Query 030865
Match_columns 170
No_of_seqs 139 out of 1126
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:45:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030865.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030865hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00060 L18_bact ribosomal p 100.0 1.2E-44 2.6E-49 277.8 15.0 110 52-167 2-113 (114)
2 PRK05593 rplR 50S ribosomal pr 100.0 1.6E-44 3.5E-49 277.7 15.7 115 50-167 2-116 (117)
3 CHL00139 rpl18 ribosomal prote 100.0 3.7E-44 8E-49 272.9 11.3 108 58-167 1-108 (109)
4 COG0256 RplR Ribosomal protein 100.0 4.7E-42 1E-46 267.0 15.0 118 48-167 5-124 (125)
5 PF00861 Ribosomal_L18p: Ribos 100.0 3.3E-39 7.2E-44 247.5 15.1 116 51-167 2-118 (119)
6 PTZ00032 60S ribosomal protein 100.0 7.5E-38 1.6E-42 260.0 12.5 97 70-167 103-210 (211)
7 cd00432 Ribosomal_L18_L5e Ribo 100.0 2.8E-36 6.1E-41 224.6 12.6 102 63-166 2-103 (103)
8 PRK08569 rpl18p 50S ribosomal 100.0 3.1E-34 6.6E-39 237.0 13.0 112 51-167 14-129 (193)
9 PTZ00069 60S ribosomal protein 99.5 7.3E-14 1.6E-18 122.1 9.7 107 59-167 31-173 (300)
10 KOG3333 Mitochondrial/chloropl 99.2 3.7E-11 8.1E-16 97.8 9.0 94 73-169 61-155 (188)
11 PTZ00090 40S ribosomal protein 97.5 0.0022 4.8E-08 54.9 11.4 89 72-167 118-207 (233)
12 TIGR03632 bact_S11 30S ribosom 97.3 0.0038 8.3E-08 47.4 10.3 86 75-167 3-88 (108)
13 PF00411 Ribosomal_S11: Riboso 97.2 0.0047 1E-07 46.9 10.0 85 75-166 3-87 (110)
14 CHL00041 rps11 ribosomal prote 97.2 0.0069 1.5E-07 46.6 10.7 87 74-167 15-101 (116)
15 PRK05309 30S ribosomal protein 96.9 0.015 3.3E-07 45.5 10.6 89 72-167 17-105 (128)
16 TIGR03628 arch_S11P archaeal r 96.5 0.048 1E-06 42.2 10.5 90 74-167 4-99 (114)
17 PRK09607 rps11p 30S ribosomal 96.2 0.061 1.3E-06 42.7 9.5 89 74-166 11-105 (132)
18 KOG0875 60S ribosomal protein 96.1 0.0091 2E-07 52.0 4.9 116 50-167 26-172 (264)
19 PTZ00129 40S ribosomal protein 95.5 0.22 4.8E-06 40.4 10.4 92 73-167 29-125 (149)
20 COG0100 RpsK Ribosomal protein 92.1 1 2.2E-05 35.8 7.7 84 75-166 21-105 (129)
21 KOG0408 Mitochondrial/chloropl 89.7 4.2 9.2E-05 34.0 9.5 90 71-167 78-167 (190)
22 KOG0407 40S ribosomal protein 80.1 11 0.00023 29.9 7.1 89 74-166 18-112 (139)
23 TIGR00725 conserved hypothetic 69.6 11 0.00023 30.1 4.9 39 117-165 16-54 (159)
24 PF07071 DUF1341: Protein of u 68.0 13 0.00027 32.1 5.2 75 85-168 106-180 (218)
25 TIGR03581 EF_0839 conserved hy 66.5 15 0.00032 32.0 5.4 73 87-168 108-180 (236)
26 TIGR01917 gly_red_sel_B glycin 62.1 32 0.00069 32.4 7.1 53 114-167 314-366 (431)
27 PF03646 FlaG: FlaG protein; 61.8 46 0.001 24.4 6.7 45 55-99 39-83 (107)
28 cd06280 PBP1_LacI_like_4 Ligan 59.4 40 0.00086 26.9 6.5 47 122-168 100-147 (263)
29 TIGR01918 various_sel_PB selen 56.1 44 0.00096 31.5 6.9 53 114-167 314-366 (431)
30 cd06319 PBP1_ABC_sugar_binding 52.0 59 0.0013 25.9 6.3 52 116-167 102-157 (277)
31 cd06276 PBP1_FucR_like Ligand- 50.0 49 0.0011 26.8 5.7 46 122-167 100-148 (247)
32 cd06286 PBP1_CcpB_like Ligand- 49.3 58 0.0013 25.8 5.9 48 116-167 97-146 (260)
33 COG1611 Predicted Rossmann fol 47.9 25 0.00054 29.4 3.6 39 118-166 33-71 (205)
34 cd06288 PBP1_sucrose_transcrip 47.9 60 0.0013 25.6 5.8 42 125-166 104-147 (269)
35 cd06296 PBP1_CatR_like Ligand- 47.6 60 0.0013 25.7 5.7 44 124-167 104-149 (270)
36 cd06285 PBP1_LacI_like_7 Ligan 45.3 73 0.0016 25.3 5.9 47 116-167 97-146 (265)
37 cd06271 PBP1_AglR_RafR_like Li 45.2 66 0.0014 25.3 5.6 45 123-167 106-152 (268)
38 cd06282 PBP1_GntR_like_2 Ligan 45.1 68 0.0015 25.2 5.6 46 122-167 101-149 (266)
39 PRK07738 flagellar protein Fla 44.5 1E+02 0.0023 23.9 6.4 40 58-97 51-90 (117)
40 TIGR00612 ispG_gcpE 1-hydroxy- 44.5 84 0.0018 28.9 6.7 55 114-169 54-125 (346)
41 cd01543 PBP1_XylR Ligand-bindi 44.4 79 0.0017 25.3 6.0 44 124-167 96-140 (265)
42 PRK10423 transcriptional repre 44.2 77 0.0017 26.2 6.1 44 124-167 161-206 (327)
43 PRK09492 treR trehalose repres 44.1 87 0.0019 25.8 6.4 49 116-168 158-209 (315)
44 PRK14987 gluconate operon tran 42.7 87 0.0019 26.2 6.2 47 116-167 163-211 (331)
45 cd06283 PBP1_RegR_EndR_KdgR_li 41.9 1E+02 0.0022 24.2 6.2 44 123-166 102-148 (267)
46 PRK10703 DNA-binding transcrip 41.1 86 0.0019 26.2 5.9 45 123-167 164-210 (341)
47 cd06267 PBP1_LacI_sugar_bindin 40.9 99 0.0021 23.9 5.9 43 124-166 103-147 (264)
48 cd01574 PBP1_LacI Ligand-bindi 40.8 1E+02 0.0022 24.3 6.1 44 124-167 103-148 (264)
49 cd01540 PBP1_arabinose_binding 40.1 1E+02 0.0022 24.8 6.1 53 115-167 105-162 (289)
50 cd06293 PBP1_LacI_like_11 Liga 39.7 1.1E+02 0.0023 24.4 6.1 48 116-167 99-148 (269)
51 PF03928 DUF336: Domain of unk 39.7 48 0.001 25.1 3.9 32 117-149 4-37 (132)
52 PRK11303 DNA-binding transcrip 39.3 1E+02 0.0023 25.5 6.1 43 124-167 166-211 (328)
53 PRK04302 triosephosphate isome 39.2 77 0.0017 26.1 5.3 45 123-168 72-117 (223)
54 cd06275 PBP1_PurR Ligand-bindi 39.1 1.1E+02 0.0025 24.1 6.1 45 123-167 103-149 (269)
55 cd06287 PBP1_LacI_like_8 Ligan 39.0 1E+02 0.0022 25.2 6.0 46 122-167 103-150 (269)
56 TIGR01481 ccpA catabolite cont 38.9 1.2E+02 0.0025 25.2 6.4 44 124-168 163-210 (329)
57 COG1908 FrhD Coenzyme F420-red 38.7 75 0.0016 25.4 4.8 45 126-170 43-96 (132)
58 PRK10014 DNA-binding transcrip 38.6 1E+02 0.0023 25.7 6.1 44 124-167 169-214 (342)
59 cd06291 PBP1_Qymf_like Ligand 38.4 1.1E+02 0.0025 24.1 6.0 45 123-167 98-145 (265)
60 cd06272 PBP1_hexuronate_repres 38.1 92 0.002 24.7 5.4 44 123-166 97-142 (261)
61 cd06294 PBP1_ycjW_transcriptio 37.9 92 0.002 24.6 5.4 45 122-166 107-153 (270)
62 PF14419 SPOUT_MTase_2: AF2226 37.7 99 0.0021 25.8 5.6 49 115-164 10-58 (173)
63 PF02878 PGM_PMM_I: Phosphoglu 37.5 1.5E+02 0.0032 22.4 6.2 49 116-167 18-70 (137)
64 cd01545 PBP1_SalR Ligand-bindi 37.3 1.3E+02 0.0028 23.7 6.2 46 122-167 103-150 (270)
65 TIGR02417 fruct_sucro_rep D-fr 37.1 1.1E+02 0.0023 25.5 5.9 42 125-167 166-210 (327)
66 cd06292 PBP1_LacI_like_10 Liga 36.1 1.6E+02 0.0034 23.4 6.5 48 116-167 105-154 (273)
67 cd06273 PBP1_GntR_like_1 This 35.9 1.5E+02 0.0033 23.4 6.4 46 122-167 101-149 (268)
68 smart00481 POLIIIAc DNA polyme 35.9 1.3E+02 0.0027 19.7 5.1 41 125-168 17-57 (67)
69 PRK10727 DNA-binding transcrip 35.6 1.2E+02 0.0026 25.5 6.0 42 125-167 164-208 (343)
70 PF00532 Peripla_BP_1: Peripla 35.2 1E+02 0.0022 25.9 5.6 43 124-166 105-150 (279)
71 PRK12548 shikimate 5-dehydroge 35.2 96 0.0021 26.6 5.4 41 123-164 136-176 (289)
72 COG1472 BglX Beta-glucosidase- 34.8 97 0.0021 28.4 5.6 54 114-168 91-163 (397)
73 cd06303 PBP1_LuxPQ_Quorum_Sens 34.7 1.4E+02 0.003 24.3 6.0 49 116-166 112-162 (280)
74 cd06281 PBP1_LacI_like_5 Ligan 34.6 1.4E+02 0.0031 23.8 6.1 42 125-167 104-148 (269)
75 PRK10339 DNA-binding transcrip 34.5 1.3E+02 0.0028 25.1 6.0 46 122-167 159-206 (327)
76 cd06274 PBP1_FruR Ligand bindi 34.4 1.4E+02 0.003 23.7 6.0 47 116-166 99-147 (264)
77 PRK07710 acetolactate synthase 34.4 64 0.0014 30.2 4.5 39 123-167 17-55 (571)
78 TIGR00730 conserved hypothetic 34.3 1.2E+02 0.0026 24.6 5.6 40 117-165 17-56 (178)
79 PRK10401 DNA-binding transcrip 34.1 1.5E+02 0.0033 24.9 6.4 48 116-167 159-208 (346)
80 cd06270 PBP1_GalS_like Ligand 33.8 1.5E+02 0.0032 23.6 6.0 43 125-167 104-148 (268)
81 PRK09526 lacI lac repressor; R 33.8 1.4E+02 0.0031 24.9 6.1 48 116-167 164-213 (342)
82 PRK11041 DNA-binding transcrip 32.8 1.5E+02 0.0033 24.1 6.1 48 116-167 135-184 (309)
83 cd06295 PBP1_CelR Ligand bindi 32.7 1.6E+02 0.0034 23.5 6.0 44 123-166 111-156 (275)
84 PF00933 Glyco_hydro_3: Glycos 32.6 86 0.0019 27.0 4.7 54 115-168 81-151 (299)
85 PF07355 GRDB: Glycine/sarcosi 32.1 76 0.0016 29.1 4.4 28 114-141 318-345 (349)
86 PRK12827 short chain dehydroge 32.0 1.3E+02 0.0027 23.6 5.3 41 122-163 16-56 (249)
87 PF00875 DNA_photolyase: DNA p 31.8 75 0.0016 24.5 3.9 42 125-167 77-119 (165)
88 TIGR02405 trehalos_R_Ecol treh 31.7 1.5E+02 0.0032 24.6 5.9 48 116-167 155-205 (311)
89 PRK12549 shikimate 5-dehydroge 31.6 1.2E+02 0.0025 26.2 5.4 37 123-163 137-173 (284)
90 cd01575 PBP1_GntR Ligand-bindi 31.4 1.7E+02 0.0036 23.0 5.9 45 123-167 102-148 (268)
91 cd01391 Periplasmic_Binding_Pr 31.0 1.9E+02 0.004 21.8 5.9 44 123-166 110-154 (269)
92 COG1052 LdhA Lactate dehydroge 30.7 75 0.0016 28.3 4.1 40 123-167 156-204 (324)
93 cd01537 PBP1_Repressors_Sugar_ 30.5 1.6E+02 0.0035 22.6 5.6 43 123-165 104-148 (264)
94 cd01292 metallo-dependent_hydr 30.3 1.3E+02 0.0028 23.4 5.0 50 116-167 28-82 (275)
95 cd00175 SNc Staphylococcal nuc 30.1 2.2E+02 0.0047 20.7 6.5 62 84-166 61-124 (129)
96 KOG3332 N-acetylglucosaminyl p 29.4 1.3E+02 0.0028 26.4 5.2 45 124-168 124-171 (247)
97 cd06308 PBP1_sensor_kinase_lik 29.3 1.7E+02 0.0036 23.4 5.6 48 116-166 103-154 (270)
98 PRK00366 ispG 4-hydroxy-3-meth 29.1 1.2E+02 0.0026 28.0 5.2 55 114-169 62-134 (360)
99 cd01541 PBP1_AraR Ligand-bindi 29.1 1.6E+02 0.0035 23.4 5.5 47 116-166 104-151 (273)
100 cd06310 PBP1_ABC_sugar_binding 28.7 1.9E+02 0.0041 23.0 5.8 49 116-167 104-156 (273)
101 cd01544 PBP1_GalR Ligand-bindi 28.5 1.9E+02 0.0042 23.1 5.9 42 125-166 100-148 (270)
102 PF02826 2-Hacid_dh_C: D-isome 28.4 68 0.0015 25.3 3.2 25 123-148 46-70 (178)
103 cd06300 PBP1_ABC_sugar_binding 27.9 2.1E+02 0.0045 22.8 5.9 50 116-167 106-158 (272)
104 cd07367 CarBb CarBb is the B s 27.8 2.8E+02 0.006 23.8 7.0 79 59-141 31-109 (268)
105 PRK12744 short chain dehydroge 27.6 1.6E+02 0.0036 23.5 5.4 40 123-163 19-58 (257)
106 smart00259 ZnF_A20 A20-like zi 27.5 27 0.00059 20.3 0.6 10 13-22 7-16 (26)
107 PF13380 CoA_binding_2: CoA bi 27.5 1.1E+02 0.0023 22.9 4.0 42 120-167 63-104 (116)
108 PF00070 Pyr_redox: Pyridine n 27.4 2E+02 0.0043 19.3 5.1 44 123-167 9-56 (80)
109 PF03900 Porphobil_deamC: Porp 27.3 2.1E+02 0.0045 19.6 5.8 61 62-134 10-74 (74)
110 PF02961 BAF: Barrier to autoi 26.9 18 0.00038 27.2 -0.4 24 118-141 21-44 (89)
111 cd06320 PBP1_allose_binding Pe 26.7 2.1E+02 0.0046 22.8 5.8 49 116-166 103-154 (275)
112 PRK08085 gluconate 5-dehydroge 26.7 1.5E+02 0.0033 23.6 5.0 38 122-164 19-56 (254)
113 PRK08452 flagellar protein Fla 26.4 2.6E+02 0.0057 21.9 6.0 36 62-97 62-97 (124)
114 PRK07523 gluconate 5-dehydroge 26.2 1.6E+02 0.0034 23.6 5.0 39 121-164 19-57 (255)
115 cd06284 PBP1_LacI_like_6 Ligan 26.2 2.2E+02 0.0048 22.3 5.8 44 123-166 101-146 (267)
116 cd06298 PBP1_CcpA_like Ligand- 26.0 2.5E+02 0.0054 22.1 6.0 47 116-166 99-148 (268)
117 PRK06114 short chain dehydroge 26.0 1.7E+02 0.0036 23.6 5.1 38 123-164 19-56 (254)
118 PRK08868 flagellar protein Fla 25.8 2.6E+02 0.0055 22.7 6.0 38 60-97 78-115 (144)
119 cd06326 PBP1_STKc_like Type I 25.7 2E+02 0.0043 23.8 5.6 46 121-167 120-166 (336)
120 TIGR02867 spore_II_P stage II 25.6 1.3E+02 0.0028 25.2 4.5 29 119-149 30-58 (196)
121 PF06370 DUF1069: Protein of u 25.6 39 0.00086 27.8 1.3 20 133-153 163-182 (206)
122 COG1609 PurR Transcriptional r 24.9 2E+02 0.0042 25.1 5.6 44 124-168 162-208 (333)
123 cd06322 PBP1_ABC_sugar_binding 24.4 2.6E+02 0.0056 22.1 5.9 49 116-167 102-153 (267)
124 PRK10936 TMAO reductase system 24.3 2.8E+02 0.0061 23.7 6.5 52 116-167 150-204 (343)
125 TIGR02801 tolR TolR protein. T 24.3 2.9E+02 0.0064 20.5 5.9 25 143-167 98-122 (129)
126 cd06311 PBP1_ABC_sugar_binding 24.3 2.5E+02 0.0053 22.5 5.8 49 116-166 108-157 (274)
127 PRK05867 short chain dehydroge 23.7 1.9E+02 0.0041 23.1 5.0 37 122-163 19-55 (253)
128 PF00106 adh_short: short chai 23.6 2.5E+02 0.0053 20.6 5.3 42 122-165 10-51 (167)
129 cd06278 PBP1_LacI_like_2 Ligan 23.2 2.9E+02 0.0062 21.6 5.9 47 116-166 98-146 (266)
130 cd06313 PBP1_ABC_sugar_binding 23.0 2.7E+02 0.0058 22.5 5.8 47 116-165 104-153 (272)
131 COG0299 PurN Folate-dependent 22.9 1.4E+02 0.0031 25.4 4.2 34 129-165 43-79 (200)
132 PRK07792 fabG 3-ketoacyl-(acyl 22.4 2E+02 0.0043 24.3 5.1 40 122-165 22-61 (306)
133 PRK08217 fabG 3-ketoacyl-(acyl 22.4 2.1E+02 0.0046 22.4 5.0 24 122-146 15-38 (253)
134 TIGR02765 crypto_DASH cryptoch 22.1 1.8E+02 0.0038 26.2 4.9 40 127-167 87-127 (429)
135 COG5611 Predicted nucleic-acid 22.1 58 0.0013 25.9 1.6 23 124-146 97-119 (130)
136 PF01488 Shikimate_DH: Shikima 22.1 2.5E+02 0.0054 21.1 5.1 34 124-161 23-56 (135)
137 cd06277 PBP1_LacI_like_1 Ligan 22.1 2.8E+02 0.0061 21.9 5.7 44 124-167 105-150 (268)
138 PLN02293 adenine phosphoribosy 22.1 2.2E+02 0.0048 23.2 5.1 36 116-151 42-77 (187)
139 cd06317 PBP1_ABC_sugar_binding 22.0 2.7E+02 0.0059 22.0 5.6 49 116-166 106-156 (275)
140 PRK07791 short chain dehydroge 21.8 2.2E+02 0.0048 23.7 5.2 43 122-165 16-63 (286)
141 PF14540 NTF-like: Nucleotidyl 21.7 39 0.00084 26.3 0.6 25 138-163 93-119 (119)
142 COG3894 Uncharacterized metal- 21.3 98 0.0021 30.3 3.2 63 74-136 166-242 (614)
143 cd06290 PBP1_LacI_like_9 Ligan 21.2 3.1E+02 0.0067 21.6 5.7 47 116-167 98-147 (265)
144 PRK08703 short chain dehydroge 21.0 2.2E+02 0.0048 22.5 4.8 37 123-164 17-53 (239)
145 PRK12738 kbaY tagatose-bisphos 20.8 2.3E+02 0.0049 25.1 5.2 41 126-167 87-130 (286)
146 PRK06124 gluconate 5-dehydroge 20.6 2.2E+02 0.0049 22.6 4.9 38 121-163 20-57 (256)
147 PF00156 Pribosyltran: Phospho 20.5 1.8E+02 0.0039 20.7 3.9 34 117-150 6-41 (125)
148 PF02662 FlpD: Methyl-viologen 20.3 1.3E+02 0.0027 23.1 3.2 49 121-170 37-95 (124)
149 cd06297 PBP1_LacI_like_12 Liga 20.3 2.3E+02 0.0051 22.7 4.9 48 115-167 96-151 (269)
150 PRK06198 short chain dehydroge 20.2 2.9E+02 0.0063 21.9 5.4 25 122-146 16-40 (260)
151 cd06279 PBP1_LacI_like_3 Ligan 20.2 3.2E+02 0.007 22.1 5.8 47 116-166 99-164 (283)
152 PF08032 SpoU_sub_bind: RNA 2' 20.0 99 0.0021 20.5 2.3 40 125-167 4-45 (76)
No 1
>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=1.2e-44 Score=277.75 Aligned_cols=110 Identities=26% Similarity=0.470 Sum_probs=104.5
Q ss_pred HHHHHHHHHHHHHHhcCCC--CCCeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHH
Q 030865 52 TESAKIRNRRIQKKFNGTP--TKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELI 129 (170)
Q Consensus 52 ~~~r~~R~~RiRkki~gt~--~rPRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lA 129 (170)
++.|.+||.|+|+||.||+ ++|||+||+||+|||||||||++++||+|+||+|++++ +++|+++|+.||++||
T Consensus 2 ~~~r~~r~~r~r~ki~gt~~~~rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~-----~~~n~~aA~~vG~~la 76 (114)
T TIGR00060 2 KSARIRRHKRIRRKLRETGEANRPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK-----YTGNKDAAKKVGKLVA 76 (114)
T ss_pred cHHHHHHHHHHHHHhcCCCCCCCcEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc-----CCCCHHHHHHHHHHHH
Confidence 4567789999999999999 89999999999999999999999999999999999876 3589999999999999
Q ss_pred HHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 130 KTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 130 kra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
++|+++||++|+ ||||||+|||||+||||++||+||.
