Query 018389
Match_columns 357
No_of_seqs 160 out of 1032
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 08:36:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018389.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018389hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00139 rpl18 ribosomal prote 100.0 1.2E-35 2.6E-40 248.5 12.9 101 237-339 9-109 (109)
2 PTZ00032 60S ribosomal protein 100.0 2E-34 4.3E-39 264.1 15.2 96 243-339 104-211 (211)
3 TIGR00060 L18_bact ribosomal p 100.0 1.4E-34 3E-39 244.4 12.7 96 238-339 19-114 (114)
4 PRK05593 rplR 50S ribosomal pr 100.0 1.1E-33 2.4E-38 239.0 12.4 98 239-339 20-117 (117)
5 cd00432 Ribosomal_L18_L5e Ribo 100.0 1.7E-31 3.7E-36 217.3 13.1 96 241-337 8-103 (103)
6 PF00861 Ribosomal_L18p: Ribos 100.0 5.1E-31 1.1E-35 221.4 13.2 95 244-339 23-119 (119)
7 COG0256 RplR Ribosomal protein 100.0 4.3E-31 9.3E-36 226.7 11.9 99 239-339 25-125 (125)
8 PRK08569 rpl18p 50S ribosomal 99.9 1.5E-27 3.2E-32 217.2 11.9 98 242-341 31-132 (193)
9 KOG3333 Mitochondrial/chloropl 99.8 1.1E-18 2.5E-23 156.4 9.7 94 246-340 62-155 (188)
10 PTZ00069 60S ribosomal protein 98.3 2.3E-06 5E-11 83.4 8.2 95 245-340 49-175 (300)
11 PF00411 Ribosomal_S11: Riboso 96.7 0.024 5.3E-07 47.7 10.9 87 247-339 3-89 (110)
12 PTZ00090 40S ribosomal protein 96.7 0.032 6.9E-07 53.4 12.3 97 238-342 113-211 (233)
13 TIGR03632 bact_S11 30S ribosom 96.3 0.058 1.3E-06 45.5 10.6 88 247-340 3-90 (108)
14 CHL00041 rps11 ribosomal prote 96.2 0.069 1.5E-06 45.7 10.6 89 246-340 15-103 (116)
15 PRK05309 30S ribosomal protein 95.7 0.17 3.6E-06 44.2 10.9 89 246-340 19-107 (128)
16 TIGR03628 arch_S11P archaeal r 92.2 2.7 5.8E-05 36.5 11.0 91 247-341 5-102 (114)
17 PRK09607 rps11p 30S ribosomal 91.8 2.9 6.2E-05 37.2 11.0 92 246-341 11-109 (132)
18 PTZ00129 40S ribosomal protein 90.0 4.5 9.7E-05 36.8 10.7 93 246-341 30-128 (149)
19 COG0100 RpsK Ribosomal protein 86.1 6.9 0.00015 34.9 9.2 84 250-340 24-108 (129)
20 KOG0408 Mitochondrial/chloropl 77.6 31 0.00067 32.6 10.4 96 240-341 75-170 (190)
21 KOG0875 60S ribosomal protein 64.4 6.2 0.00013 38.9 3.0 64 244-307 48-114 (264)
22 COG1472 BglX Beta-glucosidase- 60.1 17 0.00037 37.0 5.4 56 283-338 89-162 (397)
23 TIGR00612 ispG_gcpE 1-hydroxy- 56.1 37 0.0008 34.8 6.9 54 287-341 56-126 (346)
24 cd07039 TPP_PYR_POX Pyrimidine 51.6 32 0.00069 30.3 5.0 42 295-342 2-44 (164)
25 PF01120 Alpha_L_fucos: Alpha- 51.0 40 0.00086 33.2 6.1 49 297-345 94-160 (346)
26 PF00875 DNA_photolyase: DNA p 50.5 38 0.00082 29.1 5.2 47 295-341 76-122 (165)
27 cd06288 PBP1_sucrose_transcrip 49.1 40 0.00086 29.5 5.2 45 296-340 104-150 (269)
28 cd04906 ACT_ThrD-I_1 First of 48.1 46 0.00099 26.2 5.0 46 294-341 14-71 (85)
29 TIGR01917 gly_red_sel_B glycin 47.9 58 0.0013 34.3 7.0 53 286-339 315-367 (431)
30 PF02776 TPP_enzyme_N: Thiamin 46.9 50 0.0011 28.7 5.5 42 295-342 3-45 (172)
31 COG1611 Predicted Rossmann fol 46.7 30 0.00065 32.3 4.3 39 289-337 33-71 (205)
32 smart00812 Alpha_L_fucos Alpha 46.4 37 0.00081 34.4 5.3 50 296-345 83-150 (384)
33 PF13377 Peripla_BP_3: Peripla 45.6 43 0.00094 27.2 4.7 44 300-343 1-46 (160)
34 PRK09492 treR trehalose repres 45.1 51 0.0011 30.1 5.5 45 297-341 164-211 (315)
35 PF13727 CoA_binding_3: CoA-bi 44.3 48 0.001 27.4 4.8 42 298-341 132-173 (175)
36 PRK07449 2-succinyl-5-enolpyru 43.9 66 0.0014 33.2 6.7 45 293-343 9-54 (568)
37 PF03646 FlaG: FlaG protein; 43.8 37 0.00081 27.8 4.0 36 234-269 46-81 (107)
38 PF00933 Glyco_hydro_3: Glycos 43.1 55 0.0012 31.3 5.6 57 285-342 80-154 (299)
39 PRK10423 transcriptional repre 42.9 49 0.0011 30.3 5.1 44 296-339 162-207 (327)
40 PRK14459 ribosomal RNA large s 42.1 2E+02 0.0042 29.6 9.6 82 252-334 106-204 (373)
41 PRK14467 ribosomal RNA large s 42.0 1.4E+02 0.003 30.1 8.5 86 252-338 84-180 (348)
42 PRK07710 acetolactate synthase 41.6 50 0.0011 34.3 5.5 44 293-342 16-59 (571)
43 TIGR01918 various_sel_PB selen 41.6 82 0.0018 33.3 6.9 53 286-339 315-367 (431)
44 cd06280 PBP1_LacI_like_4 Ligan 40.6 74 0.0016 28.0 5.7 45 295-340 102-148 (263)
45 cd01543 PBP1_XylR Ligand-bindi 39.5 87 0.0019 27.7 6.0 45 295-339 96-141 (265)
46 cd06275 PBP1_PurR Ligand-bindi 38.3 84 0.0018 27.5 5.6 46 295-340 104-151 (269)
47 PRK13398 3-deoxy-7-phosphohept 37.2 61 0.0013 31.4 5.0 52 288-343 39-98 (266)
48 PF14419 SPOUT_MTase_2: AF2226 37.0 98 0.0021 29.1 6.0 52 283-335 7-58 (173)
49 cd06286 PBP1_CcpB_like Ligand- 36.9 87 0.0019 27.4 5.5 44 296-339 102-147 (260)
50 PRK00366 ispG 4-hydroxy-3-meth 36.9 72 0.0016 32.9 5.6 55 287-342 64-136 (360)
51 COG0684 MenG Demethylmenaquino 36.7 80 0.0017 30.2 5.5 89 230-340 35-123 (210)
52 cd06296 PBP1_CatR_like Ligand- 36.1 87 0.0019 27.5 5.4 45 296-340 105-151 (270)
53 KOG0407 40S ribosomal protein 36.0 1.8E+02 0.004 26.1 7.3 89 248-339 20-114 (139)
54 PRK04302 triosephosphate isome 35.8 1E+02 0.0022 28.3 6.0 48 295-342 73-120 (223)
55 PF01408 GFO_IDH_MocA: Oxidore 35.6 1E+02 0.0022 24.4 5.3 42 298-341 77-118 (120)
56 smart00481 POLIIIAc DNA polyme 34.3 1.8E+02 0.0039 21.4 6.1 42 297-341 18-59 (67)
57 PF02878 PGM_PMM_I: Phosphoglu 34.3 2.1E+02 0.0046 24.1 7.2 53 287-341 18-73 (137)
58 cd06267 PBP1_LacI_sugar_bindin 33.9 97 0.0021 26.4 5.2 44 296-339 104-149 (264)
59 PRK07523 gluconate 5-dehydroge 33.6 87 0.0019 27.8 5.0 42 292-338 19-60 (255)
60 PF06414 Zeta_toxin: Zeta toxi 33.5 1.6E+02 0.0035 26.1 6.7 51 290-343 76-126 (199)
61 PF02065 Melibiase: Melibiase; 33.4 1E+02 0.0023 31.5 6.2 45 299-344 63-125 (394)
62 TIGR00725 conserved hypothetic 33.4 87 0.0019 27.9 5.0 41 288-338 16-56 (159)
63 PRK11579 putative oxidoreducta 33.3 1.1E+02 0.0024 29.5 6.0 33 299-335 107-140 (346)
64 COG1908 FrhD Coenzyme F420-red 32.8 86 0.0019 28.4 4.8 43 295-338 41-93 (132)
65 TIGR02766 crypt_chrom_pln cryp 32.7 1.1E+02 0.0024 31.2 6.2 46 295-341 75-121 (475)
66 TIGR02571 ComEB ComE operon pr 32.6 84 0.0018 28.1 4.7 36 300-340 101-136 (151)
67 cd06319 PBP1_ABC_sugar_binding 31.8 1.7E+02 0.0036 25.8 6.4 54 287-340 102-159 (277)
68 PF08032 SpoU_sub_bind: RNA 2' 31.7 69 0.0015 23.9 3.5 44 296-342 4-49 (76)
69 cd06270 PBP1_GalS_like Ligand 31.5 1.2E+02 0.0026 26.7 5.5 44 296-339 104-149 (268)
70 PF13671 AAA_33: AAA domain; P 31.4 2.8E+02 0.006 22.4 7.3 45 295-342 58-102 (143)
71 PF00070 Pyr_redox: Pyridine n 30.8 2.4E+02 0.0051 21.3 6.5 48 294-342 9-60 (80)
72 PRK10727 DNA-binding transcrip 30.3 96 0.0021 28.9 4.9 44 296-339 164-209 (343)
73 cd06295 PBP1_CelR Ligand bindi 29.9 1.4E+02 0.0031 26.4 5.7 45 295-339 112-158 (275)
74 PRK14466 ribosomal RNA large s 29.9 71 0.0015 32.4 4.3 53 288-342 264-320 (345)
75 cd06284 PBP1_LacI_like_6 Ligan 29.6 1.1E+02 0.0024 26.5 4.9 46 295-340 102-149 (267)
76 PRK10014 DNA-binding transcrip 29.5 1.3E+02 0.0028 27.8 5.6 48 288-339 166-215 (342)
77 PRK12738 kbaY tagatose-bisphos 29.3 1.5E+02 0.0033 29.3 6.3 45 299-344 89-136 (286)
78 TIGR03457 sulphoacet_xsc sulfo 29.3 93 0.002 32.4 5.1 44 294-343 3-46 (579)
79 PRK06194 hypothetical protein; 29.2 1.2E+02 0.0025 27.5 5.2 43 291-338 14-56 (287)
80 PRK09542 manB phosphomannomuta 29.0 2.7E+02 0.0059 28.3 8.2 61 279-341 6-68 (445)
81 PF00532 Peripla_BP_1: Peripla 29.0 1.8E+02 0.0039 27.2 6.5 47 295-341 105-154 (279)
82 cd01545 PBP1_SalR Ligand-bindi 29.0 1.4E+02 0.0031 26.0 5.6 45 295-339 105-151 (270)
83 PF14488 DUF4434: Domain of un 28.6 1.4E+02 0.0031 26.8 5.5 43 300-343 26-85 (166)
84 cd06290 PBP1_LacI_like_9 Ligan 28.3 1.5E+02 0.0031 26.1 5.5 48 288-339 99-148 (265)
85 PF14871 GHL6: Hypothetical gl 28.2 1.5E+02 0.0033 25.8 5.5 48 297-344 3-65 (132)
86 COG0673 MviM Predicted dehydro 28.0 1.3E+02 0.0028 28.0 5.4 34 298-335 109-143 (342)
87 PRK10703 DNA-binding transcrip 28.0 1.4E+02 0.0029 27.8 5.5 45 296-340 166-212 (341)
88 cd01391 Periplasmic_Binding_Pr 27.9 2.2E+02 0.0047 23.7 6.2 45 295-340 111-157 (269)
89 TIGR00730 conserved hypothetic 27.8 1E+02 0.0022 28.1 4.6 43 288-339 17-59 (178)
90 PF13380 CoA_binding_2: CoA bi 27.7 1E+02 0.0022 25.8 4.3 41 292-339 65-105 (116)
91 PF07071 DUF1341: Protein of u 27.6 1.5E+02 0.0033 28.8 5.8 39 301-339 142-180 (218)
92 PF02789 Peptidase_M17_N: Cyto 27.6 2.6E+02 0.0056 22.5 6.4 52 288-339 67-119 (126)
93 cd06285 PBP1_LacI_like_7 Ligan 27.3 1.5E+02 0.0032 26.1 5.3 48 288-339 98-147 (265)
94 COG1893 ApbA Ketopantoate redu 27.3 93 0.002 30.4 4.4 43 291-343 7-49 (307)
95 PRK06048 acetolactate synthase 27.3 1.2E+02 0.0026 31.5 5.4 45 293-343 8-52 (561)
96 cd01540 PBP1_arabinose_binding 27.2 1.6E+02 0.0035 26.2 5.7 53 287-339 106-163 (289)
97 PRK06124 gluconate 5-dehydroge 27.1 1.2E+02 0.0025 26.9 4.7 42 291-337 19-60 (256)
98 cd01284 Riboflavin_deaminase-r 27.0 3.4E+02 0.0073 23.1 7.3 76 253-336 18-115 (115)
99 cd06278 PBP1_LacI_like_2 Ligan 26.8 1.8E+02 0.004 25.2 5.8 48 288-339 99-148 (266)
100 cd01575 PBP1_GntR Ligand-bindi 26.6 1.7E+02 0.0036 25.5 5.5 46 294-339 102-149 (268)
101 cd06276 PBP1_FucR_like Ligand- 26.5 1.6E+02 0.0035 26.5 5.5 46 295-340 102-150 (247)
102 PRK10860 tRNA-specific adenosi 26.3 2.2E+02 0.0048 25.9 6.4 78 256-338 35-132 (172)
103 TIGR03556 photolyase_8HDF deox 26.2 1.6E+02 0.0034 30.4 6.0 45 297-341 80-124 (471)
104 cd06282 PBP1_GntR_like_2 Ligan 26.1 1.6E+02 0.0035 25.5 5.3 46 294-339 102-150 (266)
105 PRK12744 short chain dehydroge 26.0 2.1E+02 0.0045 25.5 6.1 45 292-337 17-61 (257)
106 PRK09124 pyruvate dehydrogenas 25.7 1.2E+02 0.0026 31.6 5.1 44 293-342 3-47 (574)
107 PRK11303 DNA-binding transcrip 25.5 1.7E+02 0.0037 26.9 5.6 46 296-341 167-214 (328)
108 cd06291 PBP1_Qymf_like Ligand 25.4 1.7E+02 0.0037 25.7 5.4 46 295-340 99-147 (265)
109 TIGR02417 fruct_sucro_rep D-fr 25.3 1.6E+02 0.0035 27.1 5.4 44 296-339 166-211 (327)
110 PRK14456 ribosomal RNA large s 25.3 3.5E+02 0.0075 27.6 8.1 84 252-336 106-203 (368)
111 cd06274 PBP1_FruR Ligand bindi 25.1 1.7E+02 0.0037 25.7 5.3 49 288-340 100-150 (264)
112 PF06792 UPF0261: Uncharacteri 25.0 1.6E+02 0.0035 30.8 5.8 48 287-335 312-370 (403)
113 PRK08266 hypothetical protein; 24.8 1.3E+02 0.0027 31.0 5.1 44 294-343 5-50 (542)
114 PRK12737 gatY tagatose-bisphos 24.8 2E+02 0.0044 28.3 6.3 45 299-344 89-136 (284)
115 PRK06466 acetolactate synthase 24.7 1.2E+02 0.0027 31.5 5.0 44 294-343 5-49 (574)
116 cd04726 KGPDC_HPS 3-Keto-L-gul 24.7 2.3E+02 0.0051 24.8 6.1 42 298-342 68-109 (202)
117 PRK08085 gluconate 5-dehydroge 24.3 1.5E+02 0.0033 26.3 4.9 41 292-337 18-58 (254)
118 PRK08617 acetolactate synthase 24.1 1.4E+02 0.0031 30.8 5.3 44 294-343 6-49 (552)
119 TIGR01858 tag_bisphos_ald clas 24.0 2.2E+02 0.0048 28.1 6.3 44 300-344 88-134 (282)
120 PF13546 DDE_5: DDE superfamil 24.0 1.9E+02 0.0041 26.8 5.7 48 293-345 169-218 (273)
121 cd06292 PBP1_LacI_like_10 Liga 24.0 2.1E+02 0.0045 25.3 5.6 48 288-339 106-155 (273)
122 TIGR02765 crypto_DASH cryptoch 23.9 1.8E+02 0.004 29.1 5.9 44 297-340 86-129 (429)
123 PRK08277 D-mannonate oxidoredu 23.9 1.6E+02 0.0034 26.6 5.0 41 292-337 19-59 (278)
124 cd06271 PBP1_AglR_RafR_like Li 23.7 2.1E+02 0.0045 24.9 5.5 44 296-339 108-153 (268)
125 PF02826 2-Hacid_dh_C: D-isome 23.6 91 0.002 27.5 3.3 27 291-318 43-69 (178)
126 PRK08979 acetolactate synthase 23.5 1.6E+02 0.0035 30.7 5.6 43 294-342 5-48 (572)
127 PRK08217 fabG 3-ketoacyl-(acyl 23.4 2.2E+02 0.0047 24.8 5.6 40 292-336 14-53 (253)
128 PRK06457 pyruvate dehydrogenas 23.4 1.6E+02 0.0035 30.5 5.5 44 294-343 3-46 (549)
129 PRK15395 methyl-galactoside AB 23.4 2.8E+02 0.006 26.3 6.7 55 287-341 133-197 (330)
130 PRK07524 hypothetical protein; 23.3 1.5E+02 0.0033 30.4 5.3 43 294-342 3-45 (535)
131 PF00106 adh_short: short chai 23.3 2.1E+02 0.0045 23.5 5.2 49 291-341 8-56 (167)
132 PRK11041 DNA-binding transcrip 23.3 2E+02 0.0043 26.0 5.5 49 288-340 136-186 (309)
133 PRK06882 acetolactate synthase 23.2 1.6E+02 0.0035 30.5 5.5 44 294-343 5-49 (574)
134 cd06299 PBP1_LacI_like_13 Liga 23.1 2E+02 0.0044 25.1 5.4 45 296-340 104-150 (265)
135 PRK05835 fructose-bisphosphate 23.1 2.3E+02 0.005 28.5 6.3 44 300-344 90-136 (307)
136 TIGR02415 23BDH acetoin reduct 23.0 2.4E+02 0.0051 24.8 5.8 43 291-338 8-50 (254)
137 cd01574 PBP1_LacI Ligand-bindi 23.0 2.8E+02 0.006 24.3 6.2 46 296-341 104-151 (264)
138 PRK06725 acetolactate synthase 22.9 1.5E+02 0.0032 31.1 5.2 45 293-343 15-59 (570)
139 PF04551 GcpE: GcpE protein; 22.8 1.8E+02 0.0039 30.1 5.6 55 287-343 53-138 (359)
140 COG3669 Alpha-L-fucosidase [Ca 22.7 1.7E+02 0.0038 30.9 5.6 46 298-344 58-122 (430)
141 PLN00125 Succinyl-CoA ligase [ 22.7 1.7E+02 0.0036 29.1 5.3 45 292-339 79-124 (300)
142 TIGR02826 RNR_activ_nrdG3 anae 22.6 2.1E+02 0.0046 25.2 5.4 35 306-342 60-94 (147)
143 PLN02470 acetolactate synthase 22.6 1.4E+02 0.0031 31.1 5.0 44 293-342 13-57 (585)
144 PRK08611 pyruvate oxidase; Pro 22.6 1.6E+02 0.0035 30.8 5.4 43 294-342 5-49 (576)
145 PHA02588 cd deoxycytidylate de 22.5 1.2E+02 0.0026 27.5 4.0 38 300-341 115-152 (168)
146 PRK12827 short chain dehydroge 22.5 1.9E+02 0.0041 25.1 5.0 46 291-337 14-59 (249)
147 cd06283 PBP1_RegR_EndR_KdgR_li 22.4 2E+02 0.0043 25.0 5.2 45 295-339 103-150 (267)
148 cd06272 PBP1_hexuronate_repres 22.4 2.1E+02 0.0047 25.0 5.4 43 296-338 99-143 (261)
149 PF08357 SEFIR: SEFIR domain; 22.3 1.1E+02 0.0024 25.7 3.4 53 290-343 12-67 (150)
150 TIGR02867 spore_II_P stage II 22.3 2.6E+02 0.0057 26.2 6.2 51 291-343 31-89 (196)
151 PF11349 DUF3151: Protein of u 22.2 55 0.0012 29.5 1.7 35 296-337 39-75 (129)
152 COG0299 PurN Folate-dependent 22.1 1.7E+02 0.0037 28.1 5.0 42 300-342 43-85 (200)
153 PRK12826 3-ketoacyl-(acyl-carr 22.0 1.7E+02 0.0037 25.4 4.7 44 291-339 14-57 (251)
154 cd06293 PBP1_LacI_like_11 Liga 22.0 1.9E+02 0.0042 25.5 5.1 49 288-340 100-150 (269)
155 PRK07709 fructose-bisphosphate 21.7 2.7E+02 0.0058 27.5 6.4 44 301-345 94-140 (285)
156 PRK08610 fructose-bisphosphate 21.6 2.7E+02 0.0058 27.6 6.4 43 301-344 94-139 (286)
157 PRK13813 orotidine 5'-phosphat 21.6 4.1E+02 0.0089 23.8 7.2 45 296-343 69-113 (215)
158 COG4947 Uncharacterized protei 21.4 1.2E+02 0.0025 29.4 3.7 36 305-340 24-63 (227)
159 PRK09195 gatY tagatose-bisphos 21.4 2.7E+02 0.0058 27.5 6.3 45 299-344 89-136 (284)
160 cd01537 PBP1_Repressors_Sugar_ 21.1 2.5E+02 0.0055 23.8 5.4 43 294-336 104-148 (264)
161 cd06273 PBP1_GntR_like_1 This 21.1 2E+02 0.0044 25.1 5.0 46 294-339 102-150 (268)
162 PRK06546 pyruvate dehydrogenas 21.0 1.3E+02 0.0029 31.5 4.4 44 293-342 3-47 (578)
163 PRK10206 putative oxidoreducta 20.5 2.5E+02 0.0055 27.4 6.0 34 298-334 106-139 (344)
164 COG0821 gcpE 1-hydroxy-2-methy 20.4 1.8E+02 0.004 30.2 5.1 54 287-341 58-128 (361)
165 PRK07814 short chain dehydroge 20.4 2.5E+02 0.0055 25.2 5.6 41 293-338 20-60 (263)
166 PF02811 PHP: PHP domain; Int 20.4 2.2E+02 0.0047 23.6 4.8 42 299-343 21-62 (175)
167 PRK10887 glmM phosphoglucosami 20.4 3.8E+02 0.0083 27.1 7.4 50 288-341 19-72 (443)
168 TIGR00048 radical SAM enzyme, 20.3 7.4E+02 0.016 24.9 9.3 85 252-337 90-187 (355)
169 cd00947 TBP_aldolase_IIB Tagat 20.2 2.9E+02 0.0062 27.2 6.3 44 300-344 85-131 (276)
170 cd06326 PBP1_STKc_like Type I 20.2 2.6E+02 0.0055 25.7 5.6 46 295-340 123-168 (336)
171 cd06320 PBP1_allose_binding Pe 20.1 4E+02 0.0087 23.6 6.7 53 287-341 103-158 (275)
172 PRK13396 3-deoxy-7-phosphohept 20.0 1.8E+02 0.0039 29.7 5.0 46 298-343 119-172 (352)
173 PRK07454 short chain dehydroge 20.0 1.9E+02 0.004 25.4 4.5 38 292-334 15-52 (241)
No 1
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=100.00 E-value=1.2e-35 Score=248.53 Aligned_cols=101 Identities=26% Similarity=0.446 Sum_probs=97.2
Q ss_pred ccCCCCCCeEEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCC
Q 018389 237 LTAPYHEPFCLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPR 316 (357)
Q Consensus 237 rTd~Y~rPfRL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR 316 (357)
.++...+| ||+||+||+|||||||||.+|+||+||||.|++++..+.+++|++||..||++||+||+++||++|+|| |
T Consensus 9 i~g~~~rp-RL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~~gi~~vvfD-r 86 (109)
T CHL00139 9 IKGTAERP-RLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKKGITKVVFD-R 86 (109)
T ss_pred ecCCCCCC-EEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHHCCCCEEEEc-C
Confidence 44677888 899999999999999999999999999999999999899999999999999999999999999999999 9
Q ss_pred CCcchhhHHHHHHHHHHHcCcEE
Q 018389 317 KGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 317 ~GykYHGRVKAfADAaRE~GL~F 339 (357)
+||+|||||+||||+|||+||+|
T Consensus 87 gg~~yhGrV~a~a~~are~GL~f 109 (109)
T CHL00139 87 GGKLYHGRIKALAEAAREAGLQF 109 (109)
T ss_pred CCCccchHHHHHHHHHHHhCCCC
Confidence 99999999999999999999987
No 2
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=100.00 E-value=2e-34 Score=264.05 Aligned_cols=96 Identities=19% Similarity=0.242 Sum_probs=91.2
Q ss_pred CCeEEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccC------------CCCCHHHHHHHHHHHHHHHHhCCCCE
Q 018389 243 EPFCLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLD------------STRNATACAAVGGILAQRALADDIHD 310 (357)
Q Consensus 243 rPfRL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~------------St~NveAAa~VGkvLAeRakekGI~~ 310 (357)
|.+||+||+||+|||||||||.+|+|||+|||++++++..+. .++|++||+.||++||+||+++||++
T Consensus 104 rrPRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAerAl~kGI~k 183 (211)
T PTZ00032 104 RRPRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGISK 183 (211)
T ss_pred CcceEEEEecCCeEEEEEEECCCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHHHHHHHHHCCCCE
Confidence 334999999999999999999999999999999999988665 57899999999999999999999999
Q ss_pred EEEcCCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 311 VVYTPRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 311 VVFDpR~GykYHGRVKAfADAaRE~GL~F 339 (357)
|+|| |+||+|||||+||||+|||+||+|
T Consensus 184 VvFD-RgGy~YHGRVkALAdaARe~GLkF 211 (211)
T PTZ00032 184 VRFD-RAHYKYAGKVEALAEGARAVGLQF 211 (211)
T ss_pred EEEe-CCCCeehhHHHHHHHHHHHcCCCC
Confidence 9999 999999999999999999999987
No 3
>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=1.4e-34 Score=244.43 Aligned_cols=96 Identities=29% Similarity=0.454 Sum_probs=92.4
Q ss_pred cCCCCCCeEEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCC
Q 018389 238 TAPYHEPFCLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRK 317 (357)
Q Consensus 238 Td~Y~rPfRL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~ 317 (357)
|..|.+| ||+||+||+|||||||||.+++||+||||+|++++ .++|++||..||++||+||+++||++|+|| |+
T Consensus 19 t~~~~rp-RL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~----~~~n~~aA~~vG~~la~ra~~~gi~~vvfD-rg 92 (114)
T TIGR00060 19 TGEANRP-RLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK----YTGNKDAAKKVGKLVAERLKEKGIKDVVFD-RG 92 (114)
T ss_pred CCCCCCc-EEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc----CCCCHHHHHHHHHHHHHHHHHCCCCEEEEe-CC
Confidence 6667899 99999999999999999999999999999999987 678999999999999999999999999999 99
Q ss_pred CcchhhHHHHHHHHHHHcCcEE
Q 018389 318 GEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 318 GykYHGRVKAfADAaRE~GL~F 339 (357)
||+|||||+||||+|||+||+|
T Consensus 93 g~~YhGrv~A~a~~aRe~Gl~F 114 (114)
T TIGR00060 93 GYKYHGRVAALAEAAREAGLNF 114 (114)
T ss_pred CCcchHHHHHHHHHHHHhCCCC
Confidence 9999999999999999999987
No 4
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=100.00 E-value=1.1e-33 Score=239.04 Aligned_cols=98 Identities=28% Similarity=0.465 Sum_probs=93.2
Q ss_pred CCCCCCeEEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCC
Q 018389 239 APYHEPFCLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRKG 318 (357)
Q Consensus 239 d~Y~rPfRL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~G 318 (357)
+.-.+| ||+||+||+|||||||||.+|+||+||||+|++++..+. ++|++||..||++||+||+++||++|+|| |+|
