Query 029747
Match_columns 188
No_of_seqs 115 out of 1096
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:01:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029747.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029747hhsearch_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 1.7E-39 3.7E-44 251.0 12.9 109 74-183 1-109 (109)
2 PRK05593 rplR 50S ribosomal pr 100.0 5.9E-39 1.3E-43 250.6 12.7 115 67-183 3-117 (117)
3 TIGR00060 L18_bact ribosomal p 100.0 9.7E-39 2.1E-43 248.7 12.5 111 68-183 2-114 (114)
4 COG0256 RplR Ribosomal protein 100.0 1E-35 2.2E-40 234.9 12.8 116 67-183 8-125 (125)
5 PF00861 Ribosomal_L18p: Ribos 100.0 1.6E-35 3.5E-40 230.6 12.5 116 67-183 2-119 (119)
6 PTZ00032 60S ribosomal protein 100.0 6.3E-34 1.4E-38 239.8 11.7 132 50-183 51-211 (211)
7 cd00432 Ribosomal_L18_L5e Ribo 100.0 2.1E-33 4.6E-38 212.5 13.2 102 79-181 2-103 (103)
8 PRK08569 rpl18p 50S ribosomal 100.0 5.9E-31 1.3E-35 220.7 11.6 109 76-185 19-132 (193)
9 KOG3333 Mitochondrial/chloropl 99.8 1.3E-18 2.8E-23 142.8 10.0 95 89-184 61-155 (188)
10 PTZ00069 60S ribosomal protein 99.6 5.8E-15 1.3E-19 130.8 7.9 98 87-185 47-176 (300)
11 PTZ00090 40S ribosomal protein 97.9 0.00032 7E-09 60.8 12.5 101 82-188 112-213 (233)
12 TIGR03632 bact_S11 30S ribosom 97.5 0.0019 4.2E-08 49.8 10.9 90 91-186 3-92 (108)
13 PF00411 Ribosomal_S11: Riboso 97.5 0.002 4.4E-08 49.6 10.6 91 91-187 3-93 (110)
14 CHL00041 rps11 ribosomal prote 97.4 0.003 6.5E-08 49.4 10.9 92 90-187 15-106 (116)
15 KOG0875 60S ribosomal protein 97.4 0.00012 2.5E-09 64.5 2.9 98 86-184 46-174 (264)
16 PRK05309 30S ribosomal protein 97.2 0.0076 1.7E-07 48.0 11.0 93 89-187 18-110 (128)
17 TIGR03628 arch_S11P archaeal r 96.7 0.03 6.5E-07 44.0 10.5 96 91-188 5-105 (114)
18 PRK09607 rps11p 30S ribosomal 96.5 0.027 5.9E-07 45.4 9.4 96 90-187 11-111 (132)
19 PTZ00129 40S ribosomal protein 96.1 0.12 2.5E-06 42.6 10.9 97 90-188 30-131 (149)
20 KOG0408 Mitochondrial/chloropl 94.4 0.58 1.3E-05 39.5 10.1 98 85-188 76-173 (190)
21 COG0100 RpsK Ribosomal protein 94.3 0.51 1.1E-05 38.0 9.2 91 91-187 21-111 (129)
22 KOG0407 40S ribosomal protein 85.7 12 0.00026 30.0 9.5 93 91-185 19-116 (139)
23 PF01120 Alpha_L_fucos: Alpha- 72.8 8.5 0.00018 34.7 5.6 47 141-187 94-158 (346)
24 TIGR01917 gly_red_sel_B glycin 71.8 15 0.00032 35.1 7.0 56 128-184 313-368 (431)
25 smart00812 Alpha_L_fucos Alpha 70.7 8.6 0.00019 35.6 5.2 47 141-187 84-148 (384)
26 TIGR01918 various_sel_PB selen 67.2 21 0.00045 34.2 7.0 56 128-184 313-368 (431)
27 smart00481 POLIIIAc DNA polyme 64.1 27 0.00058 23.5 5.4 42 140-184 17-58 (67)
28 PF14419 SPOUT_MTase_2: AF2226 60.9 26 0.00056 29.6 5.7 49 130-179 10-58 (173)
29 COG1611 Predicted Rossmann fol 60.5 15 0.00032 31.3 4.4 41 133-183 33-73 (205)
30 PF13727 CoA_binding_3: CoA-bi 57.2 27 0.00059 26.6 5.0 42 142-185 132-173 (175)
31 PF02065 Melibiase: Melibiase; 56.0 33 0.00072 32.0 6.2 46 142-187 62-124 (394)
32 PF03646 FlaG: FlaG protein; 54.5 24 0.00052 26.3 4.2 41 76-116 44-84 (107)
33 PRK04302 triosephosphate isome 52.8 38 0.00083 28.4 5.6 47 138-184 72-118 (223)
34 PF00532 Peripla_BP_1: Peripla 50.2 45 0.00097 28.6 5.7 49 137-185 103-154 (279)
35 cd06288 PBP1_sucrose_transcrip 50.0 42 0.00092 27.0 5.3 45 140-184 104-150 (269)
36 cd06319 PBP1_ABC_sugar_binding 49.2 72 0.0016 25.9 6.6 55 130-184 101-159 (277)
37 PRK00366 ispG 4-hydroxy-3-meth 46.2 52 0.0011 30.8 5.7 57 130-187 63-137 (360)
38 cd06285 PBP1_LacI_like_7 Ligan 46.0 57 0.0012 26.5 5.5 45 139-183 101-147 (265)
39 cd06286 PBP1_CcpB_like Ligand- 45.8 55 0.0012 26.4 5.4 45 139-183 101-147 (260)
40 PF14871 GHL6: Hypothetical gl 45.6 81 0.0017 24.9 6.1 48 141-188 3-65 (132)
41 cd06296 PBP1_CatR_like Ligand- 43.4 60 0.0013 26.3 5.2 45 139-184 104-151 (270)
42 cd06280 PBP1_LacI_like_4 Ligan 42.6 83 0.0018 25.5 5.9 48 137-184 100-148 (263)