T Consensus 77 ~ra~~~gi~~vv-fDrgg~~YhGrv~A~a~~aRe~Gl~ 113 (114)
T TIGR00060 77 ERLKEKGIKDVV-FDRGGYKYHGRVAALAEAAREAGLN 113 (114)
T ss_pred HHHHHCCCCEEE-EeCCCCcchHHHHHHHHHHHHhCCC
Confidence 999999999999 9999999999999999999999984
No 2
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=100.00 E-value=1.6e-44 Score=277.68 Aligned_cols=115 Identities=32% Similarity=0.520 Sum_probs=109.2
Q ss_pred chHHHHHHHHHHHHHHhcCCCCCCeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHH
Q 030865 50 ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELI 129 (170)
Q Consensus 50 ~r~~~r~~R~~RiRkki~gt~~rPRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lA 129 (170)
++++.|.+||+|+|+||.||+++|||+||+||+|||||||||++++||+||||+|++++..+ .++|++||+.||++||
T Consensus 2 ~~~~~r~~r~~r~r~ki~g~~~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~--~~~n~~aa~~vG~~la 79 (117)
T PRK05593 2 DKKEARLRRHRRVRKKISGTAERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGL--KGGNKEAAKKVGKLIA 79 (117)
T ss_pred chHHHHHHHHHHHHHHhcCCCCCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhccc--cCCCHHHHHHHHHHHH
Confidence 46778999999999999999999999999999999999999999999999999999997643 2799999999999999
Q ss_pred HHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 130 KTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 130 kra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
++|+++||++|+ ||||||+|||||+||+|+|||+||-
T Consensus 80 ~ra~~~gi~~vv-fDrg~~~yhGrV~a~a~~are~Gl~ 116 (117)
T PRK05593 80 ERAKAKGIKQVV-FDRGGYKYHGRVKALADAAREAGLK 116 (117)
T ss_pred HHHHHCCCCEEE-EcCCCCcccHHHHHHHHHHHHhCCC
Confidence 999999999999 9999999999999999999999984
No 3
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=100.00 E-value=3.7e-44 Score=272.89 Aligned_cols=108 Identities=34% Similarity=0.571 Sum_probs=103.8
Q ss_pred HHHHHHHHhcCCCCCCeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCC
Q 030865 58 RNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNI 137 (170)
Q Consensus 58 R~~RiRkki~gt~~rPRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI 137 (170)
+++|+|+||.|++++|||+||+||+|||||||||.+|+||+||||+||++++++ .+++|+++|+.||++||+||+++||
T Consensus 1 ~~~r~r~ki~g~~~rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~-~~~~n~~aA~~vG~lla~ra~~~gi 79 (109)
T CHL00139 1 KRERVRKKIKGTAERPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSL-SSTSTCDASKLVGQKLAKKSLKKGI 79 (109)
T ss_pred CCeeeeeeecCCCCCCEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccc-cCCCCHHHHHHHHHHHHHHHHHCCC
Confidence 367999999999999999999999999999999999999999999999999885 4789999999999999999999999
Q ss_pred CEEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 138 TEISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 138 ~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
++|+ ||||||+|||||+||+|+|||+||.
T Consensus 80 ~~vv-fDrgg~~yhGrV~a~a~~are~GL~ 108 (109)
T CHL00139 80 TKVV-FDRGGKLYHGRIKALAEAAREAGLQ 108 (109)
T ss_pred CEEE-EcCCCCccchHHHHHHHHHHHhCCC
Confidence 9999 9999999999999999999999984
No 4
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.7e-42 Score=267.05 Aligned_cols=118 Identities=30% Similarity=0.406 Sum_probs=110.9
Q ss_pred ccchHHHHHHHHHHHHHHhcCCCCCCeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhcc--CCCCCCCcHHHHHHHH
Q 030865 48 ANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG--NGNPPCSTIEAAERIG 125 (170)
Q Consensus 48 ~~~r~~~r~~R~~RiRkki~gt~~rPRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~--~l~~s~~n~~AA~~VG 125 (170)
...|++++.+|+.|+|+||.|++++|||+||+||+|||||||||..+.||+++||++++++. + ...++|+++|++||
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 VKFRRRRRGKRAYRIRKKLLGTSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGK-KGGGGNTEAAYLVG 83 (125)
T ss_pred hhhHHHHHHhHHHHHHHhhccCCCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhcc-cCCCCCHHHHHHHH
Confidence 34688899999999999999999999999999999999999999999999999999999965 4 23568999999999
Q ss_pred HHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 126 EELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 126 ~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
+++|++|+++||++|| |||+||+|||||+|+||++||+||-
T Consensus 84 ~lia~ra~~kgi~~vV-fdr~g~~yhgRV~Ala~~AreaGL~ 124 (125)
T COG0256 84 KLIAERALAKGIEEVV-FDRGGYKYHGRVAALADGAREAGLE 124 (125)
T ss_pred HHHHHHHHHcCCcEEE-EcCCCCCcchHHHHHHHHHHHcCcC
Confidence 9999999999999999 9999999999999999999999984
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=3.3e-39 Score=247.51 Aligned_cols=116 Identities=31% Similarity=0.503 Sum_probs=109.2
Q ss_pred hHHHHHHHHHHHHHHhcCCCCCCeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCC-CCCCCcHHHHHHHHHHHH
Q 030865 51 RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNG-NPPCSTIEAAERIGEELI 129 (170)
Q Consensus 51 r~~~r~~R~~RiRkki~gt~~rPRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l-~~s~~n~~AA~~VG~~lA 129 (170)
+++++.+|+.++|+++.+++++|||+||+||+|||||||||..+.||++|||.+++++..+ ..+++|++||+.||++||
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 4578889999999999999999999999999999999999999999999999999999742 356789999999999999
Q ss_pred HHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 130 KTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 130 kra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
++|+++||+.|+ |||+|++|||||+||+|+|||+||-
T Consensus 82 ~ra~~~gi~~v~-fdr~~~~y~grv~a~~~~~re~Gl~ 118 (119)
T PF00861_consen 82 KRALEKGIAKVV-FDRGGYKYHGRVKALADGAREGGLE 118 (119)
T ss_dssp HHHHHTTSSEEE-ECTSTSSSSSHHHHHHHHHHHTTCB
T ss_pred HHHHHcCCcEEE-EcCCCCcccHHHHHHHHHHHHcCCC
Confidence 999999999999 9999999999999999999999984
No 6
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=100.00 E-value=7.5e-38 Score=259.97 Aligned_cols=97 Identities=23% Similarity=0.357 Sum_probs=90.6
Q ss_pred CCCCeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCC-----------CCCCcHHHHHHHHHHHHHHHHhCCCC
Q 030865 70 PTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGN-----------PPCSTIEAAERIGEELIKTCIALNIT 138 (170)
Q Consensus 70 ~~rPRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~-----------~s~~n~~AA~~VG~~lAkra~e~gI~ 138 (170)
-.+|||+||+||+|||||||||.+++|||++||+++++++.+. ..++|+++|+.||++||++|+++||+
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 3699999999999999999999999999999999999976432 14789999999999999999999999
Q ss_pred EEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 139 EISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 139 ~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
+|+ ||||||+|||||+||||+|||+||.
T Consensus 183 kVv-FDRgGy~YHGRVkALAdaARe~GLk 210 (211)
T PTZ00032 183 KVR-FDRAHYKYAGKVEALAEGARAVGLQ 210 (211)
T ss_pred EEE-EeCCCCeehhHHHHHHHHHHHcCCC
Confidence 999 9999999999999999999999984
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=2.8e-36 Score=224.63 Aligned_cols=102 Identities=33% Similarity=0.479 Sum_probs=96.5
Q ss_pred HHHhcCCCCCCeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEE
Q 030865 63 QKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISS 142 (170)
Q Consensus 63 Rkki~gt~~rPRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~ 142 (170)
++++.|+..+|||+||+||+|||||||||.+++||++|||.|+++++++ .+++|++||+.||++||+||+++||++|+
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 3456678899999999999999999999999999999999999999875 57899999999999999999999999999
Q ss_pred ecCCCCccchHHHHHHHHHHHcCC
Q 030865 143 YDRNGSRRGERMQAFEIPISRHGF 166 (170)
Q Consensus 143 fDRgg~~YhGrVkAladaaRe~Gl 166 (170)
||||+++|||||+||+|++||+||
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=3.1e-34 Score=237.02 Aligned_cols=112 Identities=21% Similarity=0.159 Sum_probs=101.9
Q ss_pred hHHHHHHHHHHHHHHhcCCCCCCeEEEEecCCeEEEEEE--eCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHH
Q 030865 51 RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLV--DDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEEL 128 (170)
Q Consensus 51 r~~~r~~R~~RiRkki~gt~~rPRL~V~kSNkhIyAQvI--dd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~l 128 (170)
|+|-+.-.++|+|... +++|||+||+||+||||||| ||++++||+||||+|++.++|. .+++|++||+.||++|
T Consensus 14 rRegkTdY~~R~rl~~---~~kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~-~~~~N~~AAy~vG~ll 89 (193)
T PRK08569 14 RREGKTDYRKRLKLLL---SGKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWK-GDTGNTPAAYLTGLLA 89 (193)
T ss_pred cccccccHHHHHHHHh---cCCCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhcccc-CCCCCHHHHHHHHHHH
Confidence 4555566677776654 47899999999999999999 8999999999999999998874 4689999999999999
Q ss_pred HHHHHhCCCCEEEEecCCCCccc--hHHHHHHHHHHHcCCc
Q 030865 129 IKTCIALNITEISSYDRNGSRRG--ERMQAFEIPISRHGFL 167 (170)
Q Consensus 129 Akra~e~gI~~Vv~fDRgg~~Yh--GrVkAladaaRe~Gl~ 167 (170)
|+||+++||++|+ |||||++|| |||+|+||+|||+||-
T Consensus 90 A~ral~kGi~~vv-fDrGg~~yh~gGRV~A~akgArd~GL~ 129 (193)
T PRK08569 90 GKKALKAGVEEAV-LDIGLHRPTKGSRVFAALKGAIDAGLE 129 (193)
T ss_pred HHHHHHCCCCEEE-EecCCccccCCccHHHHHHHHHHcCCc
Confidence 9999999999999 999999999 9999999999999985
No 9
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=99.51 E-value=7.3e-14 Score=122.06 Aligned_cols=107 Identities=18% Similarity=0.097 Sum_probs=92.0
Q ss_pred HHHHHHHhcCC----CCCCeEEEEecCCeEEEEEEe--CCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHH
Q 030865 59 NRRIQKKFNGT----PTKPRLSVFCSDKQLYAMLVD--DQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTC 132 (170)
Q Consensus 59 ~~RiRkki~gt----~~rPRL~V~kSNkhIyAQvId--d~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra 132 (170)
+.|.|.-+.+. +.+|||+|..||++|.|||+. .+++++|++|.|.|+.-.+| ..+.+|.+||+.+|.++|.|+
T Consensus 31 ~~R~rLi~q~knKynspK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~kyG~-k~gl~N~~AAY~TGlL~arR~ 109 (300)
T PTZ00069 31 YARRRLILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELPRFGI-PVGLTNYAAAYATGLLLARRL 109 (300)
T ss_pred HHHHHHHHccccccCCCCceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhcCc-CCCCccHHHHHHHHHHHHHHH
Confidence 45555555542 358999999999999999997 88999999999999987887 467899999999999999999
Q ss_pred HhC--------CCC--------------------EEEEecCCCCc--cchHHHHHHHHHHHcCCc
Q 030865 133 IAL--------NIT--------------------EISSYDRNGSR--RGERMQAFEIPISRHGFL 167 (170)
Q Consensus 133 ~e~--------gI~--------------------~Vv~fDRgg~~--YhGrVkAladaaRe~Gl~ 167 (170)
+++ |++ +++ +|-|..+ .++||+|...|+.++||-
T Consensus 110 L~kl~ld~~y~G~~e~~g~~y~v~e~~~~~~rpf~a~-LDiGL~rtt~G~RVFaalKGa~DgGl~ 173 (300)
T PTZ00069 110 LKKLGLDKQFEGVKEADGEYYHVDEEDDEERRPFKAI-LDVGLARTTTGNRVFGALKGAVDGGLH 173 (300)
T ss_pred HHhhcccccccCcccccCcccccccccccCCCCceEE-EeeccccCCCCceeeeehhcccccCcc
Confidence 998 773 678 9999755 588999999999999984
No 10
>KOG3333 consensus Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=99.24 E-value=3.7e-11 Score=97.79 Aligned_cols=94 Identities=18% Similarity=0.279 Sum_probs=82.1
Q ss_pred CeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCC-Cccc
Q 030865 73 PRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRNG-SRRG 151 (170)
Q Consensus 73 PRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg-~~Yh 151 (170)
++|.|-++..|+-+-|.+.++|.+ +||||.||.|+..|+ ++.|+.|+..+|.+||+||++.||+.++ +.-.. ....
T Consensus 61 h~lev~~~~~hveg~v~H~~~gvv-vSAST~EwaIk~qLY-st~dtsA~~niGRVLAqRCLqsGI~fm~-~~~t~ea~~~ 137 (188)
T KOG3333|consen 61 HRLEVIRTQHHVEGLVEHQNGGVV-VSASTREWAIKKQLY-STRDTSACENIGRVLAQRCLQSGINFMV-YQPTPEAAAS 137 (188)
T ss_pred eEEEEeecccceeeeeeEecCCEE-EEecccchHHHHHHh-hccchHHHHHHHHHHHHHHHHhCcceec-cCCChhhccc
Confidence 589999999999999998776655 799999999999886 8899999999999999999999999999 65433 3346
Q ss_pred hHHHHHHHHHHHcCCccC
Q 030865 152 ERMQAFEIPISRHGFLQQ 169 (170)
Q Consensus 152 GrVkAladaaRe~Gl~~~ 169 (170)
..++-|..++.|+|+...
T Consensus 138 s~~q~l~~a~~e~Gv~lk 155 (188)
T KOG3333|consen 138 SSMQRLQSAMTEGGVVLK 155 (188)
T ss_pred hHHHHHHHHHHhCCeeec
Confidence 789999999999999754
No 11
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=97.45 E-value=0.0022 Score=54.93 Aligned_cols=89 Identities=19% Similarity=0.185 Sum_probs=73.8
Q ss_pred CCeEEEEecCCeEEEEEEeCCCCe-EEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCcc
Q 030865 72 KPRLSVFCSDKQLYAMLVDDQNKK-CLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRNGSRR 150 (170)
Q Consensus 72 rPRL~V~kSNkhIyAQvIdd~~gk-tLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~Y 150 (170)
+.+|+|+.|-++..++|.|..+.. ||+-+|+-...+++. ..++--||+.+++.+|++|++.||.+|-.+=+|.
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 558999999999999999877775 688777777777764 3467789999999999999999999998666663
Q ss_pred chHHHHHHHHHHHcCCc
Q 030865 151 GERMQAFEIPISRHGFL 167 (170)
Q Consensus 151 hGrVkAladaaRe~Gl~ 167 (170)
+| .++...++...||.
T Consensus 192 Gg-REtALRaL~~~GLk 207 (233)
T PTZ00090 192 MR-VETVLQAFYANGLQ 207 (233)
T ss_pred Ch-HHHHHHHHHHCCCE
Confidence 34 89999999999974
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=97.32 E-value=0.0038 Score=47.38 Aligned_cols=86 Identities=15% Similarity=0.173 Sum_probs=66.8
Q ss_pred EEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHH
Q 030865 75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRNGSRRGERM 154 (170)
Q Consensus 75 L~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrV 154 (170)
+.|+.|.++..+.|-|. .|.+++.+|+-...+++. ...+.-||..+++.++++|+++||..|..+=||. -+ ||
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---KKSTPYAAQLAAEDAAKKAKEFGMKTVDVYVKGP-GA-GR- 75 (108)
T ss_pred EEEEccCCCEEEEEEcC-CCCEEEEEecCceeeCCC---ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECC-CC-cH-
Confidence 67899999999999987 456888888877677763 3577889999999999999999999888666662 22 44
Q ss_pred HHHHHHHHHcCCc
Q 030865 155 QAFEIPISRHGFL 167 (170)
Q Consensus 155 kAladaaRe~Gl~ 167 (170)
+++..++...|+.
T Consensus 76 ~~~ir~l~~~glk 88 (108)
T TIGR03632 76 ESAIRALQAAGLE 88 (108)
T ss_pred HHHHHHHHHCCCE
Confidence 5566666667763
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=97.25 E-value=0.0047 Score=46.88 Aligned_cols=85 Identities=20% Similarity=0.198 Sum_probs=65.6
Q ss_pred EEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHH
Q 030865 75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRNGSRRGERM 154 (170)
Q Consensus 75 L~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrV 154 (170)
+.|+.|.++..+.|-|.. |.++++.|+-...+++. ...+..||+.+++.++++|++.||+.|..+=+| .--||-
T Consensus 3 ihI~~s~NNt~vtlTd~~-G~~~~~~S~G~~gfK~~---rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG--~g~gr~ 76 (110)
T PF00411_consen 3 IHIKSSFNNTIVTLTDLK-GNVLFWSSAGSLGFKGA---RKSTPYAAQQAAEKIAKKAKELGIKTVRVKIKG--FGPGRE 76 (110)
T ss_dssp EEEEEESSEEEEEEEETT-SEEEEEEETTTSSTTTT---CGSSHHHHHHHHHHHHHHHHCTTEEEEEEEEES--SSTTHH
T ss_pred EEEEecCCCEEEEEECCC-CCEEEEEeccccccccc---cccCHHHHHHHHHHHHHHHHHcCCeEEEEEEcC--CCccHH
Confidence 678999999999999654 77778889887777763 357889999999999999999999988755555 223454
Q ss_pred HHHHHHHHHcCC
Q 030865 155 QAFEIPISRHGF 166 (170)
Q Consensus 155 kAladaaRe~Gl 166 (170)
. +..++...|+
T Consensus 77 ~-~lk~l~~~gl 87 (110)
T PF00411_consen 77 A-ALKALKKSGL 87 (110)
T ss_dssp H-HHHHHHHTTS
T ss_pred H-HHHHHHhcCC
Confidence 3 3366666776
No 14
>CHL00041 rps11 ribosomal protein S11
Probab=97.20 E-value=0.0069 Score=46.63 Aligned_cols=87 Identities=17% Similarity=0.145 Sum_probs=69.7
Q ss_pred eEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchH
Q 030865 74 RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRNGSRRGER 153 (170)
Q Consensus 74 RL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGr 153 (170)
.+.|+.|.++..+.|-|.. |.+|+.+|.-...+++. ..++.-||..+++.++++|++.||+.|..+=|| +- .||
T Consensus 15 i~hI~~t~NNTiiTlTd~~-G~~l~~~S~G~~gfKg~---rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I~ikG-~G-~Gr 88 (116)
T CHL00041 15 VIHIQASFNNTIVTVTDVR-GRVISWSSAGACGFKGA---RKGTPFAAQTAAENAIRTVIDQGMKRAEVMIKG-PG-LGR 88 (116)
T ss_pred EEEEEcccCCEEEEEEcCC-CCEEEEEecCceeeCCC---ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEC-CC-CcH
Confidence 7899999999999999764 67899988887777763 347788999999999999999999988856666 32 355
Q ss_pred HHHHHHHHHHcCCc
Q 030865 154 MQAFEIPISRHGFL 167 (170)
Q Consensus 154 VkAladaaRe~Gl~ 167 (170)
+++..++...||.
T Consensus 89 -~~~ir~l~~~glk 101 (116)
T CHL00041 89 -DTALRAIRRSGLK 101 (116)
T ss_pred -HHHHHHHHHCCCE
Confidence 5556777788864
No 15
>PRK05309 30S ribosomal protein S11; Validated
Probab=96.94 E-value=0.015 Score=45.51 Aligned_cols=89 Identities=12% Similarity=0.131 Sum_probs=68.8
Q ss_pred CCeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccc
Q 030865 72 KPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRNGSRRG 151 (170)
Q Consensus 72 rPRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~Yh 151 (170)
.-.+.|+.|.++..+.|-|. .|.+++..|.-...+++. ..++..||..+++.+++.|++.||+.|..+=|| .-+
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 35899999999999999975 677888888766666653 357788999999999999999999988855666 322
Q ss_pred hHHHHHHHHHHHcCCc
Q 030865 152 ERMQAFEIPISRHGFL 167 (170)
Q Consensus 152 GrVkAladaaRe~Gl~ 167 (170)
|| +++..++...|+.
T Consensus 91 Gr-~~air~L~~~glk 105 (128)
T PRK05309 91 GR-ESAIRALQAAGLE 105 (128)
T ss_pred cH-HHHHHHHHHCCCE
Confidence 44 5555566667763
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=96.53 E-value=0.048 Score=42.23 Aligned_cols=90 Identities=17% Similarity=0.063 Sum_probs=66.5
Q ss_pred eEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCC--CCc--
Q 030865 74 RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRN--GSR-- 149 (170)
Q Consensus 74 RL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRg--g~~-- 149 (170)
.+.|+-|-++....|-|..+..+|+-+|.-..-+++. ..++-=||...++.++++|+++||+.|..+=|| |.+
T Consensus 4 i~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~kg~---kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~ 80 (114)
T TIGR03628 4 IAHIYSSFNNTIITITDITGAETIARSSGGMVVKADR---DESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQK 80 (114)
T ss_pred EEEEEccCCCeEEEEEcCCCCEEEEEecCcceEeCCC---ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCC
Confidence 3568888899999999877778888888777666653 245667999999999999999999999866666 333
Q ss_pred -cc-hHHHHHHHHHHHcCCc
Q 030865 150 -RG-ERMQAFEIPISRHGFL 167 (170)
Q Consensus 150 -Yh-GrVkAladaaRe~Gl~ 167 (170)
++ || ++...++...||.