T Consensus 20 g~~~rp-RL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~~-~~n~~aa~~vG~~la~ra~~~gi~~vvfD-rg~ 96 (117)
T PRK05593 20 GTAERP-RLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGLK-GGNKEAAKKVGKLIAERAKAKGIKQVVFD-RGG 96 (117)
T ss_pred CCCCCC-EEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhcccc-CCCHHHHHHHHHHHHHHHHHCCCCEEEEc-CCC
Confidence 445777 899999999999999999999999999999999987765 89999999999999999999999999999 999
Q ss_pred cchhhHHHHHHHHHHHcCcEE
Q 018389 319 EKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 319 ykYHGRVKAfADAaRE~GL~F 339 (357)
|+|||||+||||+|||+||+|
T Consensus 97 ~~yhGrV~a~a~~are~Gl~f 117 (117)
T PRK05593 97 YKYHGRVKALADAAREAGLKF 117 (117)
T ss_pred CcccHHHHHHHHHHHHhCCCC
Confidence 999999999999999999987
No 5
>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=99.97 E-value=1.7e-31 Score=217.33 Aligned_cols=96 Identities=28% Similarity=0.367 Sum_probs=92.8
Q ss_pred CCCCeEEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcc
Q 018389 241 YHEPFCLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRKGEK 320 (357)
Q Consensus 241 Y~rPfRL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~Gyk 320 (357)
+..++||+|++||+|||||||||.+++||++|||.|++++..+++++|++||..||++||+||+++||..|+|| |+|++
T Consensus 8 ~~~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vv~D-~~~~~ 86 (103)
T cd00432 8 TQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFD-RGGYR 86 (103)
T ss_pred cCCCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEEe-CCCcc
Confidence 34567999999999999999999999999999999999999999999999999999999999999999999999 99999
Q ss_pred hhhHHHHHHHHHHHcCc
Q 018389 321 LEGKLQIVLQAIIDNGV 337 (357)
Q Consensus 321 YHGRVKAfADAaRE~GL 337 (357)
|||||+||++++||+||
T Consensus 87 ~~grv~a~~~~~r~~Gl 103 (103)
T cd00432 87 YHGRVKALAKGAREGGL 103 (103)
T ss_pred cccHHHHHHHHHHHcCC
Confidence 99999999999999997
No 6
>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=99.97 E-value=5.1e-31 Score=221.44 Aligned_cols=95 Identities=28% Similarity=0.396 Sum_probs=90.2
Q ss_pred CeEEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhccc--CCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcch
Q 018389 244 PFCLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDL--DSTRNATACAAVGGILAQRALADDIHDVVYTPRKGEKL 321 (357)
Q Consensus 244 PfRL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L--~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~GykY 321 (357)
++||+||+||+|||||||||.++.||++|||.+++|++.+ .+++|++||..||++||+||+++||..|+|| |+|++|
T Consensus 23 ~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~~vG~lla~ra~~~gi~~v~fd-r~~~~y 101 (119)
T PF00861_consen 23 RPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAYLVGELLAKRALEKGIAKVVFD-RGGYKY 101 (119)
T ss_dssp SEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHHHHHHHHHHHHHHTTSSEEEEC-TSTSSS
T ss_pred CCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHHHHHHHHHHHHHHcCCcEEEEc-CCCCcc
Confidence 3599999999999999999999999999999999999864 5678999999999999999999999999999 999999
Q ss_pred hhHHHHHHHHHHHcCcEE
Q 018389 322 EGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 322 HGRVKAfADAaRE~GL~F 339 (357)
||||+|||++|||+||+|
T Consensus 102 ~grv~a~~~~~re~Gl~f 119 (119)
T PF00861_consen 102 HGRVKALADGAREGGLEF 119 (119)
T ss_dssp SSHHHHHHHHHHHTTCB-
T ss_pred cHHHHHHHHHHHHcCCCC
Confidence 999999999999999987
No 7
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=4.3e-31 Score=226.70 Aligned_cols=99 Identities=26% Similarity=0.389 Sum_probs=92.2
Q ss_pred CCCCCCeEEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcc--cCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCC
Q 018389 239 APYHEPFCLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFD--LDSTRNATACAAVGGILAQRALADDIHDVVYTPR 316 (357)
Q Consensus 239 d~Y~rPfRL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~--L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR 316 (357)
..-.+| ||+||+||+|||||||||..+.||++|||.+++|++. +..++|++||..||.++|+||+++||++|||| |
T Consensus 25 g~~~rp-RL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~N~~aA~~vG~lia~ra~~kgi~~vVfd-r 102 (125)
T COG0256 25 GTSGRP-RLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLVGKLIAERALAKGIEEVVFD-R 102 (125)
T ss_pred cCCCCc-EEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhcccCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEc-C
Confidence 445677 9999999999999999999999999999999999863 33467999999999999999999999999999 9
Q ss_pred CCcchhhHHHHHHHHHHHcCcEE
Q 018389 317 KGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 317 ~GykYHGRVKAfADAaRE~GL~F 339 (357)
+||+|||||+||||++||+||+|
T Consensus 103 ~g~~yhgRV~Ala~~AreaGL~f 125 (125)
T COG0256 103 GGYKYHGRVAALADGAREAGLEF 125 (125)
T ss_pred CCCCcchHHHHHHHHHHHcCcCC
Confidence 99999999999999999999987
No 8
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=99.95 E-value=1.5e-27 Score=217.19 Aligned_cols=98 Identities=20% Similarity=0.187 Sum_probs=92.8
Q ss_pred CCCeEEEEEecCCeEEEEEE--eCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCc
Q 018389 242 HEPFCLDIYISKASVRACIV--HRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRKGE 319 (357)
Q Consensus 242 ~rPfRL~VfrSNKHIYAQVI--DD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~Gy 319 (357)
.+| ||+|++||+||||||| |+.+++|||||||.|+.+...+.+++|++||..||.+||+||+++||++|+|| |+|+
T Consensus 31 ~kp-RLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~~~~~N~~AAy~vG~llA~ral~kGi~~vvfD-rGg~ 108 (193)
T PRK08569 31 GKP-RLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKGDTGNTPAAYLTGLLAGKKALKAGVEEAVLD-IGLH 108 (193)
T ss_pred CCC-EEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhccccCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEe-cCCc
Confidence 345 9999999999999999 89999999999999999977677789999999999999999999999999999 8999
Q ss_pred chh--hHHHHHHHHHHHcCcEEEE
Q 018389 320 KLE--GKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 320 kYH--GRVKAfADAaRE~GL~FK~ 341 (357)
+|| |||+|||++||++||+|-.
T Consensus 109 ~yh~gGRV~A~akgArd~GL~fPh 132 (193)
T PRK08569 109 RPTKGSRVFAALKGAIDAGLEIPH 132 (193)
T ss_pred cccCCccHHHHHHHHHHcCCcCCC
Confidence 999 9999999999999999854
No 9
>KOG3333 consensus Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=99.77 E-value=1.1e-18 Score=156.42 Aligned_cols=94 Identities=30% Similarity=0.432 Sum_probs=85.9
Q ss_pred EEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHH
Q 018389 246 CLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKL 325 (357)
Q Consensus 246 RL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRV 325 (357)
+|.|.++..|+.+-|.|..+|. |+||||.||.|+++||++.|+.||.+||++||+||++.||+++++.|-....-....
T Consensus 62 ~lev~~~~~hveg~v~H~~~gv-vvSAST~EwaIk~qLYst~dtsA~~niGRVLAqRCLqsGI~fm~~~~t~ea~~~s~~ 140 (188)
T KOG3333|consen 62 RLEVIRTQHHVEGLVEHQNGGV-VVSASTREWAIKKQLYSTRDTSACENIGRVLAQRCLQSGINFMVYQPTPEAAASSSM 140 (188)
T ss_pred EEEEeecccceeeeeeEecCCE-EEEecccchHHHHHHhhccchHHHHHHHHHHHHHHHHhCcceeccCCChhhccchHH
Confidence 6999999999999999988776 559999999999999999999999999999999999999999999975555555788
Q ss_pred HHHHHHHHHcCcEEE
Q 018389 326 QIVLQAIIDNGVNVK 340 (357)
Q Consensus 326 KAfADAaRE~GL~FK 340 (357)
+-|..++.|+|+.||
T Consensus 141 q~l~~a~~e~Gv~lk 155 (188)
T KOG3333|consen 141 QRLQSAMTEGGVVLK 155 (188)
T ss_pred HHHHHHHHhCCeeec
Confidence 889999999999876
No 10
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=98.28 E-value=2.3e-06 Score=83.42 Aligned_cols=95 Identities=20% Similarity=0.170 Sum_probs=72.4
Q ss_pred eEEEEEecCCeEEEEEEeCC--CCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhC--------CCC-----
Q 018389 245 FCLDIYISKASVRACIVHRV--TSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALAD--------DIH----- 309 (357)
Q Consensus 245 fRL~VfrSNKHIYAQVIDD~--~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakek--------GI~----- 309 (357)
|||.|-+||++|.|||+... .-+|||+|.+.|..=-.-..+.+|..||...|-+||.|++.+ |++
T Consensus 49 ~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~kyG~k~gl~N~~AAY~TGlL~arR~L~kl~ld~~y~G~~e~~g~ 128 (300)
T PTZ00069 49 YRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELPRFGIPVGLTNYAAAYATGLLLARRLLKKLGLDKQFEGVKEADGE 128 (300)
T ss_pred ceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhcCcCCCCccHHHHHHHHHHHHHHHHHhhcccccccCcccccCc
Confidence 69999999999999999763 567888888877542112234689999999999999999999 874
Q ss_pred ---------------EEEEcCCCCc--chhhHHHHHHHHHHHcCcEEE
Q 018389 310 ---------------DVVYTPRKGE--KLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 310 ---------------~VVFDpR~Gy--kYHGRVKAfADAaRE~GL~FK 340 (357)
.++.|. |-. ..-+||=|.+.++-++||.+=
T Consensus 129 ~y~v~e~~~~~~rpf~a~LDi-GL~rtt~G~RVFaalKGa~DgGl~IP 175 (300)
T PTZ00069 129 YYHVDEEDDEERRPFKAILDV-GLARTTTGNRVFGALKGAVDGGLHIP 175 (300)
T ss_pred ccccccccccCCCCceEEEee-ccccCCCCceeeeehhcccccCcccC
Confidence 445553 111 111689999999999999763
No 11
>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=96.74 E-value=0.024 Score=47.68 Aligned_cols=87 Identities=17% Similarity=0.155 Sum_probs=68.7
Q ss_pred EEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHH
Q 018389 247 LDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQ 326 (357)
Q Consensus 247 L~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVK 326 (357)
+.|+.|.+.+...|.| .+|.++.++|+-.-.+|..- .....||..+++.++++|++.||..|.--.+ | .--||-.
T Consensus 3 ihI~~s~NNt~vtlTd-~~G~~~~~~S~G~~gfK~~r--k~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ik-G-~g~gr~~ 77 (110)
T PF00411_consen 3 IHIKSSFNNTIVTLTD-LKGNVLFWSSAGSLGFKGAR--KSTPYAAQQAAEKIAKKAKELGIKTVRVKIK-G-FGPGREA 77 (110)
T ss_dssp EEEEEESSEEEEEEEE-TTSEEEEEEETTTSSTTTTC--GSSHHHHHHHHHHHHHHHHCTTEEEEEEEEE-S-SSTTHHH
T ss_pred EEEEecCCCEEEEEEC-CCCCEEEEEecccccccccc--ccCHHHHHHHHHHHHHHHHHcCCeEEEEEEc-C-CCccHHH
Confidence 6788899999999987 77999999999888887743 5577999999999999999999998753322 3 2236764
Q ss_pred HHHHHHHHcCcEE
Q 018389 327 IVLQAIIDNGVNV 339 (357)
Q Consensus 327 AfADAaRE~GL~F 339 (357)
+ ..+|...||++
T Consensus 78 ~-lk~l~~~gl~I 89 (110)
T PF00411_consen 78 A-LKALKKSGLKI 89 (110)
T ss_dssp H-HHHHHHTTSEE
T ss_pred H-HHHHHhcCCEE
Confidence 4 47788899864
No 12
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=96.67 E-value=0.032 Score=53.43 Aligned_cols=97 Identities=24% Similarity=0.249 Sum_probs=74.8
Q ss_pred cCCCCCCeEEEEEecCCeEEEEEEeCCCCe--EEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcC
Q 018389 238 TAPYHEPFCLDIYISKASVRACIVHRVTSK--VVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTP 315 (357)
Q Consensus 238 Td~Y~rPfRL~VfrSNKHIYAQVIDD~~Gk--TLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDp 315 (357)
+.|-+ .|+|.|+-|-.++.++|.| ..|. ||+-+|.-.-.+|... ...--||..+++-+|+.|++.||..|.-=.
T Consensus 113 ~~p~~-~f~~vI~aSfNNTIVTlTD-~~GNv~tl~WSSAG~~GFKGsK--KsTpfAAQ~aae~aakka~~~GIk~V~V~v 188 (233)
T PTZ00090 113 IEPTD-RFMLVITTSKNNVHAQVVN-KSKNYKTVFGSFAGNVGFRKKL--QQSERCAYRIGENIAKKCRRLGIFAVDIKF 188 (233)
T ss_pred ecCCC-cEEEEEEeccCcEEEEEEe-CCCCEEEEEEEcccccCcccCc--cCCHHHHHHHHHHHHHHHHHcCCeEEEEEE
Confidence 33433 4889999999999999998 5566 5877777777777643 345689999999999999999999875331
Q ss_pred CCCcchhhHHHHHHHHHHHcCcEEEEE
Q 018389 316 RKGEKLEGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 316 R~GykYHGRVKAfADAaRE~GL~FK~~ 342 (357)
+ |- |...+.+.++..+||++..-
T Consensus 189 K-Gp---GgREtALRaL~~~GLkIt~I 211 (233)
T PTZ00090 189 R-RI---MRVETVLQAFYANGLQVTQI 211 (233)
T ss_pred e-CC---ChHHHHHHHHHHCCCEEEEE
Confidence 2 32 44889999999999987653
No 13
>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=96.31 E-value=0.058 Score=45.49 Aligned_cols=88 Identities=16% Similarity=0.127 Sum_probs=67.4
Q ss_pred EEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHH
Q 018389 247 LDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQ 326 (357)
Q Consensus 247 L~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVK 326 (357)
+-|+.|.+.+...|.|. +|.+++.+|.-...++.. .....-||..+++.++++|++.||..|..=.| |.-+ || +
T Consensus 3 ~hI~~s~NNT~itlTd~-~g~~~~~~S~G~~gfkg~--rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~k-G~G~-gr-~ 76 (108)
T TIGR03632 3 AHIHATFNNTIVTITDP-QGNVLSWASAGAVGFKGS--KKSTPYAAQLAAEDAAKKAKEFGMKTVDVYVK-GPGA-GR-E 76 (108)
T ss_pred EEEEccCCCEEEEEEcC-CCCEEEEEecCceeeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEE-CCCC-cH-H
Confidence 56888999999999884 688999988877777764 34567889999999999999999998753322 3222 65 5
Q ss_pred HHHHHHHHcCcEEE
Q 018389 327 IVLQAIIDNGVNVK 340 (357)
Q Consensus 327 AfADAaRE~GL~FK 340 (357)
++..+|...||++.
T Consensus 77 ~~ir~l~~~glkI~ 90 (108)
T TIGR03632 77 SAIRALQAAGLEVT 90 (108)
T ss_pred HHHHHHHHCCCEEE
Confidence 66777888898753
No 14
>CHL00041 rps11 ribosomal protein S11
Probab=96.20 E-value=0.069 Score=45.69 Aligned_cols=89 Identities=15% Similarity=0.156 Sum_probs=69.5
Q ss_pred EEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHH
Q 018389 246 CLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKL 325 (357)
Q Consensus 246 RL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRV 325 (357)
.+.|+.|.+.+...|.| ..|.+++.+|.-.-.++..- ....-||..+++-+++.|++.||..|..=. .|.- .||
T Consensus 15 i~hI~~t~NNTiiTlTd-~~G~~l~~~S~G~~gfKg~r--K~T~~Aa~~~a~~~~~~~~~~gi~~v~I~i-kG~G-~Gr- 88 (116)
T CHL00041 15 VIHIQASFNNTIVTVTD-VRGRVISWSSAGACGFKGAR--KGTPFAAQTAAENAIRTVIDQGMKRAEVMI-KGPG-LGR- 88 (116)
T ss_pred EEEEEcccCCEEEEEEc-CCCCEEEEEecCceeeCCCc--cCCHHHHHHHHHHHHHHHHHcCCcEEEEEE-ECCC-CcH-
Confidence 47788899999999987 56899999998877777642 456789999999999999999999875332 2332 377
Q ss_pred HHHHHHHHHcCcEEE
Q 018389 326 QIVLQAIIDNGVNVK 340 (357)
Q Consensus 326 KAfADAaRE~GL~FK 340 (357)
+++..+|+..||++.
T Consensus 89 ~~~ir~l~~~glkI~ 103 (116)
T CHL00041 89 DTALRAIRRSGLKLS 103 (116)
T ss_pred HHHHHHHHHCCCEEE
Confidence 556688899999753
No 15
>PRK05309 30S ribosomal protein S11; Validated
Probab=95.71 E-value=0.17 Score=44.19 Aligned_cols=89 Identities=16% Similarity=0.152 Sum_probs=68.3
Q ss_pred EEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHH
Q 018389 246 CLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKL 325 (357)
Q Consensus 246 RL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRV 325 (357)
.+.|+-|.+.....|.| .+|.+++.+|.-.-.++.. .....-||..+++.+++.|++.||..|..-.+ |.- -||
T Consensus 19 i~hI~~t~NNTiitlTd-~~G~~~~~~S~G~~gfKg~--rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ik-G~G-~Gr- 92 (128)
T PRK05309 19 VAHIHATFNNTIVTITD-RQGNVISWASAGGLGFKGS--RKSTPYAAQVAAEDAAKKAKEHGMKTVEVFVK-GPG-SGR- 92 (128)
T ss_pred EEEEEccCCCEEEEEEc-CCCCEEEEEecCccEeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEE-CCC-CcH-
Confidence 58899999999999987 6789999888877677663 34567899999999999999999998753322 332 266
Q ss_pred HHHHHHHHHcCcEEE
Q 018389 326 QIVLQAIIDNGVNVK 340 (357)
Q Consensus 326 KAfADAaRE~GL~FK 340 (357)
.+++-+|...||++.
T Consensus 93 ~~air~L~~~glkI~ 107 (128)
T PRK05309 93 ESAIRALQAAGLEVT 107 (128)
T ss_pred HHHHHHHHHCCCEEE
Confidence 556667777899754
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=92.18 E-value=2.7 Score=36.52 Aligned_cols=91 Identities=16% Similarity=0.165 Sum_probs=63.3
Q ss_pred EEEEecCCeEEEEEEeCCCC-eEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCC--Ccch--
Q 018389 247 LDIYISKASVRACIVHRVTS-KVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRK--GEKL-- 321 (357)
Q Consensus 247 L~VfrSNKHIYAQVIDD~~G-kTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~--GykY-- 321 (357)
+-|+-|-+.....|.| ..| .||+-+|.-....+.. ..+.--||...++-+|++|++.||..|..-.|+ |.+-
T Consensus 5 ~hI~as~NNTiitvTD-~~G~~~~~~~S~G~~g~kg~--kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~~ 81 (114)
T TIGR03628 5 AHIYSSFNNTIITITD-ITGAETIARSSGGMVVKADR--DESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKS 81 (114)
T ss_pred EEEEccCCCeEEEEEc-CCCCEEEEEecCcceEeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCCC
Confidence 4577788888888887 556 6787777666555442 234557899999999999999999998755444 2221
Q ss_pred --hhHHHHHHHHHHHcCcEEEE
Q 018389 322 --EGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 322 --HGRVKAfADAaRE~GL~FK~ 341 (357)
-||- +.+.+|+..||++..
T Consensus 82 ~G~Gr~-~air~l~~~glkI~~ 102 (114)
T TIGR03628 82 PGPGAQ-AAIRALARAGLRIGR 102 (114)
T ss_pred CCCcHH-HHHHHHHHCCCEEEE
Confidence 1554 345677889998653
No 17
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=91.83 E-value=2.9 Score=37.24 Aligned_cols=92 Identities=16% Similarity=0.124 Sum_probs=63.9
Q ss_pred EEEEEecCCeEEEEEEeCCCC-eEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCC--Ccc--
Q 018389 246 CLDIYISKASVRACIVHRVTS-KVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRK--GEK-- 320 (357)
Q Consensus 246 RL~VfrSNKHIYAQVIDD~~G-kTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~--Gyk-- 320 (357)
.+.|+-|-+.....|.| ..| .||+-+|.-....+.. .....-||...++-+|++|++.||..|..-.++ |..
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 IAHIYASFNNTIITITD-LTGAETIAKSSGGMVVKADR--DESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNGQK 87 (132)
T ss_pred EEEEEcccCCeEEEEEc-CCCCEEEEEecCcceeeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCc
Confidence 36778888888899987 567 4887777665544432 233557899999999999999999998755444 111
Q ss_pred --hhhHHHHHHHHHHHcCcEEEE
Q 018389 321 --LEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 321 --YHGRVKAfADAaRE~GL~FK~ 341 (357)
=-|+-. .+.+|...||++..
T Consensus 88 ~~G~Gr~~-airal~~~glkI~~ 109 (132)
T PRK09607 88 SPGPGAQA-AIRALARAGLRIGR 109 (132)
T ss_pred CCCCcHHH-HHHHHHHCCCEEEE
Confidence 125544 45677888998653
No 18
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=90.04 E-value=4.5 Score=36.82 Aligned_cols=93 Identities=17% Similarity=0.185 Sum_probs=67.0
Q ss_pred EEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCC--CCcch--
Q 018389 246 CLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPR--KGEKL-- 321 (357)
Q Consensus 246 RL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR--~GykY-- 321 (357)
.+.|+-|-++....|.| .+|.+++.+|+-.-.++.... .+.--||...++.+|+.|++.||..|..-.| +|..-
T Consensus 30 i~hI~as~NNTiItiTD-~~G~~~~w~SsG~~gfKg~r~-KsTpyAAq~aa~~~a~k~~~~Gi~~v~V~vr~~gg~~~kg 107 (149)
T PTZ00129 30 VAHIFASFNDTFIHVTD-LSGRETLVRVTGGMKVKADRD-ESSPYAAMMAAQDVAARCKELGINALHIKLRATGGVRTKT 107 (149)
T ss_pred EEEEEcccCCeEEEEEc-ccCCEEEEEecCcceeccccc-CCCHHHHHHHHHHHHHHHHHcCCeEEEEEEEecCCCCCCC
Confidence 46788888888889987 678888888887777765421 2345688999999999999999999764432 22222
Q ss_pred --hhHHHHHHHHHHHcCcEEEE
Q 018389 322 --EGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 322 --HGRVKAfADAaRE~GL~FK~ 341 (357)
-|+- +.+.+|..+||++..
T Consensus 108 ~GpGr~-~airaL~~~glkI~~ 128 (149)
T PTZ00129 108 PGPGAQ-AALRALARAGLKIGR 128 (149)
T ss_pred CCCCHH-HHHHHHHHCCCEEEE
Confidence 2554 456788889998754
No 19
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=86.14 E-value=6.9 Score=34.95 Aligned_cols=84 Identities=19% Similarity=0.207 Sum_probs=58.1
Q ss_pred EecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCC-CcchhhHHHHH
Q 018389 250 YISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRK-GEKLEGKLQIV 328 (357)
Q Consensus 250 frSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~-GykYHGRVKAf 328 (357)
+-|-..-...|- |.+|.+++.+|+=--.+|..- .+.--||...++.+|+.|++.||..|..-.++ | -|| .|.
T Consensus 24 ~asfNNTivtit-D~~Gn~i~wassG~~gfk~~r--k~tpyAA~~aa~~aa~~a~e~Gi~~v~v~vkgpG---~Gr-eaA 96 (129)
T COG0100 24 HASFNNTIVTIT-DLTGNVIIWASSGGMGFKGSR--KSTPYAAQLAAEDAAKKAKEHGIKSVEVKVKGPG---PGR-EAA 96 (129)
T ss_pred EcccCCcEEEec-CCCCCEEEEEecCCceEcCCC--CCCHHHHHHHHHHHHHHHHHhCccEEEEEEECCC---CcH-HHH
Confidence 334333333444 588999999999988888753 55778889999999999999999987533233 4 244 344
Q ss_pred HHHHHHcCcEEE
Q 018389 329 LQAIIDNGVNVK 340 (357)
Q Consensus 329 ADAaRE~GL~FK 340 (357)
..+|...||.+.