43 PF07713 DUF1604: Protein of u 41.6 9.3 0.0002 29.0 0.2 25 32-56 45-69 (87)
44 cd06274 PBP1_FruR Ligand bindi 41.5 71 0.0015 25.9 5.4 48 132-183 100-149 (264)
45 cd01543 PBP1_XylR Ligand-bindi 41.3 74 0.0016 25.9 5.5 45 138-183 95-141 (265)
46 cd06293 PBP1_LacI_like_11 Liga 40.8 77 0.0017 25.7 5.5 45 139-184 103-150 (269)
47 PRK10423 transcriptional repre 40.5 78 0.0017 26.7 5.7 44 139-183 161-207 (327)
48 PF00875 DNA_photolyase: DNA p 40.4 63 0.0014 25.3 4.8 46 140-186 77-123 (165)
49 COG3669 Alpha-L-fucosidase [Ca 39.9 66 0.0014 30.8 5.5 46 142-187 58-121 (430)
50 PLN03231 putative alpha-galact 39.7 70 0.0015 29.7 5.6 57 132-188 16-107 (357)
51 TIGR02571 ComEB ComE operon pr 39.2 68 0.0015 25.9 4.9 37 144-185 101-137 (151)
52 cd06267 PBP1_LacI_sugar_bindin 38.8 88 0.0019 24.6 5.4 44 140-183 104-149 (264)
53 TIGR00612 ispG_gcpE 1-hydroxy- 38.7 74 0.0016 29.7 5.5 56 130-186 55-127 (346)
54 PF00106 adh_short: short chai 38.6 1.6E+02 0.0034 22.1 6.6 48 136-185 9-56 (167)
55 cd01574 PBP1_LacI Ligand-bindi 38.4 1.1E+02 0.0024 24.6 6.0 46 139-184 103-150 (264)
56 cd06275 PBP1_PurR Ligand-bindi 38.3 98 0.0021 25.0 5.7 48 137-184 102-151 (269)
57 cd06295 PBP1_CelR Ligand bindi 38.0 94 0.002 25.3 5.6 47 137-183 110-158 (275)
58 PRK10703 DNA-binding transcrip 37.9 85 0.0019 26.8 5.5 47 138-184 164-212 (341)
59 cd06276 PBP1_FucR_like Ligand- 37.8 88 0.0019 25.8 5.5 48 137-184 100-150 (247)
60 PF13380 CoA_binding_2: CoA bi 37.7 69 0.0015 24.3 4.5 37 142-184 70-106 (116)
61 cd06282 PBP1_GntR_like_2 Ligan 37.6 86 0.0019 25.1 5.3 46 137-183 101-150 (266)
62 PLN02229 alpha-galactosidase 36.5 1.1E+02 0.0024 29.2 6.4 57 132-188 78-149 (427)
63 PRK09492 treR trehalose repres 36.4 1.1E+02 0.0024 25.7 5.9 43 141-184 164-210 (315)
64 PF09666 Sororin: Sororin prot 35.7 14 0.00031 30.9 0.4 15 42-56 100-114 (162)
65 PHA02588 cd deoxycytidylate de 35.1 86 0.0019 25.8 4.9 39 144-186 115-153 (168)
66 cd06287 PBP1_LacI_like_8 Ligan 34.8 1.1E+02 0.0025 25.4 5.8 47 138-184 104-152 (269)
67 PF07071 DUF1341: Protein of u 34.3 1.3E+02 0.0028 26.4 6.0 40 145-184 142-181 (218)
68 PRK11303 DNA-binding transcrip 34.3 1.4E+02 0.003 25.2 6.3 44 140-184 167-213 (328)
69 COG1472 BglX Beta-glucosidase- 34.2 96 0.0021 28.9 5.6 57 126-182 88-162 (397)
70 PF02811 PHP: PHP domain; Int 34.2 1.2E+02 0.0027 22.9 5.5 40 143-185 21-60 (175)
71 COG0041 PurE Phosphoribosylcar 33.9 1.7E+02 0.0038 24.5 6.5 41 144-185 22-62 (162)
72 cd01575 PBP1_GntR Ligand-bindi 33.7 1.2E+02 0.0025 24.4 5.4 46 138-183 102-149 (268)
73 cd06284 PBP1_LacI_like_6 Ligan 33.6 98 0.0021 24.8 5.0 46 138-183 101-148 (267)
74 PRK14719 bifunctional RNAse/5- 33.5 65 0.0014 29.7 4.4 39 143-184 58-99 (360)
75 cd06270 PBP1_GalS_like Ligand 33.2 1.3E+02 0.0028 24.4 5.6 44 140-183 104-149 (268)
76 cd06283 PBP1_RegR_EndR_KdgR_li 33.2 1.1E+02 0.0025 24.4 5.3 46 138-183 102-150 (267)
77 PRK10727 DNA-binding transcrip 32.9 1.1E+02 0.0025 26.1 5.6 43 140-183 164-209 (343)
78 TIGR00730 conserved hypothetic 32.5 95 0.0021 25.7 4.8 42 133-183 18-59 (178)
79 cd06273 PBP1_GntR_like_1 This 32.5 1.1E+02 0.0024 24.6 5.2 47 137-184 101-151 (268)
80 PRK13125 trpA tryptophan synth 32.4 1.4E+02 0.003 25.5 5.9 44 143-187 93-136 (244)
81 PRK07738 flagellar protein Fla 32.2 72 0.0016 25.2 3.8 38 76-113 53-90 (117)
82 PF06414 Zeta_toxin: Zeta toxi 32.1 1.9E+02 0.0042 23.3 6.5 50 135-187 77-126 (199)
83 COG3345 GalA Alpha-galactosida 31.7 61 0.0013 32.5 4.0 45 142-187 313-375 (687)
84 PRK10014 DNA-binding transcrip 31.3 1.4E+02 0.003 25.4 5.7 44 139-183 169-215 (342)
85 cd06281 PBP1_LacI_like_5 Ligan 31.2 1.5E+02 0.0032 24.2 5.7 43 140-183 104-149 (269)
86 cd06298 PBP1_CcpA_like Ligand- 31.1 1.5E+02 0.0032 23.9 5.6 45 139-183 103-150 (268)
87 cd06278 PBP1_LacI_like_2 Ligan 31.0 1.6E+02 0.0034 23.6 5.8 48 132-183 99-148 (266)
88 PRK12744 short chain dehydroge 30.9 1.8E+02 0.0039 23.8 6.2 45 138-183 19-63 (257)