T Consensus 81 ~~G~Gr-~~air~l~~~glk 99 (114)
T TIGR03628 81 SPGPGA-QAAIRALARAGLR 99 (114)
T ss_pred CCCCcH-HHHHHHHHHCCCE
Confidence 22 44 3444566667763
No 17
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=96.18 E-value=0.061 Score=42.72 Aligned_cols=89 Identities=18% Similarity=0.093 Sum_probs=65.3
Q ss_pred eEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCC--CCc--
Q 030865 74 RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRN--GSR-- 149 (170)
Q Consensus 74 RL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRg--g~~-- 149 (170)
.+.|+.|-++.+..|-|..+..||+.+|.-..-+++. ..++-=||...++.++++|+++||+.|..+=|| |..
T Consensus 11 i~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~kg~---kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~Ggn~~~ 87 (132)
T PRK09607 11 IAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADR---DESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNGQK 87 (132)
T ss_pred EEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeCCC---ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCc
Confidence 6889999999999999877667888877766555542 245667999999999999999999999866666 222
Q ss_pred -cc-hHHHHHHHHHHHcCC
Q 030865 150 -RG-ERMQAFEIPISRHGF 166 (170)
Q Consensus 150 -Yh-GrVkAladaaRe~Gl 166 (170)
++ |+ ++...++...||
T Consensus 88 ~~G~Gr-~~airal~~~gl 105 (132)
T PRK09607 88 SPGPGA-QAAIRALARAGL 105 (132)
T ss_pred CCCCcH-HHHHHHHHHCCC
Confidence 22 44 334455555665
No 18
>KOG0875 consensus 60S ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=96.12 E-value=0.0091 Score=52.04 Aligned_cols=116 Identities=14% Similarity=0.049 Sum_probs=83.4
Q ss_pred chHHHHHHHHHHHHHHhcCCCCCCeEEEEecCCeEEEEEEe--CCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHH
Q 030865 50 ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVD--DQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEE 127 (170)
Q Consensus 50 ~r~~~r~~R~~RiRkki~gt~~rPRL~V~kSNkhIyAQvId--d~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~ 127 (170)
-++.-..++|.-+.-|-.-...+.||.|..+|+.|.+||+- -+.+.+++++-+.|..-.+.. ....|-.||+..|.+
T Consensus 26 GkTdy~arkrl~~qdknk~nt~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s~elpkyg~~-~GLtNyaAay~TglL 104 (264)
T KOG0875|consen 26 GKTDYYARKRLVVQDKNKYNTPKYRMIVRVINKDIICQIAYATIEGDVIVRAAYAHELPKYGVK-VGLTNYAAAYCTGLL 104 (264)
T ss_pred CCccHHHHHHHHhhcccccCCCceEEEEEEechhhHHHHHhheecceEEEEeeccccccccccc-cccchhHHHHhhHHH
Confidence 34444444455444444333468899999999999999986 556677888899988876642 345789999999999
Q ss_pred HHHHHHh-CCCCE--------------------------EEEecCCCCc--cchHHHHHHHHHHHcCCc
Q 030865 128 LIKTCIA-LNITE--------------------------ISSYDRNGSR--RGERMQAFEIPISRHGFL 167 (170)
Q Consensus 128 lAkra~e-~gI~~--------------------------Vv~fDRgg~~--YhGrVkAladaaRe~Gl~ 167 (170)
||.|+++ .|.++ +. +|-|.-+ -+.||+...+++.++||.
T Consensus 105 LarR~l~~~gmD~~yeg~~e~~gde~~~e~idgq~~aFt~~-Ld~GLaRtttg~kvFGAlkga~dGGL~ 172 (264)
T KOG0875|consen 105 LACRLLKRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCY-LDAGLARTTTGNKVFGALKGAVDGGLS 172 (264)
T ss_pred HHHHHHHHhCcccccccceeecCcccccccccCCCCCeEEE-ecccccccCCCceeeeeeehhccccee
Confidence 9999986 55432 33 5666433 256888888888888885
No 19
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=95.54 E-value=0.22 Score=40.36 Aligned_cols=92 Identities=18% Similarity=0.174 Sum_probs=65.2
Q ss_pred CeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCC--CCcc
Q 030865 73 PRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRN--GSRR 150 (170)
Q Consensus 73 PRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRg--g~~Y 150 (170)
-.+.|+-|-++....|-|.. |.+++..|+-...+++.. ..++-=||...++.++++|+++||+.|..+=|+ |..-
T Consensus 29 Gi~hI~as~NNTiItiTD~~-G~~~~w~SsG~~gfKg~r--~KsTpyAAq~aa~~~a~k~~~~Gi~~v~V~vr~~gg~~~ 105 (149)
T PTZ00129 29 GVAHIFASFNDTFIHVTDLS-GRETLVRVTGGMKVKADR--DESSPYAAMMAAQDVAARCKELGINALHIKLRATGGVRT 105 (149)
T ss_pred EEEEEEcccCCeEEEEEccc-CCEEEEEecCcceecccc--cCCCHHHHHHHHHHHHHHHHHcCCeEEEEEEEecCCCCC
Confidence 47889999999999998765 555667777666666532 145566899999999999999999998866653 3222
Q ss_pred ch---HHHHHHHHHHHcCCc
Q 030865 151 GE---RMQAFEIPISRHGFL 167 (170)
Q Consensus 151 hG---rVkAladaaRe~Gl~ 167 (170)
+| -=++...+|...||.
T Consensus 106 kg~GpGr~~airaL~~~glk 125 (149)
T PTZ00129 106 KTPGPGAQAALRALARAGLK 125 (149)
T ss_pred CCCCCCHHHHHHHHHHCCCE
Confidence 21 234555666667764
No 20
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=92.08 E-value=1 Score=35.81 Aligned_cols=84 Identities=18% Similarity=0.199 Sum_probs=57.9
Q ss_pred EEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCC-CCccchH
Q 030865 75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRN-GSRRGER 153 (170)
Q Consensus 75 L~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRg-g~~YhGr 153 (170)
..|+.|-++-...+- |..|..+..+|+=..-+++. ..++--||...++..++.++|.||..|-++=+| |. ||
T Consensus 21 ahI~asfNNTivtit-D~~Gn~i~wassG~~gfk~~---rk~tpyAA~~aa~~aa~~a~e~Gi~~v~v~vkgpG~---Gr 93 (129)
T COG0100 21 AHIHASFNNTIVTIT-DLTGNVIIWASSGGMGFKGS---RKSTPYAAQLAAEDAAKKAKEHGIKSVEVKVKGPGP---GR 93 (129)
T ss_pred EEEEcccCCcEEEec-CCCCCEEEEEecCCceEcCC---CCCCHHHHHHHHHHHHHHHHHhCccEEEEEEECCCC---cH
Confidence 445555555444444 67788888999988888763 256777888899999999999999988755666 22 22
Q ss_pred HHHHHHHHHHcCC
Q 030865 154 MQAFEIPISRHGF 166 (170)
Q Consensus 154 VkAladaaRe~Gl 166 (170)
+|...+|-.+|+
T Consensus 94 -eaAiraL~~ag~ 105 (129)
T COG0100 94 -EAAIRALAAAGL 105 (129)
T ss_pred -HHHHHHHHHccc
Confidence 334444446665
No 21
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=89.65 E-value=4.2 Score=33.99 Aligned_cols=90 Identities=16% Similarity=0.162 Sum_probs=67.9
Q ss_pred CCCeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCcc
Q 030865 71 TKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRNGSRR 150 (170)
Q Consensus 71 ~rPRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~Y 150 (170)
+-|-..|.-|.++-..+|.| ..|+++..+|---.-+++. ..++--||.-.|-..+.+++++|+..|-+-=+| .-
T Consensus 78 eiPi~hIraS~NNTivtVtd-~kg~vi~~~ScgteGFrnt---rkgT~iAaQtaavaa~~r~v~~G~~~vrV~VkG--lG 151 (190)
T KOG0408|consen 78 EIPIIHIRASFNNTIVTVTD-VKGEVISWSSCGTEGFRNT---RKGTPIAAQTAAVAAIRRAVDQGMQTVRVRVKG--LG 151 (190)
T ss_pred ccceEEEEecCCCeEEEEEc-cCCcEEEEeeccccccccc---ccCCchhHHHHHHHHHHHHHHhcceEEEEEEec--CC
Confidence 67999999999999999985 5667776666555556653 346677899999999999999999977633444 34
Q ss_pred chHHHHHHHHHHHcCCc
Q 030865 151 GERMQAFEIPISRHGFL 167 (170)
Q Consensus 151 hGrVkAladaaRe~Gl~ 167 (170)
-||+.|+ .+++-+||.
T Consensus 152 pGRmsa~-kgl~m~Gl~ 167 (190)
T KOG0408|consen 152 PGRMSAL-KGLRMGGLL 167 (190)
T ss_pred ccHHHHH-hhhhhcceE
Confidence 5887765 677777774
No 22
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=80.10 E-value=11 Score=29.88 Aligned_cols=89 Identities=18% Similarity=0.246 Sum_probs=58.4
Q ss_pred eEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecC---CCCc-
Q 030865 74 RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDR---NGSR- 149 (170)
Q Consensus 74 RL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDR---gg~~- 149 (170)
...||-|-+..++.|-|-.+.+|++-..---+ ++.. ...++--||-+-...+|.+|++.||+.+- +.- ||.+
T Consensus 18 vahi~asfndtfvhitdlsg~eti~rvtggmk-vkad--rdesspyaamlaaqdva~kck~~gi~alh-~klratgg~kt 93 (139)
T KOG0407|consen 18 VAHIFASFNDTFVHVTDLSGKETIVRVTGGMK-VKAD--RDESSPYAAMLAAQDVAAKCKELGITALH-IKLRATGGTKT 93 (139)
T ss_pred EEEEEeecccceEEEeccCCceEEEEecCCeE-Eecc--cccCChHHHHHHHHHHHHHHHhcCeeEEE-EEEEecCCccc
Confidence 34577788888888888888899887654433 2221 22456678888899999999999999887 543 3433
Q ss_pred --cchHHHHHHHHHHHcCC
Q 030865 150 --RGERMQAFEIPISRHGF 166 (170)
Q Consensus 150 --YhGrVkAladaaRe~Gl 166 (170)
.+---++...+|-.+|+
T Consensus 94 ktpgpgaqsalralar~gm 112 (139)
T KOG0407|consen 94 KTPGPGAQSALRALARSGM 112 (139)
T ss_pred CCCCccHHHHHHHHHHhcc
Confidence 22223444444545554
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=69.59 E-value=11 Score=30.12 Aligned_cols=39 Identities=28% Similarity=0.282 Sum_probs=30.1
Q ss_pred cHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcC
Q 030865 117 TIEAAERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHG 165 (170)
Q Consensus 117 n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~G 165 (170)
-.++|+.+|+.||+ .|+ .++ + ||.. |-+.++++++.++|
T Consensus 16 ~~~~A~~lg~~La~----~g~-~lv-~--Gg~~--GlM~a~a~ga~~~g 54 (159)
T TIGR00725 16 LYEIAYRLGKELAK----KGH-ILI-N--GGRT--GVMEAVSKGAREAG 54 (159)
T ss_pred HHHHHHHHHHHHHH----CCC-EEE-c--CCch--hHHHHHHHHHHHCC
Confidence 45678888888877 487 666 5 6543 99999999999887
No 24
>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=67.96 E-value=13 Score=32.08 Aligned_cols=75 Identities=20% Similarity=0.148 Sum_probs=43.4
Q ss_pred EEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHc
Q 030865 85 YAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRH 164 (170)
Q Consensus 85 yAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~ 164 (170)
.--||.+.+..=.+-.||=...-+.. ...-.++.|. .-+++.|++.|-+|.-+|-.+-.-++|+|+++-++
T Consensus 106 VNaLvsPTG~~G~VkIsTGp~Ss~~~--~~~V~vetAi-------aml~dmG~~SiKffPm~Gl~~leE~~avAkA~a~~ 176 (218)
T PF07071_consen 106 VNALVSPTGTPGKVKISTGPLSSQGP--DAIVPVETAI-------AMLKDMGGSSIKFFPMGGLKHLEELKAVAKACARN 176 (218)
T ss_dssp EEEEEBE-SSTTEEE---STTHHGSS----EEEHHHHH-------HHHHHTT--EEEE---TTTTTHHHHHHHHHHHHHC
T ss_pred EEEEEcCCCCceEEEeccCCccccCC--CccccHHHHH-------HHHHHcCCCeeeEeecCCcccHHHHHHHHHHHHHc
Confidence 33455555544455566655443321 1223455553 34678999999999999999999999999999999
Q ss_pred CCcc
Q 030865 165 GFLQ 168 (170)
Q Consensus 165 Gl~~ 168 (170)
||..
T Consensus 177 g~~l 180 (218)
T PF07071_consen 177 GFTL 180 (218)
T ss_dssp T-EE
T ss_pred Ccee
Confidence 9864
No 25
>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=66.55 E-value=15 Score=31.96 Aligned_cols=73 Identities=23% Similarity=0.211 Sum_probs=51.3
Q ss_pred EEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCC
Q 030865 87 MLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGF 166 (170)
Q Consensus 87 QvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl 166 (170)
-||.+.+..=.+-.||-...-+.. ...-.++.| ..-+++.|++.|-+|.-+|-.+-.-++|+|+++-++||
T Consensus 108 ~LvsPTG~~G~VkISTGp~Ss~~~--~~iV~vetA-------iaml~dmG~~SiKffPM~Gl~~leE~~avA~aca~~g~ 178 (236)
T TIGR03581 108 GLVSPTGTPGLVNISTGPLSSQGK--EAIVPIETA-------IAMLKDMGGSSVKFFPMGGLKHLEEYAAVAKACAKHGF 178 (236)
T ss_pred EeecCCCccceEEeccCcccccCC--CceeeHHHH-------HHHHHHcCCCeeeEeecCCcccHHHHHHHHHHHHHcCC
Confidence 355565555566667654433321 112344444 34478899999999999999999999999999999998
Q ss_pred cc
Q 030865 167 LQ 168 (170)
Q Consensus 167 ~~ 168 (170)
..
T Consensus 179 ~l 180 (236)
T TIGR03581 179 YL 180 (236)
T ss_pred cc
Confidence 64
No 26
>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=62.11 E-value=32 Score=32.41 Aligned_cols=53 Identities=11% Similarity=0.150 Sum_probs=42.5
Q ss_pred CCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 114 PCSTIEAAERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 114 s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
.+.+.+.++..|+.||+++++.|++.|+ +--+=-.-|=-+...+..+-++||.
T Consensus 314 ~gt~~~~a~~~g~eIa~~Lk~dgVDAvI-LtstCgtCtrcga~m~keiE~~GIP 366 (431)
T TIGR01917 314 NGTAVANSKQFAKEFSKELLAAGVDAVI-LTSTUGTCTRCGATMVKEIERAGIP 366 (431)
T ss_pred CCccHHHHHHHHHHHHHHHHHcCCCEEE-EcCCCCcchhHHHHHHHHHHHcCCC
Confidence 5677788999999999999999999999 7755334555667777777778874
No 27
>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=61.79 E-value=46 Score=24.36 Aligned_cols=45 Identities=11% Similarity=0.113 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHhcCCCCCCeEEEEecCCeEEEEEEeCCCCeEEEE
Q 030865 55 AKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFF 99 (170)
Q Consensus 55 r~~R~~RiRkki~gt~~rPRL~V~kSNkhIyAQvIdd~~gktLas 99 (170)
...--.++.+.+......-+..|......++++|||.++|++|=-
T Consensus 39 l~~~v~~ln~~~~~~~~~l~F~vde~~~~~vVkViD~~T~eVIRq 83 (107)
T PF03646_consen 39 LEEAVEKLNEFLQALNTSLRFSVDEESGRVVVKVIDKETGEVIRQ 83 (107)
T ss_dssp HHHHHHHHHHHHTTSS--EEEEEEEETTEEEEEEEETTT-SEEEE
T ss_pred HHHHHHHHHHHHHhcCCceEEEEecCCCcEEEEEEECCCCcEEEe
Confidence 333445555666554456699999999999999999999999733
No 28
>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=59.43 E-value=40 Score=26.92 Aligned_cols=47 Identities=19% Similarity=0.345 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhCCCCEEEEe-cCCCCccchHHHHHHHHHHHcCCcc
Q 030865 122 ERIGEELIKTCIALNITEISSY-DRNGSRRGERMQAFEIPISRHGFLQ 168 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~f-DRgg~~YhGrVkAladaaRe~Gl~~ 168 (170)
+..|+.+++.+.+.|..++.++ +.....-..|+..|.+++.+.|+..
T Consensus 100 ~~~g~~a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~~~~~~~ 147 (263)
T cd06280 100 RAAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAP 147 (263)
T ss_pred HHHHHHHHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHHHcCCCC
Confidence 3455566666777899888844 3222233579999999999999753
No 29
>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=56.15 E-value=44 Score=31.49 Aligned_cols=53 Identities=9% Similarity=0.097 Sum_probs=42.2
Q ss_pred CCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 114 PCSTIEAAERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 114 s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
.+.+...++..|..||+++++.|++.|+ +--.=-.-|=-+...+..+-++||.
T Consensus 314 ~gt~~~~a~~~g~eIa~~Lk~dgVDAVI-LTstCgtC~r~~a~m~keiE~~GiP 366 (431)
T TIGR01918 314 NGTTVAESKQFAKEFVVELKQGGVDAVI-LTSTUGTCTRCGATMVKEIERAGIP 366 (431)
T ss_pred CCchHHHHHHHHHHHHHHHHHcCCCEEE-EcCCCCcchhHHHHHHHHHHHcCCC
Confidence 4567788999999999999999999999 7755334555666777777778874
No 30
>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=52.02 E-value=59 Score=25.90 Aligned_cols=52 Identities=15% Similarity=0.164 Sum_probs=37.7
Q ss_pred CcHHHHHHHHHHHHHHHHhC--CCCEEEEec--CCCCccchHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIAL--NITEISSYD--RNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~--gI~~Vv~fD--Rgg~~YhGrVkAladaaRe~Gl~ 167 (170)
.+.++++.+++.|++.+.+. |..++..+- .+...-.-|.+.|.+++.++|+.
T Consensus 102 d~~~~g~~~~~~l~~~~~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~ 157 (277)
T cd06319 102 DNYEGAYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCD 157 (277)
T ss_pred ccHHHHHHHHHHHHHHHHhhCCCCCcEEEEeccCCCccHHHHHHHHHHHHHhcCCc
Confidence 57788999999999998875 556766231 11122356899999999999874
No 31
>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=49.96 E-value=49 Score=26.81 Aligned_cols=46 Identities=9% Similarity=-0.016 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHh--CCCCEEEEe-cCCCCccchHHHHHHHHHHHcCCc
Q 030865 122 ERIGEELIKTCIA--LNITEISSY-DRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 122 ~~VG~~lAkra~e--~gI~~Vv~f-DRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
+..|..+++.+.+ +|.+++.++ +........|...|.++++++|+.
T Consensus 100 ~~~~~~a~~~L~~~~~G~~~Ia~i~~~~~~~~~~R~~gf~~~l~~~g~~ 148 (247)
T cd06276 100 EKAIYNALQEGLEKLKKYKKLILVFPNKTAIPKEIKRGFERFCKDYNIE 148 (247)
T ss_pred HHHHHHHHHHHHHHhcCCCEEEEEecCccHhHHHHHHHHHHHHHHcCCC
Confidence 3445566777777 899998745 322223357999999999999985
No 32
>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=49.29 E-value=58 Score=25.76 Aligned_cols=48 Identities=21% Similarity=0.199 Sum_probs=31.8
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEec-C-CCCccchHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYD-R-NGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fD-R-gg~~YhGrVkAladaaRe~Gl~ 167 (170)
.+.++++ .+++.+.+.|..++.++- . +......|...|.+++.++|+-
T Consensus 97 d~~~~~~----~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~ 146 (260)
T cd06286 97 DHYEAFY----EALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLT 146 (260)
T ss_pred CChHHHH----HHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCC
Confidence 3445554 555566667999988331 1 1233457999999999999963
No 33
>COG1611 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]
Probab=47.89 E-value=25 Score=29.44 Aligned_cols=39 Identities=23% Similarity=0.151 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCC
Q 030865 118 IEAAERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGF 166 (170)
Q Consensus 118 ~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl 166 (170)
.+.|+.||+.||++. .+| +-=| ..|-+.|.++++.++|-
T Consensus 33 ~~~a~~lg~~la~~g------~~V-~tGG---~~GiMea~~~gA~~~gg 71 (205)
T COG1611 33 YELARELGRELAKRG------LLV-ITGG---GPGVMEAVARGALEAGG 71 (205)
T ss_pred HHHHHHHHHHHHhCC------cEE-EeCC---chhhhhHHHHHHHHcCC
Confidence 467888888888876 455 4333 56999999999998874
No 34
>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=47.89 E-value=60 Score=25.64 Aligned_cols=42 Identities=12% Similarity=0.218 Sum_probs=28.5
Q ss_pred HHHHHHHHHhCCCCEEEEe-cCCCCc-cchHHHHHHHHHHHcCC
Q 030865 125 GEELIKTCIALNITEISSY-DRNGSR-RGERMQAFEIPISRHGF 166 (170)
Q Consensus 125 G~~lAkra~e~gI~~Vv~f-DRgg~~-YhGrVkAladaaRe~Gl 166 (170)
|+.+++.+.+.|..++.++ +..+.. -..|.+.|.+++.++|+
T Consensus 104 ~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~ 147 (269)
T cd06288 104 GYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQALAEAGI 147 (269)
T ss_pred HHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHHHHcCC
Confidence 4455555556688888855 222222 25699999999999986
No 35
>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=47.59 E-value=60 Score=25.73 Aligned_cols=44 Identities=11% Similarity=0.127 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhCCCCEEEEec-CCCCcc-chHHHHHHHHHHHcCCc
Q 030865 124 IGEELIKTCIALNITEISSYD-RNGSRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fD-Rgg~~Y-hGrVkAladaaRe~Gl~ 167 (170)
.|+.+++.+.++|..++.++. ..+... ..|...|.+++.+.|+.