T Consensus 97 iraL~~ag~~i~ 108 (129)
T COG0100 97 IRALAAAGLKIT 108 (129)
T ss_pred HHHHHHccceEE
Confidence 455557888653
No 20
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=77.59 E-value=31 Score=32.58 Aligned_cols=96 Identities=15% Similarity=0.156 Sum_probs=70.8
Q ss_pred CCCCCeEEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCc
Q 018389 240 PYHEPFCLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPRKGE 319 (357)
Q Consensus 240 ~Y~rPfRL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~Gy 319 (357)
+|++-....|--|..+...+|.| ..|.++..+|---..+|+.- .+..-||..-|-..+.|+.+.|+..|-.-. .|
T Consensus 75 ~f~eiPi~hIraS~NNTivtVtd-~kg~vi~~~ScgteGFrntr--kgT~iAaQtaavaa~~r~v~~G~~~vrV~V-kG- 149 (190)
T KOG0408|consen 75 NFREIPIIHIRASFNNTIVTVTD-VKGEVISWSSCGTEGFRNTR--KGTPIAAQTAAVAAIRRAVDQGMQTVRVRV-KG- 149 (190)
T ss_pred cccccceEEEEecCCCeEEEEEc-cCCcEEEEeecccccccccc--cCCchhHHHHHHHHHHHHHHhcceEEEEEE-ec-
Confidence 45554467777798999999987 88999988887777888742 234456777777889999999999875442 22
Q ss_pred chhhHHHHHHHHHHHcCcEEEE
Q 018389 320 KLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 320 kYHGRVKAfADAaRE~GL~FK~ 341 (357)
+=-||..|+ .+|+-+||.+-+
T Consensus 150 lGpGRmsa~-kgl~m~Gl~vvs 170 (190)
T KOG0408|consen 150 LGPGRMSAL-KGLRMGGLLVVS 170 (190)
T ss_pred CCccHHHHH-hhhhhcceEEEE
Confidence 224898875 789999997644
No 21
>KOG0875 consensus 60S ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=64.38 E-value=6.2 Score=38.87 Aligned_cols=64 Identities=17% Similarity=0.026 Sum_probs=44.7
Q ss_pred CeEEEEEecCCeEEEEEEeCC-CCeE-EEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHh-CC
Q 018389 244 PFCLDIYISKASVRACIVHRV-TSKV-VVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALA-DD 307 (357)
Q Consensus 244 PfRL~VfrSNKHIYAQVIDD~-~GkT-LaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRake-kG 307 (357)
.|||.|-++|+.|.+||+-.. +|-+ |++|-+.|..--.......|-+||..-|-+||.|+++ .|
T Consensus 48 kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s~elpkyg~~~GLtNyaAay~TglLLarR~l~~~g 114 (264)
T KOG0875|consen 48 KYRMIVRVINKDIICQIAYATIEGDVIVRAAYAHELPKYGVKVGLTNYAAAYCTGLLLACRLLKRFG 114 (264)
T ss_pred ceEEEEEEechhhHHHHHhheecceEEEEeeccccccccccccccchhHHHHhhHHHHHHHHHHHhC
Confidence 378999999999999997543 4443 4444444433222223457889999999999999985 45
No 22
>COG1472 BglX Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]
Probab=60.11 E-value=17 Score=36.97 Aligned_cols=56 Identities=25% Similarity=0.278 Sum_probs=42.5
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHhCCCCE-------EEEcCCCCcchhh-----------HHHHHHHHHHHcCcE
Q 018389 283 LDSTRNATACAAVGGILAQRALADDIHD-------VVYTPRKGEKLEG-----------KLQIVLQAIIDNGVN 338 (357)
Q Consensus 283 L~St~NveAAa~VGkvLAeRakekGI~~-------VVFDpR~GykYHG-----------RVKAfADAaRE~GL~ 338 (357)
|..+-+.+.+..+|+++|+-+.+.||+- |..||++|-.+.+ -..|++++++.+|+.
T Consensus 89 laa~~~~~la~~~g~~~A~Elra~Gin~~fAPvlDv~~~p~~~ri~ersfgeDP~lv~~l~~a~i~Glq~~gv~ 162 (397)
T COG1472 89 LAATWDPELARKVGRVIAKELRALGINLDFAPVLDVARDPRWGRIGERSFGEDPELVALLAAAFIKGLQGAGVA 162 (397)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHcCCCccccceeecccCCCcCccccccCCCCHHHHHHHHHHHHHHHhhCCce
Confidence 4456678999999999999999999984 4566655443332 367888999988874
No 23
>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=56.10 E-value=37 Score=34.81 Aligned_cols=54 Identities=22% Similarity=0.342 Sum_probs=48.0
Q ss_pred CCHHHHHHHHHH-----------------HHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 287 RNATACAAVGGI-----------------LAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 287 ~NveAAa~VGkv-----------------LAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
.|.++|..++.+ ||..|.++|+.++-..| +..-...+|+.+++++++.|+...+
T Consensus 56 p~~~~A~al~~I~~~~~iPlVADIHFd~~lAl~a~~~g~dkiRINP-GNig~~e~v~~vv~~ak~~~ipIRI 126 (346)
T TIGR00612 56 PDRESAAAFEAIKEGTNVPLVADIHFDYRLAALAMAKGVAKVRINP-GNIGFRERVRDVVEKARDHGKAMRI 126 (346)
T ss_pred CCHHHHHhHHHHHhCCCCCEEEeeCCCcHHHHHHHHhccCeEEECC-CCCCCHHHHHHHHHHHHHCCCCEEE
Confidence 488999999975 89999999999999995 6666778999999999999998876
No 24
>cd07039 TPP_PYR_POX Pyrimidine (PYR) binding domain of POX. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. Lactobacillus plantarum POX is a homotetramer (dimer-of-homodimers), having two active sites per homodimer lying between PYR and PP domains of differ
Probab=51.57 E-value=32 Score=30.30 Aligned_cols=42 Identities=10% Similarity=0.117 Sum_probs=33.0
Q ss_pred HHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHH-cCcEEEEE
Q 018389 295 VGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIID-NGVNVKVK 342 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE-~GL~FK~~ 342 (357)
+++.|++.+++.||+.|.-= .| +.+-.|.+++.+ .||.+-.-
T Consensus 2 ~~~~l~~~L~~~Gv~~vFgi--pG----~~~~~l~~al~~~~~i~~v~~ 44 (164)
T cd07039 2 VADVIVETLENWGVKRVYGI--PG----DSINGLMDALRREGKIEFIQV 44 (164)
T ss_pred HHHHHHHHHHHCCCCEEEEc--CC----CchHHHHHHHhhcCCCeEEEe
Confidence 68899999999999986555 35 567788888876 78887654
No 25
>PF01120 Alpha_L_fucos: Alpha-L-fucosidase; InterPro: IPR000933 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Family 29 (GH29 from CAZY) encompasses alpha-L-fucosidases (3.2.1.51 from EC) [], which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Alpha-L-fucosidase is responsible for hydrolysing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Fucosylated glycoconjugates are involved in numerous biological events, making alpha-l-fucosidases, the enzymes responsible for their processing, critically important. Deficiency in alpha-l-fucosidase activity is associated with fucosidosis, a lysosomal storage disorder characterised by rapid neurodegeneration, resulting in severe mental and motor deterioration []. The enzyme is a hexamer and displays a two-domain fold, composed of a catalytic (beta/alpha)(8)-like domain and a C-terminal beta-sandwich domain []. Drosophila melanogaster spermatozoa contains an alpha-l-fucosidase that might be involved in fertilisation by interacting with alpha-l-fucose residues on the micropyle of the eggshell []. In human sperm, membrane-associated alpha-l-fucosidase is stable for extended periods of time, which is made possible by membrane domains and compartmentalisation. These help preserve protein integrity []. ; GO: 0004560 alpha-L-fucosidase activity, 0005975 carbohydrate metabolic process; PDB: 3EYP_B 2ZX6_A 2ZWY_B 2ZX8_B 2WSP_A 2ZXA_A 2ZWZ_B 1ODU_B 1HL9_A 2ZX5_B ....
Probab=51.01 E-value=40 Score=33.24 Aligned_cols=49 Identities=18% Similarity=0.114 Sum_probs=33.7
Q ss_pred HHHHHHHHhCCCCEEEEcC--CCCc-----c---h--------hhHHHHHHHHHHHcCcEEEEEeec
Q 018389 297 GILAQRALADDIHDVVYTP--RKGE-----K---L--------EGKLQIVLQAIIDNGVNVKVKLKQ 345 (357)
Q Consensus 297 kvLAeRakekGI~~VVFDp--R~Gy-----k---Y--------HGRVKAfADAaRE~GL~FK~~lkq 345 (357)
...|+.|+++|..-||+.. -.|| . | .--|+.|++|+|+.||+|.|++-.
T Consensus 94 dqW~~~ak~aGakY~VlTakHHDGF~LW~S~~t~~~v~~~~~krDiv~El~~A~rk~Glk~G~Y~S~ 160 (346)
T PF01120_consen 94 DQWAKLAKDAGAKYVVLTAKHHDGFCLWPSKYTDYNVVNSGPKRDIVGELADACRKYGLKFGLYYSP 160 (346)
T ss_dssp HHHHHHHHHTT-SEEEEEEE-TT--BSS--TT-SSBGGGGGGTS-HHHHHHHHHHHTT-EEEEEEES
T ss_pred HHHHHHHHHcCCCEEEeehhhcCccccCCCCCCcccccCCCCCCCHHHHHHHHHHHcCCeEEEEecc
Confidence 4578899999999988542 1121 1 1 134999999999999999998754
No 26
>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=50.49 E-value=38 Score=29.12 Aligned_cols=47 Identities=15% Similarity=0.132 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 295 VGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
...+|.+-|.+.||+.|+++..-+.-...+.+++.+.+.+.||.+..
T Consensus 76 ~~~~l~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~~ 122 (165)
T PF00875_consen 76 PEEVLPELAKEYGATAVYFNEEYTPYERRRDERVRKALKKHGIKVHT 122 (165)
T ss_dssp HHHHHHHHHHHHTESEEEEE---SHHHHHHHHHHHHHHHHTTSEEEE
T ss_pred hHHHHHHHHHhcCcCeeEeccccCHHHHHHHHHHHHHHHhcceEEEE
Confidence 34566677888999999999433334447889999999999999864
No 27
>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=49.07 E-value=40 Score=29.48 Aligned_cols=45 Identities=16% Similarity=0.138 Sum_probs=30.4
Q ss_pred HHHHHHHHHhCCCCEEEE--cCCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 296 GGILAQRALADDIHDVVY--TPRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 296 GkvLAeRakekGI~~VVF--DpR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
|+.+|+.+.+.|-.+|+| .+.+......|++.|.+++.+.|+.+.
T Consensus 104 ~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~~~~ 150 (269)
T cd06288 104 GYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQALAEAGIPFD 150 (269)
T ss_pred HHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHHHHcCCCCC
Confidence 445555556668888765 322222335799999999999997653
No 28
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=48.13 E-value=46 Score=26.20 Aligned_cols=46 Identities=17% Similarity=0.180 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcch------------hhHHHHHHHHHHHcCcEEEE
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKL------------EGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykY------------HGRVKAfADAaRE~GL~FK~ 341 (357)
.+++++..-+ .++|..+.|+ +.+..+ ...+..+.+.|++.|+.+..
T Consensus 14 ~L~~ll~~l~-~anI~~~~y~-~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~ 71 (85)
T cd04906 14 SFKKFCELIG-PRNITEFNYR-YADEKDAHIFVGVSVANGAEELAELLEDLKSAGYEVVD 71 (85)
T ss_pred HHHHHHHHhC-CCceeEEEEE-ccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEE
Confidence 3444444334 7899999998 533222 35688999999999998764
No 29
>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=47.93 E-value=58 Score=34.32 Aligned_cols=53 Identities=15% Similarity=0.182 Sum_probs=44.3
Q ss_pred CCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 286 TRNATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 286 t~NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~F 339 (357)
++.+..++..|..||++|++.||..|+..+--| .-|=-+..++..+..+||..
T Consensus 315 gt~~~~a~~~g~eIa~~Lk~dgVDAvILtstCg-tCtrcga~m~keiE~~GIPv 367 (431)
T TIGR01917 315 GTAVANSKQFAKEFSKELLAAGVDAVILTSTUG-TCTRCGATMVKEIERAGIPV 367 (431)
T ss_pred CccHHHHHHHHHHHHHHHHHcCCCEEEEcCCCC-cchhHHHHHHHHHHHcCCCE
Confidence 467788999999999999999999999995333 55666788899999999865
No 30
>PF02776 TPP_enzyme_N: Thiamine pyrophosphate enzyme, N-terminal TPP binding domain; InterPro: IPR012001 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This represents the N-terminal TPP binding domain of TPP enzymes.; GO: 0030976 thiamine pyrophosphate binding; PDB: 3HWX_1 3FLM_B 3HWW_A 2JLC_A 2JLA_A 2VBG_A 2VBF_B 2Q29_A 2Q27_B 2Q28_B ....
Probab=46.91 E-value=50 Score=28.72 Aligned_cols=42 Identities=21% Similarity=0.229 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHc-CcEEEEE
Q 018389 295 VGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDN-GVNVKVK 342 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~-GL~FK~~ 342 (357)
+++.|++.+++.||+.|..=| | +.+..|.+++.+. ||.+..-
T Consensus 3 ~~~~l~~~L~~~Gv~~vfgvp--G----~~~~~l~~al~~~~~i~~i~~ 45 (172)
T PF02776_consen 3 GAEALAEALKANGVTHVFGVP--G----SGNLPLLDALEKSPGIRFIPV 45 (172)
T ss_dssp HHHHHHHHHHHTT-SEEEEE--------GGGHHHHHHHHHTTTSEEEE-
T ss_pred HHHHHHHHHHHCCCeEEEEEe--C----hhHhHHHHHhhhhcceeeecc
Confidence 688999999999999976553 5 4566799999999 7887653
No 31
>COG1611 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]
Probab=46.75 E-value=30 Score=32.33 Aligned_cols=39 Identities=26% Similarity=0.329 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCc
Q 018389 289 ATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGV 337 (357)
Q Consensus 289 veAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL 337 (357)
.+.|+.||+.||+|. .+|+. +| .-|-..|.++++.++|.
T Consensus 33 ~~~a~~lg~~la~~g------~~V~t--GG--~~GiMea~~~gA~~~gg 71 (205)
T COG1611 33 YELARELGRELAKRG------LLVIT--GG--GPGVMEAVARGALEAGG 71 (205)
T ss_pred HHHHHHHHHHHHhCC------cEEEe--CC--chhhhhHHHHHHHHcCC
Confidence 488999999999998 58888 44 25899999999997664
No 32
>smart00812 Alpha_L_fucos Alpha-L-fucosidase. O-Glycosyl hydrolases (EC 3.2.1.-) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site PUBMED:. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Family 29 encompasses alpha-L-fucosidases, which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Deficiency of alpha-L-fucosidase results in the lysosomal storage disease fucosidosis.
Probab=46.41 E-value=37 Score=34.41 Aligned_cols=50 Identities=14% Similarity=0.064 Sum_probs=36.7
Q ss_pred HHHHHHHHHhCCCCEEEEcCC--CCc--------ch--------hhHHHHHHHHHHHcCcEEEEEeec
Q 018389 296 GGILAQRALADDIHDVVYTPR--KGE--------KL--------EGKLQIVLQAIIDNGVNVKVKLKQ 345 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFDpR--~Gy--------kY--------HGRVKAfADAaRE~GL~FK~~lkq 345 (357)
.+..|+.|+++|..-||+..+ .|| .| .--|+.|++|+|+.||.|.+++-.
T Consensus 83 ~~~Wa~~~k~AGakY~vlTaKHHDGF~lw~S~~t~~n~~~~~pkrDiv~el~~A~rk~Glk~G~Y~S~ 150 (384)
T smart00812 83 PEEWADLFKKAGAKYVVLTAKHHDGFCLWDSKYSNWNAVDTGPKRDLVGELADAVRKRGLKFGLYHSL 150 (384)
T ss_pred HHHHHHHHHHcCCCeEEeeeeecCCccccCCCCCCCcccCCCCCcchHHHHHHHHHHcCCeEEEEcCH
Confidence 356799999999998875421 111 11 135999999999999999998753
No 33
>PF13377 Peripla_BP_3: Periplasmic binding protein-like domain; PDB: 3K9C_B 3BIL_B 3JVD_B 1ZAY_A 1VPW_A 1DBQ_A 2PUA_A 1QQA_A 1PNR_A 1JHZ_A ....
Probab=45.56 E-value=43 Score=27.24 Aligned_cols=44 Identities=9% Similarity=0.240 Sum_probs=34.2
Q ss_pred HHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 300 AQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 300 AeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
|+.+.++|..++.|= +.....++.|++.|.+++++.|+.+.+..
T Consensus 1 ~~~L~~~G~r~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~ 46 (160)
T PF13377_consen 1 VDYLIERGHRRIAFIGGPPNSSVSRERLEGFREALKEHGIEFEELI 46 (160)
T ss_dssp HHHHHHTT-SSEEEEESSTTSHHHHHHHHHHHHHHHHTTSEEEGEE
T ss_pred ChHHHHCCCCeEEEEecCCCChhHHHHHHHHHHHHHHCCCCCCeeE
Confidence 577889999987642 24556788999999999999999977543
No 34
>PRK09492 treR trehalose repressor; Provisional
Probab=45.09 E-value=51 Score=30.05 Aligned_cols=45 Identities=13% Similarity=0.093 Sum_probs=31.3
Q ss_pred HHHHHHHHhCCCCEEEEcC--CCCc-chhhHHHHHHHHHHHcCcEEEE
Q 018389 297 GILAQRALADDIHDVVYTP--RKGE-KLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 297 kvLAeRakekGI~~VVFDp--R~Gy-kYHGRVKAfADAaRE~GL~FK~ 341 (357)
..+++.+.+.|...|.|=- .... ....|+..|.+++++.||.+..
T Consensus 164 ~~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~ 211 (315)
T PRK09492 164 KLLMQRLYDQGHRHISYLGVDHSDVTTGKRRHQAYLAFCKQHKLTPVA 211 (315)
T ss_pred HHHHHHHHHcCCCeEEEEcCCcccchhHHHHHHHHHHHHHHcCCCcee
Confidence 3455666678999988641 1111 2258999999999999997643
No 35
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=44.28 E-value=48 Score=27.42 Aligned_cols=42 Identities=21% Similarity=0.340 Sum_probs=27.3
Q ss_pred HHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 298 ILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 298 vLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
-|.+.+.+.+|++|+... ...-++.|+.+.+.+++.|+.+++
T Consensus 132 ~l~~~~~~~~id~v~ial--~~~~~~~i~~ii~~~~~~~v~v~~ 173 (175)
T PF13727_consen 132 DLPELVREHDIDEVIIAL--PWSEEEQIKRIIEELENHGVRVRV 173 (175)
T ss_dssp GHHHHHHHHT--EEEE----TTS-HHHHHHHHHHHHTTT-EEEE
T ss_pred HHHHHHHhCCCCEEEEEc--CccCHHHHHHHHHHHHhCCCEEEE
Confidence 456677778888887663 223468889999999999988876
No 36
>PRK07449 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase; Validated
Probab=43.93 E-value=66 Score=33.19 Aligned_cols=45 Identities=9% Similarity=0.153 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHH-cCcEEEEEe
Q 018389 293 AAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIID-NGVNVKVKL 343 (357)
Q Consensus 293 a~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE-~GL~FK~~l 343 (357)
.++|..|++++.+.||+.|.-= .| +.+..|.+++.+ .||.|-.-.
T Consensus 9 ~~~a~~l~~~L~~~GV~~vFgv--pG----~~~~~l~~~l~~~~~i~~v~~~ 54 (568)
T PRK07449 9 TLWAAVILEELTRLGVRHVVIA--PG----SRSTPLTLAAAEHPRLRLHTHF 54 (568)
T ss_pred HHHHHHHHHHHHHcCCCEEEEC--CC----CccHHHHHHHHhCCCcEEEeec
Confidence 7899999999999999997665 36 678888888855 588886643
No 37
>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=43.79 E-value=37 Score=27.81 Aligned_cols=36 Identities=11% Similarity=0.252 Sum_probs=27.1
Q ss_pred cccccCCCCCCeEEEEEecCCeEEEEEEeCCCCeEE
Q 018389 234 FNQLTAPYHEPFCLDIYISKASVRACIVHRVTSKVV 269 (357)
Q Consensus 234 f~qrTd~Y~rPfRL~VfrSNKHIYAQVIDD~~GkTL 269 (357)
.|.......+..++.|....+.++.+|||..+|.||
T Consensus 46 ln~~~~~~~~~l~F~vde~~~~~vVkViD~~T~eVI 81 (107)
T PF03646_consen 46 LNEFLQALNTSLRFSVDEESGRVVVKVIDKETGEVI 81 (107)
T ss_dssp HHHHHTTSS--EEEEEEEETTEEEEEEEETTT-SEE
T ss_pred HHHHHHhcCCceEEEEecCCCcEEEEEEECCCCcEE
Confidence 344444556667899999999999999999999998
No 38
>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=43.11 E-value=55 Score=31.35 Aligned_cols=57 Identities=26% Similarity=0.309 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHhCCCCE-------EEEcCCCCcchh----------h-HHHHHHHHHHHcCcEEEEE
Q 018389 285 STRNATACAAVGGILAQRALADDIHD-------VVYTPRKGEKLE----------G-KLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 285 St~NveAAa~VGkvLAeRakekGI~~-------VVFDpR~GykYH----------G-RVKAfADAaRE~GL~FK~~ 342 (357)
.+.|.+.|..+|..+|+-++..||+- |..+|+.| ++. + -..||+++++++||---+|
T Consensus 80 at~d~~~a~~~g~~~a~el~~~Gin~~~aPv~Dv~~~p~~~-~~~rsfgeDp~~v~~~~~a~v~G~q~~gv~~~~K 154 (299)
T PF00933_consen 80 ATWDPELAYEVGRIIARELRALGINVNFAPVVDVNRNPRWG-RGERSFGEDPDLVAEMARAFVRGLQGAGVAATAK 154 (299)
T ss_dssp HHTCHHHHHHHHHHHHHHHHHTT-SEEEEEB----SSTTST-TGGGSS-SSHHHHHHHHHHHHHHHHCTTSEEEEE
T ss_pred hhccchHHHHHHHHHHHHHHHhhhccccccceeeeeecccc-ccccccchhHHHHHHHHHHHhccccccccccccc
Confidence 35688999999999999999999996 44666665 332 1 2679999999999865543
No 39
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=42.92 E-value=49 Score=30.26 Aligned_cols=44 Identities=16% Similarity=0.224 Sum_probs=31.7
Q ss_pred HHHHHHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 296 GGILAQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~F 339 (357)
|+.+++.+++.|-.+|.|= +........|+..|.+++.+.|+.+
T Consensus 162 ~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~ 207 (327)
T PRK10423 162 GDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNI 207 (327)
T ss_pred HHHHHHHHHHcCCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCC
Confidence 5566677777899988763 2222234579999999999999864
No 40
>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=42.11 E-value=2e+02 Score=29.56 Aligned_cols=82 Identities=18% Similarity=0.257 Sum_probs=60.2
Q ss_pred cCCeEEEEEEeCCCCeEEEEEcccchhhhcccC------CCCCHHHHHHHHHHHHHHH-HhC--------CCCEEEEcCC
Q 018389 252 SKASVRACIVHRVTSKVVVVAHSISKDMKFDLD------STRNATACAAVGGILAQRA-LAD--------DIHDVVYTPR 316 (357)
Q Consensus 252 SNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~------St~NveAAa~VGkvLAeRa-kek--------GI~~VVFDpR 316 (357)
.+..|.+-+|....+.||+..|+.-=.++-... -..|..+...|+++++-+. ... .|+.|+|. -
T Consensus 106 Dg~~iEtV~i~~~~~~tlCvSsQvGC~m~C~FCatg~~g~~RnLt~~EIv~Qv~~~~~~~~~~~~~~~~~~i~nVvfm-G 184 (373)
T PRK14459 106 DGTLVESVLMRYPDRATLCISSQAGCGMACPFCATGQGGLTRNLSTAEIVEQVRAAARALRDGEVPGGPGRLSNVVFM-G 184 (373)
T ss_pred CCCEEEEEEEEEcCCceEEEEecCCCCCcCCCCCCCCCCCCCccCHHHHHHHHHHHHHHhhhcccccCCCceeEEEEe-c
Confidence 688999999999999999887777666644322 2357899999999987543 222 28999999 3
Q ss_pred CCcchh--hHHHHHHHHHHH
Q 018389 317 KGEKLE--GKLQIVLQAIID 334 (357)
Q Consensus 317 ~GykYH--GRVKAfADAaRE 334 (357)
-|+..+ .-|..+++.+.+
T Consensus 185 mGEPLlN~d~V~~~i~~l~~ 204 (373)
T PRK14459 185 MGEPLANYKRVVAAVRRITA 204 (373)
T ss_pred CCcchhhHHHHHHHHHHHhC
Confidence 388664 667777787776
No 41
>PRK14467 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=42.00 E-value=1.4e+02 Score=30.07 Aligned_cols=86 Identities=13% Similarity=0.280 Sum_probs=62.5
Q ss_pred cCCeEEEEEEeCCCCeEEEEEcccchhhhcccCC------CCCHHHHHHHHHHHHHHHH--hCCCCEEEEcCCCCcchh-
Q 018389 252 SKASVRACIVHRVTSKVVVVAHSISKDMKFDLDS------TRNATACAAVGGILAQRAL--ADDIHDVVYTPRKGEKLE- 322 (357)
Q Consensus 252 SNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~S------t~NveAAa~VGkvLAeRak--ekGI~~VVFDpR~GykYH- 322 (357)
.+..|.+-+|-+..+.||+..|+.-=.++-.... ..|..+...|++++.-+.. ..+|..|||- .-|+..+
T Consensus 84 dg~~vE~V~i~~~~~~t~cvSsq~GC~l~C~FC~t~~~G~~rnlt~~EIv~Qv~~~~~~~~~~~v~~Vvfm-GmGEPL~N 162 (348)
T PRK14467 84 DGHTIETVLIKERDHLTLCVSSQVGCAVGCKFCATAKDGLIRNLRTAEIIDQYIQVQKFLGENRIRNVVFM-GMGEPLAN 162 (348)
T ss_pred CCCEEEEEEEEeCCCcEEEEEcCCCCCCcCcCCCCCCCCCcCCCCHHHHHHHHHHHHHHhccCCCCeEEEE-ccChhhcC
Confidence 5788999999988899998877776656443221 2488899999999876653 2469999999 3377655
Q ss_pred -hHHHHHHHHHHH-cCcE
Q 018389 323 -GKLQIVLQAIID-NGVN 338 (357)
Q Consensus 323 -GRVKAfADAaRE-~GL~ 338 (357)
.-|..+++.+.+ .||.