89 cd06294 PBP1_ycjW_transcriptio 30.6 1.1E+02 0.0024 24.6 4.9 46 137-182 107-154 (270)
90 cd01545 PBP1_SalR Ligand-bindi 30.6 1.5E+02 0.0032 23.8 5.6 47 137-183 103-151 (270)
91 PLN02808 alpha-galactosidase 30.6 1.2E+02 0.0026 28.5 5.6 58 131-188 46-118 (386)
92 COG1609 PurR Transcriptional r 30.3 1.3E+02 0.0028 26.7 5.6 44 139-183 162-208 (333)
93 PRK12738 kbaY tagatose-bisphos 30.1 1.5E+02 0.0033 26.6 6.0 45 141-186 87-134 (286)
94 PRK11041 DNA-binding transcrip 29.9 1.5E+02 0.0033 24.6 5.7 50 131-184 135-186 (309)
95 PLN02692 alpha-galactosidase 29.3 1.2E+02 0.0027 28.8 5.5 57 132-188 71-142 (412)
96 COG2131 ComEB Deoxycytidylate 28.7 1.2E+02 0.0027 25.4 4.8 41 143-185 110-150 (164)
97 cd06320 PBP1_allose_binding Pe 28.7 2.5E+02 0.0053 22.8 6.7 54 130-185 102-158 (275)
98 cd06272 PBP1_hexuronate_repres 28.4 1.3E+02 0.0028 24.3 4.9 46 138-183 97-144 (261)
99 PRK12827 short chain dehydroge 28.3 2.1E+02 0.0046 22.7 6.1 44 137-181 16-59 (249)
100 PF00933 Glyco_hydro_3: Glycos 28.2 1E+02 0.0022 27.0 4.5 57 128-184 79-152 (299)
101 COG1683 Uncharacterized conser 28.1 1.5E+02 0.0032 24.8 5.2 56 130-185 77-146 (156)
102 cd06310 PBP1_ABC_sugar_binding 28.1 2.3E+02 0.0049 22.9 6.3 50 132-184 105-158 (273)
103 PF07355 GRDB: Glycine/sarcosi 28.0 1E+02 0.0022 28.8 4.6 31 128-158 317-347 (349)
104 cd01540 PBP1_arabinose_binding 28.0 2E+02 0.0042 23.6 6.0 54 130-183 105-163 (289)
105 PRK07523 gluconate 5-dehydroge 27.8 2.1E+02 0.0045 23.3 6.1 43 136-183 19-61 (255)
106 cd06290 PBP1_LacI_like_9 Ligan 27.8 1.7E+02 0.0038 23.5 5.6 48 131-183 98-148 (265)
107 PF08032 SpoU_sub_bind: RNA 2' 27.7 91 0.002 21.1 3.4 43 140-185 4-48 (76)
108 cd06271 PBP1_AglR_RafR_like Li 27.7 1.5E+02 0.0033 23.6 5.2 46 138-183 106-153 (268)
109 TIGR01858 tag_bisphos_ald clas 27.7 1.8E+02 0.0039 26.0 6.0 43 143-186 87-132 (282)
110 TIGR01481 ccpA catabolite cont 27.5 1.6E+02 0.0035 24.8 5.5 44 140-184 164-211 (329)
111 PF02593 dTMP_synthase: Thymid 27.4 1.8E+02 0.004 25.2 5.8 44 140-185 65-108 (217)
112 PLN00125 Succinyl-CoA ligase [ 27.3 1.4E+02 0.0031 26.9 5.3 40 143-183 85-124 (300)
113 cd06277 PBP1_LacI_like_1 Ligan 27.3 1.7E+02 0.0037 23.7 5.4 45 139-184 105-152 (268)
114 PRK14987 gluconate operon tran 27.2 2E+02 0.0042 24.5 6.0 43 140-182 168-211 (331)
115 cd04906 ACT_ThrD-I_1 First of 27.2 1.9E+02 0.0042 20.4 5.1 36 149-185 24-71 (85)
116 COG0821 gcpE 1-hydroxy-2-methy 26.9 1.5E+02 0.0032 27.9 5.4 56 130-186 57-129 (361)
117 TIGR02766 crypt_chrom_pln cryp 26.9 1.7E+02 0.0037 27.3 6.0 48 139-187 75-123 (475)
118 cd01391 Periplasmic_Binding_Pr 26.5 2.8E+02 0.0061 21.2 6.3 47 138-184 110-157 (269)
119 PLN02899 alpha-galactosidase 26.2 1.3E+02 0.0028 30.3 5.2 58 131-188 45-134 (633)
120 COG1908 FrhD Coenzyme F420-red 25.9 1.4E+02 0.0029 24.3 4.4 42 141-183 43-94 (132)
121 cd06292 PBP1_LacI_like_10 Liga 25.6 2.2E+02 0.0048 23.0 5.8 48 131-183 105-155 (273)
122 PRK07710 acetolactate synthase 25.2 1.6E+02 0.0035 28.1 5.6 41 138-184 17-57 (571)
123 cd00946 FBP_aldolase_IIA Class 25.2 3.4E+02 0.0074 25.1 7.5 54 133-187 105-161 (345)
124 cd01541 PBP1_AraR Ligand-bindi 25.2 1.9E+02 0.0041 23.4 5.4 44 139-182 108-152 (273)
125 PRK12737 gatY tagatose-bisphos 25.1 2.1E+02 0.0046 25.6 6.0 44 143-187 89-135 (284)
126 COG0299 PurN Folate-dependent 24.9 1.7E+02 0.0037 25.3 5.1 41 144-185 43-84 (200)
127 PLN02591 tryptophan synthase 24.8 2.3E+02 0.0049 24.8 6.0 43 141-187 96-138 (250)
128 cd06299 PBP1_LacI_like_13 Liga 24.3 2.1E+02 0.0045 23.0 5.4 44 140-183 104-149 (265)
129 cd06291 PBP1_Qymf_like Ligand 24.2 2.2E+02 0.0048 22.9 5.6 47 138-184 98-147 (265)
130 cd06308 PBP1_sensor_kinase_lik 24.2 3.2E+02 0.007 22.1 6.6 52 131-184 103-157 (270)
131 cd07939 DRE_TIM_NifV Streptomy 24.1 2.3E+02 0.0049 24.2 5.9 69 111-182 85-154 (259)
132 cd06322 PBP1_ABC_sugar_binding 23.9 3.1E+02 0.0066 22.1 6.3 51 132-184 103-155 (267)