T Consensus 104 ~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~ 149 (270)
T cd06296 104 GGLAATEHLLELGHRRIGFITGPPDLLCSRARLDGYRAALAEAGIP 149 (270)
T ss_pred HHHHHHHHHHHcCCCcEEEEcCCCcchhHHHHHHHHHHHHHHcCCC
Confidence 455556666667999998552 222223 57999999999998863
No 36
>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=45.32 E-value=73 Score=25.33 Aligned_cols=47 Identities=13% Similarity=0.231 Sum_probs=30.8
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCCC---CccchHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRNG---SRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg---~~YhGrVkAladaaRe~Gl~ 167 (170)
.|-++++.++ +.+.+.|..++.++ -+. .....|++.|.+++.++|+-
T Consensus 97 d~~~ag~~a~----~~L~~~g~~~i~~i-~~~~~~~~~~~R~~Gf~~~~~~~~~~ 146 (265)
T cd06285 97 DDVLGGRLAT----RHLLDLGHRRIAVL-AGPDYASTARDRLAGFRAALAEAGIE 146 (265)
T ss_pred CcHHHHHHHH----HHHHHCCCccEEEE-eCCcccccHHHHHHHHHHHHHHcCCC
Confidence 3555555554 44555688888834 232 22357999999999999973
No 37
>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=45.19 E-value=66 Score=25.34 Aligned_cols=45 Identities=13% Similarity=0.191 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHhCCCCEEEEecC-CCCcc-chHHHHHHHHHHHcCCc
Q 030865 123 RIGEELIKTCIALNITEISSYDR-NGSRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDR-gg~~Y-hGrVkAladaaRe~Gl~ 167 (170)
..|+.+++.+.+.|..++.++-- ..... ..|.+.|.+++.++|+.
T Consensus 106 ~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 152 (268)
T cd06271 106 AAAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEAGLP 152 (268)
T ss_pred HHHHHHHHHHHHcCCCcEEEecCccccchHHHHHHHHHHHHHHhCCC
Confidence 44555566666779999885532 22222 46899999999999874
No 38
>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=45.14 E-value=68 Score=25.24 Aligned_cols=46 Identities=17% Similarity=0.286 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHhCCCCEEEEe-cCCC-C-ccchHHHHHHHHHHHcCCc
Q 030865 122 ERIGEELIKTCIALNITEISSY-DRNG-S-RRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~f-DRgg-~-~YhGrVkAladaaRe~Gl~ 167 (170)
+..|..+++.+.+.|..+|..+ .+.. . ..+.|.++|.+.+.++|+-
T Consensus 101 ~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~ 149 (266)
T cd06282 101 RAAARDVAQALAALGHRRIAMLAGRLAASDRARQRYAGYRAAMRAAGLA 149 (266)
T ss_pred HHHHHHHHHHHHHcCcccEEEeccccccCchHHHHHHHHHHHHHHcCCC
Confidence 4455556666666799988834 2211 2 2357999999999999974
No 39
>PRK07738 flagellar protein FlaG; Provisional
Probab=44.53 E-value=1e+02 Score=23.94 Aligned_cols=40 Identities=10% Similarity=0.237 Sum_probs=32.0
Q ss_pred HHHHHHHHhcCCCCCCeEEEEecCCeEEEEEEeCCCCeEE
Q 030865 58 RNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCL 97 (170)
Q Consensus 58 R~~RiRkki~gt~~rPRL~V~kSNkhIyAQvIdd~~gktL 97 (170)
--.++-+.+......-+..|+.....++++|||..+|++|
T Consensus 51 aveklN~~l~~~~~~L~F~vdeet~~~vVkVvD~~T~EVI 90 (117)
T PRK07738 51 VVDGMNELLEPSQTSLKFELHEKLNEYYVQVVDERTNEVI 90 (117)
T ss_pred HHHHHHHHHHhcCCceEEEEecCCCcEEEEEEECCCCeee
Confidence 3345555555555677999999999999999999999996
No 40
>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=44.50 E-value=84 Score=28.89 Aligned_cols=55 Identities=15% Similarity=0.140 Sum_probs=45.6
Q ss_pred CCCcHHHHHHHHHH-----------------HHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCCccC
Q 030865 114 PCSTIEAAERIGEE-----------------LIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGFLQQ 169 (170)
Q Consensus 114 s~~n~~AA~~VG~~-----------------lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~~~ 169 (170)
...+.++|..++++ +|-.+.+.|++++- ..=|..-...+|+.+++.+++.|+.-|
T Consensus 54 avp~~~~A~al~~I~~~~~iPlVADIHFd~~lAl~a~~~g~dkiR-INPGNig~~e~v~~vv~~ak~~~ipIR 125 (346)
T TIGR00612 54 TVPDRESAAAFEAIKEGTNVPLVADIHFDYRLAALAMAKGVAKVR-INPGNIGFRERVRDVVEKARDHGKAMR 125 (346)
T ss_pred cCCCHHHHHhHHHHHhCCCCCEEEeeCCCcHHHHHHHHhccCeEE-ECCCCCCCHHHHHHHHHHHHHCCCCEE
Confidence 34677888888864 88889999999999 777766667899999999999998643
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=44.40 E-value=79 Score=25.28 Aligned_cols=44 Identities=23% Similarity=0.385 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhCCCCEEEEecCCCCcc-chHHHHHHHHHHHcCCc
Q 030865 124 IGEELIKTCIALNITEISSYDRNGSRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDRgg~~Y-hGrVkAladaaRe~Gl~ 167 (170)
.|+.+++.+.+.|..++.++-..+... ..|.++|.+++.++|+.
T Consensus 96 ~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~ 140 (265)
T cd01543 96 IGRMAAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEAGYE 140 (265)
T ss_pred HHHHHHHHHHHCCCcEEEEEcCCCCHHHHHHHHHHHHHHHHcCCc
Confidence 455556666778999998442222222 46899999999999974
No 42
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=44.18 E-value=77 Score=26.22 Aligned_cols=44 Identities=16% Similarity=0.231 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhCCCCEEEEec-C-CCCccchHHHHHHHHHHHcCCc
Q 030865 124 IGEELIKTCIALNITEISSYD-R-NGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fD-R-gg~~YhGrVkAladaaRe~Gl~ 167 (170)
-|+.+++.+.+.|..+|.++- - +......|...|.+++.++|+.
T Consensus 161 ~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~ 206 (327)
T PRK10423 161 GGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLN 206 (327)
T ss_pred HHHHHHHHHHHcCCCeEEEEeCCccccchHHHHHHHHHHHHHcCCC
Confidence 356666677778999998442 1 1122356999999999999974
No 43
>PRK09492 treR trehalose repressor; Provisional
Probab=44.05 E-value=87 Score=25.80 Aligned_cols=49 Identities=16% Similarity=0.091 Sum_probs=32.9
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCCC-C--ccchHHHHHHHHHHHcCCcc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRNG-S--RRGERMQAFEIPISRHGFLQ 168 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg-~--~YhGrVkAladaaRe~Gl~~ 168 (170)
.|..+++ .+++.+.+.|..++.++.-.. . ....|...|.+++.++|+.+
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 4555554 455556678999999552111 1 12579999999999999853
No 44
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=42.67 E-value=87 Score=26.16 Aligned_cols=47 Identities=21% Similarity=0.304 Sum_probs=31.8
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCC--CCccchHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRN--GSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRg--g~~YhGrVkAladaaRe~Gl~ 167 (170)
.|.+++ +.+++.+.+.|..++. |=-+ ......|...|.+++.++|+.
T Consensus 163 Dn~~~~----~~a~~~L~~~Gh~~I~-~i~~~~~~~~~~R~~Gf~~al~~~g~~ 211 (331)
T PRK14987 163 DNFEAA----RQMTTAIIARGHRHIA-YLGARLDERTIIKQKGYEQAMLDAGLV 211 (331)
T ss_pred CcHHHH----HHHHHHHHHCCCceEE-EEcCCCcccHHHHHHHHHHHHHHcCCC
Confidence 355554 4455556678999988 4322 122346899999999999974
No 45
>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=41.90 E-value=1e+02 Score=24.24 Aligned_cols=44 Identities=18% Similarity=0.223 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhCCCCEEEEec-CCC-Ccc-chHHHHHHHHHHHcCC
Q 030865 123 RIGEELIKTCIALNITEISSYD-RNG-SRR-GERMQAFEIPISRHGF 166 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fD-Rgg-~~Y-hGrVkAladaaRe~Gl 166 (170)
..|+.+++.+.+.|..++.++- ... ... +.|...|.+.+.++|+
T Consensus 102 ~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~~~~~~ 148 (267)
T cd06283 102 EAAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEALAEHGI 148 (267)
T ss_pred HHHHHHHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHHHHcCC
Confidence 3467777777788999887552 222 222 4799999999999985
No 46
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=41.11 E-value=86 Score=26.24 Aligned_cols=45 Identities=11% Similarity=0.038 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhCCCCEEEEec--CCCCccchHHHHHHHHHHHcCCc
Q 030865 123 RIGEELIKTCIALNITEISSYD--RNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fD--Rgg~~YhGrVkAladaaRe~Gl~ 167 (170)
.-|+.+++.+.+.|..++.++- .+....+.|...|.+++.++|+.
T Consensus 164 ~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~ 210 (341)
T PRK10703 164 EGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIK 210 (341)
T ss_pred HHHHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHHHHHHHcCCC
Confidence 4466666777778988888442 11123357999999999999974
No 47
>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=40.86 E-value=99 Score=23.87 Aligned_cols=43 Identities=14% Similarity=0.166 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhCCCCEEEEecCC-CCcc-chHHHHHHHHHHHcCC
Q 030865 124 IGEELIKTCIALNITEISSYDRN-GSRR-GERMQAFEIPISRHGF 166 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDRg-g~~Y-hGrVkAladaaRe~Gl 166 (170)
.|+.+++.+.+.|..+|.++.-. +..+ +.|.+.|.+.+.++|+
T Consensus 103 ~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~ 147 (264)
T cd06267 103 GAYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAGI 147 (264)
T ss_pred HHHHHHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHHHcCC
Confidence 35555555666788888845322 2233 5799999999999984
No 48
>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=40.76 E-value=1e+02 Score=24.31 Aligned_cols=44 Identities=9% Similarity=0.070 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhCCCCEEEEecCC-CCc-cchHHHHHHHHHHHcCCc
Q 030865 124 IGEELIKTCIALNITEISSYDRN-GSR-RGERMQAFEIPISRHGFL 167 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDRg-g~~-YhGrVkAladaaRe~Gl~ 167 (170)
.|+.+++.+.+.|..+|.++.-. +.. ...|...|.+++.+.|+.
T Consensus 103 ~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~ 148 (264)
T cd01574 103 GARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALEAAGIA 148 (264)
T ss_pred HHHHHHHHHHHCCCCEEEEEecCCccchHHHHHHHHHHHHHHCCCC
Confidence 34444555555788888856322 222 246899999999998874
No 49
>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=40.09 E-value=1e+02 Score=24.80 Aligned_cols=53 Identities=15% Similarity=0.170 Sum_probs=38.7
Q ss_pred CCcHHHHHHHHHHHHHHHHhCCC--CEEEEecC---CCCccchHHHHHHHHHHHcCCc
Q 030865 115 CSTIEAAERIGEELIKTCIALNI--TEISSYDR---NGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 115 ~~n~~AA~~VG~~lAkra~e~gI--~~Vv~fDR---gg~~YhGrVkAladaaRe~Gl~ 167 (170)
..+.++++.+|+.|++.+.+.|. .++.++.- ....-..|+..|.+++.+.|+.
T Consensus 105 ~d~~~~g~~~~~~l~~~~~~~g~~~~~i~~i~~~~~~~~~~~~R~~G~~~~l~~~~~~ 162 (289)
T cd01540 105 MSATKIGEQVGEAIADEMKKRGWDPKEVGALRITYDELDTAKPRTDGALEALKAPGFP 162 (289)
T ss_pred CCHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecCCCCcchhhHHHHHHHHHhcCCCC
Confidence 46889999999999999988887 55542322 1122356899999999998863
No 50
>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=39.72 E-value=1.1e+02 Score=24.44 Aligned_cols=48 Identities=6% Similarity=0.029 Sum_probs=31.0
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEec-CCCCcc-chHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYD-RNGSRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fD-Rgg~~Y-hGrVkAladaaRe~Gl~ 167 (170)
.+.++++. +++.+.++|..++.++- ...... ..|.+.|.+++.++|+.
T Consensus 99 d~~~~~~~----~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~ 148 (269)
T cd06293 99 DNEQGGRL----ATRHLARAGHRRIAFVGGPDALISARERYAGYREALAEAHIP 148 (269)
T ss_pred CCHHHHHH----HHHHHHHCCCceEEEEecCcccccHHHHHHHHHHHHHHcCCC
Confidence 35555554 45555567999988442 222222 36899999999999974
No 51
>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=39.69 E-value=48 Score=25.14 Aligned_cols=32 Identities=19% Similarity=0.299 Sum_probs=25.2
Q ss_pred cHHHHHHHHHHHHHHHHhCC--CCEEEEecCCCCc
Q 030865 117 TIEAAERIGEELIKTCIALN--ITEISSYDRNGSR 149 (170)
Q Consensus 117 n~~AA~~VG~~lAkra~e~g--I~~Vv~fDRgg~~ 149 (170)
+.+.|..++...-+.|.+.| +.-.| .|++|+.
T Consensus 4 ~~~~A~~l~~~a~~~a~~~g~~v~iaV-vd~~G~~ 37 (132)
T PF03928_consen 4 TLEDAWKLGDAAVEEARERGLPVSIAV-VDAGGHL 37 (132)
T ss_dssp -HHHHHHHHHHHHHHHHHTT---EEEE-EETTS-E
T ss_pred CHHHHHHHHHHHHHHHHHhCCCeEEEE-EECCCCE
Confidence 56899999999999999999 44555 7999854
No 52
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=39.34 E-value=1e+02 Score=25.50 Aligned_cols=43 Identities=19% Similarity=0.042 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhCCCCEEEEecCCC---CccchHHHHHHHHHHHcCCc
Q 030865 124 IGEELIKTCIALNITEISSYDRNG---SRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDRgg---~~YhGrVkAladaaRe~Gl~ 167 (170)
-|..+++.+.+.|..+|.++ .+. .....|.+.|.+++.++|+.
T Consensus 166 ~~~~a~~~L~~~G~r~I~~i-~~~~~~~~~~~R~~Gf~~al~~~g~~ 211 (328)
T PRK11303 166 DAEMLAESLLKFPAESILLL-GALPELSVSFEREQGFRQALKDDPRE 211 (328)
T ss_pred HHHHHHHHHHHCCCCeEEEE-eCccccccHHHHHHHHHHHHHHcCCC
Confidence 35556777778899998844 221 12346999999999999974
No 53
>PRK04302 triosephosphate isomerase; Provisional
Probab=39.17 E-value=77 Score=26.09 Aligned_cols=45 Identities=9% Similarity=0.017 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCC-CCccchHHHHHHHHHHHcCCcc
Q 030865 123 RIGEELIKTCIALNITEISSYDRN-GSRRGERMQAFEIPISRHGFLQ 168 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRg-g~~YhGrVkAladaaRe~Gl~~ 168 (170)
-.|+..++.+.+.|++-|+ .+.. -..+++.+..+.+.+.+.|+.+
T Consensus 72 ~tg~~~~~~l~~~G~~~vi-i~~ser~~~~~e~~~~v~~a~~~Gl~~ 117 (223)
T PRK04302 72 HTGHILPEAVKDAGAVGTL-INHSERRLTLADIEAVVERAKKLGLES 117 (223)
T ss_pred chhhhHHHHHHHcCCCEEE-EeccccccCHHHHHHHHHHHHHCCCeE
Confidence 4577779999999999999 6642 2467778999999999999854
No 54
>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=39.11 E-value=1.1e+02 Score=24.13 Aligned_cols=45 Identities=16% Similarity=0.210 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhCCCCEEEEec-C-CCCccchHHHHHHHHHHHcCCc
Q 030865 123 RIGEELIKTCIALNITEISSYD-R-NGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fD-R-gg~~YhGrVkAladaaRe~Gl~ 167 (170)
..|+.+++.+.+.|..++.++. . +...-.-|.+.|.+++.++|+.
T Consensus 103 ~~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~ 149 (269)
T cd06275 103 EGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLP 149 (269)
T ss_pred HHHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCC
Confidence 4445555666677988888443 2 2223356899999999999864
No 55
>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=39.02 E-value=1e+02 Score=25.18 Aligned_cols=46 Identities=15% Similarity=0.093 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHhCCCCEEEEec-CCC-CccchHHHHHHHHHHHcCCc
Q 030865 122 ERIGEELIKTCIALNITEISSYD-RNG-SRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fD-Rgg-~~YhGrVkAladaaRe~Gl~ 167 (170)
+..|..+++.+.++|..++.++. ... .....|..+|.++++++|+.
T Consensus 103 ~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~~ 150 (269)
T cd06287 103 AATARMLLEHLRAQGARQIALIVGSARRNSYLEAEAAYRAFAAEHGMP 150 (269)
T ss_pred HHHHHHHHHHHHHcCCCcEEEEeCCcccccHHHHHHHHHHHHHHcCCC
Confidence 34577778888888999987552 221 22356899999999999974
No 56
>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=38.92 E-value=1.2e+02 Score=25.23 Aligned_cols=44 Identities=14% Similarity=0.212 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhCCCCEEEEecCCC--Cc--cchHHHHHHHHHHHcCCcc
Q 030865 124 IGEELIKTCIALNITEISSYDRNG--SR--RGERMQAFEIPISRHGFLQ 168 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDRgg--~~--YhGrVkAladaaRe~Gl~~ 168 (170)
-|..+++.+.+.|..++.++ -|. .. ...|...|.+++.++|+..
T Consensus 163 ~~~~a~~~L~~~G~~~I~~i-~g~~~~~~~~~~R~~Gf~~~l~~~g~~~ 210 (329)
T TIGR01481 163 ATKEAVGELIAKGHKSIAFV-GGPLSDSINGEDRLEGYKEALNKAGIQF 210 (329)
T ss_pred HHHHHHHHHHHCCCCeEEEE-ecCcccccchHHHHHHHHHHHHHcCCCC
Confidence 35556666777899999844 221 22 2579999999999999753
No 57
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=38.66 E-value=75 Score=25.44 Aligned_cols=45 Identities=13% Similarity=0.223 Sum_probs=35.7
Q ss_pred HHHHHHHHhCCCCEEEE---------ecCCCCccchHHHHHHHHHHHcCCccCC
Q 030865 126 EELIKTCIALNITEISS---------YDRNGSRRGERMQAFEIPISRHGFLQQR 170 (170)
Q Consensus 126 ~~lAkra~e~gI~~Vv~---------fDRgg~~YhGrVkAladaaRe~Gl~~~~ 170 (170)
-.++-+|+..|++-|.+ |++|.|+-.-|+..+.+.|-|-||=+.|
T Consensus 43 ~~fvl~Al~~GaDGV~v~GC~~geCHy~~GN~ka~rR~~~lke~l~elgie~eR 96 (132)
T COG1908 43 PEFVLKALRKGADGVLVAGCKIGECHYISGNYKAKRRMELLKELLKELGIEPER 96 (132)
T ss_pred HHHHHHHHHcCCCeEEEecccccceeeeccchHHHHHHHHHHHHHHHhCCCcce
Confidence 34666788888875532 8898888899999999999999987654
No 58
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=38.57 E-value=1e+02 Score=25.66 Aligned_cols=44 Identities=18% Similarity=0.230 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhCCCCEEEEecC-CCC-ccchHHHHHHHHHHHcCCc
Q 030865 124 IGEELIKTCIALNITEISSYDR-NGS-RRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDR-gg~-~YhGrVkAladaaRe~Gl~ 167 (170)
.|+.+++.+.+.|..+|.++.- ... ....|+..|.+++.++|+.
T Consensus 169 ~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~ 214 (342)
T PRK10014 169 AAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATLLKFGLP 214 (342)
T ss_pred HHHHHHHHHHHCCCCEEEEEcCCcccccHHHHHHHHHHHHHHcCCC
Confidence 3444555556679999884421 112 2257999999999999974
No 59
>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=38.37 E-value=1.1e+02 Score=24.12 Aligned_cols=45 Identities=13% Similarity=0.114 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCCC--cc-chHHHHHHHHHHHcCCc
Q 030865 123 RIGEELIKTCIALNITEISSYDRNGS--RR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg~--~Y-hGrVkAladaaRe~Gl~ 167 (170)
..|+.+++.+.+.|..++.++.-... .. ..|.+.|.+++.++|+.
