q Consensus 125 A~~VG~~LAkra~e~GI~~VvfDRgg 150 (171)
.--||..+++.+.+.|..-+..+|+.
T Consensus 18 sg~IG~~~a~~l~~~G~~Vi~~~r~~ 43 (258)
T PRK06949 18 SSGLGARFAQVLAQAGAKVVLASRRV 43 (258)
T ss_pred CcHHHHHHHHHHHHCCCEEEEEeCCH
Confidence 34689999999999998766788863
Done!