133 TIGR02417 fruct_sucro_rep D-fr 23.9 2.3E+02 0.005 23.9 5.8 43 140-183 166-211 (327)
134 PF14488 DUF4434: Domain of un 23.9 2.4E+02 0.0052 23.0 5.7 44 143-187 25-85 (166)
135 cd07940 DRE_TIM_IPMS 2-isoprop 23.6 2.3E+02 0.0049 24.4 5.8 49 133-182 109-158 (268)
136 COG0007 CysG Uroporphyrinogen- 23.6 1.6E+02 0.0035 26.0 4.9 46 138-186 69-115 (244)
137 PRK09195 gatY tagatose-bisphos 23.1 2.5E+02 0.0054 25.2 6.1 44 142-186 88-134 (284)
138 cd01537 PBP1_Repressors_Sugar_ 23.1 2.4E+02 0.0052 22.0 5.4 43 138-180 104-148 (264)
139 PRK05835 fructose-bisphosphate 23.0 2.5E+02 0.0055 25.5 6.2 44 143-187 89-135 (307)
140 PRK08610 fructose-bisphosphate 22.9 2.6E+02 0.0056 25.1 6.1 42 144-186 93-137 (286)
141 PF04551 GcpE: GcpE protein; 22.4 1.9E+02 0.0041 27.1 5.3 55 130-186 52-137 (359)
142 CHL00200 trpA tryptophan synth 22.3 2.3E+02 0.005 24.9 5.6 42 141-186 109-150 (263)
143 cd06303 PBP1_LuxPQ_Quorum_Sens 22.2 3.8E+02 0.0083 22.1 6.7 51 131-183 112-164 (280)
144 cd06300 PBP1_ABC_sugar_binding 22.2 3.6E+02 0.0077 21.8 6.4 52 131-184 106-160 (272)
145 cd06297 PBP1_LacI_like_12 Liga 22.2 1.7E+02 0.0037 24.0 4.5 50 130-184 96-153 (269)
146 PRK07709 fructose-bisphosphate 22.1 2.7E+02 0.006 24.9 6.1 43 144-187 93-138 (285)
147 cd00947 TBP_aldolase_IIB Tagat 22.1 2.7E+02 0.0058 24.9 6.0 44 143-187 84-130 (276)
148 PRK11858 aksA trans-homoaconit 22.1 2.3E+02 0.0049 26.0 5.7 66 114-182 94-160 (378)
149 PRK12452 cardiolipin synthetas 22.0 2.8E+02 0.0061 26.6 6.5 48 136-187 179-227 (509)
150 PRK08452 flagellar protein Fla 21.4 1.3E+02 0.0028 24.0 3.5 38 76-113 60-97 (124)
151 PRK08195 4-hyroxy-2-oxovalerat 21.4 2.5E+02 0.0053 25.5 5.8 42 144-185 150-194 (337)
152 PRK10401 DNA-binding transcrip 21.4 2.7E+02 0.0058 23.9 5.8 48 131-183 159-209 (346)
153 TIGR00640 acid_CoA_mut_C methy 21.3 2.6E+02 0.0057 21.9 5.3 12 141-152 71-82 (132)
154 PRK13111 trpA tryptophan synth 21.3 2.7E+02 0.0058 24.4 5.8 42 141-186 107-148 (258)
155 cd07945 DRE_TIM_CMS Leptospira 21.2 2.6E+02 0.0057 24.6 5.8 69 112-182 91-162 (280)
156 smart00822 PKS_KR This enzymat 20.9 3.4E+02 0.0073 19.7 6.1 47 137-184 10-56 (180)
157 PF00352 TBP: Transcription fa 20.9 3.2E+02 0.007 19.5 6.6 34 89-124 39-72 (86)
158 cd07937 DRE_TIM_PC_TC_5S Pyruv 20.9 2.7E+02 0.0058 24.2 5.7 43 143-185 154-197 (275)
159 cd06413 GH25_muramidase_1 Unch 20.8 2.5E+02 0.0055 22.7 5.3 39 148-186 21-60 (191)
160 cd07938 DRE_TIM_HMGL 3-hydroxy 20.7 2.6E+02 0.0057 24.4 5.6 36 144-179 155-190 (274)
161 TIGR02717 AcCoA-syn-alpha acet 20.6 2.2E+02 0.0047 26.7 5.4 40 143-183 80-124 (447)
162 PRK05692 hydroxymethylglutaryl 20.6 2.5E+02 0.0055 24.8 5.6 15 168-182 156-170 (287)
163 PF01408 GFO_IDH_MocA: Oxidore 20.5 3.1E+02 0.0067 19.6 5.2 43 141-185 76-118 (120)
164 TIGR03581 EF_0839 conserved hy 20.5 2.3E+02 0.0049 25.2 5.1 39 145-183 142-180 (236)
165 PF01346 FKBP_N: Domain amino 20.4 1E+02 0.0022 23.2 2.6 25 130-154 20-44 (124)
166 cd06314 PBP1_tmGBP Periplasmic 20.3 3.7E+02 0.0079 21.9 6.2 52 132-184 102-154 (271)
167 PF00857 Isochorismatase: Isoc 20.3 1.8E+02 0.0038 22.5 4.1 46 140-188 100-145 (174)
168 PRK07998 gatY putative fructos 20.1 3.2E+02 0.0069 24.5 6.1 43 143-186 89-134 (283)
169 cd06326 PBP1_STKc_like Type I 20.0 3.2E+02 0.007 22.9 5.9 48 136-184 120-168 (336)
170 TIGR00725 conserved hypothetic 20.0 3.5E+02 0.0075 21.8 5.8 42 132-183 16-57 (159)
No 1
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=100.00 E-value=1.7e-39 Score=250.98 Aligned_cols=109 Identities=21% Similarity=0.344 Sum_probs=105.9
Q ss_pred chhhhcccccccCCCceEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCC
Q 029747 74 KHISFKQRTVAYMEPFTLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVY 153 (188)
Q Consensus 74 rh~r~rkr~~~~~~~pRL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~ 153 (188)