T Consensus 98 ~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~ 145 (265)
T cd06291 98 EGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLE 145 (265)
T ss_pred HHHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHHHcCCC
Confidence 34555566666679999985532222 22 37899999999999874
No 60
>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=38.14 E-value=92 Score=24.69 Aligned_cols=44 Identities=14% Similarity=0.092 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCC-C-CccchHHHHHHHHHHHcCC
Q 030865 123 RIGEELIKTCIALNITEISSYDRN-G-SRRGERMQAFEIPISRHGF 166 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRg-g-~~YhGrVkAladaaRe~Gl 166 (170)
..|+.+++.+.+.|..+|.++.-. . ....-|...|.+++.+.|+
T Consensus 97 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~ 142 (261)
T cd06272 97 KAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDENGI 142 (261)
T ss_pred HHHHHHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHHHcCC
Confidence 345566666677799998855322 2 2335689999999999996
No 61
>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=37.92 E-value=92 Score=24.61 Aligned_cols=45 Identities=18% Similarity=0.278 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhCCCCEEEEec-CCCCc-cchHHHHHHHHHHHcCC
Q 030865 122 ERIGEELIKTCIALNITEISSYD-RNGSR-RGERMQAFEIPISRHGF 166 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fD-Rgg~~-YhGrVkAladaaRe~Gl 166 (170)
+..|+.+++.+.+.|..+|.++. ..++. -+-|.+.|.+++++.|+
T Consensus 107 ~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~ 153 (270)
T cd06294 107 IQAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALEDHGI 153 (270)
T ss_pred HHHHHHHHHHHHHcCCccEEEecCCcccHHHHHHHHHHHHHHHHcCC
Confidence 34555556666666888888563 22222 24589999999999996
No 62
>PF14419 SPOUT_MTase_2: AF2226-like SPOUT RNA Methylase fused to THUMP
Probab=37.70 E-value=99 Score=25.82 Aligned_cols=49 Identities=12% Similarity=0.234 Sum_probs=35.1
Q ss_pred CCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHc
Q 030865 115 CSTIEAAERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRH 164 (170)
Q Consensus 115 ~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~ 164 (170)
-++.+||+..|+-|+..+....+.+.+.-..+ +.-.=-+..|++|++++
T Consensus 10 lGd~~a~r~mGerIGRaaQ~FEV~eLiiap~~-~vda~eL~~Fl~gV~~G 58 (173)
T PF14419_consen 10 LGDLKACRKMGERIGRAAQAFEVKELIIAPKE-KVDAYELMEFLRGVREG 58 (173)
T ss_pred cCCHHHHHHHHHHHhHHHhhcchheEEEeccC-ccCHHHHHHHHHHHHHh
Confidence 47889999999999999999999999822222 11122355677777664
No 63
>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=37.46 E-value=1.5e+02 Score=22.37 Aligned_cols=49 Identities=16% Similarity=0.130 Sum_probs=37.9
Q ss_pred CcHHHHHHHHHHHHHHHHhC--CCCEEEEecCCCCccchH--HHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIAL--NITEISSYDRNGSRRGER--MQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~--gI~~Vv~fDRgg~~YhGr--VkAladaaRe~Gl~ 167 (170)
-|.+.+..+|..++.-..+. +-.-+|.+|. ++++. .++++++++..|+.
T Consensus 18 lt~~~~~~~~~a~~~~~~~~~~~~~VvVg~D~---R~~s~~~~~~~~~~l~~~G~~ 70 (137)
T PF02878_consen 18 LTPEFAARLAQAFASYLKEKGNGSRVVVGRDT---RPSSPMLAKALAAGLRANGVD 70 (137)
T ss_dssp BSHHHHHHHHHHHHHHHHHTTTSSEEEEEE-S---STTHHHHHHHHHHHHHHTTEE
T ss_pred CCHHHHHHHHHHHHHhhcccCCCCeEEEEEcc---cCCHHHHHHHHHHHHhhcccc
Confidence 58899999999999999985 4555565665 45554 68899999999974
No 64
>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=37.26 E-value=1.3e+02 Score=23.73 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhCCCCEEEEe-cCCCCcc-chHHHHHHHHHHHcCCc
Q 030865 122 ERIGEELIKTCIALNITEISSY-DRNGSRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~f-DRgg~~Y-hGrVkAladaaRe~Gl~ 167 (170)
+..|+.+++.+.+.|..++.++ +..++.. ..|...|.+++.+.|+.
T Consensus 103 ~~~g~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~ 150 (270)
T cd01545 103 RAAAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALAEAGLP 150 (270)
T ss_pred HHHHHHHHHHHHHCCCceEEEEeCCCCchhHHHHHHHHHHHHHHcCCC
Confidence 4456666666777798988844 2223332 36789999999998864
No 65
>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=37.06 E-value=1.1e+02 Score=25.50 Aligned_cols=42 Identities=17% Similarity=0.227 Sum_probs=31.6
Q ss_pred HHHHHHHHHhCCCCEEEEecCCC---CccchHHHHHHHHHHHcCCc
Q 030865 125 GEELIKTCIALNITEISSYDRNG---SRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 125 G~~lAkra~e~gI~~Vv~fDRgg---~~YhGrVkAladaaRe~Gl~ 167 (170)
|..+++.+.+.|..+|.++ .+. .....|...|.+++.++|+.
T Consensus 166 ~~~~~~~L~~~G~~~I~~i-~~~~~~~~~~~R~~Gf~~al~~~~~~ 210 (327)
T TIGR02417 166 AAELIERLLSQHADEFWYL-GAQPELSVSRDRLAGFRQALKQATLE 210 (327)
T ss_pred HHHHHHHHHHCCCCeEEEE-eCcccchhHHHHHHHHHHHHHHcCCC
Confidence 5667778888999999844 332 22357999999999999974
No 66
>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=36.12 E-value=1.6e+02 Score=23.43 Aligned_cols=48 Identities=17% Similarity=0.198 Sum_probs=31.4
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEec-CCCCc-cchHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYD-RNGSR-RGERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fD-Rgg~~-YhGrVkAladaaRe~Gl~ 167 (170)
.|..+++.+++.| .++|..++.++- ..... -+.|...|.+++.++|+.
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 4555555555554 556999988442 22222 247899999999999964
No 67
>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=35.94 E-value=1.5e+02 Score=23.36 Aligned_cols=46 Identities=17% Similarity=0.174 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhCCCCEEEEecCCC-C-cc-chHHHHHHHHHHHcCCc
Q 030865 122 ERIGEELIKTCIALNITEISSYDRNG-S-RR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fDRgg-~-~Y-hGrVkAladaaRe~Gl~ 167 (170)
+..|..+++.+.+.|..+|.++.-.. . .+ ..|...|.+.+.++|+.
T Consensus 101 ~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~ 149 (268)
T cd06273 101 REAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAALAEAGLE 149 (268)
T ss_pred HHHHHHHHHHHHHCCCCeEEEEeccccCCccHHHHHHHHHHHHHHcCCC
Confidence 34455555555667999998664221 1 12 25899999999999864
No 68
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=35.87 E-value=1.3e+02 Score=19.74 Aligned_cols=41 Identities=22% Similarity=0.250 Sum_probs=29.3
Q ss_pred HHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCCcc
Q 030865 125 GEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGFLQ 168 (170)
Q Consensus 125 G~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~~ 168 (170)
-+.+.++|++.|++.+..-|.+ .+.|-. .+.+.+++.||.+
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 3467899999999999877887 445544 4445667777753
No 69
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=35.56 E-value=1.2e+02 Score=25.54 Aligned_cols=42 Identities=17% Similarity=0.150 Sum_probs=30.3
Q ss_pred HHHHHHHHHhCCCCEEEEecCCC---CccchHHHHHHHHHHHcCCc
Q 030865 125 GEELIKTCIALNITEISSYDRNG---SRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 125 G~~lAkra~e~gI~~Vv~fDRgg---~~YhGrVkAladaaRe~Gl~ 167 (170)
|..+++.+.+.|..++.++- +. .....|...|.+++.++|+.
T Consensus 164 ~~~a~~~L~~~G~~~I~~i~-~~~~~~~~~~R~~Gf~~al~~~gi~ 208 (343)
T PRK10727 164 AWLATRHLIQQGHTRIGYLC-SNHSISDAEDRLQGYYDALAESGIP 208 (343)
T ss_pred HHHHHHHHHHCCCccEEEEe-CCccccchHHHHHHHHHHHHHCCCC
Confidence 55566667778999888442 21 22357999999999999974
No 70
>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=35.23 E-value=1e+02 Score=25.89 Aligned_cols=43 Identities=19% Similarity=0.220 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhCCCCE-EEEecCCCCc--cchHHHHHHHHHHHcCC
Q 030865 124 IGEELIKTCIALNITE-ISSYDRNGSR--RGERMQAFEIPISRHGF 166 (170)
Q Consensus 124 VG~~lAkra~e~gI~~-Vv~fDRgg~~--YhGrVkAladaaRe~Gl 166 (170)
-|+.+++.+.+.|..+ |.++...... ...|++.|.+++.++|+
T Consensus 105 a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl 150 (279)
T PF00532_consen 105 AGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGL 150 (279)
T ss_dssp HHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCC
Confidence 3456677788889999 7734443222 35699999999999998
No 71
>PRK12548 shikimate 5-dehydrogenase; Provisional
Probab=35.18 E-value=96 Score=26.64 Aligned_cols=41 Identities=15% Similarity=0.150 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHc
Q 030865 123 RIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRH 164 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~ 164 (170)
-.|+.++..+.+.|+++|+.+||+. .+..+.+.+++.+.+.
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 4566788888889999887799973 2345677777766543
No 72
>COG1472 BglX Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]
Probab=34.77 E-value=97 Score=28.41 Aligned_cols=54 Identities=30% Similarity=0.332 Sum_probs=39.2
Q ss_pred CCCcHHHHHHHHHHHHHHHHhCCCCE-------EEEec----CCCCc-cch-------HHHHHHHHHHHcCCcc
Q 030865 114 PCSTIEAAERIGEELIKTCIALNITE-------ISSYD----RNGSR-RGE-------RMQAFEIPISRHGFLQ 168 (170)
Q Consensus 114 s~~n~~AA~~VG~~lAkra~e~gI~~-------Vv~fD----Rgg~~-YhG-------rVkAladaaRe~Gl~~ 168 (170)
..-+.+.++.+|+++|+-+.+.||+- |. .| |.+.+ |+. =..|+++|+...|+.+
T Consensus 91 a~~~~~la~~~g~~~A~Elra~Gin~~fAPvlDv~-~~p~~~ri~ersfgeDP~lv~~l~~a~i~Glq~~gv~a 163 (397)
T COG1472 91 ATWDPELARKVGRVIAKELRALGINLDFAPVLDVA-RDPRWGRIGERSFGEDPELVALLAAAFIKGLQGAGVAA 163 (397)
T ss_pred hcCCHHHHHHHHHHHHHHHHHcCCCccccceeecc-cCCCcCccccccCCCCHHHHHHHHHHHHHHHhhCCcee
Confidence 44678999999999999999999972 11 11 22233 432 2678899999999875
No 73
>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=34.70 E-value=1.4e+02 Score=24.31 Aligned_cols=49 Identities=14% Similarity=0.097 Sum_probs=31.0
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEe-cCCCCccchHHHHHHHHHHHc-CC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSY-DRNGSRRGERMQAFEIPISRH-GF 166 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~f-DRgg~~YhGrVkAladaaRe~-Gl 166 (170)
.|.++++.+++.|.+.+ .|..++.++ .-..+..+.|+..|.+++.++ |+
T Consensus 112 d~~~~g~~~~~~L~~~~--~g~~~i~~l~~~~~~~~~~R~~gf~~al~~~~~~ 162 (280)
T cd06303 112 DHAAGARLLADYFIKRY--PNHARYAMLYFSPGYISTARGDTFIDCVHARNNW 162 (280)
T ss_pred CHHHHHHHHHHHHHHhc--CCCcEEEEEECCCCcchhHHHHHHHHHHHhCCCc
Confidence 45555555555554432 677777734 111244577999999999998 75
No 74
>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=34.60 E-value=1.4e+02 Score=23.77 Aligned_cols=42 Identities=19% Similarity=0.321 Sum_probs=28.6
Q ss_pred HHHHHHHHHhCCCCEEEEecCCCCc---cchHHHHHHHHHHHcCCc
Q 030865 125 GEELIKTCIALNITEISSYDRNGSR---RGERMQAFEIPISRHGFL 167 (170)
Q Consensus 125 G~~lAkra~e~gI~~Vv~fDRgg~~---YhGrVkAladaaRe~Gl~ 167 (170)
|+.+++.+.+.|..++..+ .+... ..-|+..|.+++.++|+.
T Consensus 104 g~~a~~~l~~~G~~~i~~l-~~~~~~~~~~~R~~Gf~~~~~~~~~~ 148 (269)
T cd06281 104 MRQAVEYLISLGHRRIALV-GGGSNTRPGRERLEGYKAAFAAAGLP 148 (269)
T ss_pred HHHHHHHHHHCCCcEEEEe-cCccccccHHHHHHHHHHHHHHcCCC
Confidence 4555666666799998834 33211 235889999999999974
No 75
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=34.50 E-value=1.3e+02 Score=25.10 Aligned_cols=46 Identities=20% Similarity=0.188 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHhCCCCEEEEecC-CCC-ccchHHHHHHHHHHHcCCc
Q 030865 122 ERIGEELIKTCIALNITEISSYDR-NGS-RRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fDR-gg~-~YhGrVkAladaaRe~Gl~ 167 (170)
+..|..+++.+.++|..++.++.- ... ....|..+|.+++.++|+.
T Consensus 159 ~~~~~~a~~~l~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~g~~ 206 (327)
T PRK10339 159 ARISKEIIDFYINQGVNRIGFIGGEDEPGKADIREVAFAEYGRLKQVV 206 (327)
T ss_pred HHHHHHHHHHHHHCCCCeEEEeCCccccchhhHHHHHHHHHHHHcCCC
Confidence 566788888999999999986622 112 2346899999999999874
No 76
>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=34.44 E-value=1.4e+02 Score=23.68 Aligned_cols=47 Identities=21% Similarity=0.295 Sum_probs=30.1
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEe-cCCC-CccchHHHHHHHHHHHcCC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSY-DRNG-SRRGERMQAFEIPISRHGF 166 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~f-DRgg-~~YhGrVkAladaaRe~Gl 166 (170)
.|.++++.+++.|+ +.|..++.++ ...+ ..-+-|.++|.+.+.++|+
T Consensus 99 d~~~~g~~~~~~l~----~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~ 147 (264)
T cd06274 99 DNRDGAAELTRELL----AAPPEEVLFLGGLPELSPSRERLAGFRQALADAGL 147 (264)
T ss_pred ccHHHHHHHHHHHH----HCCCCcEEEEeCCCcccchHHHHHHHHHHHHHcCC
Confidence 35555555555554 4788887734 2212 2235699999999999986
No 77
>PRK07710 acetolactate synthase catalytic subunit; Reviewed
Probab=34.40 E-value=64 Score=30.23 Aligned_cols=39 Identities=13% Similarity=0.038 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 123 RIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
.+++.|++.+++.||+.|. -..++.+..|.|++.+.|+.
T Consensus 17 ~~~~~i~~~L~~~Gv~~vF------g~pG~~~~~l~~al~~~~i~ 55 (571)
T PRK07710 17 TGAQMLIEALEKEGVEVIF------GYPGGAVLPLYDALYDCGIP 55 (571)
T ss_pred hHHHHHHHHHHHcCCCEEE------eCCCcchHHHHHHHHhcCCc
Confidence 4799999999999999999 46677888899998777753
No 78
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to 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 that the branches may have distinct functions.
Probab=34.30 E-value=1.2e+02 Score=24.63 Aligned_cols=40 Identities=23% Similarity=0.165 Sum_probs=30.2
Q ss_pred cHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcC
Q 030865 117 TIEAAERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHG 165 (170)
Q Consensus 117 n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~G 165 (170)
-.++|+.+|+.||++ |++=|. || -..|-+.|++++++++|
T Consensus 17 ~~~~A~~lG~~la~~----g~~lV~----GG-g~~GlM~a~a~ga~~~g 56 (178)
T TIGR00730 17 YKELAAELGAYLAGQ----GWGLVY----GG-GRVGLMGAIADAAMENG 56 (178)
T ss_pred HHHHHHHHHHHHHHC----CCEEEE----CC-ChHhHHHHHHHHHHhcC
Confidence 446888888888774 666555 43 35799999999999976
No 79
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=34.07 E-value=1.5e+02 Score=24.89 Aligned_cols=48 Identities=10% Similarity=0.207 Sum_probs=31.5
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecC-CC-CccchHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDR-NG-SRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDR-gg-~~YhGrVkAladaaRe~Gl~ 167 (170)
.|..+++ .+++.+.+.|..++.++-- .. .....|++.|.+++.++|+.
T Consensus 159 D~~~~~~----~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~ 208 (346)
T PRK10401 159 DNVSGAR----MATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWMSALKEQGII 208 (346)
T ss_pred CcHHHHH----HHHHHHHHCCCCeEEEEeCCCcCcchHHHHHHHHHHHHHcCCC
Confidence 3444544 4445556679998875521 11 22357999999999999974
No 80
>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=33.83 E-value=1.5e+02 Score=23.61 Aligned_cols=43 Identities=16% Similarity=0.183 Sum_probs=28.8
Q ss_pred HHHHHHHHHhCCCCEEEEec-CCCC-ccchHHHHHHHHHHHcCCc
Q 030865 125 GEELIKTCIALNITEISSYD-RNGS-RRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 125 G~~lAkra~e~gI~~Vv~fD-Rgg~-~YhGrVkAladaaRe~Gl~ 167 (170)
|+.+++.+.+.|-.++.++- ..+. .-.-|.+.|.+.++++|+.
T Consensus 104 ~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 148 (268)
T cd06270 104 GYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEAGIA 148 (268)
T ss_pred HHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCC
Confidence 44555555667888887442 2222 2246899999999999974
No 81
>PRK09526 lacI lac repressor; Reviewed
Probab=33.75 E-value=1.4e+02 Score=24.85 Aligned_cols=48 Identities=6% Similarity=0.047 Sum_probs=31.3
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEec--CCCCccchHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYD--RNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fD--Rgg~~YhGrVkAladaaRe~Gl~ 167 (170)
.|.++++. +++.+.+.|..++.++- .+......|...|.+++.++|+.
T Consensus 164 d~~~~~~~----a~~~L~~~G~~~I~~l~g~~~~~~~~~R~~Gf~~al~~~gi~ 213 (342)
T PRK09526 164 DPEDGTRL----GVEHLVELGHQRIALLAGPESSVSARLRLAGWLEYLTDYQLQ 213 (342)
T ss_pred CcHHHHHH----HHHHHHHCCCCeEEEEeCCCccccHHHHHHHHHHHHHHcCCC
Confidence 44455444 45555567999988441 12122357899999999999974
No 82
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=32.80 E-value=1.5e+02 Score=24.13 Aligned_cols=48 Identities=17% Similarity=0.124 Sum_probs=30.9
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEec-CCCCc-cchHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYD-RNGSR-RGERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fD-Rgg~~-YhGrVkAladaaRe~Gl~ 167 (170)
.|..+++..++. +.+.|..++.++- ..... -+.|.+.|.++++++|+.
T Consensus 135 Dn~~~g~~a~~~----l~~~G~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~ 184 (309)
T PRK11041 135 DNLTAAFEAVNY----LHELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGIT 184 (309)
T ss_pred CcHHHHHHHHHH----HHHcCCceEEEEeCCccccchHHHHHHHHHHHHHcCCC
Confidence 455555555444 4556888888442 22222 246999999999999973
No 83
>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=32.69 E-value=1.6e+02 Score=23.55 Aligned_cols=44 Identities=14% Similarity=0.183 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCC-CCcc-chHHHHHHHHHHHcCC
Q 030865 123 RIGEELIKTCIALNITEISSYDRN-GSRR-GERMQAFEIPISRHGF 166 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRg-g~~Y-hGrVkAladaaRe~Gl 166 (170)
..|+.+|+.+.+.|..+|.++--. .... +-|...|.++++++|+
T Consensus 111 ~~g~~~a~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~ 156 (275)
T cd06295 111 GGGRLATEHLLARGRRRIAFLGGPQDMPEGEERLEGYREALAEAGL 156 (275)
T ss_pred HHHHHHHHHHHHCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHcCC
Confidence 445555666667798888844221 2222 3689999999999984
No 84
>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=32.61 E-value=86 Score=26.98 Aligned_cols=54 Identities=22% Similarity=0.182 Sum_probs=36.7
Q ss_pred CCcHHHHHHHHHHHHHHHHhCCCCEEEE----ecCCC------Cccc------h-HHHHHHHHHHHcCCcc
Q 030865 115 CSTIEAAERIGEELIKTCIALNITEISS----YDRNG------SRRG------E-RMQAFEIPISRHGFLQ 168 (170)
Q Consensus 115 ~~n~~AA~~VG~~lAkra~e~gI~~Vv~----fDRgg------~~Yh------G-rVkAladaaRe~Gl~~ 168 (170)
+.|.+.++.+|..+|+-+.+.||+-... ..|+. ..|+ + -..|+.+++.++||.+
T Consensus 81 t~d~~~a~~~g~~~a~el~~~Gin~~~aPv~Dv~~~p~~~~~~rsfgeDp~~v~~~~~a~v~G~q~~gv~~ 151 (299)
T PF00933_consen 81 TWDPELAYEVGRIIARELRALGINVNFAPVVDVNRNPRWGRGERSFGEDPDLVAEMARAFVRGLQGAGVAA 151 (299)
T ss_dssp HTCHHHHHHHHHHHHHHHHHTT-SEEEEEB----SSTTSTTGGGSS-SSHHHHHHHHHHHHHHHHCTTSEE
T ss_pred hccchHHHHHHHHHHHHHHHhhhccccccceeeeeeccccccccccchhHHHHHHHHHHHhcccccccccc
Confidence 4688999999999999999999985210 22221 1121 1 2568999999999875
No 85
>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=32.13 E-value=76 Score=29.14 Aligned_cols=28 Identities=18% Similarity=0.279 Sum_probs=25.3
Q ss_pred CCCcHHHHHHHHHHHHHHHHhCCCCEEE
Q 030865 114 PCSTIEAAERIGEELIKTCIALNITEIS 141 (170)
Q Consensus 114 s~~n~~AA~~VG~~lAkra~e~gI~~Vv 141 (170)
.+.+.+.++..|..||+.+++.|++.|+
T Consensus 318 ~gt~~~~~~~~g~eIa~~Lk~dgVDAVI 345 (349)
T PF07355_consen 318 NGTAVANAKRFGPEIAKELKEDGVDAVI 345 (349)
T ss_pred CCccHHHHHHHHHHHHHHHHHcCCCEEE
Confidence 4567788999999999999999999998
No 86
>PRK12827 short chain dehydrogenase; Provisional
Probab=31.98 E-value=1.3e+02 Score=23.62 Aligned_cols=41 Identities=17% Similarity=0.103 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHH
Q 030865 122 ERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISR 163 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe 163 (170)
--+|..+|+.+.+.|.+-++ .||....-......+.+.+.+
T Consensus 16 g~iG~~la~~l~~~g~~v~~-~~~~~~~~~~~~~~~~~~~~~ 56 (249)
T PRK12827 16 GGLGRAIAVRLAADGADVIV-LDIHPMRGRAEADAVAAGIEA 56 (249)
T ss_pred ChHHHHHHHHHHHCCCeEEE-EcCcccccHHHHHHHHHHHHh
Confidence 45788899999888887656 787543334455555554443
No 87
>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=31.76 E-value=75 Score=24.49 Aligned_cols=42 Identities=14% Similarity=0.203 Sum_probs=29.3
Q ss_pred HHHHHHHHHhCCCCEEEEecCCCCcc-chHHHHHHHHHHHcCCc
Q 030865 125 GEELIKTCIALNITEISSYDRNGSRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 125 G~~lAkra~e~gI~~Vv~fDRgg~~Y-hGrVkAladaaRe~Gl~ 167 (170)
.+.|.+-|.+.||+.|+ +++..-.| ..+.+.+.+.+.+.|+.