T Consensus 163 ~d~v~~~l~~l~~~~gl~ 180 (348)
T PRK14467 163 YENVRKAVQIMTSPWGLD 180 (348)
T ss_pred HHHHHHHHHHHcChhccC
Confidence 667777777765 6764
No 42
>PRK07710 acetolactate synthase catalytic subunit; Reviewed
Probab=41.63 E-value=50 Score=34.25 Aligned_cols=44 Identities=14% Similarity=0.197 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEE
Q 018389 293 AAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 293 a~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~ 342 (357)
..++..|++++++.||+.|.-= .| |.+..|.+++.+.||.+-..
T Consensus 16 ~~~~~~i~~~L~~~Gv~~vFg~--pG----~~~~~l~~al~~~~i~~i~~ 59 (571)
T PRK07710 16 MTGAQMLIEALEKEGVEVIFGY--PG----GAVLPLYDALYDCGIPHILT 59 (571)
T ss_pred chHHHHHHHHHHHcCCCEEEeC--CC----cchHHHHHHHHhcCCcEEEe
Confidence 3579999999999999996555 46 78889999998889987654
No 43
>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=41.57 E-value=82 Score=33.28 Aligned_cols=53 Identities=11% Similarity=0.112 Sum_probs=44.2
Q ss_pred CCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 286 TRNATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 286 t~NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~F 339 (357)
++.+..++..|..||+++++.||..|+..+--| .-|=-+...+..+..+||..
T Consensus 315 gt~~~~a~~~g~eIa~~Lk~dgVDAVILTstCg-tC~r~~a~m~keiE~~GiPv 367 (431)
T TIGR01918 315 GTTVAESKQFAKEFVVELKQGGVDAVILTSTUG-TCTRCGATMVKEIERAGIPV 367 (431)
T ss_pred CchHHHHHHHHHHHHHHHHHcCCCEEEEcCCCC-cchhHHHHHHHHHHHcCCCE
Confidence 467788899999999999999999999995323 55666788899999999865
No 44
>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=40.56 E-value=74 Score=28.05 Aligned_cols=45 Identities=9% Similarity=0.016 Sum_probs=32.6
Q ss_pred HHHHHHHHHHhCCCCEEEE--cCCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 295 VGGILAQRALADDIHDVVY--TPRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVF--DpR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
.|+.+|+.+++.|-.++.| . ........|++.|.+++.+.|+.+.
T Consensus 102 ~g~~a~~~L~~~g~~~i~~~~~-~~~~~~~~R~~gf~~~~~~~~~~~~ 148 (263)
T cd06280 102 AARTLVEHLVAQGYRRIGGLFG-NASTTGAERRAGYEDAMRRHGLAPD 148 (263)
T ss_pred HHHHHHHHHHHCCCceEEEEeC-CCCCCHHHHHHHHHHHHHHcCCCCC
Confidence 4556677777789888764 3 2233445899999999999998764
No 45
>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=39.51 E-value=87 Score=27.73 Aligned_cols=45 Identities=13% Similarity=0.234 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhCCCCEEEEcCCCCc-chhhHHHHHHHHHHHcCcEE
Q 018389 295 VGGILAQRALADDIHDVVYTPRKGE-KLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFDpR~Gy-kYHGRVKAfADAaRE~GL~F 339 (357)
.|+.+|+.+.+.|...|.|=-..+. -...|+++|.+++++.|+.+
T Consensus 96 ~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~~ 141 (265)
T cd01543 96 IGRMAAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEAGYEC 141 (265)
T ss_pred HHHHHHHHHHHCCCcEEEEEcCCCCHHHHHHHHHHHHHHHHcCCcc
Confidence 4556677777889998876411222 22478999999999999876
No 46
>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=38.31 E-value=84 Score=27.53 Aligned_cols=46 Identities=13% Similarity=0.159 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhCCCCEEEE--cCCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 295 VGGILAQRALADDIHDVVY--TPRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVF--DpR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
.|+.+|+.+.+.|..+|.| ........+-|.+.|.+++.+.|+.+.
T Consensus 104 ~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~ 151 (269)
T cd06275 104 GGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPVN 151 (269)
T ss_pred HHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCCCC
Confidence 3445556666678888765 222333445689999999999998754
No 47
>PRK13398 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=37.22 E-value=61 Score=31.36 Aligned_cols=52 Identities=15% Similarity=0.266 Sum_probs=36.5
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEE---EEcCCCC-cchhh----HHHHHHHHHHHcCcEEEEEe
Q 018389 288 NATACAAVGGILAQRALADDIHDV---VYTPRKG-EKLEG----KLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~V---VFDpR~G-ykYHG----RVKAfADAaRE~GL~FK~~l 343 (357)
+.+++.. .|+++++.|+.-| .|+||+- +-|.| -++.+.+.+++.||.|-..+
T Consensus 39 ~~~~~~~----~A~~lk~~g~~~~r~~~~kpRTs~~s~~G~g~~gl~~l~~~~~~~Gl~~~te~ 98 (266)
T PRK13398 39 SEEQMVK----VAEKLKELGVHMLRGGAFKPRTSPYSFQGLGEEGLKILKEVGDKYNLPVVTEV 98 (266)
T ss_pred CHHHHHH----HHHHHHHcCCCEEEEeeecCCCCCCccCCcHHHHHHHHHHHHHHcCCCEEEee
Confidence 4455544 4666677888755 3888876 55554 57889999999999886543
No 48
>PF14419 SPOUT_MTase_2: AF2226-like SPOUT RNA Methylase fused to THUMP
Probab=36.96 E-value=98 Score=29.13 Aligned_cols=52 Identities=17% Similarity=0.300 Sum_probs=41.4
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHc
Q 018389 283 LDSTRNATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDN 335 (357)
Q Consensus 283 L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~ 335 (357)
+..-++.+||+++|+-|+.-+....|.+.+--| .|+.--=-+..|+++++++
T Consensus 7 ~pYlGd~~a~r~mGerIGRaaQ~FEV~eLiiap-~~~vda~eL~~Fl~gV~~G 58 (173)
T PF14419_consen 7 MPYLGDLKACRKMGERIGRAAQAFEVKELIIAP-KEKVDAYELMEFLRGVREG 58 (173)
T ss_pred ccccCCHHHHHHHHHHHhHHHhhcchheEEEec-cCccCHHHHHHHHHHHHHh
Confidence 455679999999999999999999999988774 4443334577888888876
No 49
>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=36.94 E-value=87 Score=27.39 Aligned_cols=44 Identities=9% Similarity=0.090 Sum_probs=30.6
Q ss_pred HHHHHHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 296 GGILAQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~F 339 (357)
|..+++.+.+.|..++.|= +......+.|+..|.+++++.|+.+
T Consensus 102 ~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~ 147 (260)
T cd06286 102 FYEALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTP 147 (260)
T ss_pred HHHHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCCC
Confidence 4455566667798888653 1122344589999999999999765
No 50
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=36.89 E-value=72 Score=32.93 Aligned_cols=55 Identities=22% Similarity=0.294 Sum_probs=47.2
Q ss_pred CCHHHHHHHHHH-----------------HHHHHHhCCCCEEEEcCCCCcch-hhHHHHHHHHHHHcCcEEEEE
Q 018389 287 RNATACAAVGGI-----------------LAQRALADDIHDVVYTPRKGEKL-EGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 287 ~NveAAa~VGkv-----------------LAeRakekGI~~VVFDpR~GykY-HGRVKAfADAaRE~GL~FK~~ 342 (357)
.|.++|..++.+ ||..|.+.|+..+-..| +.... ..+|+++++++++.|+...+=
T Consensus 64 ~~~~~a~al~~I~~~~~iPlvADIHFd~~lAl~a~~~G~~~iRINP-GNig~~~~~v~~vv~~ak~~~ipIRIG 136 (360)
T PRK00366 64 PDMEAAAALPEIKKQLPVPLVADIHFDYRLALAAAEAGADALRINP-GNIGKRDERVREVVEAAKDYGIPIRIG 136 (360)
T ss_pred CCHHHHHhHHHHHHcCCCCEEEecCCCHHHHHHHHHhCCCEEEECC-CCCCchHHHHHHHHHHHHHCCCCEEEe
Confidence 488999999975 88999999999999996 44444 789999999999999988763
No 51
>COG0684 MenG Demethylmenaquinone methyltransferase [Coenzyme metabolism]
Probab=36.71 E-value=80 Score=30.16 Aligned_cols=89 Identities=12% Similarity=0.068 Sum_probs=62.7
Q ss_pred CCcccccccCCCCCCeEEEEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCC
Q 018389 230 RTPTFNQLTAPYHEPFCLDIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIH 309 (357)
Q Consensus 230 ~~~sf~qrTd~Y~rPfRL~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~ 309 (357)
....|.+++..+=+-+.+.++-.+-.++..|-....|.+|+....-+ + .++.+|.+||..|+..||.
T Consensus 35 ~i~p~~~~~~~~G~A~TV~~~~~d~~~~~al~~~~~GdVLVid~~g~------------~-~~A~~Gd~la~~a~~~G~~ 101 (210)
T COG0684 35 GIRPFGGRSSFVGPAVTVRCFPDDWLLHVALEQAGPGDVLVIDGGGD------------L-RRALWGDLLATLAKVRGWA 101 (210)
T ss_pred ccccCCCCCcceeEEEEEEEeCCCchhhheeecCCCCCEEEEeCCCC------------c-ceeehHHHHHHHHHHcCcc
Confidence 45556666666666677888888888888666667888887765322 1 5678999999999999999
Q ss_pred EEEEcCCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 310 DVVYTPRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 310 ~VVFDpR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
-+|-| ++ |.- ++.++|-|+.+.
T Consensus 102 GvVid--G~------vRD-v~~l~el~~pv~ 123 (210)
T COG0684 102 GVVID--GA------VRD-VDELRELDFPVF 123 (210)
T ss_pred EEEEe--ce------eec-hHHHhhcCCCeE
Confidence 99988 22 222 345666665443
No 52
>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=36.09 E-value=87 Score=27.47 Aligned_cols=45 Identities=13% Similarity=0.109 Sum_probs=30.9
Q ss_pred HHHHHHHHHhCCCCEEEEc-CCCCcc-hhhHHHHHHHHHHHcCcEEE
Q 018389 296 GGILAQRALADDIHDVVYT-PRKGEK-LEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD-pR~Gyk-YHGRVKAfADAaRE~GL~FK 340 (357)
|+.+++.+.++|..++.|= ...+.. ...|...|.+++++.|+.+.
T Consensus 105 ~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~ 151 (270)
T cd06296 105 GLAATEHLLELGHRRIGFITGPPDLLCSRARLDGYRAALAEAGIPVD 151 (270)
T ss_pred HHHHHHHHHHcCCCcEEEEcCCCcchhHHHHHHHHHHHHHHcCCCCC
Confidence 5555666667788888753 122332 34889999999999998653
No 53
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=35.97 E-value=1.8e+02 Score=26.10 Aligned_cols=89 Identities=18% Similarity=0.194 Sum_probs=51.0
Q ss_pred EEEecCCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEcCC--CCcchh---
Q 018389 248 DIYISKASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGILAQRALADDIHDVVYTPR--KGEKLE--- 322 (357)
Q Consensus 248 ~VfrSNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvLAeRakekGI~~VVFDpR--~GykYH--- 322 (357)
.||-|-.-....|.|-....||+-. |---.+|.+ ..-+..-||-.-+.-.|.+|++.||+.+.+-.| +|-+-.
T Consensus 20 hi~asfndtfvhitdlsg~eti~rv-tggmkvkad-rdesspyaamlaaqdva~kck~~gi~alh~klratgg~ktktpg 97 (139)
T KOG0407|consen 20 HIFASFNDTFVHVTDLSGKETIVRV-TGGMKVKAD-RDESSPYAAMLAAQDVAAKCKELGITALHIKLRATGGTKTKTPG 97 (139)
T ss_pred EEEeecccceEEEeccCCceEEEEe-cCCeEEecc-cccCChHHHHHHHHHHHHHHHhcCeeEEEEEEEecCCcccCCCC
Confidence 3555555556666665555566543 333333332 122355677777888999999999999887653 222111
Q ss_pred -hHHHHHHHHHHHcCcEE
Q 018389 323 -GKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 323 -GRVKAfADAaRE~GL~F 339 (357)
| -++-+.+|-.+|+.+
T Consensus 98 pg-aqsalralar~gmri 114 (139)
T KOG0407|consen 98 PG-AQSALRALARSGMRI 114 (139)
T ss_pred cc-HHHHHHHHHHhccee
Confidence 2 233344555566654
No 54
>PRK04302 triosephosphate isomerase; Provisional
Probab=35.77 E-value=1e+02 Score=28.26 Aligned_cols=48 Identities=13% Similarity=0.120 Sum_probs=34.3
Q ss_pred HHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEE
Q 018389 295 VGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~ 342 (357)
-|++.++.+++.|+.-|.........+.+.+..+...+++.||..-+-
T Consensus 73 tg~~~~~~l~~~G~~~vii~~ser~~~~~e~~~~v~~a~~~Gl~~I~~ 120 (223)
T PRK04302 73 TGHILPEAVKDAGAVGTLINHSERRLTLADIEAVVERAKKLGLESVVC 120 (223)
T ss_pred hhhhHHHHHHHcCCCEEEEeccccccCHHHHHHHHHHHHHCCCeEEEE
Confidence 355668888888888887763223466677888888888888876653
No 55
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=35.58 E-value=1e+02 Score=24.35 Aligned_cols=42 Identities=21% Similarity=0.235 Sum_probs=32.4
Q ss_pred HHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 298 ILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 298 vLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
-++..|+++|+ .|.-+ ...-.--.-.+.+++.+++.|+.+-|
T Consensus 77 ~~~~~~l~~g~-~v~~E-KP~~~~~~~~~~l~~~a~~~~~~~~V 118 (120)
T PF01408_consen 77 EIAKKALEAGK-HVLVE-KPLALTLEEAEELVEAAKEKGVKVMV 118 (120)
T ss_dssp HHHHHHHHTTS-EEEEE-SSSSSSHHHHHHHHHHHHHHTSCEEE
T ss_pred HHHHHHHHcCC-EEEEE-cCCcCCHHHHHHHHHHHHHhCCEEEE
Confidence 46899999999 56666 34444447789999999999998765
No 56
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=34.27 E-value=1.8e+02 Score=21.39 Aligned_cols=42 Identities=19% Similarity=0.218 Sum_probs=29.5
Q ss_pred HHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 297 GILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 297 kvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
+-++++|++.|+..|.+.-.+ -+.|-+ .+.+.+++.||++-.
T Consensus 18 ~~~~~~a~~~g~~~v~iTDh~--~~~~~~-~~~~~~~~~gi~~i~ 59 (67)
T smart00481 18 EELVKRAKELGLKAIAITDHG--NLFGAV-EFYKAAKKAGIKPII 59 (67)
T ss_pred HHHHHHHHHcCCCEEEEeeCC--cccCHH-HHHHHHHHcCCeEEE
Confidence 457899999999999876222 344544 555777888887654
No 57
>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=34.27 E-value=2.1e+02 Score=24.11 Aligned_cols=53 Identities=15% Similarity=0.039 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHHHHHHHHhC-CCCEE--EEcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 287 RNATACAAVGGILAQRALAD-DIHDV--VYTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 287 ~NveAAa~VGkvLAeRakek-GI~~V--VFDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
-+.+.+..+|..+|.-..+. +-..| -+|.|.. -.--.++++++|+..|+.+..
T Consensus 18 lt~~~~~~~~~a~~~~~~~~~~~~~VvVg~D~R~~--s~~~~~~~~~~l~~~G~~V~~ 73 (137)
T PF02878_consen 18 LTPEFAARLAQAFASYLKEKGNGSRVVVGRDTRPS--SPMLAKALAAGLRANGVDVID 73 (137)
T ss_dssp BSHHHHHHHHHHHHHHHHHTTTSSEEEEEE-SSTT--HHHHHHHHHHHHHHTTEEEEE
T ss_pred CCHHHHHHHHHHHHHhhcccCCCCeEEEEEcccCC--HHHHHHHHHHHHhhccccccc
Confidence 47899999999999998885 33343 4885443 112368999999999998764
No 58
>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=33.90 E-value=97 Score=26.42 Aligned_cols=44 Identities=7% Similarity=0.108 Sum_probs=29.8
Q ss_pred HHHHHHHHHhCCCCEEEE-cCCCCc-chhhHHHHHHHHHHHcCcEE
Q 018389 296 GGILAQRALADDIHDVVY-TPRKGE-KLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 296 GkvLAeRakekGI~~VVF-DpR~Gy-kYHGRVKAfADAaRE~GL~F 339 (357)
|+.+|+.+.+.|..+|.+ ....+. -.+.|.+.|.+++.+.|+.+
T Consensus 104 g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~~~ 149 (264)
T cd06267 104 AYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAGIPL 149 (264)
T ss_pred HHHHHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHHHcCCCC
Confidence 555666666678888764 212332 34589999999999999644
No 59
>PRK07523 gluconate 5-dehydrogenase; Provisional
Probab=33.55 E-value=87 Score=27.82 Aligned_cols=42 Identities=17% Similarity=0.252 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcE
Q 018389 292 CAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVN 338 (357)
Q Consensus 292 Aa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~ 338 (357)
+.-||..||+++.+.|.+=++.+ |+. .++.++.+.+++.|..
T Consensus 19 ~g~iG~~ia~~l~~~G~~V~~~~-r~~----~~~~~~~~~i~~~~~~ 60 (255)
T PRK07523 19 SQGIGYALAEGLAQAGAEVILNG-RDP----AKLAAAAESLKGQGLS 60 (255)
T ss_pred cchHHHHHHHHHHHcCCEEEEEe-CCH----HHHHHHHHHHHhcCce
Confidence 45789999999999998655677 554 4566677777766643
No 60
>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []. It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.
Probab=33.53 E-value=1.6e+02 Score=26.15 Aligned_cols=51 Identities=12% Similarity=0.225 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 290 TACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 290 eAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
..|..+...+.+.|.+.|.+ |+|| +...-...+..+++.++++|-.+.+.+
T Consensus 76 ~~a~~~~~~~~~~a~~~~~n-ii~E--~tl~~~~~~~~~~~~~k~~GY~v~l~~ 126 (199)
T PF06414_consen 76 KEASRLAEKLIEYAIENRYN-IIFE--GTLSNPSKLRKLIREAKAAGYKVELYY 126 (199)
T ss_dssp HHHHHHHHHHHHHHHHCT---EEEE----TTSSHHHHHHHHHHHCTT-EEEEEE
T ss_pred HHHHHHHHHHHHHHHHcCCC-EEEe--cCCCChhHHHHHHHHHHcCCceEEEEE
Confidence 45666777788888999984 6677 223323566669999999998877654
No 61
>PF02065 Melibiase: Melibiase; InterPro: IPR000111 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycosyl hydrolase family 27, family 31 and family 36 alpha-galactosidases form the glycosyl hydrolase clan GH-D (acc_GH from CAZY), a superfamily of alpha-galactosidases, alpha-N-acetylgalactosaminidases, and isomaltodextranases which are likely to share a common catalytic mechanism and structural topology. Alpha-galactosidase (3.2.1.22 from EC) (melibiase) [] catalyzes the hydrolysis of melibiose into galactose and glucose. In man, the deficiency of this enzyme is the cause of Fabry's disease (X-linked sphingolipidosis). Alpha-galactosidase is present in a variety of organisms. There is a considerable degree of similarity in the sequence of alpha-galactosidase from various eukaryotic species. Escherichia coli alpha-galactosidase (gene melA), which requires NAD and magnesium as cofactors, is not structurally related to the eukaryotic enzymes; by contrast, an Escherichia coli plasmid encoded alpha-galactosidase (gene rafA P16551 from SWISSPROT) [] contains a region of about 50 amino acids which is similar to a domain of the eukaryotic alpha-galactosidases. Alpha-N-acetylgalactosaminidase (3.2.1.49 from EC) [] catalyzes the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D- galactosaminides. In man, the deficiency of this enzyme is the cause of Schindler and Kanzaki diseases. The sequence of this enzyme is highly related to that of the eukaryotic alpha-galactosidases.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1KTC_A 1KTB_A 1UAS_A 3H55_A 3H53_A 3IGU_B 3H54_A 3LRM_A 3LRL_A 3LRK_A ....
Probab=33.45 E-value=1e+02 Score=31.52 Aligned_cols=45 Identities=18% Similarity=0.072 Sum_probs=32.9
Q ss_pred HHHHHHhCCCCEEEEcCCCCc------------------chhhHHHHHHHHHHHcCcEEEEEee
Q 018389 299 LAQRALADDIHDVVYTPRKGE------------------KLEGKLQIVLQAIIDNGVNVKVKLK 344 (357)
Q Consensus 299 LAeRakekGI~~VVFDpR~Gy------------------kYHGRVKAfADAaRE~GL~FK~~lk 344 (357)
+|+.|++.||+-++-| -+.+ ++=+-+++|++.+++.|++|.+-+-
T Consensus 63 ~a~~~~~~G~e~fviD-DGW~~~r~~d~~~~GdW~~~~~kFP~Gl~~l~~~i~~~Gmk~GlW~e 125 (394)
T PF02065_consen 63 LADAAAELGYEYFVID-DGWFGGRDDDNAGLGDWEPDPKKFPNGLKPLADYIHSLGMKFGLWFE 125 (394)
T ss_dssp HHHHHHHHT-SEEEE--SSSBCTESTTTSTTSBECBBTTTSTTHHHHHHHHHHHTT-EEEEEEE
T ss_pred HHHHHHHhCCEEEEEc-CccccccCCCcccCCceeEChhhhCCcHHHHHHHHHHCCCeEEEEec
Confidence 4788899999999977 3433 2323499999999999999999873
No 62
>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=33.40 E-value=87 Score=27.87 Aligned_cols=41 Identities=17% Similarity=0.178 Sum_probs=31.2
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVN 338 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~ 338 (357)
-.++|..+|+.||++ |+ .|++- |. -|--.+.++++.++|-.
T Consensus 16 ~~~~A~~lg~~La~~----g~-~lv~G---g~--~GlM~a~a~ga~~~gg~ 56 (159)
T TIGR00725 16 LYEIAYRLGKELAKK----GH-ILING---GR--TGVMEAVSKGAREAGGL 56 (159)
T ss_pred HHHHHHHHHHHHHHC----CC-EEEcC---Cc--hhHHHHHHHHHHHCCCe
Confidence 458899999999884 76 56663 42 39999999999888753
No 63
>PRK11579 putative oxidoreductase; Provisional
Probab=33.32 E-value=1.1e+02 Score=29.46 Aligned_cols=33 Identities=9% Similarity=0.043 Sum_probs=15.6
Q ss_pred HHHHHHhCCCCEEE-EcCCCCcchhhHHHHHHHHHHHc
Q 018389 299 LAQRALADDIHDVV-YTPRKGEKLEGKLQIVLQAIIDN 335 (357)
Q Consensus 299 LAeRakekGI~~VV-FDpR~GykYHGRVKAfADAaRE~ 335 (357)
|.+.|.+.|+.-++ |. ++|+.-+..+-+.+.++
T Consensus 107 l~~~a~~~g~~l~v~~~----~R~~p~~~~~k~~i~~g 140 (346)
T PRK11579 107 LDALAKSAGRVLSVFHN----RRWDSDFLTLKALLAEG 140 (346)
T ss_pred HHHHHHHhCCEEEEEee----ccCCHHHHHHHHHHhcC
Confidence 34445555655333 33 34445555555554443
No 64
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=32.80 E-value=86 Score=28.36 Aligned_cols=43 Identities=16% Similarity=0.290 Sum_probs=36.4
Q ss_pred HHHHHHHHHHhCCCCEE----------EEcCCCCcchhhHHHHHHHHHHHcCcE
Q 018389 295 VGGILAQRALADDIHDV----------VYTPRKGEKLEGKLQIVLQAIIDNGVN 338 (357)
Q Consensus 295 VGkvLAeRakekGI~~V----------VFDpR~GykYHGRVKAfADAaRE~GL~ 338 (357)
|--.++.+|+..|+.-| .|+ ++.|+-.-|+..+.+.|.|-||.
T Consensus 41 vn~~fvl~Al~~GaDGV~v~GC~~geCHy~-~GN~ka~rR~~~lke~l~elgie 93 (132)
T COG1908 41 VNPEFVLKALRKGADGVLVAGCKIGECHYI-SGNYKAKRRMELLKELLKELGIE 93 (132)
T ss_pred cCHHHHHHHHHcCCCeEEEecccccceeee-ccchHHHHHHHHHHHHHHHhCCC
Confidence 33457788999998875 488 89999999999999999999985
No 65
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=32.71 E-value=1.1e+02 Score=31.25 Aligned_cols=46 Identities=7% Similarity=0.095 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhCCCCEEEEcCCCCcchh-hHHHHHHHHHHHcCcEEEE
Q 018389 295 VGGILAQRALADDIHDVVYTPRKGEKLE-GKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFDpR~GykYH-GRVKAfADAaRE~GL~FK~ 341 (357)
...+|.+-|.+.||+.|++. +....|. -|-+++.+.+++.||.+..
T Consensus 75 ~~~~l~~l~~~~~i~~v~~~-~~~~~~~~~rd~~v~~~l~~~gi~~~~ 121 (475)
T TIGR02766 75 TVAALLDCVRSTGATRLFFN-HLYDPVSLVRDHRAKEVLTAQGISVQS 121 (475)
T ss_pred HHHHHHHHHHHcCCCEEEEe-cccCHHHHHHHHHHHHHHHHcCCEEEE
Confidence 44567888899999999999 5555554 5678899999999998864
No 66
>TIGR02571 ComEB ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.
Probab=32.59 E-value=84 Score=28.08 Aligned_cols=36 Identities=14% Similarity=0.296 Sum_probs=25.6
Q ss_pred HHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 300 AQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 300 AeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
|..+..+||.+|+|- ..|...+ +-.+-|+++||.+.