+|.|+|+++.++.++|||+|++||+|||||||||.+|+||+||||.||++++++++++|++||+.||++||+||+++||+
T Consensus 1 ~~~r~r~ki~g~~~rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~~gi~ 80 (109)
T CHL00139 1 KRERVRKKIKGTAERPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKKGIT 80 (109)
T ss_pred CCeeeeeeecCCCCCCEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHHCCCC
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 154 TASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 154 ~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
+|+| |||+++|||||+||+|++||+||+|
T Consensus 81 ~vvf-Drgg~~yhGrV~a~a~~are~GL~f 109 (109)
T CHL00139 81 KVVF-DRGGKLYHGRIKALAEAAREAGLQF 109 (109)
T ss_pred EEEE-cCCCCccchHHHHHHHHHHHhCCCC
Confidence 9999 7999999999999999999999987
No 2
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=100.00 E-value=5.9e-39 Score=250.56 Aligned_cols=115 Identities=26% Similarity=0.427 Sum_probs=108.6
Q ss_pred hhhccccchhhhcccccccCCCceEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHH
Q 029747 67 KKSKNTTKHISFKQRTVAYMEPFTLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAER 146 (188)
Q Consensus 67 ~~~kr~~rh~r~rkr~~~~~~~pRL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~R 146 (188)
+++.|.+||.|+|+++.++.++|||+|++||+|||||||||++++||+||||.||+++..+. ++|++||+.||++||+|
T Consensus 3 ~~~~r~~r~~r~r~ki~g~~~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~~-~~n~~aa~~vG~~la~r 81 (117)
T PRK05593 3 KKEARLRRHRRVRKKISGTAERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGLK-GGNKEAAKKVGKLIAER 81 (117)
T ss_pred hHHHHHHHHHHHHHHhcCCCCCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhcccc-CCCHHHHHHHHHHHHHH
Confidence 34567788999999999999999999999999999999999999999999999999976554 89999999999999999
Q ss_pred HHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 147 AREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 147 akeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
|+++||++|+| |||+++|||||+||+|++||+||+|
T Consensus 82 a~~~gi~~vvf-Drg~~~yhGrV~a~a~~are~Gl~f 117 (117)
T PRK05593 82 AKAKGIKQVVF-DRGGYKYHGRVKALADAAREAGLKF 117 (117)
T ss_pred HHHCCCCEEEE-cCCCCcccHHHHHHHHHHHHhCCCC
Confidence 99999999999 7999999999999999999999987
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=9.7e-39 Score=248.66 Aligned_cols=111 Identities=23% Similarity=0.354 Sum_probs=105.4
Q ss_pred hhccccchhhhcccccccC--CCceEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHH
Q 029747 68 KSKNTTKHISFKQRTVAYM--EPFTLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAE 145 (188)
Q Consensus 68 ~~kr~~rh~r~rkr~~~~~--~~pRL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~ 145 (188)
+++|.+||.|+|+++.++. ++|||+|++||+|||||||||++++||+||||+|++++ +++|++||+.||++||+
T Consensus 2 ~~~r~~r~~r~r~ki~gt~~~~rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~----~~~n~~aA~~vG~~la~ 77 (114)
T TIGR00060 2 KSARIRRHKRIRRKLRETGEANRPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK----YTGNKDAAKKVGKLVAE 77 (114)
T ss_pred cHHHHHHHHHHHHHhcCCCCCCCcEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc----CCCCHHHHHHHHHHHHH
Confidence 3456688999999999998 89999999999999999999999999999999999976 68899999999999999
Q ss_pred HHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 146 RAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 146 RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
||+++||++|+| |||+++|||||+||+|++||+||+|
T Consensus 78 ra~~~gi~~vvf-Drgg~~YhGrv~A~a~~aRe~Gl~F 114 (114)
T TIGR00060 78 RLKEKGIKDVVF-DRGGYKYHGRVAALAEAAREAGLNF 114 (114)
T ss_pred HHHHCCCCEEEE-eCCCCcchHHHHHHHHHHHHhCCCC
Confidence 999999999999 7999999999999999999999987
No 4
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-35 Score=234.88 Aligned_cols=116 Identities=19% Similarity=0.316 Sum_probs=109.9
Q ss_pred hhhccccchhhhcccccccCCCceEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhh--hhcCCCCHHHHHHHHHHHH