T Consensus 77 ~~~l~~l~~~~~~~~V~-~~~~~~~~~~~rd~~v~~~l~~~~i~ 119 (165)
T PF00875_consen 77 EEVLPELAKEYGATAVY-FNEEYTPYERRRDERVRKALKKHGIK 119 (165)
T ss_dssp HHHHHHHHHHHTESEEE-EE---SHHHHHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHhcCcCeeE-eccccCHHHHHHHHHHHHHHHhcceE
Confidence 34455566678999999 99984444 35788999999988875
No 88
>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=31.70 E-value=1.5e+02 Score=24.64 Aligned_cols=48 Identities=15% Similarity=0.005 Sum_probs=32.8
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCCC--Ccc-chHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRNG--SRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg--~~Y-hGrVkAladaaRe~Gl~ 167 (170)
.|..++ +.+++.+.++|..++.++.-.. ..+ ..|.++|.++++++|+.
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 454454 4556666778999999553111 222 46999999999999984
No 89
>PRK12549 shikimate 5-dehydrogenase; Reviewed
Probab=31.57 E-value=1.2e+02 Score=26.24 Aligned_cols=37 Identities=14% Similarity=0.313 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHH
Q 030865 123 RIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISR 163 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe 163 (170)
-+|..++..+.+.|+.+|+.+||. .+|.+++++.+.+
T Consensus 137 Gaaraia~aL~~~G~~~I~I~nR~----~~ka~~la~~l~~ 173 (284)
T PRK12549 137 GAGAAVAHALLTLGVERLTIFDVD----PARAAALADELNA 173 (284)
T ss_pred HHHHHHHHHHHHcCCCEEEEECCC----HHHHHHHHHHHHh
Confidence 356667777778999988889997 3678888877643
No 90
>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=31.39 E-value=1.7e+02 Score=23.02 Aligned_cols=45 Identities=16% Similarity=0.290 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCC--CccchHHHHHHHHHHHcCCc
Q 030865 123 RIGEELIKTCIALNITEISSYDRNG--SRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg--~~YhGrVkAladaaRe~Gl~ 167 (170)
..|+.+++.+.+.|..++.++.-.. ..-+.|...|.+++.++|+.
T Consensus 102 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~ 148 (268)
T cd01575 102 EAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLD 148 (268)
T ss_pred HHHHHHHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCC
Confidence 4455555666667888777443222 22356899999999999863
No 91
>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=31.00 E-value=1.9e+02 Score=21.78 Aligned_cols=44 Identities=14% Similarity=0.256 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCC-CccchHHHHHHHHHHHcCC
Q 030865 123 RIGEELIKTCIALNITEISSYDRNG-SRRGERMQAFEIPISRHGF 166 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg-~~YhGrVkAladaaRe~Gl 166 (170)
..|+.+++.+.+.|..++..+--.. ...+.++.+|.+++.+.|+
T Consensus 110 ~~~~~~~~~l~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~ 154 (269)
T cd01391 110 QAGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAGI 154 (269)
T ss_pred HHHHHHHHHHHHhCCceEEEEecCCcchhhHHHHHHHHHHHhcCc
Confidence 4466666666777788776443222 3346789999999999884
No 92
>COG1052 LdhA Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]
Probab=30.74 E-value=75 Score=28.33 Aligned_cols=40 Identities=18% Similarity=0.409 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCC---------CccchHHHHHHHHHHHcCCc
Q 030865 123 RIGEELIKTCIALNITEISSYDRNG---------SRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg---------~~YhGrVkAladaaRe~Gl~ 167 (170)
.+|+.+|++++..|.+-+. |||.. +.|+. +.|-+.+..++
T Consensus 156 rIG~avA~r~~~Fgm~v~y-~~~~~~~~~~~~~~~~y~~----l~ell~~sDii 204 (324)
T COG1052 156 RIGQAVARRLKGFGMKVLY-YDRSPNPEAEKELGARYVD----LDELLAESDII 204 (324)
T ss_pred HHHHHHHHHHhcCCCEEEE-ECCCCChHHHhhcCceecc----HHHHHHhCCEE
Confidence 5899999999977776666 99986 33333 66666666554
No 93
>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=30.53 E-value=1.6e+02 Score=22.56 Aligned_cols=43 Identities=19% Similarity=0.182 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCC-CCcc-chHHHHHHHHHHHcC
Q 030865 123 RIGEELIKTCIALNITEISSYDRN-GSRR-GERMQAFEIPISRHG 165 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRg-g~~Y-hGrVkAladaaRe~G 165 (170)
..|..+++.+.+.|..+|.++... .+.+ ..+...|.+++.+.|
T Consensus 104 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~ 148 (264)
T cd01537 104 QAGYLAGEHLAEKGHRRIALLAGPLGSSTARERVAGFKDALKEAG 148 (264)
T ss_pred HHHHHHHHHHHHhcCCcEEEEECCCCCCcHHHHHHHHHHHHHHcC
Confidence 577778888888888888755433 3233 468999999999887
No 94
>cd01292 metallo-dependent_hydrolases Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others.
Probab=30.29 E-value=1.3e+02 Score=23.37 Aligned_cols=50 Identities=12% Similarity=0.064 Sum_probs=37.9
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccc----hHHHHHHHHHHHc-CCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRNGSRRG----ERMQAFEIPISRH-GFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~Yh----GrVkAladaaRe~-Gl~ 167 (170)
.+.+..+...+...+.+.+.||+.|+ |.+....+ ..+.++++.+.+. |+.
T Consensus 28 ~~~~~~~~~~~~~~~~~~~~Gvttv~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (275)
T cd01292 28 LSPEDLYEDTLRALEALLAGGVTTVV--DMGSTPPPTTTKAAIEAVAEAARASAGIR 82 (275)
T ss_pred cCHHHHHHHHHHHHHHHHhcCceEEE--eeEeecCccccchHHHHHHHHHHHhcCee
Confidence 45677788889999999999999998 55533333 3688888888887 654
No 95
>cd00175 SNc Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.
Probab=30.13 E-value=2.2e+02 Score=20.72 Aligned_cols=62 Identities=8% Similarity=-0.021 Sum_probs=42.5
Q ss_pred EEEEEE-eCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCC-ccchHHHHHHHHH
Q 030865 84 LYAMLV-DDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNITEISSYDRNGS-RRGERMQAFEIPI 161 (170)
Q Consensus 84 IyAQvI-dd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~-~YhGrVkAladaa 161 (170)
|+..+. .|..|..|+.+..-+ |.-+++.+++.|.-.+. ...... .|+....+..+.|
T Consensus 61 V~i~~~~~d~~gr~la~v~~~~--------------------~~~v~~~Lv~~G~A~~~-~~~~~~~~~~~~l~~ae~~A 119 (129)
T cd00175 61 VQVEVDSKDRYGRTLGTVYLNG--------------------GENIAEELVKEGLARVY-RYYPDDSEYYDELLEAEEAA 119 (129)
T ss_pred EEEEEccCCCCCCEEEEEEeCC--------------------CCcHHHHHHhcCCEEEE-EECCCCcHHHHHHHHHHHHH
Confidence 333333 377888888774321 34567888889988887 444433 6889999999999
Q ss_pred HHcCC
Q 030865 162 SRHGF 166 (170)
Q Consensus 162 Re~Gl 166 (170)
++.++
T Consensus 120 k~~k~ 124 (129)
T cd00175 120 KKARK 124 (129)
T ss_pred HHhCc
Confidence 88754
No 96
>KOG3332 consensus N-acetylglucosaminyl phosphatidylinositol de-N-acetylase [Cell wall/membrane/envelope biogenesis]
Probab=29.35 E-value=1.3e+02 Score=26.44 Aligned_cols=45 Identities=20% Similarity=0.101 Sum_probs=32.6
Q ss_pred HHHHHHHHHHhCCCCEEEEecCCC---CccchHHHHHHHHHHHcCCcc
Q 030865 124 IGEELIKTCIALNITEISSYDRNG---SRRGERMQAFEIPISRHGFLQ 168 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDRgg---~~YhGrVkAladaaRe~Gl~~ 168 (170)
|.+.+-+.---.+|+.+++||..| +.-|=.+.+-++.+-+.+..|
T Consensus 124 v~~~l~~~ie~~~~~~iiTFD~~GVSgH~NH~~~y~av~~l~~~~k~p 171 (247)
T KOG3332|consen 124 VASILLQHIEVLNIDTIITFDNYGVSGHCNHIACYAAVDCLIDGLKLP 171 (247)
T ss_pred HHHHHHHHHHccCccEEEEecCCCcCCCCccHhhhhhHHHHhhhccCC
Confidence 444555555557899999999976 666777877777777776655
No 97
>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=29.28 E-value=1.7e+02 Score=23.38 Aligned_cols=48 Identities=21% Similarity=0.217 Sum_probs=32.0
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCC--CCcc-chHHHHHHHHHHHc-CC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRN--GSRR-GERMQAFEIPISRH-GF 166 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRg--g~~Y-hGrVkAladaaRe~-Gl 166 (170)
.+.++++.+++.|.+.+ .|..+|.++ .+ +... +.|.+.|.+++.++ |+
T Consensus 103 d~~~~g~~~~~~l~~~~--~g~~~i~~l-~~~~~~~~~~~R~~g~~~~l~~~~~~ 154 (270)
T cd06308 103 DNYEIGRQAGEYIANLL--PGKGNILEI-WGLEGSSPAIERHDGFKEALSKYPKI 154 (270)
T ss_pred CcHHHHHHHHHHHHHHc--CCCceEEEE-ECCCCCchHHHHHHHHHHHHHHCCCC
Confidence 45566666666666544 477888744 33 2222 56899999999999 76
No 98
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=29.08 E-value=1.2e+02 Score=27.99 Aligned_cols=55 Identities=15% Similarity=0.158 Sum_probs=44.8
Q ss_pred CCCcHHHHHHHHHH-----------------HHHHHHhCCCCEEEEecCCCCcc-chHHHHHHHHHHHcCCccC
Q 030865 114 PCSTIEAAERIGEE-----------------LIKTCIALNITEISSYDRNGSRR-GERMQAFEIPISRHGFLQQ 169 (170)
Q Consensus 114 s~~n~~AA~~VG~~-----------------lAkra~e~gI~~Vv~fDRgg~~Y-hGrVkAladaaRe~Gl~~~ 169 (170)
...+.++|..++++ +|-.|.+.|++++- ..=|.... ..+|..+++.+++.|+.-|
T Consensus 62 av~~~~~a~al~~I~~~~~iPlvADIHFd~~lAl~a~~~G~~~iR-INPGNig~~~~~v~~vv~~ak~~~ipIR 134 (360)
T PRK00366 62 AVPDMEAAAALPEIKKQLPVPLVADIHFDYRLALAAAEAGADALR-INPGNIGKRDERVREVVEAAKDYGIPIR 134 (360)
T ss_pred ccCCHHHHHhHHHHHHcCCCCEEEecCCCHHHHHHHHHhCCCEEE-ECCCCCCchHHHHHHHHHHHHHCCCCEE
Confidence 35678888888864 78899999999998 66665555 6799999999999998643
No 99
>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=29.08 E-value=1.6e+02 Score=23.42 Aligned_cols=47 Identities=21% Similarity=0.274 Sum_probs=29.7
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecC-CCCccchHHHHHHHHHHHcCC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDR-NGSRRGERMQAFEIPISRHGF 166 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDR-gg~~YhGrVkAladaaRe~Gl 166 (170)
.|..+++.+++.| .++|..++.++-. .....+-|...|.+++.++|+
T Consensus 104 D~~~~g~~~~~~l----~~~G~~~i~~l~~~~~~~~~~r~~g~~~~l~~~~~ 151 (273)
T cd01541 104 DDEKGGYKATEYL----IELGHRKIAGIFKADDLQGVKRMKGFIKAYREHGI 151 (273)
T ss_pred CcHHHHHHHHHHH----HHcCCcCEEEecCCCcccHHHHHHHHHHHHHHcCC
Confidence 4545555555544 5568888863322 112235689999999999986
No 100
>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=28.70 E-value=1.9e+02 Score=22.96 Aligned_cols=49 Identities=14% Similarity=0.108 Sum_probs=31.1
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCCC--Ccc-chHHHHHHHHHHHc-CCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRNG--SRR-GERMQAFEIPISRH-GFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg--~~Y-hGrVkAladaaRe~-Gl~ 167 (170)
.+.++++.+++.|++++ .|..++.++ .+. +.. .-|.++|.+++.++ |+.
T Consensus 104 d~~~~~~~~~~~l~~~~--~g~~~i~~i-~~~~~~~~~~~r~~gf~~a~~~~~~~~ 156 (273)
T cd06310 104 DNVAAGKLAAEALAELL--GKKGKVAVI-SFVPGSSTTDQREEGFLEGLKEYPGIE 156 (273)
T ss_pred ChHHHHHHHHHHHHHHc--CCCceEEEE-eCCCCCccHHHHHHHHHHHHHhCCCcE
Confidence 35556666666666553 377888834 332 211 35889999999998 863
No 101
>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=28.54 E-value=1.9e+02 Score=23.14 Aligned_cols=42 Identities=19% Similarity=0.199 Sum_probs=29.3
Q ss_pred HHHHHHHHHhCCCCEEEEecCCCC-------ccchHHHHHHHHHHHcCC
Q 030865 125 GEELIKTCIALNITEISSYDRNGS-------RRGERMQAFEIPISRHGF 166 (170)
Q Consensus 125 G~~lAkra~e~gI~~Vv~fDRgg~-------~YhGrVkAladaaRe~Gl 166 (170)
|..+++.+.+.|..++.++--... ..+.|...|.+++.++|+
T Consensus 100 ~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~ 148 (270)
T cd01544 100 VEKALDYLLELGHTRIGFIGGEEKTTDGHEYIEDPRETAFREYMKEKGL 148 (270)
T ss_pred HHHHHHHHHHcCCCcEEEECCCcccccccchhhhHHHHHHHHHHHHcCC
Confidence 555566666689998874532211 236689999999999995
No 102
>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=28.39 E-value=68 Score=25.33 Aligned_cols=25 Identities=28% Similarity=0.555 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCCC
Q 030865 123 RIGEELIKTCIALNITEISSYDRNGS 148 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg~ 148 (170)
.+|+.+|++++..|. +|++|||...
T Consensus 46 ~IG~~vA~~l~~fG~-~V~~~d~~~~ 70 (178)
T PF02826_consen 46 RIGRAVARRLKAFGM-RVIGYDRSPK 70 (178)
T ss_dssp HHHHHHHHHHHHTT--EEEEEESSCH
T ss_pred CCcCeEeeeeecCCc-eeEEecccCC
Confidence 589999999999999 4555999754
No 103
>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=27.85 E-value=2.1e+02 Score=22.81 Aligned_cols=50 Identities=12% Similarity=0.023 Sum_probs=30.1
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEe-cCCCCc-cchHHHHHHHHHHHcC-Cc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSY-DRNGSR-RGERMQAFEIPISRHG-FL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~f-DRgg~~-YhGrVkAladaaRe~G-l~ 167 (170)
.+..+++..++.|.+++ .|..++.++ ...... ...|.+.|.+++.++| +.
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 45556555555555443 266766633 111222 2478999999999988 53
No 104
>cd07367 CarBb CarBb is the B subunit of the Class III Extradiol ring-cleavage dioxygenase, 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBb is the B subunit of 2-aminophenol 1,6-dioxygenase (CarB), which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. It is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, it has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=27.76 E-value=2.8e+02 Score=23.78 Aligned_cols=79 Identities=9% Similarity=0.126 Sum_probs=45.4
Q ss_pred HHHHHHHhcCCCCCCeEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHhCCCC
Q 030865 59 NRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIALNIT 138 (170)
Q Consensus 59 ~~RiRkki~gt~~rPRL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e~gI~ 138 (170)
-.+++..+.. .+|...|..|+.|....-.+....-++.+..+.. ++..... +....+....+++.|++.+.+.||+
T Consensus 31 l~~~~~~l~~--~~Pd~ivvis~dH~~~~~~~~~p~~~i~~~~~~~-~~~~~g~-p~~~~~gd~~LA~~i~~~l~~~g~~ 106 (268)
T cd07367 31 MAEIGRRVRE--SRPDVLVVISSDHLFNINLSLQPPFVVGTADSYT-PFGDMDI-PRELFPGHREFARAFVRQAAEDGFD 106 (268)
T ss_pred HHHHHHHHHH--cCCCEEEEEeCchhhhcccccCCceEEeeccccc-cCCcCCC-CcccCCCCHHHHHHHHHHHHHcCCC
Confidence 3556666653 5799999999989644433333333332222222 2221111 1122344556888889999999997
Q ss_pred EEE
Q 030865 139 EIS 141 (170)
Q Consensus 139 ~Vv 141 (170)
-+.
T Consensus 107 ~~~ 109 (268)
T cd07367 107 LAQ 109 (268)
T ss_pred eee
Confidence 665
No 105
>PRK12744 short chain dehydrogenase; Provisional
Probab=27.63 E-value=1.6e+02 Score=23.55 Aligned_cols=40 Identities=8% Similarity=0.112 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHH
Q 030865 123 RIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISR 163 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe 163 (170)
-+|..+|+.+.+.|.+-++ .++.........+.+++.+..
T Consensus 19 gIG~~~a~~l~~~G~~vv~-i~~~~~~~~~~~~~~~~~l~~ 58 (257)
T PRK12744 19 NLGGLIARDLAAQGAKAVA-IHYNSAASKADAEETVAAVKA 58 (257)
T ss_pred hHHHHHHHHHHHCCCcEEE-EecCCccchHHHHHHHHHHHH
Confidence 4888888888888887566 665443334455555555443
No 106
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=27.52 E-value=27 Score=20.33 Aligned_cols=10 Identities=50% Similarity=1.135 Sum_probs=8.2
Q ss_pred ccccccCCCC
Q 030865 13 NACDFFGTKA 22 (170)
Q Consensus 13 ~~~~~~~~~~ 22 (170)
.+|+|||+..
T Consensus 7 ~~CgF~G~~~ 16 (26)
T smart00259 7 PGCGFFGNPA 16 (26)
T ss_pred CCCCCcCChh
Confidence 5899999863
No 107
>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=27.48 E-value=1.1e+02 Score=22.87 Aligned_cols=42 Identities=10% Similarity=0.122 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 120 AAERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 120 AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
........+.+.|.++|+..|+ |=-| ..-..+.+.++++|+.
T Consensus 63 ~~~~~~~~~v~~~~~~g~~~v~-~~~g-----~~~~~~~~~a~~~gi~ 104 (116)
T PF13380_consen 63 VPPDKVPEIVDEAAALGVKAVW-LQPG-----AESEELIEAAREAGIR 104 (116)
T ss_dssp S-HHHHHHHHHHHHHHT-SEEE-E-TT-----S--HHHHHHHHHTT-E
T ss_pred cCHHHHHHHHHHHHHcCCCEEE-EEcc-----hHHHHHHHHHHHcCCE
Confidence 3344455567888899999999 6655 6778889999999985
No 108
>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=27.36 E-value=2e+02 Score=19.32 Aligned_cols=44 Identities=18% Similarity=0.167 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCCCcc----chHHHHHHHHHHHcCCc
Q 030865 123 RIGEELIKTCIALNITEISSYDRNGSRR----GERMQAFEIPISRHGFL 167 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg~~Y----hGrVkAladaaRe~Gl~ 167 (170)
.+|-.+|.-+.+.|.+-.+ ++|+.... .---+.+.+.+++.|+-
T Consensus 9 ~ig~E~A~~l~~~g~~vtl-i~~~~~~~~~~~~~~~~~~~~~l~~~gV~ 56 (80)
T PF00070_consen 9 FIGIELAEALAELGKEVTL-IERSDRLLPGFDPDAAKILEEYLRKRGVE 56 (80)
T ss_dssp HHHHHHHHHHHHTTSEEEE-EESSSSSSTTSSHHHHHHHHHHHHHTTEE
T ss_pred HHHHHHHHHHHHhCcEEEE-EeccchhhhhcCHHHHHHHHHHHHHCCCE
Confidence 3567777777888876656 99987554 22356667888888874
No 109
>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=27.30 E-value=2.1e+02 Score=19.58 Aligned_cols=61 Identities=23% Similarity=0.331 Sum_probs=34.9
Q ss_pred HHHHhcCCCCCC--eEEEEecCC--eEEEEEEeCCCCeEEEEEechhhhhccCCCCCCCcHHHHHHHHHHHHHHHHh
Q 030865 62 IQKKFNGTPTKP--RLSVFCSDK--QLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIEAAERIGEELIKTCIA 134 (170)
Q Consensus 62 iRkki~gt~~rP--RL~V~kSNk--hIyAQvIdd~~gktLasaST~ek~ik~~l~~s~~n~~AA~~VG~~lAkra~e 134 (170)
+-+.+.|.=.-| -...+..+. ++.+.+.++++.+.+..++-. ++.+.+..+|+.+|+.+++
T Consensus 10 fl~~l~ggC~~Piga~a~~~~~~~l~l~~~v~~~dG~~~~~~~~~~------------~~~~~a~~lg~~la~~l~~ 74 (74)
T PF03900_consen 10 FLKELGGGCHSPIGAYAKIEGDERLRLRAMVGSPDGSRIIIRVEIT------------GPIEDAEELGKKLAEELLA 74 (74)
T ss_dssp HHHHCT--TTSSEEEEEEEETTE-EEEEEEEE-TTSSSEEEEEEEE------------E-GGGHCCHHHHHHHHHHH
T ss_pred HHHHhCCCCCCceeeEEEEcCCCEEEEEEEEECCCCCEEEEEEEEE------------cCHHHHHHHHHHHHHHHhC
Confidence 445566654556 466666666 667777776665523333211 2456777889998888764
No 110
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=26.93 E-value=18 Score=27.19 Aligned_cols=24 Identities=17% Similarity=0.073 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHhCCCCEEE
Q 030865 118 IEAAERIGEELIKTCIALNITEIS 141 (170)
Q Consensus 118 ~~AA~~VG~~lAkra~e~gI~~Vv 141 (170)
+..-.=||+.+++++.++|+++..