T Consensus 101 a~ai~~agI~~Vvy~--~~~~~~~---~~~~~l~~~gi~v~ 136 (151)
T TIGR02571 101 TKSIIQAGIKKIYYA--QDYHNHP---YAIELFEQAGVELK 136 (151)
T ss_pred HHHHHHhCCCEEEEc--cCCCCcH---HHHHHHHHCCCEEE
Confidence 445567899999996 2343332 34689999999886
No 67
>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=31.77 E-value=1.7e+02 Score=25.82 Aligned_cols=54 Identities=19% Similarity=0.196 Sum_probs=38.9
Q ss_pred CCHHHHHHHHHHHHHHHHhC--CCCEEEE--cCCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 287 RNATACAAVGGILAQRALAD--DIHDVVY--TPRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 287 ~NveAAa~VGkvLAeRakek--GI~~VVF--DpR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
.+..++..+++.|++++.+. |-.+|.| .+.......-|++.|.+++.+.|+.+.
T Consensus 102 d~~~~g~~~~~~l~~~~~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~ 159 (277)
T cd06319 102 DNYEGAYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCDLA 159 (277)
T ss_pred ccHHHHHHHHHHHHHHHHhhCCCCCcEEEEeccCCCccHHHHHHHHHHHHHhcCCceE
Confidence 46788899999999998865 4455543 211222345889999999999998754
No 68
>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=31.67 E-value=69 Score=23.87 Aligned_cols=44 Identities=20% Similarity=0.307 Sum_probs=30.9
Q ss_pred HHHHHHHHHhCC--CCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEE
Q 018389 296 GGILAQRALADD--IHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 296 GkvLAeRakekG--I~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~ 342 (357)
|.-+.+-|++.| |..|.+.. + ....++..+.+.+++.|+.+.+-
T Consensus 4 G~~~V~eaL~~~~~i~~l~~~~-~--~~~~~~~~i~~~~~~~~i~v~~v 49 (76)
T PF08032_consen 4 GRHAVEEALKSGPRIKKLFVTE-E--KADKRIKEILKLAKKKGIPVYEV 49 (76)
T ss_dssp SHHHHHHHHHCTGGEEEEEEET-T-----CCTHHHHHHHHHCT-EEEEE
T ss_pred EHHHHHHHHcCCCCccEEEEEc-C--ccchhHHHHHHHHHHcCCeEEEe
Confidence 555667777777 78888883 3 55567889999999999988764
No 69
>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=31.50 E-value=1.2e+02 Score=26.72 Aligned_cols=44 Identities=11% Similarity=0.132 Sum_probs=30.0
Q ss_pred HHHHHHHHHhCCCCEEEEc-CCCCc-chhhHHHHHHHHHHHcCcEE
Q 018389 296 GGILAQRALADDIHDVVYT-PRKGE-KLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD-pR~Gy-kYHGRVKAfADAaRE~GL~F 339 (357)
|+.+|+.+.+.|-..|.|= ...+. .-.-|.+.|.+++++.|+.+
T Consensus 104 ~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 149 (268)
T cd06270 104 GYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEAGIAL 149 (268)
T ss_pred HHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 5555666666787777642 12222 33478999999999999876
No 70
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=31.42 E-value=2.8e+02 Score=22.35 Aligned_cols=45 Identities=16% Similarity=0.111 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEE
Q 018389 295 VGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~ 342 (357)
+-..++..+++.|+. +++| ++.........+.+.+++.|..+.+-
T Consensus 58 ~~~~~~~~~l~~g~~-~vvd--~~~~~~~~r~~~~~~~~~~~~~~~~v 102 (143)
T PF13671_consen 58 ILNAAIRKALRNGNS-VVVD--NTNLSREERARLRELARKHGYPVRVV 102 (143)
T ss_dssp HHHHHHHHHHHTT-E-EEEE--SS--SHHHHHHHHHHHHHCTEEEEEE
T ss_pred HHHHHHHHHHHcCCC-ceec--cCcCCHHHHHHHHHHHHHcCCeEEEE
Confidence 333446677789988 6668 34455566689999999999876654
No 71
>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=30.80 E-value=2.4e+02 Score=21.32 Aligned_cols=48 Identities=19% Similarity=0.168 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcch----hhHHHHHHHHHHHcCcEEEEE
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKL----EGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykY----HGRVKAfADAaRE~GL~FK~~ 342 (357)
.+|--+|.-+.+.|.+-.+++ +..... .---+.+.+.+++.||++..-
T Consensus 9 ~ig~E~A~~l~~~g~~vtli~-~~~~~~~~~~~~~~~~~~~~l~~~gV~v~~~ 60 (80)
T PF00070_consen 9 FIGIELAEALAELGKEVTLIE-RSDRLLPGFDPDAAKILEEYLRKRGVEVHTN 60 (80)
T ss_dssp HHHHHHHHHHHHTTSEEEEEE-SSSSSSTTSSHHHHHHHHHHHHHTTEEEEES
T ss_pred HHHHHHHHHHHHhCcEEEEEe-ccchhhhhcCHHHHHHHHHHHHHCCCEEEeC
Confidence 456677777788898777788 555544 233566778999999988754
No 72
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=30.26 E-value=96 Score=28.92 Aligned_cols=44 Identities=14% Similarity=0.205 Sum_probs=31.1
Q ss_pred HHHHHHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 296 GGILAQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~F 339 (357)
|..+++.+.+.|-..|.|= +........|...|.+++.+.||.+
T Consensus 164 ~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~ 209 (343)
T PRK10727 164 AWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPA 209 (343)
T ss_pred HHHHHHHHHHCCCccEEEEeCCccccchHHHHHHHHHHHHHCCCCC
Confidence 4556667777898887753 1111234579999999999999864
No 73
>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=29.92 E-value=1.4e+02 Score=26.37 Aligned_cols=45 Identities=16% Similarity=0.224 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCCCCEEEEcC-CCCcc-hhhHHHHHHHHHHHcCcEE
Q 018389 295 VGGILAQRALADDIHDVVYTP-RKGEK-LEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFDp-R~Gyk-YHGRVKAfADAaRE~GL~F 339 (357)
.|+.+|+.+.+.|...|.|=. ..+.. -+.|...|.+++++.|+.+
T Consensus 112 ~g~~~a~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~ 158 (275)
T cd06295 112 GGRLATEHLLARGRRRIAFLGGPQDMPEGEERLEGYREALAEAGLPL 158 (275)
T ss_pred HHHHHHHHHHHCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHcCCCC
Confidence 455566667778988887531 12212 2378999999999999653
No 74
>PRK14466 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=29.88 E-value=71 Score=32.35 Aligned_cols=53 Identities=11% Similarity=0.203 Sum_probs=39.9
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchh----hHHHHHHHHHHHcCcEEEEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYTPRKGEKLE----GKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYH----GRVKAfADAaRE~GL~FK~~ 342 (357)
+.+.|..++++|... ...|.=+-|.|+.|..|. .+|.+|++.|++.||...|.
T Consensus 264 ~~e~a~~L~~ll~~~--~~~VNLIp~Np~~~~~~~~~s~~~~~~F~~~L~~~gi~~tvR 320 (345)
T PRK14466 264 SLKHAKELVKLLRGI--DCRVNLIRFHAIPGVDLEGSDMARMEAFRDYLTSHGVFTTIR 320 (345)
T ss_pred CHHHHHHHHHHHcCC--CceEEEEecCCCCCCCCcCCCHHHHHHHHHHHHHCCCcEEEe
Confidence 456788888877532 244556679988886665 79999999999999977664
No 75
>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=29.57 E-value=1.1e+02 Score=26.54 Aligned_cols=46 Identities=11% Similarity=0.161 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhCCCCEEEE-cCCCCc-chhhHHHHHHHHHHHcCcEEE
Q 018389 295 VGGILAQRALADDIHDVVY-TPRKGE-KLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVF-DpR~Gy-kYHGRVKAfADAaRE~GL~FK 340 (357)
.|+.+|+.+.+.|-.+|+| ....+. -.+.|+..|.+++.+.|+.+.
T Consensus 102 ~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~~~~~~~~~~ 149 (267)
T cd06284 102 AARLAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAEAGLPAD 149 (267)
T ss_pred HHHHHHHHHHHcCCceEEEEcCCccchhHHHHHHHHHHHHHHcCCCCC
Confidence 3455555666678888764 212232 235799999999999997543
No 76
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=29.47 E-value=1.3e+02 Score=27.80 Aligned_cols=48 Identities=8% Similarity=0.173 Sum_probs=31.1
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEcC-CCCc-chhhHHHHHHHHHHHcCcEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYTP-RKGE-KLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFDp-R~Gy-kYHGRVKAfADAaRE~GL~F 339 (357)
|..++.. +++.+++.|-.+|.|=. .... -...|+..|.+++.+.|+.+
T Consensus 166 ~~~~~~~----a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~ 215 (342)
T PRK10014 166 NMQAAQL----LTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPF 215 (342)
T ss_pred CHHHHHH----HHHHHHHCCCCEEEEEcCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 4454444 45555667888887631 1112 23579999999999999865
No 77
>PRK12738 kbaY tagatose-bisphosphate aldolase; Reviewed
Probab=29.31 E-value=1.5e+02 Score=29.29 Aligned_cols=45 Identities=9% Similarity=0.093 Sum_probs=37.1
Q ss_pred HHHHHHhCCCCEEEEcCCCCcchhh---HHHHHHHHHHHcCcEEEEEee
Q 018389 299 LAQRALADDIHDVVYTPRKGEKLEG---KLQIVLQAIIDNGVNVKVKLK 344 (357)
Q Consensus 299 LAeRakekGI~~VVFDpR~GykYHG---RVKAfADAaRE~GL~FK~~lk 344 (357)
+..+|+++|.+.|.|| .+...|+. ..+.+++-+...|+.+...|=
T Consensus 89 ~i~~ai~~GFtSVM~D-gS~lp~eeNi~~T~evv~~Ah~~gv~VEaElG 136 (286)
T PRK12738 89 DIRRKVHAGVRSAMID-GSHFPFAENVKLVKSVVDFCHSQDCSVEAELG 136 (286)
T ss_pred HHHHHHHcCCCeEeec-CCCCCHHHHHHHHHHHHHHHHHcCCeEEEEEE
Confidence 5678999999999999 67788885 456788888999998877664
No 78
>TIGR03457 sulphoacet_xsc sulfoacetaldehyde acetyltransferase. Members of this protein family are sulfoacetaldehyde acetyltransferase, an enzyme of taurine utilization. Taurine, or 2-aminoethanesulfonate, can be used by bacteria as a source of carbon, nitrogen, and sulfur.
Probab=29.28 E-value=93 Score=32.41 Aligned_cols=44 Identities=7% Similarity=0.139 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
.+|.+||+++++.||+. +|-. .| +.+-.|.|++.+.||.+..-.
T Consensus 3 ~~~~~l~~~L~~~GV~~-vFGi-pG----~~~~~l~dal~~~~i~~i~~r 46 (579)
T TIGR03457 3 TPSEAFVEVLVANGVTH-AFGI-MG----SAFMDAMDLFPPAGIRFIPVV 46 (579)
T ss_pred cHHHHHHHHHHHCCCCE-EEEc-cC----cchHHHHHHHhhcCCeEEEec
Confidence 46899999999999987 5552 45 456668889988899887643
No 79
>PRK06194 hypothetical protein; Provisional
Probab=29.21 E-value=1.2e+02 Score=27.51 Aligned_cols=43 Identities=16% Similarity=0.159 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcE
Q 018389 291 ACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVN 338 (357)
Q Consensus 291 AAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~ 338 (357)
++.-||..||+++.+.|..-++.| |.. .....+++.+...|..
T Consensus 14 asggIG~~la~~l~~~G~~V~~~~-r~~----~~~~~~~~~~~~~~~~ 56 (287)
T PRK06194 14 AASGFGLAFARIGAALGMKLVLAD-VQQ----DALDRAVAELRAQGAE 56 (287)
T ss_pred CccHHHHHHHHHHHHCCCEEEEEe-CCh----HHHHHHHHHHHhcCCe
Confidence 456799999999999998766778 554 4455566666555544
No 80
>PRK09542 manB phosphomannomutase/phosphoglucomutase; Reviewed
Probab=29.02 E-value=2.7e+02 Score=28.25 Aligned_cols=61 Identities=15% Similarity=0.139 Sum_probs=41.9
Q ss_pred hhcccCCCCCHHHHHHHHHHHHHHHHhCCCCEEE--EcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 279 MKFDLDSTRNATACAAVGGILAQRALADDIHDVV--YTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 279 IK~~L~St~NveAAa~VGkvLAeRakekGI~~VV--FDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
||......-+.+.|..||..+|.-..+.+-..|+ +|.|.. -.---.|++.+|..+|+.+..
T Consensus 6 iRG~~~~~lt~~~v~~l~~a~~~~l~~~~~~~VvVg~D~R~~--s~~l~~a~~~gL~s~G~~V~~ 68 (445)
T PRK09542 6 VRGVVGEQIDEDLVRDVGAAFARLMRAEGATTVVIGHDMRDS--SPELAAAFAEGVTAQGLDVVR 68 (445)
T ss_pred cccccCCCcCHHHHHHHHHHHHHHHHHcCCCeEEEEeCCCCC--HHHHHHHHHHHHHHCCCEEEE
Confidence 4433333347789999999999988765444444 785443 112368999999999998764
No 81
>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=28.99 E-value=1.8e+02 Score=27.21 Aligned_cols=47 Identities=13% Similarity=0.220 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhCCCCE-EEEc--CCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 295 VGGILAQRALADDIHD-VVYT--PRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 295 VGkvLAeRakekGI~~-VVFD--pR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
-|..+++.+++.|-.+ |.|= +..-.-...|++.|.+++.+.||.+.-
T Consensus 105 a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~~~~ 154 (279)
T PF00532_consen 105 AGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLPIDE 154 (279)
T ss_dssp HHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSCEEE
T ss_pred HHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCCCCc
Confidence 3456778888888888 6643 122223457899999999999996544
No 82
>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=28.99 E-value=1.4e+02 Score=26.00 Aligned_cols=45 Identities=7% Similarity=0.160 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCCCCEEEEc-CCCCcch-hhHHHHHHHHHHHcCcEE
Q 018389 295 VGGILAQRALADDIHDVVYT-PRKGEKL-EGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFD-pR~GykY-HGRVKAfADAaRE~GL~F 339 (357)
.|+.+|+.+.+.|-.+|++= ...++.. ..|...|.+++++.|+.+
T Consensus 105 ~g~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 151 (270)
T cd01545 105 AAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALAEAGLPL 151 (270)
T ss_pred HHHHHHHHHHHCCCceEEEEeCCCCchhHHHHHHHHHHHHHHcCCCC
Confidence 45556666666788887642 1234432 378899999999999876
No 83
>PF14488 DUF4434: Domain of unknown function (DUF4434)
Probab=28.57 E-value=1.4e+02 Score=26.80 Aligned_cols=43 Identities=23% Similarity=0.209 Sum_probs=31.2
Q ss_pred HHHHHhCCCCEEEEcCCCCc------chhh-----------HHHHHHHHHHHcCcEEEEEe
Q 018389 300 AQRALADDIHDVVYTPRKGE------KLEG-----------KLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 300 AeRakekGI~~VVFDpR~Gy------kYHG-----------RVKAfADAaRE~GL~FK~~l 343 (357)
-...++.||..|+.- +.|+ .-.+ -|.+++++|.+.|++|-|-|
T Consensus 26 ~~~m~~~GidtlIlq-~~~~~~~~~yps~~~~~~~~~~~~d~l~~~L~~A~~~Gmkv~~Gl 85 (166)
T PF14488_consen 26 FRAMKAIGIDTLILQ-WTGYGGFAFYPSKLSPGGFYMPPVDLLEMILDAADKYGMKVFVGL 85 (166)
T ss_pred HHHHHHcCCcEEEEE-EeecCCcccCCccccCccccCCcccHHHHHHHHHHHcCCEEEEeC
Confidence 345678899998744 2222 1123 68999999999999998866
No 84
>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=28.29 E-value=1.5e+02 Score=26.08 Aligned_cols=48 Identities=17% Similarity=0.138 Sum_probs=30.5
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~F 339 (357)
+.+++..++ +.+.++|-..|.|= +.....-..|++.|.+++.+.|+.+
T Consensus 99 ~~~a~~~~~----~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~ 148 (265)
T cd06290 99 NFQGGYLAT----QHLIDLGHRRIAHITGPRGHIDARDRLAGYRKALEEAGLEV 148 (265)
T ss_pred cHHHHHHHH----HHHHHCCCCeEEEEeCccccchhhHHHHHHHHHHHHcCCCC
Confidence 455555544 44555688887653 1111222378999999999999864
No 85
>PF14871 GHL6: Hypothetical glycosyl hydrolase 6
Probab=28.18 E-value=1.5e+02 Score=25.83 Aligned_cols=48 Identities=10% Similarity=0.143 Sum_probs=37.1
Q ss_pred HHHHHHHHhCCCCEEEEcCC--CCcchh-------------hHHHHHHHHHHHcCcEEEEEee
Q 018389 297 GILAQRALADDIHDVVYTPR--KGEKLE-------------GKLQIVLQAIIDNGVNVKVKLK 344 (357)
Q Consensus 297 kvLAeRakekGI~~VVFDpR--~GykYH-------------GRVKAfADAaRE~GL~FK~~lk 344 (357)
+.+++-++++|+..|+...+ +|+-|. .-+..+.+++++.||.+-+.+-
T Consensus 3 ~~~~~~lk~~~v~si~i~a~~h~g~ayYPt~~~~~hp~L~~Dllge~v~a~h~~Girv~ay~~ 65 (132)
T PF14871_consen 3 EQFVDTLKEAHVNSITIFAKCHGGYAYYPTKVGPRHPGLKRDLLGEQVEACHERGIRVPAYFD 65 (132)
T ss_pred HHHHHHHHHhCCCEEEEEcccccEEEEccCCCCcCCCCCCcCHHHHHHHHHHHCCCEEEEEEe
Confidence 35678889999999887545 555544 3479999999999999988763
No 86
>COG0673 MviM Predicted dehydrogenases and related proteins [General function prediction only]
Probab=28.01 E-value=1.3e+02 Score=28.03 Aligned_cols=34 Identities=15% Similarity=0.214 Sum_probs=19.8
Q ss_pred HHHHHHHhCCCCEEE-EcCCCCcchhhHHHHHHHHHHHc
Q 018389 298 ILAQRALADDIHDVV-YTPRKGEKLEGKLQIVLQAIIDN 335 (357)
Q Consensus 298 vLAeRakekGI~~VV-FDpR~GykYHGRVKAfADAaRE~ 335 (357)
.|.+.|.++|+.-+| |. ++|+.-+.++-+.+.++
T Consensus 109 ~l~~~a~~~~~~l~v~~~----~Rf~p~~~~~k~li~~g 143 (342)
T COG0673 109 ELVELARKAGVKLMVGFN----RRFDPAVQALKELIDSG 143 (342)
T ss_pred HHHHHHHHcCCceeeehh----hhcCHHHHHHHHHHhcC
Confidence 455666666755444 44 55666666666666544
No 87
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=27.98 E-value=1.4e+02 Score=27.77 Aligned_cols=45 Identities=16% Similarity=0.253 Sum_probs=31.3
Q ss_pred HHHHHHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 296 GGILAQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
|..+|+.+.+.|-.+|.|= ..+....+.|+..|.+++.+.|+.+.
T Consensus 166 g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~~~ 212 (341)
T PRK10703 166 GYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVP 212 (341)
T ss_pred HHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHHHHHHHcCCCCC
Confidence 5566666677788877642 11222345899999999999998753
No 88
>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=27.87 E-value=2.2e+02 Score=23.65 Aligned_cols=45 Identities=20% Similarity=0.226 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhCCCCEEE--EcCCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 295 VGGILAQRALADDIHDVV--YTPRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 295 VGkvLAeRakekGI~~VV--FDpR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
.|+++++.+.+.|..+|. ++ ......+.++.+|.+++++.|+.+.
T Consensus 111 ~~~~~~~~l~~~~~~~i~~i~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (269)
T cd01391 111 AGEAAAEYLAEKGWKRVALIYG-DDGAYGRERLEGFKAALKKAGIEVV 157 (269)
T ss_pred HHHHHHHHHHHhCCceEEEEec-CCcchhhHHHHHHHHHHHhcCcEEE
Confidence 455666666666777764 33 2224567899999999999996553
No 89
>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=27.80 E-value=1e+02 Score=28.05 Aligned_cols=43 Identities=26% Similarity=0.392 Sum_probs=32.3
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~F 339 (357)
-.++|..+|+.||++ | ..+||- +| ..|-..|++++++++|-..
T Consensus 17 ~~~~A~~lG~~la~~----g-~~lV~G--Gg--~~GlM~a~a~ga~~~gG~v 59 (178)
T TIGR00730 17 YKELAAELGAYLAGQ----G-WGLVYG--GG--RVGLMGAIADAAMENGGTA 59 (178)
T ss_pred HHHHHHHHHHHHHHC----C-CEEEEC--CC--hHhHHHHHHHHHHhcCCeE
Confidence 347899999999986 4 346776 32 3589999999999887543
No 90
>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=27.72 E-value=1e+02 Score=25.76 Aligned_cols=41 Identities=24% Similarity=0.332 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 292 CAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 292 Aa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~F 339 (357)
+..+..+ .+.|.++|+..|.|-+ | ..-..+.+.++++||.+
T Consensus 65 ~~~~~~~-v~~~~~~g~~~v~~~~--g----~~~~~~~~~a~~~gi~v 105 (116)
T PF13380_consen 65 PDKVPEI-VDEAAALGVKAVWLQP--G----AESEELIEAAREAGIRV 105 (116)
T ss_dssp HHHHHHH-HHHHHHHT-SEEEE-T--T----S--HHHHHHHHHTT-EE
T ss_pred HHHHHHH-HHHHHHcCCCEEEEEc--c----hHHHHHHHHHHHcCCEE
Confidence 3344444 5667788999999994 4 77789999999999976
No 91
>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=27.59 E-value=1.5e+02 Score=28.83 Aligned_cols=39 Identities=21% Similarity=0.178 Sum_probs=29.9
Q ss_pred HHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 301 QRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 301 eRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~F 339 (357)
.-+++.|++.|-|=|=+|-.+-.-++|+|+++-++|+.+
T Consensus 142 aml~dmG~~SiKffPm~Gl~~leE~~avAkA~a~~g~~l 180 (218)
T PF07071_consen 142 AMLKDMGGSSIKFFPMGGLKHLEELKAVAKACARNGFTL 180 (218)
T ss_dssp HHHHHTT--EEEE---TTTTTHHHHHHHHHHHHHCT-EE
T ss_pred HHHHHcCCCeeeEeecCCcccHHHHHHHHHHHHHcCcee
Confidence 457899999998888899999999999999999999876
No 92
>PF02789 Peptidase_M17_N: Cytosol aminopeptidase family, N-terminal domain; InterPro: IPR008283 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The two zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3PEI_A 1GYT_C 3JRU_A 3H8F_D 3H8G_F 3H8E_A 3KZW_L 1LAP_A 1LAN_A 1LCP_B ....
Probab=27.57 E-value=2.6e+02 Score=22.48 Aligned_cols=52 Identities=12% Similarity=0.107 Sum_probs=38.7
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEcCC-CCcchhhHHHHHHHHHHHcCcEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYTPR-KGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFDpR-~GykYHGRVKAfADAaRE~GL~F 339 (357)
+.+..+.+|..+++.+...++..|.++.. .+.....-+.++++++..+.-.|
T Consensus 67 ~~~~~r~a~~~~~~~l~~~~~~~v~i~l~~~~~~~~~~~~~~~~g~~l~~Y~f 119 (126)
T PF02789_consen 67 TAESLRKAGAAAARALKKLKVKSVAIDLPIDGENSDEAAEAAAEGALLGSYRF 119 (126)
T ss_dssp CHHHHHHHHHHHHHHHHHTT-SEEEEEGCSSBTTCHHHHHHHHHHHHHHT---
T ss_pred CHHHHHHHHHHHHHHHhhCCceEEEEeCcccccCcHHHHHHHHHHHHHcCccC
Confidence 67889999999999999999999987753 22222388999999998877665
No 93
>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=27.29 E-value=1.5e+02 Score=26.15 Aligned_cols=48 Identities=13% Similarity=0.156 Sum_probs=31.1
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~F 339 (357)
|..++..++ +.+.+.|-.++.|= +.+......|++.|.+++++.|+.+
T Consensus 98 ~~~ag~~a~----~~L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 147 (265)
T cd06285 98 DVLGGRLAT----RHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEAGIEV 147 (265)
T ss_pred cHHHHHHHH----HHHHHCCCccEEEEeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 445555444 44455687777643 1222234589999999999999865
No 94
>COG1893 ApbA Ketopantoate reductase [Coenzyme metabolism]
Probab=27.28 E-value=93 Score=30.42 Aligned_cols=43 Identities=23% Similarity=0.393 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 291 ACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 291 AAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
.|-.||-++|-++.++| +.|.+.. |-+- ++++++.||.+.-.-
T Consensus 7 GaGAvG~l~g~~L~~~g-~~V~~~~--------R~~~-~~~l~~~GL~i~~~~ 49 (307)
T COG1893 7 GAGAIGSLLGARLAKAG-HDVTLLV--------RSRR-LEALKKKGLRIEDEG 49 (307)
T ss_pred CCcHHHHHHHHHHHhCC-CeEEEEe--------cHHH-HHHHHhCCeEEecCC
Confidence 35689999999999999 9999983 3344 889999999876543
No 95
>PRK06048 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=27.26 E-value=1.2e+02 Score=31.49 Aligned_cols=45 Identities=9% Similarity=0.087 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 293 AAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 293 a~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
..+|..|++++++.||..|.== .| +.+-.|.++|.+.||.+..-.