Q 029747 67 KKSKNTTKHISFKQRTVAYMEPFTLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKA--VLRSRSDIPACLAIGRILA 144 (188)
Q Consensus 67 ~~~kr~~rh~r~rkr~~~~~~~pRL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~--~L~s~~n~~AA~~vG~lLA 144 (188)
++.++.+||.++|.++.++.++|||+|++||+|||||||||..+.|+++|||.++++++ |...++|++||++||+++|
T Consensus 8 rr~~~~kr~~r~R~kl~g~~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~N~~aA~~vG~lia 87 (125)
T COG0256 8 RRRRRGKRAYRIRKKLLGTSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLVGKLIA 87 (125)
T ss_pred HHHHHHhHHHHHHHhhccCCCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhcccCCCCCHHHHHHHHHHHH
Confidence 66677888999999999999999999999999999999999999999999999999965 6667889999999999999
Q ss_pred HHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 145 ERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 145 ~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
+||+++||++|+| ||++++|||||+|++|++||+||+|
T Consensus 88 ~ra~~kgi~~vVf-dr~g~~yhgRV~Ala~~AreaGL~f 125 (125)
T COG0256 88 ERALAKGIEEVVF-DRGGYKYHGRVAALADGAREAGLEF 125 (125)
T ss_pred HHHHHcCCcEEEE-cCCCCCcchHHHHHHHHHHHcCcCC
Confidence 9999999999999 7999999999999999999999987
No 5
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=100.00 E-value=1.6e-35 Score=230.61 Aligned_cols=116 Identities=23% Similarity=0.387 Sum_probs=109.1
Q ss_pred hhhccccchhhhcccccccCCCceEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhh--hcCCCCHHHHHHHHHHHH
Q 029747 67 KKSKNTTKHISFKQRTVAYMEPFTLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAV--LRSRSDIPACLAIGRILA 144 (188)
Q Consensus 67 ~~~kr~~rh~r~rkr~~~~~~~pRL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~--L~s~~n~~AA~~vG~lLA 144 (188)
++.++.+|+.++++++.++.++|||+|++||+|||||||||.++.++++|||.|++++.. ..+++|++||+.||++||
T Consensus 2 k~~~~~~r~~~~r~~~~~~~~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~~vG~lla 81 (119)
T PF00861_consen 2 KKRRRRRRKLRIRRKIKGTAERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAYLVGELLA 81 (119)
T ss_dssp SCHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHhcCCCCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHHHHHHHHH
Confidence 566777888999999999999999999999999999999999999999999999999964 477889999999999999
Q ss_pred HHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 145 ERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 145 ~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
+||+++||..|+| |+++++|||+|+||+|++||+||+|
T Consensus 82 ~ra~~~gi~~v~f-dr~~~~y~grv~a~~~~~re~Gl~f 119 (119)
T PF00861_consen 82 KRALEKGIAKVVF-DRGGYKYHGRVKALADGAREGGLEF 119 (119)
T ss_dssp HHHHHTTSSEEEE-CTSTSSSSSHHHHHHHHHHHTTCB-
T ss_pred HHHHHcCCcEEEE-cCCCCcccHHHHHHHHHHHHcCCCC
Confidence 9999999999999 7999999999999999999999987
No 6
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=100.00 E-value=6.3e-34 Score=239.83 Aligned_cols=132 Identities=17% Similarity=0.228 Sum_probs=110.8
Q ss_pred ccccCCCCCCcccchhhhh-hccccchhhh----------------cccccccCCCceEEEEecCCeEEEEEEECCCCeE
Q 029747 50 EDFLDDDNSRPYTYKKEKK-SKNTTKHISF----------------KQRTVAYMEPFTLDVFISKRFVSASLTHRVTSKQ 112 (188)
Q Consensus 50 ~df~~~~~~~~~~y~~~~~-~kr~~rh~r~----------------rkr~~~~~~~pRL~V~kSNkhiyAqVidd~~g~t 112 (188)
-+|+.++ ++++++++.++ .+.+-+..-+ =+-|..-.++|||+|++||+|||||||||.+++|
T Consensus 51 ~~~~~k~-~~~~~~~~~r~l~~~~~~~~~~ee~~~~~~~~~~~~~~~~~i~~gkrrPRLsV~RSnkHIYAQIIDD~~~~T 129 (211)
T PTZ00032 51 KLLLTKR-SKLKGIPKPRKLHKHGFWAEIFEEKVEREELGNPCKDLDKDIIKGKRRPRLTLKNTNNQMYATIVDDYTRHV 129 (211)
T ss_pred HHHHHHH-HhhcCCcchHHHHhhhhhhhhhhhhhhhcccCCCcccccHHHHcCCCcceEEEEecCCeEEEEEEECCCCCE
Confidence 3577777 88888887633 3333332222 2222333688999999999999999999999999
Q ss_pred EEEEecchhhhhhhhc------------CCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCC
Q 029747 113 VAVAGTNSKDIKAVLR------------SRSDIPACLAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNG 180 (188)