T Consensus 21 V~~laGIG~~lg~~L~~~GfdKAy 44 (89)
T PF02961_consen 21 VTELAGIGPVLGKRLEEKGFDKAY 44 (89)
T ss_dssp GGGSTT--HHHHHHHHHTT--BHH
T ss_pred ccccCCcCHHHHHHHHHCCCcHHH
Confidence 334445999999999999988753
No 111
>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=26.74 E-value=2.1e+02 Score=22.76 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=30.4
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEe-cCCC-CccchHHHHHHHHHHHc-CC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSY-DRNG-SRRGERMQAFEIPISRH-GF 166 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~f-DRgg-~~YhGrVkAladaaRe~-Gl 166 (170)
.+.++++.+++.|.++. .|-.++.++ .... ..-..|.++|.+.+.++ |+
T Consensus 103 d~~~~g~~~~~~l~~~~--~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~ 154 (275)
T cd06320 103 DNKANGVRGAEWIIDKL--AEGGKVAIIEGKAGAFAAEQRTEGFTEAIKKASGI 154 (275)
T ss_pred CcHHHHHHHHHHHHHHh--CCCceEEEEeCCCCCccHHHHHHHHHHHHhhCCCc
Confidence 45566666666666553 256666633 2222 22256899999999998 86
No 112
>PRK08085 gluconate 5-dehydrogenase; Provisional
Probab=26.66 E-value=1.5e+02 Score=23.61 Aligned_cols=38 Identities=18% Similarity=0.111 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHc
Q 030865 122 ERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRH 164 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~ 164 (170)
.-+|..+++++.+.|.+-++ .||+. .+...+++.+++.
T Consensus 19 ~giG~~ia~~L~~~G~~vvl-~~r~~----~~~~~~~~~l~~~ 56 (254)
T PRK08085 19 QGIGFLLATGLAEYGAEIII-NDITA----ERAELAVAKLRQE 56 (254)
T ss_pred ChHHHHHHHHHHHcCCEEEE-EcCCH----HHHHHHHHHHHhc
Confidence 46899999999999976555 88862 3444555555443
No 113
>PRK08452 flagellar protein FlaG; Provisional
Probab=26.41 E-value=2.6e+02 Score=21.87 Aligned_cols=36 Identities=14% Similarity=0.135 Sum_probs=27.7
Q ss_pred HHHHhcCCCCCCeEEEEecCCeEEEEEEeCCCCeEE
Q 030865 62 IQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCL 97 (170)
Q Consensus 62 iRkki~gt~~rPRL~V~kSNkhIyAQvIdd~~gktL 97 (170)
+-+.+......-+..+......+|++|+|..+|+++
T Consensus 62 lN~~~~~~~~~L~F~~de~~~~~vVkVvD~~T~eVI 97 (124)
T PRK08452 62 LNEEMKRLDTNIRFGYNDKIKGLVVSVKEANGGKVI 97 (124)
T ss_pred HHHHHHhhCCceEEEEcCCCCcEEEEEEECCCCcee
Confidence 333344344567889999999999999999999996
No 114
>PRK07523 gluconate 5-dehydrogenase; Provisional
Probab=26.23 E-value=1.6e+02 Score=23.60 Aligned_cols=39 Identities=15% Similarity=0.164 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHc
Q 030865 121 AERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRH 164 (170)
Q Consensus 121 A~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~ 164 (170)
+.-+|..+++++.+.|.+=++ +||+. .+.+++.+.+++.
T Consensus 19 ~g~iG~~ia~~l~~~G~~V~~-~~r~~----~~~~~~~~~i~~~ 57 (255)
T PRK07523 19 SQGIGYALAEGLAQAGAEVIL-NGRDP----AKLAAAAESLKGQ 57 (255)
T ss_pred cchHHHHHHHHHHHcCCEEEE-EeCCH----HHHHHHHHHHHhc
Confidence 346899999999999986444 88873 2344455555443
No 115
>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=26.16 E-value=2.2e+02 Score=22.27 Aligned_cols=44 Identities=11% Similarity=0.254 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhCCCCEEEEecC-CCCc-cchHHHHHHHHHHHcCC
Q 030865 123 RIGEELIKTCIALNITEISSYDR-NGSR-RGERMQAFEIPISRHGF 166 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDR-gg~~-YhGrVkAladaaRe~Gl 166 (170)
..|+.+++.+.+.|..++..+.- .... .+.|...|.+++.+.|+
T Consensus 101 ~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~~~~~~~ 146 (267)
T cd06284 101 AAARLAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAEAGL 146 (267)
T ss_pred HHHHHHHHHHHHcCCceEEEEcCCccchhHHHHHHHHHHHHHHcCC
Confidence 33444555555678888884432 2222 35699999999999985
No 116
>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=26.01 E-value=2.5e+02 Score=22.06 Aligned_cols=47 Identities=17% Similarity=0.097 Sum_probs=30.6
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEec-CCC-Cc-cchHHHHHHHHHHHcCC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYD-RNG-SR-RGERMQAFEIPISRHGF 166 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fD-Rgg-~~-YhGrVkAladaaRe~Gl 166 (170)
.|.++++. +++.+.+.|..++.++- ..+ .. -+.|.+.|.+.+.++|+
T Consensus 99 d~~~~~~~----~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~gf~~~~~~~~~ 148 (268)
T cd06298 99 DYKKAAFE----ATELLIKNGHKKIAFISGPLEDSINGDERLAGYKEALSEANI 148 (268)
T ss_pred CcHHHHHH----HHHHHHHcCCceEEEEeCCcccccchhHHHHHHHHHHHHcCC
Confidence 34455554 45555557888888553 222 22 35799999999999985
No 117
>PRK06114 short chain dehydrogenase; Provisional
Probab=25.96 E-value=1.7e+02 Score=23.55 Aligned_cols=38 Identities=11% Similarity=0.090 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHc
Q 030865 123 RIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRH 164 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~ 164 (170)
-+|..+|+++.+.|.+-++ .||+.. .....+++.+.+.
T Consensus 19 gIG~~ia~~l~~~G~~v~~-~~r~~~---~~~~~~~~~l~~~ 56 (254)
T PRK06114 19 GIGQRIAIGLAQAGADVAL-FDLRTD---DGLAETAEHIEAA 56 (254)
T ss_pred hHHHHHHHHHHHCCCEEEE-EeCCcc---hHHHHHHHHHHhc
Confidence 5899999999999986666 898642 2344445544443
No 118
>PRK08868 flagellar protein FlaG; Provisional
Probab=25.79 E-value=2.6e+02 Score=22.65 Aligned_cols=38 Identities=3% Similarity=-0.011 Sum_probs=30.2
Q ss_pred HHHHHHhcCCCCCCeEEEEecCCeEEEEEEeCCCCeEE
Q 030865 60 RRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCL 97 (170)
Q Consensus 60 ~RiRkki~gt~~rPRL~V~kSNkhIyAQvIdd~~gktL 97 (170)
.++.+.+......-+..|......++++|||..+|.+|
T Consensus 78 eklNe~~~~~n~~L~F~vdeetgr~VVkViD~~T~EVI 115 (144)
T PRK08868 78 EQMNEFVKSINKGLSFRVDEESGRDVVTIYEASTGDII 115 (144)
T ss_pred HHHHHHHHhhcCceEEEEecCCCCEEEEEEECCCCcee
Confidence 44445555445667999999999999999999999986
No 119
>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=25.75 E-value=2e+02 Score=23.81 Aligned_cols=46 Identities=9% Similarity=0.215 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEecCCCCcc-chHHHHHHHHHHHcCCc
Q 030865 121 AERIGEELIKTCIALNITEISSYDRNGSRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 121 A~~VG~~lAkra~e~gI~~Vv~fDRgg~~Y-hGrVkAladaaRe~Gl~ 167 (170)
....+..+++.+++.|.++|..+ ...+.| ..+.++|.+.+.+.|+-
T Consensus 120 ~~~~~~~~~~~l~~~g~~~v~~l-~~~~~~~~~~~~~~~~~~~~~G~~ 166 (336)
T cd06326 120 YADEIAAIVRHLVTLGLKRIAVF-YQDDAFGKDGLAGVEKALAARGLK 166 (336)
T ss_pred hHHHHHHHHHHHHHhCCceEEEE-EecCcchHHHHHHHHHHHHHcCCC
Confidence 34456677777888899998744 333344 47899999999999963
No 120
>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=25.64 E-value=1.3e+02 Score=25.16 Aligned_cols=29 Identities=21% Similarity=0.264 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHhCCCCEEEEecCCCCc
Q 030865 119 EAAERIGEELIKTCIALNITEISSYDRNGSR 149 (170)
Q Consensus 119 ~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~ 149 (170)
-.-..||+.|++.+.+.||.-+. |+.-+.
T Consensus 30 ~~V~~VG~~L~~~Le~~Gi~vih--d~t~~~ 58 (196)
T TIGR02867 30 GNITKVGDRLAKELEEKGIGVIH--DKTVHD 58 (196)
T ss_pred CcHHHHHHHHHHHHHHCCCeEEE--eCCccC
Confidence 35678999999999999998766 887433
No 121
>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=25.57 E-value=39 Score=27.83 Aligned_cols=20 Identities=20% Similarity=0.463 Sum_probs=16.8
Q ss_pred HhCCCCEEEEecCCCCccchH
Q 030865 133 IALNITEISSYDRNGSRRGER 153 (170)
Q Consensus 133 ~e~gI~~Vv~fDRgg~~YhGr 153 (170)
...|+++|. |--||.+|||-
T Consensus 163 sgigvdevt-yasggdryhgg 182 (206)
T PF06370_consen 163 SGIGVDEVT-YASGGDRYHGG 182 (206)
T ss_pred cCccceeEE-eccCCccccCC
Confidence 346789999 99999999983
No 122
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=24.87 E-value=2e+02 Score=25.09 Aligned_cols=44 Identities=16% Similarity=0.184 Sum_probs=33.9
Q ss_pred HHHHHHHHHHhCCCCEEEEecCCC---CccchHHHHHHHHHHHcCCcc
Q 030865 124 IGEELIKTCIALNITEISSYDRNG---SRRGERMQAFEIPISRHGFLQ 168 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDRgg---~~YhGrVkAladaaRe~Gl~~ 168 (170)
-|+.+++.+.++|..++. |=-++ .....|...|.+++.++|+.+
T Consensus 162 ~~~~a~~~L~~~G~~~i~-~i~~~~~~~~~~~R~~Gf~~al~~~~~~~ 208 (333)
T COG1609 162 GAYLATEHLIELGHRRIA-FIGGPLDSSASRERLEGYRAALREAGLPI 208 (333)
T ss_pred HHHHHHHHHHHCCCceEE-EEeCCCccccHhHHHHHHHHHHHHCCCCC
Confidence 355667778889999888 54443 345789999999999999863
No 123
>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=24.40 E-value=2.6e+02 Score=22.11 Aligned_cols=49 Identities=12% Similarity=0.104 Sum_probs=30.9
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCCC--CccchHHHHHHHHHHHc-CCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRNG--SRRGERMQAFEIPISRH-GFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg--~~YhGrVkAladaaRe~-Gl~ 167 (170)
.+.++++..++.|+++. .|..++.++- +. ..-..|.++|.+++.++ |+.
T Consensus 102 d~~~~g~~~~~~l~~~~--~g~~~i~~i~-~~~~~~~~~R~~gf~~~~~~~~~~~ 153 (267)
T cd06322 102 DNYAGGVLAGELAAKVL--NGKGQVAIID-YPTVQSVVDRVRGFKEALADYPNIK 153 (267)
T ss_pred ChHHHHHHHHHHHHHHh--CCCceEEEEe-cCCCccHHHHHHHHHHHHHhCCCcE
Confidence 35556666666666653 3667777442 21 11235899999999998 874
No 124
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=24.32 E-value=2.8e+02 Score=23.71 Aligned_cols=52 Identities=13% Similarity=0.056 Sum_probs=36.1
Q ss_pred CcHHHHHHHHHHHHHHHHh-CCCCEEEEec-CCCCcc-chHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIA-LNITEISSYD-RNGSRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e-~gI~~Vv~fD-Rgg~~Y-hGrVkAladaaRe~Gl~ 167 (170)
.|.++++..++.|++.... .|..++.++- ..+... ..|++.|.+++++.|+.
T Consensus 150 D~~~~g~~aa~~L~~~~~~~~g~~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~~i~ 204 (343)
T PRK10936 150 SWYQMGYQAGRYLAQWHPKGSKPLNVALLPGPEGAGGSKAVEQGFRAAIAGSDVR 204 (343)
T ss_pred ChHHHHHHHHHHHHHHHHhcCCCceEEEEECCCCCchHHHHHHHHHHHHhcCCCE
Confidence 5778888888888887643 3567776442 222333 36899999999999873
No 125
>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=24.27 E-value=2.9e+02 Score=20.52 Aligned_cols=25 Identities=4% Similarity=-0.045 Sum_probs=20.5
Q ss_pred ecCCCCccchHHHHHHHHHHHcCCc
Q 030865 143 YDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 143 fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
..--....+|.|-.+.|.++++|+.
T Consensus 98 i~aD~~~~~~~vv~vmd~~~~~G~~ 122 (129)
T TIGR02801 98 IRADKTVPYGEVIKVMALLKQAGIE 122 (129)
T ss_pred EEcCCCCCHHHHHHHHHHHHHcCCC
Confidence 4444468999999999999999984
No 126
>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=24.25 E-value=2.5e+02 Score=22.45 Aligned_cols=49 Identities=16% Similarity=0.144 Sum_probs=32.0
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEec-CCCCccchHHHHHHHHHHHcCC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYD-RNGSRRGERMQAFEIPISRHGF 166 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fD-Rgg~~YhGrVkAladaaRe~Gl 166 (170)
.|.++.+..++.|++++. |-.+|.++- .....-+-|++.|.+.+.++|+
T Consensus 108 d~~~~g~~aa~~l~~~~~--g~~~i~~~~g~~~~~~~~R~~gf~~~l~~~~~ 157 (274)
T cd06311 108 DNYGMGRVAGEYIATKLG--GNGNIVVLRGIPTPIDNERVDAFDAAIAKYPI 157 (274)
T ss_pred CcHHHHHHHHHHHHHHhC--CCCeEEEEECCCCcchhHHHHHHHHHHhhCCc
Confidence 566677777777766542 555666452 1113335789999999999985
No 127
>PRK05867 short chain dehydrogenase; Provisional
Probab=23.70 E-value=1.9e+02 Score=23.13 Aligned_cols=37 Identities=11% Similarity=0.130 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHH
Q 030865 122 ERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISR 163 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe 163 (170)
.-+|..+++++.+.|.+-++ .||+. .+.+.+++.+.+
T Consensus 19 ~gIG~~ia~~l~~~G~~V~~-~~r~~----~~~~~~~~~l~~ 55 (253)
T PRK05867 19 TGIGKRVALAYVEAGAQVAI-AARHL----DALEKLADEIGT 55 (253)
T ss_pred chHHHHHHHHHHHCCCEEEE-EcCCH----HHHHHHHHHHHh
Confidence 35788888888888876555 77752 344555555444
No 128
>PF00106 adh_short: short chain dehydrogenase alcohol dehydrogenase superfamily signature glucose/ribitol dehydrogenase family signature; InterPro: IPR002198 The short-chain dehydrogenases/reductases family (SDR) [] is a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases. As the first member of this family to be characterised was Drosophila alcohol dehydrogenase, this family used to be called [, , ] 'insect-type', or 'short-chain' alcohol dehydrogenases. Most member of this family are proteins of about 250 to 300 amino acid residues. Most dehydrogenases possess at least 2 domains [], the first binding the coenzyme, often NAD, and the second binding the substrate. This latter domain determines the substrate specificity and contains amino acids involved in catalysis. Little sequence similarity has been found in the coenzyme binding domain although there is a large degree of structural similarity, and it has therefore been suggested that the structure of dehydrogenases has arisen through gene fusion of a common ancestral coenzyme nucleotide sequence with various substrate specific domains [].; GO: 0016491 oxidoreductase activity, 0008152 metabolic process; PDB: 3QWI_D 3QWF_G 3IS3_A 3QWH_C 3ITD_A 3L77_A 1HDC_C 2HSD_C 3KVO_A 3KZV_A ....
Probab=23.59 E-value=2.5e+02 Score=20.62 Aligned_cols=42 Identities=17% Similarity=0.179 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcC
Q 030865 122 ERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHG 165 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~G 165 (170)
.-+|+.+++...+.|-..|+..+|+ .--.....+++.+.+.|
T Consensus 10 ~giG~~~a~~l~~~g~~~v~~~~r~--~~~~~~~~l~~~l~~~~ 51 (167)
T PF00106_consen 10 SGIGRALARALARRGARVVILTSRS--EDSEGAQELIQELKAPG 51 (167)
T ss_dssp SHHHHHHHHHHHHTTTEEEEEEESS--CHHHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHhcCceEEEEeeec--ccccccccccccccccc
Confidence 4589999999999988777756776 33455666666666544
No 129
>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=23.22 E-value=2.9e+02 Score=21.61 Aligned_cols=47 Identities=17% Similarity=0.199 Sum_probs=29.4
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEec-CCCCcc-chHHHHHHHHHHHcCC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYD-RNGSRR-GERMQAFEIPISRHGF 166 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fD-Rgg~~Y-hGrVkAladaaRe~Gl 166 (170)
.+.++++.++ +.+.+.|..+|.++- ..+..+ .-|...|.+.+.+.|+
T Consensus 98 d~~~~g~~~~----~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~ 146 (266)
T cd06278 98 DNYEAGRLAA----ELLLAKGCRRIAFIGGPADTSTSRERERGFRDALAAAGV 146 (266)
T ss_pred ChHHHHHHHH----HHHHHCCCceEEEEcCCCcccchHHHHHHHHHHHHHcCC
Confidence 4555555554 444556888888442 212222 3588999999999886
No 130
>cd06313 PBP1_ABC_sugar_binding_like_5 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=23.00 E-value=2.7e+02 Score=22.51 Aligned_cols=47 Identities=13% Similarity=0.099 Sum_probs=30.3
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCCC--C-ccchHHHHHHHHHHHcC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRNG--S-RRGERMQAFEIPISRHG 165 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg--~-~YhGrVkAladaaRe~G 165 (170)
.+.++.+..++.|.+++ .|..+|.++ .+. . .-..|...|.+++.++|
T Consensus 104 d~~~~g~~~~~~l~~~~--~g~~~i~~l-~g~~~~~~~~~R~~gf~~~~~~~~ 153 (272)
T cd06313 104 DNYFMGASVAQALCNAM--GGKGKIAML-QGALGHTGAQGRAQGFNDVIKKYP 153 (272)
T ss_pred CcHHHHHHHHHHHHHHc--CCCceEEEE-ECCCCCcchhHHHHHHHHHHHhCC
Confidence 45666666666666653 277777744 222 1 12468999999999886
No 131
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=22.89 E-value=1.4e+02 Score=25.39 Aligned_cols=34 Identities=18% Similarity=0.254 Sum_probs=25.6
Q ss_pred HHHHHhCCCCEEEEecCCCCccchH---HHHHHHHHHHcC
Q 030865 129 IKTCIALNITEISSYDRNGSRRGER---MQAFEIPISRHG 165 (170)
Q Consensus 129 Akra~e~gI~~Vv~fDRgg~~YhGr---VkAladaaRe~G 165 (170)
.+||.+.||..++ ||+..|. +| =.++++.+++.+
T Consensus 43 lerA~~~gIpt~~-~~~k~~~--~r~~~d~~l~~~l~~~~ 79 (200)
T COG0299 43 LERAAKAGIPTVV-LDRKEFP--SREAFDRALVEALDEYG 79 (200)
T ss_pred HHHHHHcCCCEEE-eccccCC--CHHHHHHHHHHHHHhcC
Confidence 5789999999999 9998654 43 356677776655
No 132
>PRK07792 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=22.44 E-value=2e+02 Score=24.30 Aligned_cols=40 Identities=15% Similarity=0.047 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHcC
Q 030865 122 ERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRHG 165 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~G 165 (170)
.-+|..+|+.+.+.|..-++ .|++. ...++.+++.+++.|
T Consensus 22 ~gIG~~ia~~L~~~Ga~Vv~-~~~~~---~~~~~~~~~~i~~~g 61 (306)
T PRK07792 22 AGLGRAEALGLARLGATVVV-NDVAS---ALDASDVLDEIRAAG 61 (306)
T ss_pred ChHHHHHHHHHHHCCCEEEE-ecCCc---hhHHHHHHHHHHhcC
Confidence 35889999999999986555 78752 234556666665544
No 133
>PRK08217 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=22.43 E-value=2.1e+02 Score=22.39 Aligned_cols=24 Identities=13% Similarity=0.097 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHhCCCCEEEEecCC
Q 030865 122 ERIGEELIKTCIALNITEISSYDRN 146 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fDRg 146 (170)
.-+|..+++.+.+.|..-++ +||.