T Consensus 8 ~~~~~~l~~~L~~~Gv~~vFgi--pG----~~~~~l~~al~~~~i~~v~~~ 52 (561)
T PRK06048 8 MTGARAIIKCLEKEGVEVIFGY--PG----GAIIPVYDELYDSDLRHILVR 52 (561)
T ss_pred ccHHHHHHHHHHHcCCCEEEEC--CC----cchHHHHHHHhhCCCeEEEec
Confidence 4679999999999999985444 46 677888999988898886543
No 96
>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=27.23 E-value=1.6e+02 Score=26.21 Aligned_cols=53 Identities=15% Similarity=0.094 Sum_probs=38.2
Q ss_pred CCHHHHHHHHHHHHHHHHhCCC--CEEEE---cCCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 287 RNATACAAVGGILAQRALADDI--HDVVY---TPRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 287 ~NveAAa~VGkvLAeRakekGI--~~VVF---DpR~GykYHGRVKAfADAaRE~GL~F 339 (357)
.+.+++..+|+.|++.+...|. .++.| .+.....-..|+..|.+++.+.|+.+
T Consensus 106 d~~~~g~~~~~~l~~~~~~~g~~~~~i~~i~~~~~~~~~~~~R~~G~~~~l~~~~~~~ 163 (289)
T cd01540 106 SATKIGEQVGEAIADEMKKRGWDPKEVGALRITYDELDTAKPRTDGALEALKAPGFPE 163 (289)
T ss_pred CHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecCCCCcchhhHHHHHHHHHhcCCCCc
Confidence 4778889999999998888786 44432 21221233579999999999999864
No 97
>PRK06124 gluconate 5-dehydrogenase; Provisional
Probab=27.06 E-value=1.2e+02 Score=26.94 Aligned_cols=42 Identities=19% Similarity=0.237 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCc
Q 018389 291 ACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGV 337 (357)
Q Consensus 291 AAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL 337 (357)
++.-||..||+++.+.|..=+.++ |.. ..+.++++.+++.|-
T Consensus 19 as~~IG~~la~~l~~~G~~v~~~~-r~~----~~~~~~~~~~~~~~~ 60 (256)
T PRK06124 19 SARGLGFEIARALAGAGAHVLVNG-RNA----ATLEAAVAALRAAGG 60 (256)
T ss_pred CCchHHHHHHHHHHHcCCeEEEEe-CCH----HHHHHHHHHHHhcCC
Confidence 345689999999999998766788 554 455666666666553
No 98
>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Probab=27.05 E-value=3.4e+02 Score=23.11 Aligned_cols=76 Identities=14% Similarity=0.063 Sum_probs=40.0
Q ss_pred CCeEEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHH----------------------HHHHHHHhCCCCE
Q 018389 253 KASVRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGG----------------------ILAQRALADDIHD 310 (357)
Q Consensus 253 NKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGk----------------------vLAeRakekGI~~ 310 (357)
+--|-|-|+++. |.+|+.+....... ...-+.|....++ .-+..+..+||..
T Consensus 18 ~~pvGaviv~~~-g~iv~~g~n~~~~~-----~HAE~~ai~~a~~~~l~g~tly~TlEPC~~~~~~~mC~~ai~~~gi~~ 91 (115)
T cd01284 18 NPPVGCVIVDDD-GEIVGEGYHRKAGG-----PHAEVNALASAGEKLARGATLYVTLEPCSHHGKTPPCVDAIIEAGIKR 91 (115)
T ss_pred CCCEEEEEEeCC-CeEEEEecCCCCCc-----ccHHHHHHHHHhhcCCCCeEEEEeCCCCCCCCCchHHHHHHHHHCcCE
Confidence 334677777643 88887765554210 1123333333333 2355667789999
Q ss_pred EEEcCCCCcchhhHHHHHHHHHHHcC
Q 018389 311 VVYTPRKGEKLEGKLQIVLQAIIDNG 336 (357)
Q Consensus 311 VVFDpR~GykYHGRVKAfADAaRE~G 336 (357)
|+|-. ..... |....-++.|++.|
T Consensus 92 Vv~g~-~~~~~-~~~~~g~~~l~~~g 115 (115)
T cd01284 92 VVVGV-RDPNP-LVAGKGAERLRAAG 115 (115)
T ss_pred EEEEe-cCCCc-ccccHHHHHHHHCc
Confidence 98763 22222 22234455566655
No 99
>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=26.77 E-value=1.8e+02 Score=25.20 Aligned_cols=48 Identities=19% Similarity=0.192 Sum_probs=30.2
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEc-CCCCc-chhhHHHHHHHHHHHcCcEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYT-PRKGE-KLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFD-pR~Gy-kYHGRVKAfADAaRE~GL~F 339 (357)
+..++..+++.| .+.|..+|.|= ...+. --.-|...|.+++.+.|+.+
T Consensus 99 ~~~~g~~~~~~l----~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 148 (266)
T cd06278 99 NYEAGRLAAELL----LAKGCRRIAFIGGPADTSTSRERERGFRDALAAAGVPV 148 (266)
T ss_pred hHHHHHHHHHHH----HHCCCceEEEEcCCCcccchHHHHHHHHHHHHHcCCCh
Confidence 445555555544 45687887652 11222 23468999999999999864
No 100
>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=26.58 E-value=1.7e+02 Score=25.51 Aligned_cols=46 Identities=15% Similarity=0.255 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhCCCCEEEE--cCCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 294 AVGGILAQRALADDIHDVVY--TPRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVF--DpR~GykYHGRVKAfADAaRE~GL~F 339 (357)
..|+.+++.+.+.|-..+.| ++.....-+.|...|.+++++.|+.+
T Consensus 102 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~ 149 (268)
T cd01575 102 EAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDP 149 (268)
T ss_pred HHHHHHHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCCC
Confidence 34555566666678777653 32221344578999999999999743
No 101
>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=26.47 E-value=1.6e+02 Score=26.45 Aligned_cols=46 Identities=11% Similarity=0.012 Sum_probs=33.3
Q ss_pred HHHHHHHHHHh--CCCCEEEEc-CCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 295 VGGILAQRALA--DDIHDVVYT-PRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 295 VGkvLAeRake--kGI~~VVFD-pR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
.|..+++.+++ .|-.++.|= .........|+..|.+++++.|+.+.
T Consensus 102 ~~~~a~~~L~~~~~G~~~Ia~i~~~~~~~~~~R~~gf~~~l~~~g~~~~ 150 (247)
T cd06276 102 AIYNALQEGLEKLKKYKKLILVFPNKTAIPKEIKRGFERFCKDYNIETE 150 (247)
T ss_pred HHHHHHHHHHHHhcCCCEEEEEecCccHhHHHHHHHHHHHHHHcCCCcc
Confidence 45566777777 899998643 12224456899999999999999764
No 102
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=26.31 E-value=2.2e+02 Score=25.95 Aligned_cols=78 Identities=18% Similarity=0.207 Sum_probs=41.8
Q ss_pred EEEEEEeCCCCeEEEEEcccchhhhcccCCCCCHHHHHHHHHHH--------------------HHHHHhCCCCEEEEcC
Q 018389 256 VRACIVHRVTSKVVVVAHSISKDMKFDLDSTRNATACAAVGGIL--------------------AQRALADDIHDVVYTP 315 (357)
Q Consensus 256 IYAQVIDD~~GkTLaSAST~EkdIK~~L~St~NveAAa~VGkvL--------------------AeRakekGI~~VVFDp 315 (357)
|-|-||+ +|.+|+++...-..-.. .....-+.|....++.+ +..+..+||.+|+|-.
T Consensus 35 vGAVIV~--~g~IIa~g~N~~~~~~d-~~~HAEi~Ai~~a~~~~~~~~l~g~tlY~TlEPC~MC~~aii~agI~rVvyg~ 111 (172)
T PRK10860 35 VGAVLVH--NNRVIGEGWNRPIGRHD-PTAHAEIMALRQGGLVLQNYRLLDATLYVTLEPCVMCAGAMVHSRIGRLVFGA 111 (172)
T ss_pred EEEEEEe--CCEEEEEeeCCCCCCCC-CccCHHHHHHHHHHHhcCCCCcCCcEEEeeCCCcHHHHHHHHHhCCCEEEEee
Confidence 6676775 47888776554221110 00112334444444443 6677889999999862
Q ss_pred CCCcchhhHHHHHHHHHHHcCcE
Q 018389 316 RKGEKLEGKLQIVLQAIIDNGVN 338 (357)
Q Consensus 316 R~GykYHGRVKAfADAaRE~GL~ 338 (357)
......| +....+.++..||.
T Consensus 112 -~d~~~g~-~g~~~~~l~~~~~~ 132 (172)
T PRK10860 112 -RDAKTGA-AGSLMDVLHHPGMN 132 (172)
T ss_pred -cCCCCCC-CCcHHHHhhcccCC
Confidence 3333322 23335566767754
No 103
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=26.23 E-value=1.6e+02 Score=30.42 Aligned_cols=45 Identities=16% Similarity=0.104 Sum_probs=34.8
Q ss_pred HHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 297 GILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 297 kvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
.+|.+-+.+.||+.|+|+..-+..-.-+-+++++.+++.||.+..
T Consensus 80 ~vl~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~~ 124 (471)
T TIGR03556 80 QLIPQLAQQLGAKAVYWNLDVEPYGRKRDRAVAAALKEAGIAVVT 124 (471)
T ss_pred HHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHCCCEEEE
Confidence 467777888899999998433332236789999999999999876
No 104
>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=26.07 E-value=1.6e+02 Score=25.52 Aligned_cols=46 Identities=13% Similarity=0.011 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhCCCCEEEEc--CCCCc-chhhHHHHHHHHHHHcCcEE
Q 018389 294 AVGGILAQRALADDIHDVVYT--PRKGE-KLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFD--pR~Gy-kYHGRVKAfADAaRE~GL~F 339 (357)
..|+.+|+.+.+.|..+|+|= +.... ..+.|.++|.+++.+.|+..
T Consensus 102 ~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~ 150 (266)
T cd06282 102 AAARDVAQALAALGHRRIAMLAGRLAASDRARQRYAGYRAAMRAAGLAP 150 (266)
T ss_pred HHHHHHHHHHHHcCcccEEEeccccccCchHHHHHHHHHHHHHHcCCCC
Confidence 345555556666688887653 11112 24579999999999999863
No 105
>PRK12744 short chain dehydrogenase; Provisional
Probab=25.98 E-value=2.1e+02 Score=25.52 Aligned_cols=45 Identities=16% Similarity=0.261 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCc
Q 018389 292 CAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGV 337 (357)
Q Consensus 292 Aa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL 337 (357)
+.-||..||+.+.+.|.+-++.+ +...........+++.+...|.
T Consensus 17 ~~gIG~~~a~~l~~~G~~vv~i~-~~~~~~~~~~~~~~~~l~~~~~ 61 (257)
T PRK12744 17 AKNLGGLIARDLAAQGAKAVAIH-YNSAASKADAEETVAAVKAAGA 61 (257)
T ss_pred CchHHHHHHHHHHHCCCcEEEEe-cCCccchHHHHHHHHHHHHhCC
Confidence 34589999999999998866666 3333334556666666665553
No 106
>PRK09124 pyruvate dehydrogenase; Provisional
Probab=25.68 E-value=1.2e+02 Score=31.55 Aligned_cols=44 Identities=9% Similarity=0.074 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHc-CcEEEEE
Q 018389 293 AAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDN-GVNVKVK 342 (357)
Q Consensus 293 a~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~-GL~FK~~ 342 (357)
..+|..|++++.+.||+.|.-= .| |.+-.|.++|++. ||.+..-
T Consensus 3 ~~~a~~l~~~L~~~GV~~vFg~--pG----~~~~~l~dal~~~~~i~~i~~ 47 (574)
T PRK09124 3 QTVADYIAKTLEQAGVKRIWGV--TG----DSLNGLSDSLRRMGTIEWMHT 47 (574)
T ss_pred ccHHHHHHHHHHHcCCCEEEEC--CC----CchHHHHHHHhccCCCcEEEe
Confidence 3689999999999999985544 46 6778899999764 8886543
No 107
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=25.51 E-value=1.7e+02 Score=26.87 Aligned_cols=46 Identities=17% Similarity=0.040 Sum_probs=31.4
Q ss_pred HHHHHHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 296 GGILAQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
|..+|+.+.+.|-..|.|= +........|++.|.+++.+.|+.+.+
T Consensus 167 ~~~a~~~L~~~G~r~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~ 214 (328)
T PRK11303 167 AEMLAESLLKFPAESILLLGALPELSVSFEREQGFRQALKDDPREVHY 214 (328)
T ss_pred HHHHHHHHHHCCCCeEEEEeCccccccHHHHHHHHHHHHHHcCCCceE
Confidence 4456677777898887653 111122357999999999999986543
No 108
>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=25.45 E-value=1.7e+02 Score=25.66 Aligned_cols=46 Identities=13% Similarity=0.228 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCCCCEEEEc-CCCC--cchhhHHHHHHHHHHHcCcEEE
Q 018389 295 VGGILAQRALADDIHDVVYT-PRKG--EKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFD-pR~G--ykYHGRVKAfADAaRE~GL~FK 340 (357)
.|+.+|+.+.+.|..+|.|= .... .....|.+.|.+++.+.|+.+.
T Consensus 99 ~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~ 147 (265)
T cd06291 99 GGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLEVR 147 (265)
T ss_pred HHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHHHcCCCCC
Confidence 44555555666788887642 1222 2234789999999999998764
No 109
>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=25.30 E-value=1.6e+02 Score=27.08 Aligned_cols=44 Identities=18% Similarity=0.179 Sum_probs=32.0
Q ss_pred HHHHHHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 296 GGILAQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~F 339 (357)
|..+++.+.+.|-.+|.|= +......+.|+..|.+++.+.|+..
T Consensus 166 ~~~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~ 211 (327)
T TIGR02417 166 AAELIERLLSQHADEFWYLGAQPELSVSRDRLAGFRQALKQATLEV 211 (327)
T ss_pred HHHHHHHHHHCCCCeEEEEeCcccchhHHHHHHHHHHHHHHcCCCh
Confidence 5667788888998888753 1111234579999999999999853
No 110
>PRK14456 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=25.25 E-value=3.5e+02 Score=27.57 Aligned_cols=84 Identities=15% Similarity=0.215 Sum_probs=54.2
Q ss_pred cCCeEEEEEEeCCCCeEEEEEcccchhhhccc------CCCCCHHHHHHHHHHHHH------HHHhCCCCEEEEcCCCCc
Q 018389 252 SKASVRACIVHRVTSKVVVVAHSISKDMKFDL------DSTRNATACAAVGGILAQ------RALADDIHDVVYTPRKGE 319 (357)
Q Consensus 252 SNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L------~St~NveAAa~VGkvLAe------RakekGI~~VVFDpR~Gy 319 (357)
.+..|.+-+|....+.|++.+|+.-=.++-.. ....|..+...++.+++- ...+.||..|+|. --|+
T Consensus 106 dg~~iEtV~i~~~~~~t~ciSsq~GCnl~C~FC~tg~~g~~rnLt~~EI~~qv~~~~~~~~~~~~~~~v~nIvfm-GmGE 184 (368)
T PRK14456 106 DGELVETVLIPGPERMTACISSQAGCALRCSFCATGQMGFRRNLTAGEITGQVFALSDMLAERNRERGITNIVFM-GMGE 184 (368)
T ss_pred CCCEEEEEEEecCCceEEEEEecCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHhhhccCCccEEEEe-CcCc
Confidence 68899999999888888877665443332221 122356677777776532 2235689999999 3377
Q ss_pred chh--hHHHHHHHHHHHcC
Q 018389 320 KLE--GKLQIVLQAIIDNG 336 (357)
Q Consensus 320 kYH--GRVKAfADAaRE~G 336 (357)
... ..|..+++.|.+.|
T Consensus 185 PLln~d~v~~~i~~l~~~~ 203 (368)
T PRK14456 185 PLLNTDNVFEAVLTLSTRK 203 (368)
T ss_pred cccCHHHHHHHHHHHhccc
Confidence 544 24777777776654
No 111
>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=25.05 E-value=1.7e+02 Score=25.70 Aligned_cols=49 Identities=22% Similarity=0.218 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
|..++..+++.|+ +.|-..|.|= +......+.|+++|.+++.+.|+.+.
T Consensus 100 ~~~~g~~~~~~l~----~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~ 150 (264)
T cd06274 100 NRDGAAELTRELL----AAPPEEVLFLGGLPELSPSRERLAGFRQALADAGLPVQ 150 (264)
T ss_pred cHHHHHHHHHHHH----HCCCCcEEEEeCCCcccchHHHHHHHHHHHHHcCCCCC
Confidence 4455555555544 4677776543 12223345799999999999997653
No 112
>PF06792 UPF0261: Uncharacterised protein family (UPF0261); InterPro: IPR008322 The proteins in this entry are functionally uncharacterised.
Probab=25.02 E-value=1.6e+02 Score=30.79 Aligned_cols=48 Identities=15% Similarity=0.231 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHHHHHHh-CCCCEEE--------EcCCCCcchhh-H-HHHHHHHHHHc
Q 018389 287 RNATACAAVGGILAQRALA-DDIHDVV--------YTPRKGEKLEG-K-LQIVLQAIIDN 335 (357)
Q Consensus 287 ~NveAAa~VGkvLAeRake-kGI~~VV--------FDpR~GykYHG-R-VKAfADAaRE~ 335 (357)
++.+-++.+|+.||+|+.. .|-..|. .| +.|..+|. . -+||.++|+++
T Consensus 312 tt~eE~~~~g~~ia~kLn~~~gpv~v~lP~~G~S~~d-~~G~~f~Dpead~al~~~l~~~ 370 (403)
T PF06792_consen 312 TTPEENRQLGEFIAEKLNRAKGPVRVLLPLGGVSALD-RPGGPFYDPEADEALFDALREN 370 (403)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCCEEEEECCCCCcccC-CCCCcCcChhHHHHHHHHHHHh
Confidence 4678899999999999997 4555554 45 34444442 2 47899998764
No 113
>PRK08266 hypothetical protein; Provisional
Probab=24.80 E-value=1.3e+02 Score=30.98 Aligned_cols=44 Identities=16% Similarity=0.204 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHc--CcEEEEEe
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDN--GVNVKVKL 343 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~--GL~FK~~l 343 (357)
.+|.+|++++.+.||+.|.-= .| +.+-.|.++|.+. ||.+-.-.
T Consensus 5 ~~~~~l~~~L~~~Gv~~vFg~--pG----~~~~~l~~al~~~~~~i~~v~~~ 50 (542)
T PRK08266 5 TGGEAIVAGLVAHGVDTVFGL--PG----AQLYWLFDALYKAGDRIRVIHTR 50 (542)
T ss_pred cHHHHHHHHHHHcCCCEEEEC--CC----cchHHHHHHHHhcCCCCeEEeec
Confidence 578999999999999986554 46 6788899999764 78776543
No 114
>PRK12737 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=24.79 E-value=2e+02 Score=28.28 Aligned_cols=45 Identities=13% Similarity=0.151 Sum_probs=36.7
Q ss_pred HHHHHHhCCCCEEEEcCCCCcchhhH---HHHHHHHHHHcCcEEEEEee
Q 018389 299 LAQRALADDIHDVVYTPRKGEKLEGK---LQIVLQAIIDNGVNVKVKLK 344 (357)
Q Consensus 299 LAeRakekGI~~VVFDpR~GykYHGR---VKAfADAaRE~GL~FK~~lk 344 (357)
...+|+++|.+.|.|| -+...|..- .+.+++-++..|+.+...|=
T Consensus 89 ~i~~ai~~GftSVMiD-gS~lp~eeNi~~T~~vv~~Ah~~gvsVEaElG 136 (284)
T PRK12737 89 DIKKKVRAGIRSVMID-GSHLSFEENIAIVKEVVEFCHRYDASVEAELG 136 (284)
T ss_pred HHHHHHHcCCCeEEec-CCCCCHHHHHHHHHHHHHHHHHcCCEEEEEEe
Confidence 4589999999999999 577777754 56788889999998887663
No 115
>PRK06466 acetolactate synthase 3 catalytic subunit; Validated
Probab=24.70 E-value=1.2e+02 Score=31.47 Aligned_cols=44 Identities=11% Similarity=0.161 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHH-cCcEEEEEe
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIID-NGVNVKVKL 343 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE-~GL~FK~~l 343 (357)
..|..|++++++.||+.|.-= .| +.+-.|.++|.+ .||.+..-.
T Consensus 5 ~~a~~l~~~L~~~Gv~~vFgi--pG----~~~~~l~~al~~~~~i~~i~~r 49 (574)
T PRK06466 5 SGAEMLVRALRDEGVEYIYGY--PG----GAVLHIYDALFKQDKVEHILVR 49 (574)
T ss_pred cHHHHHHHHHHHcCCCEEEEC--CC----cchhHHHHHhhccCCceEEEeC
Confidence 368999999999999885544 46 678889999854 588886643
No 116
>cd04726 KGPDC_HPS 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for L-ascorbate utilization in some eubacteria. HPS catalyzes the formation of D-arabino-3-hexulose-6-phosphate from D-ribulose 5-phosphate and formaldehyde in microorganisms that can use formaldehyde as a carbon source. Both catalyze reactions that involve the Mg2+-assisted formation and stabilization of 1,2-enediolate reaction intermediates.
Probab=24.65 E-value=2.3e+02 Score=24.75 Aligned_cols=42 Identities=17% Similarity=0.124 Sum_probs=31.8
Q ss_pred HHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEE
Q 018389 298 ILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 298 vLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~ 342 (357)
..++.|.++|...+++....+ .+-+..+++.+++.|+.+-+.
T Consensus 68 ~~~~~~~~aGad~i~~h~~~~---~~~~~~~i~~~~~~g~~~~v~ 109 (202)
T cd04726 68 LEAEMAFKAGADIVTVLGAAP---LSTIKKAVKAAKKYGKEVQVD 109 (202)
T ss_pred HHHHHHHhcCCCEEEEEeeCC---HHHHHHHHHHHHHcCCeEEEE
Confidence 356888999999998873332 245788899999999988874
No 117
>PRK08085 gluconate 5-dehydrogenase; Provisional
Probab=24.33 E-value=1.5e+02 Score=26.25 Aligned_cols=41 Identities=10% Similarity=0.210 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCc
Q 018389 292 CAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGV 337 (357)
Q Consensus 292 Aa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL 337 (357)
+.-||..+|+++.+.|..-+..+ |+. .++..+++.+++.|.
T Consensus 18 s~giG~~ia~~L~~~G~~vvl~~-r~~----~~~~~~~~~l~~~~~ 58 (254)
T PRK08085 18 AQGIGFLLATGLAEYGAEIIIND-ITA----ERAELAVAKLRQEGI 58 (254)
T ss_pred CChHHHHHHHHHHHcCCEEEEEc-CCH----HHHHHHHHHHHhcCC
Confidence 35799999999999998766777 553 566667777766553
No 118
>PRK08617 acetolactate synthase; Reviewed
Probab=24.10 E-value=1.4e+02 Score=30.79 Aligned_cols=44 Identities=18% Similarity=0.265 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
..+.+|++++++.||+.|.== .| +.+-.|.+++++.||.+..-.
T Consensus 6 ~~~~~l~~~L~~~GV~~vFg~--pG----~~~~~l~~al~~~~i~~i~~~ 49 (552)
T PRK08617 6 YGADLVVDSLINQGVKYVFGI--PG----AKIDRVFDALEDSGPELIVTR 49 (552)
T ss_pred cHHHHHHHHHHHcCCCEEEeC--CC----ccHHHHHHHHhhCCCCEEEec
Confidence 468999999999999985433 46 778889999988899886644
No 119
>TIGR01858 tag_bisphos_ald class II aldolase, tagatose bisphosphate family. This model describes tagatose-1,6-bisphosphate aldolases, and perhaps other closely related class II aldolases. This tetrameric, Zn2+-dependent enzyme is related to the class II fructose bisphosphate aldolase; fructose 1,6-bisphosphate and tagatose 1,6 bisphosphate differ only in chirality at C4.
Probab=24.03 E-value=2.2e+02 Score=28.07 Aligned_cols=44 Identities=7% Similarity=0.087 Sum_probs=36.3
Q ss_pred HHHHHhCCCCEEEEcCCCCcchhh---HHHHHHHHHHHcCcEEEEEee
Q 018389 300 AQRALADDIHDVVYTPRKGEKLEG---KLQIVLQAIIDNGVNVKVKLK 344 (357)
Q Consensus 300 AeRakekGI~~VVFDpR~GykYHG---RVKAfADAaRE~GL~FK~~lk 344 (357)
..+|++.|.+.|.|| -+...|.- ..+.+++-++..|+.+.-.|=
T Consensus 88 i~~ai~~GFtSVM~D-gS~lp~eeNi~~T~~vv~~Ah~~gv~VEaElG 134 (282)
T TIGR01858 88 IRQKVHAGVRSAMID-GSHFPFAQNVKLVKEVVDFCHRQDCSVEAELG 134 (282)
T ss_pred HHHHHHcCCCEEeec-CCCCCHHHHHHHHHHHHHHHHHcCCeEEEEEE
Confidence 589999999999999 67778875 456788888899998877664
No 120
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=24.03 E-value=1.9e+02 Score=26.83 Aligned_cols=48 Identities=17% Similarity=0.126 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhCCCC--EEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEEeec
Q 018389 293 AAVGGILAQRALADDIH--DVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVKLKQ 345 (357)
Q Consensus 293 a~VGkvLAeRakekGI~--~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~lkq 345 (357)
-.++..+.+++...||. -|++| .+| |.-.+|..+|++.|+.+-+.|+.
T Consensus 169 ~~la~~~i~~a~~~g~~~~~vvaD--s~y---~~~~~f~~~l~~~~~~~i~~vr~ 218 (273)
T PF13546_consen 169 PELALEMIDRARQAGIPARWVVAD--SWY---GSSPAFRKALRERGLHYIGRVRS 218 (273)
T ss_pred HHHHHHHHHHHHhcccccceEEec--ccc---CChHHHHHHHHHCCceEEEeecc
Confidence 35666677778888863 38899 454 57889999999999999888864
No 121
>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=24.02 E-value=2.1e+02 Score=25.26 Aligned_cols=48 Identities=15% Similarity=0.057 Sum_probs=30.6
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEc-CCCCc-chhhHHHHHHHHHHHcCcEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYT-PRKGE-KLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFD-pR~Gy-kYHGRVKAfADAaRE~GL~F 339 (357)
|..++..+++.| .++|-.+++|= ...+. .-+.|.+.|.+++.+.|+.+
T Consensus 106 ~~~~~~~~~~~l----~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 155 (273)
T cd06292 106 DALAMRLAVRHL----VALGHRRIGFASGPGRTVPRRRKIAGFRAALEEAGLEP 155 (273)
T ss_pred cHHHHHHHHHHH----HHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 555555555544 45688887653 11222 23478999999999999753
No 122
>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=23.91 E-value=1.8e+02 Score=29.07 Aligned_cols=44 Identities=16% Similarity=0.242 Sum_probs=32.3
Q ss_pred HHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 297 GILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 297 kvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
.+|.+-|.+.||+.|+++..-+....-+-.++++.+.+.||.+.