Q Consensus 113 VaSAST~Ek~ik~~L~------------s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~G 180 (188)
||+|||+++++++.+. .++|++||+.||++||+||+++||++|+| ||+||+|||||+||||++||+|
T Consensus 130 LasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAerAl~kGI~kVvF-DRgGy~YHGRVkALAdaARe~G 208 (211)
T PTZ00032 130 LCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGISKVRF-DRAHYKYAGKVEALAEGARAVG 208 (211)
T ss_pred EEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEE-eCCCCeehhHHHHHHHHHHHcC
Confidence 9999999999987665 57899999999999999999999999999 7999999999999999999999
Q ss_pred cEe
Q 029747 181 IDV 183 (188)
Q Consensus 181 L~f 183 (188)
|+|
T Consensus 209 LkF 211 (211)
T PTZ00032 209 LQF 211 (211)
T ss_pred CCC
Confidence 987
No 7
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=100.00 E-value=2.1e-33 Score=212.48 Aligned_cols=102 Identities=25% Similarity=0.384 Sum_probs=97.7
Q ss_pred cccccccCCCceEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEe
Q 029747 79 KQRTVAYMEPFTLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYT 158 (188)
Q Consensus 79 rkr~~~~~~~pRL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfd 158 (188)
+++..+++.+|||+|++||+||||||+||.+++||++|||.||++++++++++|++||+.||++||+||+++||.+|+|
T Consensus 2 ~~~~~~~~~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vv~- 80 (103)
T cd00432 2 RRKRLGTQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVF- 80 (103)
T ss_pred ceEecCcCCCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEE-
Confidence 4555678899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCchhhHHHHHHHHHHHCCc
Q 029747 159 PRERDKFEGKIRAVVQSLIDNGI 181 (188)
Q Consensus 159 DRgg~kyhGrVkA~adalRe~GL 181 (188)
|+++++|||||+||+|++||+||
T Consensus 81 D~~~~~~~grv~a~~~~~r~~Gl 103 (103)
T cd00432 81 DRGGYRYHGRVKALAKGAREGGL 103 (103)
T ss_pred eCCCcccccHHHHHHHHHHHcCC
Confidence 79999999999999999999997
No 8
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=99.97 E-value=5.9e-31 Score=220.70 Aligned_cols=109 Identities=17% Similarity=0.178 Sum_probs=100.1
Q ss_pred hhhcccccc-cCCCceEEEEecCCeEEEEEE--ECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCC
Q 029747 76 ISFKQRTVA-YMEPFTLDVFISKRFVSASLT--HRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADV 152 (188)
Q Consensus 76 ~r~rkr~~~-~~~~pRL~V~kSNkhiyAqVi--dd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI 152 (188)
+.+.+|... +..+|||+|++||+||||||| |+++++||+||||.|++.++|..+++|++||+.||.+||+||+++||
T Consensus 19 TdY~~R~rl~~~~kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~~~~~N~~AAy~vG~llA~ral~kGi 98 (193)
T PRK08569 19 TDYRKRLKLLLSGKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKGDTGNTPAAYLTGLLAGKKALKAGV 98 (193)
T ss_pred ccHHHHHHHHhcCCCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhccccCCCCCHHHHHHHHHHHHHHHHHCCC
Confidence 444444433 468899999999999999999 89999999999999999999988999999999999999999999999
Q ss_pred CEEEEecCCCCchh--hHHHHHHHHHHHCCcEeEe
Q 029747 153 YTASYTPRERDKFE--GKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 153 ~~vvfdDRgg~kyh--GrVkA~adalRe~GL~f~~ 185 (188)
++|+| |+|+++|| |||+|+++++||+||+|+.
T Consensus 99 ~~vvf-DrGg~~yh~gGRV~A~akgArd~GL~fPh 132 (193)
T PRK08569 99 EEAVL-DIGLHRPTKGSRVFAALKGAIDAGLEIPH 132 (193)
T ss_pred CEEEE-ecCCccccCCccHHHHHHHHHHcCCcCCC
Confidence 99999 79999999 9999999999999999974
No 9
>KOG3333 consensus Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=99.77 E-value=1.3e-18 Score=142.83 Aligned_cols=95 Identities=25% Similarity=0.397 Sum_probs=85.5
Q ss_pred ceEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhH
Q 029747 89 FTLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPRERDKFEGK 168 (188)
Q Consensus 89 pRL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGr 168 (188)
++|.|..+..|+.+-|.|..+| +|+||||.||+|+.+||++.|+.||.+||++||+||+++||+.+++.+.--..-...