T Consensus 15 g~iG~~~a~~l~~~G~~vi~-~~r~ 38 (253)
T PRK08217 15 QGLGRAMAEYLAQKGAKLAL-IDLN 38 (253)
T ss_pred chHHHHHHHHHHHCCCEEEE-EeCC
Confidence 45899999999999976445 8886
No 134
>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=22.10 E-value=1.8e+02 Score=26.23 Aligned_cols=40 Identities=10% Similarity=0.116 Sum_probs=29.4
Q ss_pred HHHHHHHhCCCCEEEEecCCCCcc-chHHHHHHHHHHHcCCc
Q 030865 127 ELIKTCIALNITEISSYDRNGSRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 127 ~lAkra~e~gI~~Vv~fDRgg~~Y-hGrVkAladaaRe~Gl~ 167 (170)
.|.+-+.+.||+.|+ +|+..-.| ..+-..+++.+.+.|+.
T Consensus 87 vl~~L~~~~~~~~V~-~~~~~~~~~~~rd~~v~~~l~~~~i~ 127 (429)
T TIGR02765 87 VLPELIKELGVRTVF-LHQEVGSEEKSVERLLQQALARLGIH 127 (429)
T ss_pred HHHHHHHHhCCCEEE-EeccCCHHHHHHHHHHHHHHHhcCce
Confidence 445556677999999 99984333 23488899999888875
No 135
>COG5611 Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]
Probab=22.09 E-value=58 Score=25.93 Aligned_cols=23 Identities=13% Similarity=0.281 Sum_probs=19.0
Q ss_pred HHHHHHHHHHhCCCCEEEEecCC
Q 030865 124 IGEELIKTCIALNITEISSYDRN 146 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDRg 146 (170)
.-.+++...+.+||+++++||+-
T Consensus 97 ~D~li~~~g~~~g~~e~vTFdk~ 119 (130)
T COG5611 97 LDCLISVKGKKMGIKEVVTFDKR 119 (130)
T ss_pred HHHHHHhhhhhcCceeeEeecHH
Confidence 34567788888999999999986
No 136
>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=22.08 E-value=2.5e+02 Score=21.14 Aligned_cols=34 Identities=24% Similarity=0.282 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHH
Q 030865 124 IGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPI 161 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaa 161 (170)
.|+.++..+.+.|+++|..++|+ ..|.++|++.+
T Consensus 23 ~ar~v~~~L~~~g~~~i~i~nRt----~~ra~~l~~~~ 56 (135)
T PF01488_consen 23 AARAVAAALAALGAKEITIVNRT----PERAEALAEEF 56 (135)
T ss_dssp HHHHHHHHHHHTTSSEEEEEESS----HHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCEEEEEECC----HHHHHHHHHHc
Confidence 56777888888899988889986 46788888877
No 137
>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=22.08 E-value=2.8e+02 Score=21.95 Aligned_cols=44 Identities=14% Similarity=0.046 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhCCCCEEEEecCCCC--ccchHHHHHHHHHHHcCCc
Q 030865 124 IGEELIKTCIALNITEISSYDRNGS--RRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 124 VG~~lAkra~e~gI~~Vv~fDRgg~--~YhGrVkAladaaRe~Gl~ 167 (170)
.|+.+++.+.+.|-.+|.++.-... ...-|.+.|.+++.++|+.
T Consensus 105 ~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 150 (268)
T cd06277 105 GAYAATEYLIEKGHRKIGFVGDPLYSPSFEERYEGYKKALLDHGIP 150 (268)
T ss_pred HHHHHHHHHHHCCCCcEEEECCCCCCcchHHHHHHHHHHHHHcCCC
Confidence 4555566667779888885632111 2235889999999999874
No 138
>PLN02293 adenine phosphoribosyltransferase
Probab=22.05 E-value=2.2e+02 Score=23.23 Aligned_cols=36 Identities=11% Similarity=0.123 Sum_probs=31.4
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCCCCccc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRNGSRRG 151 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg~~Yh 151 (170)
.+-+....++..|+++..+.+++.|+..|.+|....
T Consensus 42 ~~p~~~~~~~~~l~~~~~~~~~d~Ivg~e~~Gi~lA 77 (187)
T PLN02293 42 LDPKAFKDTIDLFVERYRDMGISVVAGIEARGFIFG 77 (187)
T ss_pred hCHHHHHHHHHHHHHHHhhcCCCEEEEeCCCchHHH
Confidence 467889999999999999999999998888887655
No 139
>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=22.01 E-value=2.7e+02 Score=21.96 Aligned_cols=49 Identities=22% Similarity=0.189 Sum_probs=30.1
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecC-CCC-ccchHHHHHHHHHHHcCC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDR-NGS-RRGERMQAFEIPISRHGF 166 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDR-gg~-~YhGrVkAladaaRe~Gl 166 (170)
.|.++++.+++.+++.+ .|-.+|.++-- ..+ ....|+++|.+++.++|.
T Consensus 106 d~~~~g~~~~~~l~~~~--~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~ 156 (275)
T cd06317 106 DDISQGERSAEAMCKAL--GGKGQIVVIAGQPGNGTAIERQKGFEDELAEVCP 156 (275)
T ss_pred cHHHHHHHHHHHHHHHc--CCCceEEEEecCCCCchHHHHHHHHHHHHHhhCC
Confidence 34556666666665543 26667774421 122 234789999999999974
No 140
>PRK07791 short chain dehydrogenase; Provisional
Probab=21.81 E-value=2.2e+02 Score=23.70 Aligned_cols=43 Identities=21% Similarity=0.099 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCEEEEecCCCC-----ccchHHHHHHHHHHHcC
Q 030865 122 ERIGEELIKTCIALNITEISSYDRNGS-----RRGERMQAFEIPISRHG 165 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fDRgg~-----~YhGrVkAladaaRe~G 165 (170)
.-+|..+|+++.+.|.+-++ .||+.. .-......+++.+++.|
T Consensus 16 ~GIG~aia~~la~~G~~vii-~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 63 (286)
T PRK07791 16 GGIGRAHALAFAAEGARVVV-NDIGVGLDGSASGGSAAQAVVDEIVAAG 63 (286)
T ss_pred chHHHHHHHHHHHCCCEEEE-eeCCccccccccchhHHHHHHHHHHhcC
Confidence 46899999999999987666 887631 11245666666665544
No 141
>PF14540 NTF-like: Nucleotidyltransferase-like; PDB: 3C18_A.
Probab=21.69 E-value=39 Score=26.35 Aligned_cols=25 Identities=24% Similarity=0.313 Sum_probs=15.3
Q ss_pred CEEEEecCCCCcc--chHHHHHHHHHHH
Q 030865 138 TEISSYDRNGSRR--GERMQAFEIPISR 163 (170)
Q Consensus 138 ~~Vv~fDRgg~~Y--hGrVkAladaaRe 163 (170)
.+|+ |||+.|.. .-++..|-+..|+
T Consensus 93 G~Il-fDRneyl~~Lr~~l~~FP~~~R~ 119 (119)
T PF14540_consen 93 GKIL-FDRNEYLHNLRQRLLEFPEEERE 119 (119)
T ss_dssp SEEE-EESTTHHHHHHHHTT---HHHH-
T ss_pred CEEE-EehhHHHHHHHHHHHHcChhhcC
Confidence 4899 99998764 5666666666654
No 142
>COG3894 Uncharacterized metal-binding protein [General function prediction only]
Probab=21.33 E-value=98 Score=30.31 Aligned_cols=63 Identities=19% Similarity=0.125 Sum_probs=43.5
Q ss_pred eEEEEecCCeEEEEEEeCCCCeEEEEEechhhhhccC--C---------C---CCCCcHHHHHHHHHHHHHHHHhCC
Q 030865 74 RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGN--G---------N---PPCSTIEAAERIGEELIKTCIALN 136 (170)
Q Consensus 74 RL~V~kSNkhIyAQvIdd~~gktLasaST~ek~ik~~--l---------~---~s~~n~~AA~~VG~~lAkra~e~g 136 (170)
=+.+=--...|-||+||-.+|+++.++.|....+... + . ...-.+++-+.+-.+|++-|-|.+
T Consensus 166 GvAvDlGTS~i~aqlVDL~sgevv~t~~T~n~ql~~Ge~m~sr~~~i~~~~D~a~~l~~~vVe~i~~~id~~~~e~~ 242 (614)
T COG3894 166 GVAVDLGTSGIRAQLVDLKSGEVVATVITSNPQLPGGEVMDSRDFAIMMGPDGAEGLQIAVVEAINQLIDKLCEEGE 242 (614)
T ss_pred eeEEecccceeeeEEEeccCCcEEEeeeccCCCCCCchhhHHHHHHHHhCcchhhhhHHHHHHHHHHHHhhhchhcc
Confidence 3444455667899999999999999999988766541 0 0 112334566667777777777766
No 143
>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=21.18 E-value=3.1e+02 Score=21.62 Aligned_cols=47 Identities=11% Similarity=0.187 Sum_probs=30.6
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEecCCC--Ccc-chHHHHHHHHHHHcCCc
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYDRNG--SRR-GERMQAFEIPISRHGFL 167 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fDRgg--~~Y-hGrVkAladaaRe~Gl~ 167 (170)
.+.++++.+++. +.++|..+|.++ .+. ... ..|.+.|.+.+.+.|+.
T Consensus 98 d~~~a~~~~~~~----l~~~g~~~i~~i-~~~~~~~~~~~r~~gf~~~~~~~~~~ 147 (265)
T cd06290 98 DNFQGGYLATQH----LIDLGHRRIAHI-TGPRGHIDARDRLAGYRKALEEAGLE 147 (265)
T ss_pred CcHHHHHHHHHH----HHHCCCCeEEEE-eCccccchhhHHHHHHHHHHHHcCCC
Confidence 455666655554 555688888844 221 222 36899999999998863
No 144
>PRK08703 short chain dehydrogenase; Provisional
Probab=20.99 E-value=2.2e+02 Score=22.47 Aligned_cols=37 Identities=22% Similarity=0.258 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHHc
Q 030865 123 RIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISRH 164 (170)
Q Consensus 123 ~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe~ 164 (170)
-+|..+++.+.+.|..-++ .||+. .+..++.+.+++.
T Consensus 17 giG~~la~~l~~~g~~V~~-~~r~~----~~~~~~~~~l~~~ 53 (239)
T PRK08703 17 GLGEQVAKAYAAAGATVIL-VARHQ----KKLEKVYDAIVEA 53 (239)
T ss_pred cHHHHHHHHHHHcCCEEEE-EeCCh----HHHHHHHHHHHHc
Confidence 5888999999999986555 89874 2445555555443
No 145
>PRK12738 kbaY tagatose-bisphosphate aldolase; Reviewed
Probab=20.76 E-value=2.3e+02 Score=25.07 Aligned_cols=41 Identities=7% Similarity=-0.069 Sum_probs=32.6
Q ss_pred HHHHHHHHhCCCCEEEEecCCCCccch---HHHHHHHHHHHcCCc
Q 030865 126 EELIKTCIALNITEISSYDRNGSRRGE---RMQAFEIPISRHGFL 167 (170)
Q Consensus 126 ~~lAkra~e~gI~~Vv~fDRgg~~YhG---rVkAladaaRe~Gl~ 167 (170)
....++|++.|.+.|. ||-....|.. ..+.+.+-+...|+.
T Consensus 87 ~e~i~~ai~~GFtSVM-~DgS~lp~eeNi~~T~evv~~Ah~~gv~ 130 (286)
T PRK12738 87 LDDIRRKVHAGVRSAM-IDGSHFPFAENVKLVKSVVDFCHSQDCS 130 (286)
T ss_pred HHHHHHHHHcCCCeEe-ecCCCCCHHHHHHHHHHHHHHHHHcCCe
Confidence 4567889999999999 9999888875 456677777777764
No 146
>PRK06124 gluconate 5-dehydrogenase; Provisional
Probab=20.65 E-value=2.2e+02 Score=22.62 Aligned_cols=38 Identities=16% Similarity=0.213 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEecCCCCccchHHHHHHHHHHH
Q 030865 121 AERIGEELIKTCIALNITEISSYDRNGSRRGERMQAFEIPISR 163 (170)
Q Consensus 121 A~~VG~~lAkra~e~gI~~Vv~fDRgg~~YhGrVkAladaaRe 163 (170)
..-+|..+++.+.+.|..=+. +||+. ....++++.+++
T Consensus 20 s~~IG~~la~~l~~~G~~v~~-~~r~~----~~~~~~~~~~~~ 57 (256)
T PRK06124 20 ARGLGFEIARALAGAGAHVLV-NGRNA----ATLEAAVAALRA 57 (256)
T ss_pred CchHHHHHHHHHHHcCCeEEE-EeCCH----HHHHHHHHHHHh
Confidence 345788888888888875444 88863 334444444443
No 147
>PF00156 Pribosyltran: Phosphoribosyl transferase domain; InterPro: IPR000836 The name PRT comes from phosphoribosyltransferase (PRTase) enzymes, which carry out phosphoryl transfer reactions on 5-phosphoribosyl-alpha1-pyrophosphate PRPP, an activated form of ribose-5-phosphate. Members of Phosphoribosyltransferase (PRT) are catalytic and are regulatory proteins involved in nucleotide synthesis and salvage []. This includes a range of diverse phosphoribosyl transferase enzymes including adenine phosphoribosyltransferase (2.4.2.7 from EC); hypoxanthine-guanine-xanthine phosphoribosyltransferase; hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC); ribose-phosphate pyrophosphokinase (2.7.6.1 from EC); amidophosphoribosyltransferase (2.4.2.14 from EC); orotate phosphoribosyltransferase (2.4.2.10 from EC);uracil phosphoribosyltransferase (2.4.2.9 from EC); and xanthine-guanine phosphoribosyltransferase (2.4.2.22 from EC). Not all PRT proteins are enzymes. For example, in some bacteria PRT proteins regulate the expression of purine and pyrimidine synthetic genes. Members of PRT are defined by the protein fold and by a short 13-residue sequence motif, The motif consists of four hydrophobic amino acids, two acidic amino acids and seven amino acids of variable character, usually including glycine and threonine. The motif has been predicted to be a PRPP-binding site in advance of structural information [, ]. Apart of this motif, different PRT proteins have a low level of sequence identity, less than 15%. The PRT sequence motif is only found in PRTases from the nucleotide synthesis and salvage pathways. Other PRTases, from the tryptophan, histidine and nicotinamide synthetic and salvage pathways, lack the PRT sequence motif and appear to be unrelated to each other and unrelated to the PRT family.; GO: 0009116 nucleoside metabolic process; PDB: 2JBH_A 1Y0B_D 2FXV_B 1GPH_1 1AO0_D 1ORO_B 1VCH_C 2WNS_A 2PRZ_B 2PS1_A ....
Probab=20.52 E-value=1.8e+02 Score=20.67 Aligned_cols=34 Identities=21% Similarity=0.171 Sum_probs=28.3
Q ss_pred cHHHHHHHHHHHHHHHHhCCCCE--EEEecCCCCcc
Q 030865 117 TIEAAERIGEELIKTCIALNITE--ISSYDRNGSRR 150 (170)
Q Consensus 117 n~~AA~~VG~~lAkra~e~gI~~--Vv~fDRgg~~Y 150 (170)
+-+....+++.+|++..+.+.+. ++..++||..+
T Consensus 6 ~~~~~~~~~~~la~~i~~~~~~~~~ivgi~~~G~~~ 41 (125)
T PF00156_consen 6 SPEQIEALAERLAEQIKESGFDFDVIVGIPRGGIPL 41 (125)
T ss_dssp BHHHHHHHHHHHHHHHHHHTTTSSEEEEETTTTHHH
T ss_pred cHHHHHHHHHHHHHHHHHhCCCCCEEEeehhccHHH
Confidence 55678889999999999998876 88899988653
No 148
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=20.33 E-value=1.3e+02 Score=23.08 Aligned_cols=49 Identities=14% Similarity=0.224 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEe--cC--------CCCccchHHHHHHHHHHHcCCccCC
Q 030865 121 AERIGEELIKTCIALNITEISSY--DR--------NGSRRGERMQAFEIPISRHGFLQQR 170 (170)
Q Consensus 121 A~~VG~~lAkra~e~gI~~Vv~f--DR--------gg~~YhGrVkAladaaRe~Gl~~~~ 170 (170)
+-.|-..+.-+|.+.|.+.|. . +. |.+....||+.+-+.|.+.||-|.|
T Consensus 37 ~Grv~~~~il~Af~~GADGV~-V~gC~~g~Ch~~~Gn~~a~~Rv~~~k~~L~~~Gi~~eR 95 (124)
T PF02662_consen 37 SGRVDPEFILRAFEKGADGVL-VAGCHPGDCHYREGNYRAEKRVERLKKLLEELGIEPER 95 (124)
T ss_pred CCccCHHHHHHHHHcCCCEEE-EeCCCCCCCCcchhhHHHHHHHHHHHHHHHHcCCChhH
Confidence 334556778889999999888 4 22 2233467899999999999998765
No 149
>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=20.25 E-value=2.3e+02 Score=22.71 Aligned_cols=48 Identities=15% Similarity=0.104 Sum_probs=31.5
Q ss_pred CCcHHHHHHHHHHHHHHHHhCCCCEEEEe--cCCCC------ccchHHHHHHHHHHHcCCc
Q 030865 115 CSTIEAAERIGEELIKTCIALNITEISSY--DRNGS------RRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 115 ~~n~~AA~~VG~~lAkra~e~gI~~Vv~f--DRgg~------~YhGrVkAladaaRe~Gl~ 167 (170)
..|.++++..++.|.++ ..++.++ +-+.. .-+.|.+.|.+++.++|+-
T Consensus 96 ~d~~~~g~~a~~~L~~~-----~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~~~~~~~g~~ 151 (269)
T cd06297 96 LDNRLGGRLAGAYLADF-----PGRIGAITVEEEPDRAFRRTVFAERRAGFQQALKDAGRP 151 (269)
T ss_pred ECcHHHHHHHHHHHHHh-----CCceEEEeCccccccccccccHHHHHHHHHHHHHHcCCC
Confidence 35777877777777776 3344422 21112 2357999999999999974
No 150
>PRK06198 short chain dehydrogenase; Provisional
Probab=20.23 E-value=2.9e+02 Score=21.95 Aligned_cols=25 Identities=12% Similarity=0.256 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHhCCCCEEEEecCC
Q 030865 122 ERIGEELIKTCIALNITEISSYDRN 146 (170)
Q Consensus 122 ~~VG~~lAkra~e~gI~~Vv~fDRg 146 (170)
.-+|..+++++.+.|...|+.+||.
T Consensus 16 g~iG~~la~~l~~~G~~~V~~~~r~ 40 (260)
T PRK06198 16 QGLGAAIARAFAERGAAGLVICGRN 40 (260)
T ss_pred chHHHHHHHHHHHCCCCeEEEEcCC
Confidence 3588999999999998856558886
No 151
>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=20.18 E-value=3.2e+02 Score=22.07 Aligned_cols=47 Identities=17% Similarity=0.205 Sum_probs=29.0
Q ss_pred CcHHHHHHHHHHHHHHHHhCCCCEEEEec-CC-----------------CCcc-chHHHHHHHHHHHcCC
Q 030865 116 STIEAAERIGEELIKTCIALNITEISSYD-RN-----------------GSRR-GERMQAFEIPISRHGF 166 (170)
Q Consensus 116 ~n~~AA~~VG~~lAkra~e~gI~~Vv~fD-Rg-----------------g~~Y-hGrVkAladaaRe~Gl 166 (170)
.+.++++.. ++.+.++|..++.++. .. ++.. ..|...|.+++.++|+
T Consensus 99 d~~~~g~~~----~~~L~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~ 164 (283)
T cd06279 99 DDRAAAREA----ARHLLDLGHRRIGILGLRLGRDRNTGRVTDERLASATFSVARERLEGYLEALEEAGI 164 (283)
T ss_pred CcHHHHHHH----HHHHHHcCCCcEEEecCcccccccccccccccccccccccHHHHHHHHHHHHHHcCC
Confidence 344555554 4445557888877442 11 1122 4689999999999985
No 152
>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=20.03 E-value=99 Score=20.50 Aligned_cols=40 Identities=10% Similarity=0.259 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCC--CCEEEEecCCCCccchHHHHHHHHHHHcCCc
Q 030865 125 GEELIKTCIALN--ITEISSYDRNGSRRGERMQAFEIPISRHGFL 167 (170)
Q Consensus 125 G~~lAkra~e~g--I~~Vv~fDRgg~~YhGrVkAladaaRe~Gl~ 167 (170)
|.-+...|++.| |.++. ++.+ ..+.++..+.+.+.+.|+.
T Consensus 4 G~~~V~eaL~~~~~i~~l~-~~~~--~~~~~~~~i~~~~~~~~i~ 45 (76)
T PF08032_consen 4 GRHAVEEALKSGPRIKKLF-VTEE--KADKRIKEILKLAKKKGIP 45 (76)
T ss_dssp SHHHHHHHHHCTGGEEEEE-EETT-----CCTHHHHHHHHHCT-E
T ss_pred EHHHHHHHHcCCCCccEEE-EEcC--ccchhHHHHHHHHHHcCCe
Confidence 445566677766 77887 7776 4555577777777777753
Done!