T Consensus 86 ~vl~~L~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~ 129 (429)
T TIGR02765 86 DVLPELIKELGVRTVFLHQEVGSEEKSVERLLQQALARLGIHVE 129 (429)
T ss_pred HHHHHHHHHhCCCEEEEeccCCHHHHHHHHHHHHHHHhcCceEE
Confidence 45667777889999999932222222459999999999999864
No 123
>PRK08277 D-mannonate oxidoreductase; Provisional
Probab=23.85 E-value=1.6e+02 Score=26.64 Aligned_cols=41 Identities=20% Similarity=0.270 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCc
Q 018389 292 CAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGV 337 (357)
Q Consensus 292 Aa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL 337 (357)
+.-||..||+++.+.|..-++.+ |+. ...+.+++.+.+.|-
T Consensus 19 s~giG~~ia~~l~~~G~~V~~~~-r~~----~~~~~~~~~~~~~~~ 59 (278)
T PRK08277 19 GGVLGGAMAKELARAGAKVAILD-RNQ----EKAEAVVAEIKAAGG 59 (278)
T ss_pred CchHHHHHHHHHHHCCCEEEEEe-CCH----HHHHHHHHHHHhcCC
Confidence 45689999999999998766677 553 345555666655553
No 124
>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=23.69 E-value=2.1e+02 Score=24.94 Aligned_cols=44 Identities=11% Similarity=0.085 Sum_probs=29.4
Q ss_pred HHHHHHHHHhCCCCEEEEc-CCCCc-chhhHHHHHHHHHHHcCcEE
Q 018389 296 GGILAQRALADDIHDVVYT-PRKGE-KLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD-pR~Gy-kYHGRVKAfADAaRE~GL~F 339 (357)
|..+++.+.+.|..+|.|= ...+. -...|++.|.+++.+.|+..
T Consensus 108 ~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 153 (268)
T cd06271 108 AYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEAGLPL 153 (268)
T ss_pred HHHHHHHHHHcCCCcEEEecCccccchHHHHHHHHHHHHHHhCCCC
Confidence 4455555566788888752 11222 22478999999999999864
No 125
>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=23.60 E-value=91 Score=27.47 Aligned_cols=27 Identities=22% Similarity=0.297 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHhCCCCEEEEcCCCC
Q 018389 291 ACAAVGGILAQRALADDIHDVVYTPRKG 318 (357)
Q Consensus 291 AAa~VGkvLAeRakekGI~~VVFDpR~G 318 (357)
.+-.||+.+|++++..|.+-++|| |..
T Consensus 43 G~G~IG~~vA~~l~~fG~~V~~~d-~~~ 69 (178)
T PF02826_consen 43 GYGRIGRAVARRLKAFGMRVIGYD-RSP 69 (178)
T ss_dssp STSHHHHHHHHHHHHTT-EEEEEE-SSC
T ss_pred EEcCCcCeEeeeeecCCceeEEec-ccC
Confidence 345799999999999999888999 454
No 126
>PRK08979 acetolactate synthase 3 catalytic subunit; Validated
Probab=23.51 E-value=1.6e+02 Score=30.71 Aligned_cols=43 Identities=9% Similarity=0.290 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHH-cCcEEEEE
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIID-NGVNVKVK 342 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE-~GL~FK~~ 342 (357)
..|.+|++++++.||+.|.-= .| |.+-.|.+++++ .||.+-.-
T Consensus 5 ~~~~~l~~~L~~~Gv~~vFgv--pG----~~~~~l~~al~~~~~i~~v~~ 48 (572)
T PRK08979 5 SGASMIVRSLIDEGVKHIFGY--PG----GSVLDIYDALHEKSGIEHILV 48 (572)
T ss_pred cHHHHHHHHHHHcCCCEEEEc--CC----cchHHHHHHHhhcCCCeEEEe
Confidence 458999999999999995544 35 667789999976 48887654
No 127
>PRK08217 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=23.44 E-value=2.2e+02 Score=24.82 Aligned_cols=40 Identities=13% Similarity=0.085 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcC
Q 018389 292 CAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNG 336 (357)
Q Consensus 292 Aa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~G 336 (357)
+.-||..||+++.+.|..-++.+ |.. .++...++.+++.|
T Consensus 14 ~g~iG~~~a~~l~~~G~~vi~~~-r~~----~~~~~~~~~~~~~~ 53 (253)
T PRK08217 14 AQGLGRAMAEYLAQKGAKLALID-LNQ----EKLEEAVAECGALG 53 (253)
T ss_pred CchHHHHHHHHHHHCCCEEEEEe-CCH----HHHHHHHHHHHhcC
Confidence 46789999999999998766777 443 44555555555544
No 128
>PRK06457 pyruvate dehydrogenase; Provisional
Probab=23.39 E-value=1.6e+02 Score=30.48 Aligned_cols=44 Identities=14% Similarity=0.163 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
.+|.+|++++.+.||+.|.== .| +.+-.|.|++...||.+-.-.
T Consensus 3 ~~a~~l~~~L~~~GV~~vFg~--pG----~~~~~l~dal~~~~i~~v~~~ 46 (549)
T PRK06457 3 SVAEVIIRVLEDNGIQRIYGI--PG----DSIDPLVDAIRKSKVKYVQVR 46 (549)
T ss_pred cHHHHHHHHHHHcCCCEEEEc--CC----cchHHHHHHHHhcCCeEEEeC
Confidence 478999999999999995544 46 678889999988888876644
No 129
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=23.36 E-value=2.8e+02 Score=26.33 Aligned_cols=55 Identities=16% Similarity=0.241 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHHHHHH--------hCCCCEEEE-cCCCCcch-hhHHHHHHHHHHHcCcEEEE
Q 018389 287 RNATACAAVGGILAQRAL--------ADDIHDVVY-TPRKGEKL-EGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 287 ~NveAAa~VGkvLAeRak--------ekGI~~VVF-DpR~GykY-HGRVKAfADAaRE~GL~FK~ 341 (357)
.|..++...|+.|++.+. ..|-..++| ....+... ..|...|.+++++.|+.+..
T Consensus 133 D~~~ag~~a~~~l~~~~~~~~~~~~~~~g~~~i~~i~g~~~~~~~~~R~~G~~~al~~~g~~~~~ 197 (330)
T PRK15395 133 DSKESGIIQGDLIAKHWKANPAWDLNKDGKIQYVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQ 197 (330)
T ss_pred ChHHHHHHHHHHHHHHHhhccccccCCCCceEEEEEecCCCCchHHHHHHHHHHHHHhcCCCeee
Confidence 477888888888888876 346444433 21222333 36999999999999987654
No 130
>PRK07524 hypothetical protein; Provisional
Probab=23.28 E-value=1.5e+02 Score=30.40 Aligned_cols=43 Identities=14% Similarity=0.137 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEE
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~ 342 (357)
.+|..|++++.+.||+.|.-= .| +.+-.|.+++.+.||.+..-
T Consensus 3 ~~a~~l~~~L~~~Gv~~vFg~--pG----~~~~~~~dal~~~~i~~i~~ 45 (535)
T PRK07524 3 TCGEALVRLLEAYGVETVFGI--PG----VHTVELYRGLAGSGIRHVTP 45 (535)
T ss_pred cHHHHHHHHHHHcCCCEEEeC--CC----cchHHHHHHHhhcCCcEEEe
Confidence 578999999999999885444 46 67888899998888877653
No 131
>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=23.28 E-value=2.1e+02 Score=23.45 Aligned_cols=49 Identities=20% Similarity=0.268 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 291 ACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 291 AAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
++..||+-||+++.+.|-..|+..-|+ .-..++.++++.+++.|.++.+
T Consensus 8 a~~giG~~~a~~l~~~g~~~v~~~~r~--~~~~~~~~l~~~l~~~~~~~~~ 56 (167)
T PF00106_consen 8 ASSGIGRALARALARRGARVVILTSRS--EDSEGAQELIQELKAPGAKITF 56 (167)
T ss_dssp TTSHHHHHHHHHHHHTTTEEEEEEESS--CHHHHHHHHHHHHHHTTSEEEE
T ss_pred CCCHHHHHHHHHHHhcCceEEEEeeec--cccccccccccccccccccccc
Confidence 345799999999999988887765355 2237788888888888865544
No 132
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=23.25 E-value=2e+02 Score=26.03 Aligned_cols=49 Identities=18% Similarity=0.079 Sum_probs=31.5
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEc-CCCCcc-hhhHHHHHHHHHHHcCcEEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYT-PRKGEK-LEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFD-pR~Gyk-YHGRVKAfADAaRE~GL~FK 340 (357)
|..++..+ |+.+.+.|-..|.|= ...+.. -+.|...|.+++++.|+.+.
T Consensus 136 n~~~g~~a----~~~l~~~G~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~ 186 (309)
T PRK11041 136 NLTAAFEA----VNYLHELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGITVD 186 (309)
T ss_pred cHHHHHHH----HHHHHHcCCceEEEEeCCccccchHHHHHHHHHHHHHcCCCCC
Confidence 44555544 444455687887642 123333 34699999999999998753
No 133
>PRK06882 acetolactate synthase 3 catalytic subunit; Validated
Probab=23.16 E-value=1.6e+02 Score=30.50 Aligned_cols=44 Identities=16% Similarity=0.186 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHH-cCcEEEEEe
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIID-NGVNVKVKL 343 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE-~GL~FK~~l 343 (357)
..+.+|++++.+.||+.|.-= .| +.+..|.+++.+ .||.+..-.
T Consensus 5 ~~a~~l~~~L~~~GV~~vFg~--pG----~~~~~l~~al~~~~~i~~v~~~ 49 (574)
T PRK06882 5 SGAEMVVQSLRDEGVEYVFGY--PG----GSVLDIYDAIHTLGGIEHVLVR 49 (574)
T ss_pred cHHHHHHHHHHHcCCCEEEeC--CC----cchHHHHHHHhhcCCCeEEEec
Confidence 468999999999999986554 36 677889999877 588886654
No 134
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=23.10 E-value=2e+02 Score=25.09 Aligned_cols=45 Identities=18% Similarity=0.134 Sum_probs=29.9
Q ss_pred HHHHHHHHHhCCCCEEEE--cCCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 296 GGILAQRALADDIHDVVY--TPRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 296 GkvLAeRakekGI~~VVF--DpR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
|..+++.+.+.|..+|.| .+.....-..|+..|.+++.+.|+.+.
T Consensus 104 ~~~~~~~l~~~g~~~I~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~ 150 (265)
T cd06299 104 MTEAVSLLVALGHKKIGYISGPQDTSTGRERLEAFRQACASLGLEVN 150 (265)
T ss_pred HHHHHHHHHHcCCCcEEEEeCCCCcccHHHHHHHHHHHHHHCCCCCC
Confidence 344556666778878764 222223335889999999999997543
No 135
>PRK05835 fructose-bisphosphate aldolase; Provisional
Probab=23.08 E-value=2.3e+02 Score=28.46 Aligned_cols=44 Identities=18% Similarity=0.276 Sum_probs=35.9
Q ss_pred HHHHHhCCCCEEEEcCCCCcchh---hHHHHHHHHHHHcCcEEEEEee
Q 018389 300 AQRALADDIHDVVYTPRKGEKLE---GKLQIVLQAIIDNGVNVKVKLK 344 (357)
Q Consensus 300 AeRakekGI~~VVFDpR~GykYH---GRVKAfADAaRE~GL~FK~~lk 344 (357)
..+|+++|.+.|.|| -+...|. -..+.+++-+...|+.+...|=
T Consensus 90 i~~ai~~GftSVM~D-gS~l~~eeNi~~T~~vve~Ah~~gv~VEaElG 136 (307)
T PRK05835 90 CEKAVKAGFTSVMID-ASHHAFEENLELTSKVVKMAHNAGVSVEAELG 136 (307)
T ss_pred HHHHHHcCCCEEEEe-CCCCCHHHHHHHHHHHHHHHHHcCCEEEEEec
Confidence 567999999999999 5666777 4567788999999998877663
No 136
>TIGR02415 23BDH acetoin reductases. One member of this family, as characterized in Klebsiella terrigena, is described as able to interconvert acetoin + NADH with meso-2,3-butanediol + NAD(+). It is also called capable of irreversible reduction of diacetyl with NADH to acetoin. Blomqvist, et al. decline to specify either EC 1.1.1.4 which is (R,R)-butanediol dehydrogenase, or EC 1.1.1.5, which is acetoin dehydrogenase without a specified stereochemistry, for this enzyme. This enzyme is a homotetramer in the family of short chain dehydrogenases (pfam00106). Another member of this family, from Corynebacterium glutamicum, is called L-2,3-butanediol dehydrogenase (PubMed:11577733).
Probab=23.02 E-value=2.4e+02 Score=24.81 Aligned_cols=43 Identities=16% Similarity=0.146 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcE
Q 018389 291 ACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVN 338 (357)
Q Consensus 291 AAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~ 338 (357)
++.-||..||+++.+.|..-+..+ |+. .+...++..+++.|..
T Consensus 8 ~sg~iG~~la~~l~~~G~~v~~~~-r~~----~~~~~~~~~l~~~~~~ 50 (254)
T TIGR02415 8 GAQGIGKGIAERLAKDGFAVAVAD-LNE----ETAKETAKEINQAGGK 50 (254)
T ss_pred CCchHHHHHHHHHHHCCCEEEEEe-CCH----HHHHHHHHHHHhcCCe
Confidence 345789999999999998766777 553 5666777777776644
No 137
>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=22.96 E-value=2.8e+02 Score=24.25 Aligned_cols=46 Identities=9% Similarity=0.001 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCCCEEEEc-CCCCc-chhhHHHHHHHHHHHcCcEEEE
Q 018389 296 GGILAQRALADDIHDVVYT-PRKGE-KLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD-pR~Gy-kYHGRVKAfADAaRE~GL~FK~ 341 (357)
|+.+|+.+.+.|-.+|+|= ...+. ....|...|.+++++.|+.+..
T Consensus 104 g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~ 151 (264)
T cd01574 104 ARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALEAAGIAPPP 151 (264)
T ss_pred HHHHHHHHHHCCCCEEEEEecCCccchHHHHHHHHHHHHHHCCCCcce
Confidence 3444555555787777643 11222 2347899999999999986643
No 138
>PRK06725 acetolactate synthase 3 catalytic subunit; Validated
Probab=22.94 E-value=1.5e+02 Score=31.14 Aligned_cols=45 Identities=18% Similarity=0.184 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 293 AAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 293 a~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
..+|..|++++++.||+.|.== .| +.+-.|.|++.+.||.+..-.
T Consensus 15 ~~~a~~l~~~L~~~GV~~vFGi--pG----~~~~~l~dal~~~~i~~i~~r 59 (570)
T PRK06725 15 VTGAGHVIQCLKKLGVTTVFGY--PG----GAILPVYDALYESGLKHILTR 59 (570)
T ss_pred ccHHHHHHHHHHHcCCCEEEEc--CC----cchHHHHHHHHhcCCcEEEec
Confidence 4579999999999999985433 46 667789999988898886543
No 139
>PF04551 GcpE: GcpE protein; InterPro: IPR004588 This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is largely restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.; GO: 0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity, 0016114 terpenoid biosynthetic process, 0055114 oxidation-reduction process; PDB: 2Y0F_C 3NOY_A.
Probab=22.79 E-value=1.8e+02 Score=30.13 Aligned_cols=55 Identities=16% Similarity=0.322 Sum_probs=39.1
Q ss_pred CCHHHHHHHHHHHH----------------------HHHHhCCCCEEEEcCCCCc--------c-hhhHHHHHHHHHHHc
Q 018389 287 RNATACAAVGGILA----------------------QRALADDIHDVVYTPRKGE--------K-LEGKLQIVLQAIIDN 335 (357)
Q Consensus 287 ~NveAAa~VGkvLA----------------------eRakekGI~~VVFDpR~Gy--------k-YHGRVKAfADAaRE~ 335 (357)
.+.++|+.++++-. ..|.+. +.+|-..| +.. . ...+++.++++++|.
T Consensus 53 p~~~~a~al~~I~~~l~~~g~~iPlVADIHFd~~lAl~a~~~-v~kiRINP-GNi~~~~~~~~g~~~~~~~~vv~~ake~ 130 (359)
T PF04551_consen 53 PDMEAAEALKEIKKRLRALGSPIPLVADIHFDYRLALEAIEA-VDKIRINP-GNIVDEFQEELGSIREKVKEVVEAAKER 130 (359)
T ss_dssp -SHHHHHHHHHHHHHHHCTT-SS-EEEEESTTCHHHHHHHHC--SEEEE-T-TTSS----SS-SS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHhhccCCCCCCeeeecCCCHHHHHHHHHH-hCeEEECC-CcccccccccccchHHHHHHHHHHHHHC
Confidence 47888888887644 467777 88888885 433 2 378999999999999
Q ss_pred CcEEEEEe
Q 018389 336 GVNVKVKL 343 (357)
Q Consensus 336 GL~FK~~l 343 (357)
|+...+=.
T Consensus 131 ~ipIRIGv 138 (359)
T PF04551_consen 131 GIPIRIGV 138 (359)
T ss_dssp T-EEEEEE
T ss_pred CCCEEEec
Confidence 99888743
No 140
>COG3669 Alpha-L-fucosidase [Carbohydrate transport and metabolism]
Probab=22.71 E-value=1.7e+02 Score=30.94 Aligned_cols=46 Identities=13% Similarity=0.103 Sum_probs=34.5
Q ss_pred HHHHHHHhCCCCEEE--------EcCCCCcchh-----------hHHHHHHHHHHHcCcEEEEEee
Q 018389 298 ILAQRALADDIHDVV--------YTPRKGEKLE-----------GKLQIVLQAIIDNGVNVKVKLK 344 (357)
Q Consensus 298 vLAeRakekGI~~VV--------FDpR~GykYH-----------GRVKAfADAaRE~GL~FK~~lk 344 (357)
-.|.-.+++|-+.|+ |+. -+-.|| .-|..+|.|+|+.||.|.|++-
T Consensus 58 eWar~fK~aGAKyvilvakHHDGFaL-w~t~ys~wnsvk~GpKrDlvgela~Avr~qGL~FGvy~s 122 (430)
T COG3669 58 EWARLFKEAGAKYVILVAKHHDGFAL-WPTDYSVWNSVKRGPKRDLVGELAKAVREQGLRFGVYLS 122 (430)
T ss_pred HHHHHHHHcCCcEEEEeeeecCCeee-cccccccccccccCCcccHHHHHHHHHHHcCCeeeEeec
Confidence 467888999988765 221 112444 3499999999999999999986
No 141
>PLN00125 Succinyl-CoA ligase [GDP-forming] subunit alpha
Probab=22.66 E-value=1.7e+02 Score=29.13 Aligned_cols=45 Identities=11% Similarity=0.079 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHhCCCCEEE-EcCCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 292 CAAVGGILAQRALADDIHDVV-YTPRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 292 Aa~VGkvLAeRakekGI~~VV-FDpR~GykYHGRVKAfADAaRE~GL~F 339 (357)
+..|-.. .+.|.++||..++ +. .|+..+|....+.+.+|++|+.+
T Consensus 79 a~~v~~a-l~e~~~~Gvk~~vIis--aGf~e~g~~~~~~~~ar~~girv 124 (300)
T PLN00125 79 PPFAAAA-ILEAMEAELDLVVCIT--EGIPQHDMVRVKAALNRQSKTRL 124 (300)
T ss_pred HHHHHHH-HHHHHHcCCCEEEEEC--CCCCcccHHHHHHHHHhhcCCEE
Confidence 3444444 4558899999765 55 79999997777778899999854
No 142
>TIGR02826 RNR_activ_nrdG3 anaerobic ribonucleoside-triphosphate reductase activating protein. Members of this family represent a set of proteins related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR) as described in model TIGR02491. Members of this family are found paired with members of a similarly divergent set of anaerobic ribonucleoside-triphosphate reductases. Identification of this protein as an RNR activitating protein is partly from pairing with a candidate RNR. It is further supported by our finding that upstream of these operons are examples of a conserved regulatory element (described Rodionov and Gelfand) that is found in nearly all bacteria and that occurs specifically upstream of operons for all three classes of RNR genes.
Probab=22.64 E-value=2.1e+02 Score=25.23 Aligned_cols=35 Identities=20% Similarity=0.226 Sum_probs=27.8
Q ss_pred CCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEE
Q 018389 306 DDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 306 kGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~ 342 (357)
..+..|+|. ||+..+.-+..|++.+++.|+.+.+.
T Consensus 60 ~~~~gVt~S--GGEl~~~~l~~ll~~lk~~Gl~i~l~ 94 (147)
T TIGR02826 60 SLISCVLFL--GGEWNREALLSLLKIFKEKGLKTCLY 94 (147)
T ss_pred CCCCEEEEe--chhcCHHHHHHHHHHHHHCCCCEEEE
Confidence 347789999 88855577999999999999876553
No 143
>PLN02470 acetolactate synthase
Probab=22.62 E-value=1.4e+02 Score=31.15 Aligned_cols=44 Identities=16% Similarity=0.143 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHc-CcEEEEE
Q 018389 293 AAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDN-GVNVKVK 342 (357)
Q Consensus 293 a~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~-GL~FK~~ 342 (357)
..++.+|++++++.||+.|.-= .| +.+-.|.++|.+. ||.+..-
T Consensus 13 ~~~a~~l~~~L~~~GV~~vFg~--pG----~~~~~l~dal~~~~~i~~i~~ 57 (585)
T PLN02470 13 RKGADILVEALEREGVDTVFAY--PG----GASMEIHQALTRSNCIRNVLC 57 (585)
T ss_pred ccHHHHHHHHHHHcCCCEEEEc--CC----cccHHHHHHHhccCCceEEEe
Confidence 4678999999999999996544 46 6788899999654 8888664
No 144
>PRK08611 pyruvate oxidase; Provisional
Probab=22.58 E-value=1.6e+02 Score=30.78 Aligned_cols=43 Identities=16% Similarity=0.163 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHH--cCcEEEEE
Q 018389 294 AVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIID--NGVNVKVK 342 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE--~GL~FK~~ 342 (357)
.+|..|++++.+.||+.|.-= .| +.+-.|.+++++ .||.+.+-
T Consensus 5 ~~~~~l~~~L~~~GV~~vFgi--pG----~~~~~l~dal~~~~~~i~~i~~ 49 (576)
T PRK08611 5 KAGEALVKLLQDWGIDHVYGI--PG----DSIDAVVDALRKEQDKIKFIQV 49 (576)
T ss_pred cHHHHHHHHHHHcCCCEEEec--CC----cchHHHHHHHHhcCCCCeEEEe
Confidence 478999999999999985544 46 678889999975 68888664
No 145
>PHA02588 cd deoxycytidylate deaminase; Provisional
Probab=22.54 E-value=1.2e+02 Score=27.46 Aligned_cols=38 Identities=18% Similarity=0.170 Sum_probs=25.3
Q ss_pred HHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 300 AQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 300 AeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
|..+..+||..|+|-. .-....+ --++-|++.||++..
T Consensus 115 a~aI~~~gI~rVvy~~-~~~~~~~---~~~~~L~~~Gi~v~~ 152 (168)
T PHA02588 115 AKAIAQSGIKKLVYCE-KYDRNGP---GWDDILRKSGIEVIQ 152 (168)
T ss_pred HHHHHHhCCCEEEEee-ccCCCcH---HHHHHHHHCCCEEEE
Confidence 4555678999999862 2111122 247889999999875
No 146
>PRK12827 short chain dehydrogenase; Provisional
Probab=22.53 E-value=1.9e+02 Score=25.13 Aligned_cols=46 Identities=20% Similarity=0.183 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCc
Q 018389 291 ACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGV 337 (357)
Q Consensus 291 AAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL 337 (357)
|+.-||..||+.+.+.|-.-++.+ |....-......+++.+.+.|-
T Consensus 14 asg~iG~~la~~l~~~g~~v~~~~-~~~~~~~~~~~~~~~~~~~~~~ 59 (249)
T PRK12827 14 GSGGLGRAIAVRLAADGADVIVLD-IHPMRGRAEADAVAAGIEAAGG 59 (249)
T ss_pred CCChHHHHHHHHHHHCCCeEEEEc-CcccccHHHHHHHHHHHHhcCC
Confidence 345689999999999998766666 3322223455555555555443
No 147
>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=22.45 E-value=2e+02 Score=24.99 Aligned_cols=45 Identities=9% Similarity=0.206 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhCCCCEEEE--cCCCCcc-hhhHHHHHHHHHHHcCcEE
Q 018389 295 VGGILAQRALADDIHDVVY--TPRKGEK-LEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVF--DpR~Gyk-YHGRVKAfADAaRE~GL~F 339 (357)
.|+.+|+.+.+.|-.+|+| .+..+.. -+.|+..|.+++.+.|+.+
T Consensus 103 ~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~~~~~~~~ 150 (267)
T cd06283 103 AAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEALAEHGIGV 150 (267)
T ss_pred HHHHHHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHHHHcCCCC
Confidence 3667777777889888653 3222122 2489999999999999654
No 148
>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=22.37 E-value=2.1e+02 Score=25.04 Aligned_cols=43 Identities=9% Similarity=0.142 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCCCEEEEc--CCCCcchhhHHHHHHHHHHHcCcE
Q 018389 296 GGILAQRALADDIHDVVYT--PRKGEKLEGKLQIVLQAIIDNGVN 338 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFD--pR~GykYHGRVKAfADAaRE~GL~ 338 (357)
|+.+|+.+.+.|..+|.|= +......+-|...|.+++++.|+.
T Consensus 99 ~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 143 (261)
T cd06272 99 MELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDENGIS 143 (261)
T ss_pred HHHHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHHHcCCC
Confidence 5556666667788887642 112233456899999999999974
No 149
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=22.34 E-value=1.1e+02 Score=25.74 Aligned_cols=53 Identities=11% Similarity=-0.015 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHhC-CCCEEE--EcCCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 290 TACAAVGGILAQRALAD-DIHDVV--YTPRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 290 eAAa~VGkvLAeRakek-GI~~VV--FDpR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
++-...=..||+.+.+. ||+-++ |+ .+.-.-.|...=+.+.+++++..+-|--
T Consensus 12 ~~h~~~V~~la~~L~~~~g~~V~lD~~~-~~~i~~~g~~~W~~~~~~~ad~Vliv~S 67 (150)
T PF08357_consen 12 EEHKEWVLALAEFLRQNCGIDVILDQWE-LNEIARQGPPRWMERQIREADKVLIVCS 67 (150)
T ss_pred HHHHHHHHHHHHHHHhccCCceeecHHh-hcccccCCHHHHHHHHHhcCCEEEEEec
Confidence 33334444456777766 666442 33 1111133666667777777776655543
No 150
>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=22.34 E-value=2.6e+02 Score=26.20 Aligned_cols=51 Identities=18% Similarity=0.229 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHhCCCCEEEEcCCC-------CcchhhHHHHHHHHHHHcC-cEEEEEe
Q 018389 291 ACAAVGGILAQRALADDIHDVVYTPRK-------GEKLEGKLQIVLQAIIDNG-VNVKVKL 343 (357)
Q Consensus 291 AAa~VGkvLAeRakekGI~~VVFDpR~-------GykYHGRVKAfADAaRE~G-L~FK~~l 343 (357)
.-..||..|++.+.+.||.- ++| +. ..-|.---..+.+.|.+++ |++-+.|
T Consensus 31 ~V~~VG~~L~~~Le~~Gi~v-ihd-~t~~~~~~y~~sY~~Sr~tv~~~l~~~p~i~~viDi 89 (196)
T TIGR02867 31 NITKVGDRLAKELEEKGIGV-IHD-KTVHDGLNYEQSYDRSRETVKKALKENKDLKYIIDL 89 (196)
T ss_pred cHHHHHHHHHHHHHHCCCeE-EEe-CCccCCccHHHHHHHHHHHHHHHHHHCCCceEEEEe
Confidence 34679999999999999875 555 34 2234334455666666664 5555555
No 151
>PF11349 DUF3151: Protein of unknown function (DUF3151); InterPro: IPR014487 This group represents an uncharacterised conserved protein.
Probab=22.23 E-value=55 Score=29.48 Aligned_cols=35 Identities=34% Similarity=0.468 Sum_probs=23.3
Q ss_pred HHHHHHHHHhCC--CCEEEEcCCCCcchhhHHHHHHHHHHHcCc
Q 018389 296 GGILAQRALADD--IHDVVYTPRKGEKLEGKLQIVLQAIIDNGV 337 (357)
Q Consensus 296 GkvLAeRakekG--I~~VVFDpR~GykYHGRVKAfADAaRE~GL 337 (357)
=.+||+++++.| |..-.|- |.||.- | +|.||.+|-
T Consensus 39 WA~LAe~al~~g~~v~AYAyA-RTGYHR-G-----LD~LRr~GW 75 (129)
T PF11349_consen 39 WAALAEEALAAGRPVTAYAYA-RTGYHR-G-----LDQLRRNGW 75 (129)
T ss_pred HHHHHHHHHhCCCchhhhhhh-hccccc-c-----HHHHHHCCC
Confidence 356999999998 3344577 888532 3 466666663
No 152
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=22.14 E-value=1.7e+02 Score=28.09 Aligned_cols=42 Identities=26% Similarity=0.239 Sum_probs=32.8
Q ss_pred HHHHHhCCCCEEEEcCCCCcch-hhHHHHHHHHHHHcCcEEEEE
Q 018389 300 AQRALADDIHDVVYTPRKGEKL-EGKLQIVLQAIIDNGVNVKVK 342 (357)
Q Consensus 300 AeRakekGI~~VVFDpR~GykY-HGRVKAfADAaRE~GL~FK~~ 342 (357)
.+||++.||..++|+ +..|.- .--=.++++.+++.|..+-|-
T Consensus 43 lerA~~~gIpt~~~~-~k~~~~r~~~d~~l~~~l~~~~~dlvvL 85 (200)
T COG0299 43 LERAAKAGIPTVVLD-RKEFPSREAFDRALVEALDEYGPDLVVL 85 (200)
T ss_pred HHHHHHcCCCEEEec-cccCCCHHHHHHHHHHHHHhcCCCEEEE
Confidence 589999999999999 566541 123478999999999988763
No 153
>PRK12826 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed
Probab=22.01 E-value=1.7e+02 Score=25.43 Aligned_cols=44 Identities=20% Similarity=0.222 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEE
Q 018389 291 ACAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 291 AAa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~F 339 (357)
|+..||..||+.+.+.|-+-++.+ |+. .++..+++.+++.|-.+
T Consensus 14 asg~iG~~l~~~l~~~g~~V~~~~-r~~----~~~~~~~~~l~~~~~~~ 57 (251)
T PRK12826 14 AARGIGRAIAVRLAADGAEVIVVD-ICG----DDAAATAELVEAAGGKA 57 (251)
T ss_pred CCCcHHHHHHHHHHHCCCEEEEEe-CCH----HHHHHHHHHHHhcCCeE
Confidence 346789999999999997666777 653 56677777777776544
No 154
>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=22.01 E-value=1.9e+02 Score=25.45 Aligned_cols=49 Identities=4% Similarity=0.001 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEcC-CCCc-chhhHHHHHHHHHHHcCcEEE
Q 018389 288 NATACAAVGGILAQRALADDIHDVVYTP-RKGE-KLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~VVFDp-R~Gy-kYHGRVKAfADAaRE~GL~FK 340 (357)
+.+++.. +++++.++|..++.|=. ..+. ....|.+.|.+++.+.|+.+.
T Consensus 100 ~~~~~~~----~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~ 150 (269)
T cd06293 100 NEQGGRL----ATRHLARAGHRRIAFVGGPDALISARERYAGYREALAEAHIPEV 150 (269)
T ss_pred CHHHHHH----HHHHHHHCCCceEEEEecCcccccHHHHHHHHHHHHHHcCCCCC
Confidence 4455444 55555667988887541 1121 224789999999999998653
No 155
>PRK07709 fructose-bisphosphate aldolase; Provisional
Probab=21.67 E-value=2.7e+02 Score=27.52 Aligned_cols=44 Identities=16% Similarity=0.215 Sum_probs=35.7
Q ss_pred HHHHhCCCCEEEEcCCCCcchhh---HHHHHHHHHHHcCcEEEEEeec
Q 018389 301 QRALADDIHDVVYTPRKGEKLEG---KLQIVLQAIIDNGVNVKVKLKQ 345 (357)
Q Consensus 301 eRakekGI~~VVFDpR~GykYHG---RVKAfADAaRE~GL~FK~~lkq 345 (357)
.+|+++|.+.|.|| -+...|.. ..+.+++-+...|+.+...|=+
T Consensus 94 ~~ai~~GftSVM~D-gS~lp~eeNi~~Trevv~~Ah~~gv~VEaElG~ 140 (285)
T PRK07709 94 KEAIDAGFTSVMID-ASHHPFEENVETTKKVVEYAHARNVSVEAELGT 140 (285)
T ss_pred HHHHHcCCCEEEEe-CCCCCHHHHHHHHHHHHHHHHHcCCEEEEEEec
Confidence 38999999999999 57777774 5567888899999998877643
No 156
>PRK08610 fructose-bisphosphate aldolase; Reviewed
Probab=21.61 E-value=2.7e+02 Score=27.59 Aligned_cols=43 Identities=19% Similarity=0.299 Sum_probs=35.0
Q ss_pred HHHHhCCCCEEEEcCCCCcchhhH---HHHHHHHHHHcCcEEEEEee
Q 018389 301 QRALADDIHDVVYTPRKGEKLEGK---LQIVLQAIIDNGVNVKVKLK 344 (357)
Q Consensus 301 eRakekGI~~VVFDpR~GykYHGR---VKAfADAaRE~GL~FK~~lk 344 (357)
++|+++|.+.|.|| -+...|..- .+.+++-+...|+.+.-.|=
T Consensus 94 ~~ai~~GftSVM~D-gS~l~~eeNi~~T~~vve~Ah~~gv~VEaElG 139 (286)
T PRK08610 94 KEAIDAGFTSVMID-ASHSPFEENVATTKKVVEYAHEKGVSVEAELG 139 (286)
T ss_pred HHHHHcCCCEEEEe-CCCCCHHHHHHHHHHHHHHHHHcCCEEEEEEe
Confidence 67999999999999 677888854 56778888889998876653
No 157
>PRK13813 orotidine 5'-phosphate decarboxylase; Provisional
Probab=21.57 E-value=4.1e+02 Score=23.85 Aligned_cols=45 Identities=16% Similarity=0.283 Sum_probs=34.0
Q ss_pred HHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 296 GGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 296 GkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
....++.+.++|..-|.+....| -+.++++++.+++.|+.+.+.+
T Consensus 69 ~~~~~~~~~~~gad~vtvh~e~g---~~~l~~~i~~~~~~g~~~~v~~ 113 (215)
T PRK13813 69 NRLICEAVFEAGAWGIIVHGFTG---RDSLKAVVEAAAESGGKVFVVV 113 (215)
T ss_pred HHHHHHHHHhCCCCEEEEcCcCC---HHHHHHHHHHHHhcCCeEEEEE
Confidence 34455777788999888886555 2458889999999999887766
No 158
>COG4947 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.39 E-value=1.2e+02 Score=29.44 Aligned_cols=36 Identities=22% Similarity=0.208 Sum_probs=30.4
Q ss_pred hCCCCEEEEcCCCCcchh----hHHHHHHHHHHHcCcEEE
Q 018389 305 ADDIHDVVYTPRKGEKLE----GKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 305 ekGI~~VVFDpR~GykYH----GRVKAfADAaRE~GL~FK 340 (357)
-+||.-|||-.++|.-|+ |-|.|+|+-+.++=|+|-
T Consensus 24 HaG~pVvvFpts~Grf~eyed~G~v~ala~fie~G~vQlf 63 (227)
T COG4947 24 HAGIPVVVFPTSGGRFNEYEDFGMVDALASFIEEGLVQLF 63 (227)
T ss_pred CCCCcEEEEecCCCcchhhhhcccHHHHHHHHhcCcEEEE
Confidence 479999999988887655 999999999988877763
No 159
>PRK09195 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=21.35 E-value=2.7e+02 Score=27.51 Aligned_cols=45 Identities=11% Similarity=0.101 Sum_probs=36.1
Q ss_pred HHHHHHhCCCCEEEEcCCCCcchhhH---HHHHHHHHHHcCcEEEEEee
Q 018389 299 LAQRALADDIHDVVYTPRKGEKLEGK---LQIVLQAIIDNGVNVKVKLK 344 (357)
Q Consensus 299 LAeRakekGI~~VVFDpR~GykYHGR---VKAfADAaRE~GL~FK~~lk 344 (357)
+..+|+++|.+.|.|| -+...|..- .+.+++-+...|+.+.-.|=
T Consensus 89 ~i~~Ai~~GftSVM~D-gS~l~~eeNi~~T~~vv~~Ah~~gv~VEaElG 136 (284)
T PRK09195 89 DIAQKVRSGVRSVMID-GSHLPFAQNISLVKEVVDFCHRFDVSVEAELG 136 (284)
T ss_pred HHHHHHHcCCCEEEeC-CCCCCHHHHHHHHHHHHHHHHHcCCEEEEEEe
Confidence 4788999999999999 677777754 56778888889988876664
No 160
>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=21.11 E-value=2.5e+02 Score=23.83 Aligned_cols=43 Identities=9% Similarity=0.131 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhCCCCEEEEc-CCCC-cchhhHHHHHHHHHHHcC
Q 018389 294 AVGGILAQRALADDIHDVVYT-PRKG-EKLEGKLQIVLQAIIDNG 336 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFD-pR~G-ykYHGRVKAfADAaRE~G 336 (357)
..|..+|+.+.+.|..+|.+= .... .-...+...|.+++.+.|
T Consensus 104 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~ 148 (264)
T cd01537 104 QAGYLAGEHLAEKGHRRIALLAGPLGSSTARERVAGFKDALKEAG 148 (264)
T ss_pred HHHHHHHHHHHHhcCCcEEEEECCCCCCcHHHHHHHHHHHHHHcC
Confidence 467778888888888876532 1223 233478999999999998
No 161
>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=21.07 E-value=2e+02 Score=25.11 Aligned_cols=46 Identities=13% Similarity=0.154 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhCCCCEEEEcC-CCCc-c-hhhHHHHHHHHHHHcCcEE
Q 018389 294 AVGGILAQRALADDIHDVVYTP-RKGE-K-LEGKLQIVLQAIIDNGVNV 339 (357)
Q Consensus 294 ~VGkvLAeRakekGI~~VVFDp-R~Gy-k-YHGRVKAfADAaRE~GL~F 339 (357)
..|..+++.+.+.|..+|.|=- .... . -..|...|.+++.+.|+.+
T Consensus 102 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~ 150 (268)
T cd06273 102 EAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAALAEAGLEL 150 (268)
T ss_pred HHHHHHHHHHHHCCCCeEEEEeccccCCccHHHHHHHHHHHHHHcCCCC
Confidence 3455555666667888876431 1111 1 1258999999999999654
No 162
>PRK06546 pyruvate dehydrogenase; Provisional
Probab=20.96 E-value=1.3e+02 Score=31.47 Aligned_cols=44 Identities=18% Similarity=0.314 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHc-CcEEEEE
Q 018389 293 AAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDN-GVNVKVK 342 (357)
Q Consensus 293 a~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~-GL~FK~~ 342 (357)
..+|.+|++++.+.||+.| |- -.| +.+-.|.|++.+. ||.+..-
T Consensus 3 ~t~~~~l~~~L~~~GV~~v-Fg-~pG----~~~~~l~dal~~~~~i~~i~~ 47 (578)
T PRK06546 3 KTVAEQLVEQLVAAGVKRI-YG-IVG----DSLNPIVDAVRRTGGIEWVHV 47 (578)
T ss_pred ccHHHHHHHHHHHcCCCEE-EE-CCC----CchHHHHHHHhccCCCeEEEe
Confidence 4689999999999999985 55 246 5677789999776 8887654
No 163
>PRK10206 putative oxidoreductase; Provisional
Probab=20.54 E-value=2.5e+02 Score=27.39 Aligned_cols=34 Identities=15% Similarity=0.134 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHH
Q 018389 298 ILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIID 334 (357)
Q Consensus 298 vLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE 334 (357)
.|.+.|.+.|+.-++.- ..+|+.-+..+-+.+++
T Consensus 106 ~l~~~a~~~~~~l~v~~---~~R~~p~~~~~k~li~~ 139 (344)
T PRK10206 106 ELFALAKSKGLTVTPYQ---NRRFDSCFLTAKKAIES 139 (344)
T ss_pred HHHHHHHHhCCEEEEEE---eeeECHHHHHHHHHHHc
Confidence 33445555665544322 14555555555555544
No 164
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=20.44 E-value=1.8e+02 Score=30.16 Aligned_cols=54 Identities=22% Similarity=0.356 Sum_probs=44.4
Q ss_pred CCHHHHHHHHHH-----------------HHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEE
Q 018389 287 RNATACAAVGGI-----------------LAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 287 ~NveAAa~VGkv-----------------LAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~ 341 (357)
.+.++|..+.++ ||..+.+.|+..+--.| +..-..-+|+++++++++.|+...+
T Consensus 58 ~~~e~A~A~~~Ik~~~~vPLVaDiHf~~rla~~~~~~g~~k~RINP-GNig~~~~v~~vVe~Ak~~g~piRI 128 (361)
T COG0821 58 PDMEAAEALKEIKQRLNVPLVADIHFDYRLALEAAECGVDKVRINP-GNIGFKDRVREVVEAAKDKGIPIRI 128 (361)
T ss_pred CCHHHHHHHHHHHHhCCCCEEEEeeccHHHHHHhhhcCcceEEECC-cccCcHHHHHHHHHHHHHcCCCEEE
Confidence 467788777764 78888999999999885 6566667899999999999998876
No 165
>PRK07814 short chain dehydrogenase; Provisional
Probab=20.43 E-value=2.5e+02 Score=25.23 Aligned_cols=41 Identities=17% Similarity=0.205 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcE
Q 018389 293 AAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVN 338 (357)
Q Consensus 293 a~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~ 338 (357)
.-||..+|+.+.+.|.+=++.+ |+. .....+++.++..|..
T Consensus 20 ggIG~~~a~~l~~~G~~Vi~~~-r~~----~~~~~~~~~l~~~~~~ 60 (263)
T PRK07814 20 RGLGAAIALAFAEAGADVLIAA-RTE----SQLDEVAEQIRAAGRR 60 (263)
T ss_pred ChHHHHHHHHHHHCCCEEEEEe-CCH----HHHHHHHHHHHhcCCc
Confidence 4689999999999998666688 664 4556666666554433
No 166
>PF02811 PHP: PHP domain; InterPro: IPR004013 The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. This family is often associated with an N-terminal region IPR003141 from INTERPRO.; GO: 0003824 catalytic activity; PDB: 2WJE_A 3QY8_A 2WJD_A 2WJF_A 1PB0_B 1M68_A 1M65_A 3E38_B 2W9M_A 3E0F_A ....
Probab=20.42 E-value=2.2e+02 Score=23.58 Aligned_cols=42 Identities=12% Similarity=0.232 Sum_probs=30.8
Q ss_pred HHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEEEEe
Q 018389 299 LAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 299 LAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK~~l 343 (357)
++++|++.|++.|++... ..+.| +..+.+.+++.||.+.+=+
T Consensus 21 ~v~~A~~~Gl~~i~iTDH--~~~~~-~~~~~~~~~~~~i~vi~G~ 62 (175)
T PF02811_consen 21 YVEQAKEKGLDAIAITDH--NNFAG-YPDFYKEAKKKGIKVIPGV 62 (175)
T ss_dssp HHHHHHHTTESEEEEEEE--TTTTT-HHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHcCCCEEEEcCC--ccccc-chHHHHHHHhcCCceEEeE
Confidence 459999999999987733 33444 6777788888998776543
No 167
>PRK10887 glmM phosphoglucosamine mutase; Provisional
Probab=20.36 E-value=3.8e+02 Score=27.13 Aligned_cols=50 Identities=14% Similarity=0.084 Sum_probs=37.4
Q ss_pred CHHHHHHHHHHHHHHHHhCCCCEE--EEcCCCCcchhhH--HHHHHHHHHHcCcEEEE
Q 018389 288 NATACAAVGGILAQRALADDIHDV--VYTPRKGEKLEGK--LQIVLQAIIDNGVNVKV 341 (357)
Q Consensus 288 NveAAa~VGkvLAeRakekGI~~V--VFDpR~GykYHGR--VKAfADAaRE~GL~FK~ 341 (357)
+.+-|..||..+|..+...|...| -+|.|. .|+ -.||+.+|..+|+++..
T Consensus 19 tpe~~~~lg~a~a~~l~~~~~~~VvVg~D~R~----ss~~l~~a~~~gL~s~Gv~V~~ 72 (443)
T PRK10887 19 TPDFVLKLGWAAGKVLARQGRPKVLIGKDTRI----SGYMLESALEAGLAAAGVDVLL 72 (443)
T ss_pred CHHHHHHHHHHHHHHHHhCCCCcEEEEeCCCC----CHHHHHHHHHHHHHHCCCeEEE
Confidence 668899999999998876544444 488543 344 47899999999998754
No 168
>TIGR00048 radical SAM enzyme, Cfr family. A Staphylococcus sciuri plasmid-borne member of this family, Cfr, has been identified as essential to transferrable resistance to chloramphenicol and florfenicol by an unknown mechanism. A 14-15 residue cluster with four perfectly conserved Cys residues suggests this protein may be an enzyme with an iron-sulfur cluster. The Cys cluster is part of the radical SAM domain, suggested to provide a general mechanism by which the Fe-S center cleaves S-adenosylmethionine to initiate radical-based catalysis. Members of this family lack apparent transmembrane domains.
Probab=20.26 E-value=7.4e+02 Score=24.93 Aligned_cols=85 Identities=16% Similarity=0.319 Sum_probs=56.1
Q ss_pred cCCeEEEEEEeCCCCeEEEEEcccchhhhcccC------CCCCHHHHHHHHHHHHHHHH----hCCCCEEEEcCCCCcch
Q 018389 252 SKASVRACIVHRVTSKVVVVAHSISKDMKFDLD------STRNATACAAVGGILAQRAL----ADDIHDVVYTPRKGEKL 321 (357)
Q Consensus 252 SNKHIYAQVIDD~~GkTLaSAST~EkdIK~~L~------St~NveAAa~VGkvLAeRak----ekGI~~VVFDpR~GykY 321 (357)
.+..|.+-+|....+.||+..|...=.++-... -..|..+...|.+++.-+.. ..+|+.|+|- -.|+..
T Consensus 90 dg~~iE~V~i~~~~~~t~cVSsQ~GC~l~C~fC~t~~~g~~r~lt~~Eiv~qv~~~~~~~~~~~~~v~nVvfm-GmGEPL 168 (355)
T TIGR00048 90 DGQTIETVLIPEKDRATVCVSSQVGCALGCTFCATAKGGFNRNLEASEIIGQVLRVQKINNETGERVSNVVFM-GMGEPL 168 (355)
T ss_pred CCCEEEEEEEEeCCCcEEEEecCCCCCCcCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHhhhcCCCeeEEEEe-cCCchh
Confidence 689999999999999999776664444433221 12367888888887754431 2458899999 447744
Q ss_pred h--hHHHHHHHHHHH-cCc
Q 018389 322 E--GKLQIVLQAIID-NGV 337 (357)
Q Consensus 322 H--GRVKAfADAaRE-~GL 337 (357)
. .-|..+++.+.+ .|+
T Consensus 169 ln~d~v~~~l~~l~~~~g~ 187 (355)
T TIGR00048 169 LNLNEVVKAMEIMNDDFGL 187 (355)
T ss_pred hCHHHHHHHHHHhhccccc
Confidence 4 346666666653 553
No 169
>cd00947 TBP_aldolase_IIB Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. The type A and type B Class II FBPA's differ in the presence and absence of distinct indels in the sequence that result in differing loop lengths in the structures.
Probab=20.20 E-value=2.9e+02 Score=27.20 Aligned_cols=44 Identities=23% Similarity=0.274 Sum_probs=35.6
Q ss_pred HHHHHhCCCCEEEEcCCCCcchhh---HHHHHHHHHHHcCcEEEEEee
Q 018389 300 AQRALADDIHDVVYTPRKGEKLEG---KLQIVLQAIIDNGVNVKVKLK 344 (357)
Q Consensus 300 AeRakekGI~~VVFDpR~GykYHG---RVKAfADAaRE~GL~FK~~lk 344 (357)
..+|+++|.+.|.|| -+...|.. ..+.+++-++..|+.+...|=
T Consensus 85 i~~ai~~GftSVMiD-~S~l~~eeNi~~t~~vv~~ah~~gv~VEaElG 131 (276)
T cd00947 85 IKRAIRAGFSSVMID-GSHLPFEENVAKTKEVVELAHAYGVSVEAELG 131 (276)
T ss_pred HHHHHHhCCCEEEeC-CCCCCHHHHHHHHHHHHHHHHHcCCeEEEEEe
Confidence 458899999999999 67777775 456788889999998887663
No 170
>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=20.19 E-value=2.6e+02 Score=25.67 Aligned_cols=46 Identities=9% Similarity=0.014 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHHcCcEEE
Q 018389 295 VGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIIDNGVNVK 340 (357)
Q Consensus 295 VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE~GL~FK 340 (357)
.+..+++.+++.|..+|++=......-..++++|.+++++.|+.+.
T Consensus 123 ~~~~~~~~l~~~g~~~v~~l~~~~~~~~~~~~~~~~~~~~~G~~~~ 168 (336)
T cd06326 123 EIAAIVRHLVTLGLKRIAVFYQDDAFGKDGLAGVEKALAARGLKPV 168 (336)
T ss_pred HHHHHHHHHHHhCCceEEEEEecCcchHHHHHHHHHHHHHcCCCeE
Confidence 4566777777789888753311111235789999999999998753
No 171
>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=20.07 E-value=4e+02 Score=23.56 Aligned_cols=53 Identities=13% Similarity=0.059 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHHHHHHhCCCCEEEE--cCCCCcchhhHHHHHHHHHHHc-CcEEEE
Q 018389 287 RNATACAAVGGILAQRALADDIHDVVY--TPRKGEKLEGKLQIVLQAIIDN-GVNVKV 341 (357)
Q Consensus 287 ~NveAAa~VGkvLAeRakekGI~~VVF--DpR~GykYHGRVKAfADAaRE~-GL~FK~ 341 (357)
.+..++..+++.|++++. |-.++.| .+....--..|.++|.+++++. |+.+..
T Consensus 103 d~~~~g~~~~~~l~~~~~--g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~ 158 (275)
T cd06320 103 DNKANGVRGAEWIIDKLA--EGGKVAIIEGKAGAFAAEQRTEGFTEAIKKASGIEVVA 158 (275)
T ss_pred CcHHHHHHHHHHHHHHhC--CCceEEEEeCCCCCccHHHHHHHHHHHHhhCCCcEEEE
Confidence 355667777777766542 4445543 3222223357899999999999 998653
No 172
>PRK13396 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=20.01 E-value=1.8e+02 Score=29.75 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=34.0
Q ss_pred HHHHHHHhCCCCEE---EEcCCCC-cchhh----HHHHHHHHHHHcCcEEEEEe
Q 018389 298 ILAQRALADDIHDV---VYTPRKG-EKLEG----KLQIVLQAIIDNGVNVKVKL 343 (357)
Q Consensus 298 vLAeRakekGI~~V---VFDpR~G-ykYHG----RVKAfADAaRE~GL~FK~~l 343 (357)
-+|+++++.|+.-+ .|+||.. |-|.| -++.|+++..+.||.|-..+
T Consensus 119 ~~A~~lk~~g~~~~r~g~~kpRtsp~sf~G~g~~gl~~L~~~~~e~Gl~~~tev 172 (352)
T PRK13396 119 ETAKRVKAAGAKFLRGGAYKPRTSPYAFQGHGESALELLAAAREATGLGIITEV 172 (352)
T ss_pred HHHHHHHHcCCCEEEeeeecCCCCCcccCCchHHHHHHHHHHHHHcCCcEEEee
Confidence 34777888898765 5999754 44554 48899999999999886543
No 173
>PRK07454 short chain dehydrogenase; Provisional
Probab=20.01 E-value=1.9e+02 Score=25.41 Aligned_cols=38 Identities=11% Similarity=0.090 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHhCCCCEEEEcCCCCcchhhHHHHHHHHHHH
Q 018389 292 CAAVGGILAQRALADDIHDVVYTPRKGEKLEGKLQIVLQAIID 334 (357)
Q Consensus 292 Aa~VGkvLAeRakekGI~~VVFDpR~GykYHGRVKAfADAaRE 334 (357)
+..||..||+++.+.|-.-++.+ |+. .....+++.+.+
T Consensus 15 sg~iG~~la~~l~~~G~~V~~~~-r~~----~~~~~~~~~~~~ 52 (241)
T PRK07454 15 SSGIGKATALAFAKAGWDLALVA-RSQ----DALEALAAELRS 52 (241)
T ss_pred CchHHHHHHHHHHHCCCEEEEEe-CCH----HHHHHHHHHHHh
Confidence 35789999999999998655677 664 334445554444
Done!