T Consensus 61 h~lev~~~~~hveg~v~H~~~g-vvvSAST~EwaIk~qLYst~dtsA~~niGRVLAqRCLqsGI~fm~~~~t~ea~~~s~ 139 (188)
T KOG3333|consen 61 HRLEVIRTQHHVEGLVEHQNGG-VVVSASTREWAIKKQLYSTRDTSACENIGRVLAQRCLQSGINFMVYQPTPEAAASSS 139 (188)
T ss_pred eEEEEeecccceeeeeeEecCC-EEEEecccchHHHHHHhhccchHHHHHHHHHHHHHHHHhCcceeccCCChhhccchH
Confidence 5899999999999999997666 789999999999999999999999999999999999999999999943333445668
Q ss_pred HHHHHHHHHHCCcEeE
Q 029747 169 IRAVVQSLIDNGIDVK 184 (188)
Q Consensus 169 VkA~adalRe~GL~f~ 184 (188)
.+-|..++.|+|+.|+
T Consensus 140 ~q~l~~a~~e~Gv~lk 155 (188)
T KOG3333|consen 140 MQRLQSAMTEGGVVLK 155 (188)
T ss_pred HHHHHHHHHhCCeeec
Confidence 8889999999999986
No 10
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=99.57 E-value=5.8e-15 Score=130.76 Aligned_cols=98 Identities=17% Similarity=0.183 Sum_probs=88.5
Q ss_pred CCceEEEEecCCeEEEEEEE--CCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhc--------CCC---
Q 029747 87 EPFTLDVFISKRFVSASLTH--RVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREA--------DVY--- 153 (188)
Q Consensus 87 ~~pRL~V~kSNkhiyAqVid--d~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~Rakea--------GI~--- 153 (188)
.+|||+|.+||++|.|||+. -++++||++|+|.|+.-.+|..+.+|.+||+.+|.++|.|++++ |++
T Consensus 47 pK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~kyG~k~gl~N~~AAY~TGlL~arR~L~kl~ld~~y~G~~e~~ 126 (300)
T PTZ00069 47 PKYRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELPRFGIPVGLTNYAAAYATGLLLARRLLKKLGLDKQFEGVKEAD 126 (300)
T ss_pred CCceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhcCcCCCCccHHHHHHHHHHHHHHHHHhhcccccccCccccc
Confidence 36999999999999999999 47889999999999998999999999999999999999999998 773
Q ss_pred -----------------EEEEecCCCCc--hhhHHHHHHHHHHHCCcEeEe
Q 029747 154 -----------------TASYTPRERDK--FEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 154 -----------------~vvfdDRgg~k--yhGrVkA~adalRe~GL~f~~ 185 (188)
++++ |.|..+ .++||+|+++|+.++||+++-
T Consensus 127 g~~y~v~e~~~~~~rpf~a~L-DiGL~rtt~G~RVFaalKGa~DgGl~IPh 176 (300)
T PTZ00069 127 GEYYHVDEEDDEERRPFKAIL-DVGLARTTTGNRVFGALKGAVDGGLHIPH 176 (300)
T ss_pred CcccccccccccCCCCceEEE-eeccccCCCCceeeeehhcccccCcccCC
Confidence 6788 688754 577999999999999999864
No 11
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=97.87 E-value=0.00032 Score=60.82 Aligned_cols=101 Identities=17% Similarity=0.246 Sum_probs=77.6
Q ss_pred ccccCCCceEEEEecCCeEEEEEEECCCCe-EEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecC
Q 029747 82 TVAYMEPFTLDVFISKRFVSASLTHRVTSK-QVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPR 160 (188)
Q Consensus 82 ~~~~~~~pRL~V~kSNkhiyAqVidd~~g~-tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDR 160 (188)
|.--..++.|+|.-|-+++.++|.|..++. ||+-+|+-..-+|+. ..+.-=||+.+++-+|+.|++.||..|..--+
T Consensus 112 i~~p~~~f~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~GFKGs--KKsTpfAAQ~aae~aakka~~~GIk~V~V~vK 189 (233)
T PTZ00090 112 IIEPTDRFMLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKK--LQQSERCAYRIGENIAKKCRRLGIFAVDIKFR 189 (233)
T ss_pred EecCCCcEEEEEEeccCcEEEEEEeCCCCEEEEEEEcccccCcccC--ccCCHHHHHHHHHHHHHHHHHcCCeEEEEEEe
Confidence 333457899999999999999999965553 577777666667653 23446688889999999999999998875223
Q ss_pred CCCchhhHHHHHHHHHHHCCcEeEeecC
Q 029747 161 ERDKFEGKIRAVVQSLIDNGIDVKIYLD 188 (188)
Q Consensus 161 gg~kyhGrVkA~adalRe~GL~f~~~~~ 188 (188)
|. |...+++.++..+||++..-.|
T Consensus 190 Gp----GgREtALRaL~~~GLkIt~I~D 213 (233)
T PTZ00090 190 RI----MRVETVLQAFYANGLQVTQIIH 213 (233)
T ss_pred CC----ChHHHHHHHHHHCCCEEEEEEE
Confidence 43 3499999999999999976554
No 12
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=97.52 E-value=0.0019 Score=49.79 Aligned_cols=90 Identities=14% Similarity=0.167 Sum_probs=70.5
Q ss_pred EEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHH
Q 029747 91 LDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPRERDKFEGKIR 170 (188)
Q Consensus 91 L~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVk 170 (188)
+.|+-|.+.+.+.|.|. +|.+++.+|+-...+++. .....-||..+++.++++|++.||..+..--+|. - -|+ +
T Consensus 3 ~hI~~s~NNT~itlTd~-~g~~~~~~S~G~~gfkg~--rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~kG~-G-~gr-~ 76 (108)
T TIGR03632 3 AHIHATFNNTIVTITDP-QGNVLSWASAGAVGFKGS--KKSTPYAAQLAAEDAAKKAKEFGMKTVDVYVKGP-G-AGR-E 76 (108)
T ss_pred EEEEccCCCEEEEEEcC-CCCEEEEEecCceeeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECC-C-CcH-H
Confidence 56888999999999996 566888888877777764 3556888999999999999999999877522443 2 244 6
Q ss_pred HHHHHHHHCCcEeEee
Q 029747 171 AVVQSLIDNGIDVKIY 186 (188)
Q Consensus 171 A~adalRe~GL~f~~~ 186 (188)
+++.+|...||++..-
T Consensus 77 ~~ir~l~~~glkI~~I 92 (108)
T TIGR03632 77 SAIRALQAAGLEVTSI 92 (108)
T ss_pred HHHHHHHHCCCEEEEE
Confidence 7888899999988654
No 13
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=97.48 E-value=0.002 Score=49.62 Aligned_cols=91 Identities=16% Similarity=0.155 Sum_probs=72.0
Q ss_pred EEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHH
Q 029747 91 LDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPRERDKFEGKIR 170 (188)
Q Consensus 91 L~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVk 170 (188)
+.|+-|.+.+.++|.| ..|.++.+.|+-...+|+. ......||..+++.++++|++.||+.|..--+| .-.||-
T Consensus 3 ihI~~s~NNt~vtlTd-~~G~~~~~~S~G~~gfK~~--rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG--~g~gr~- 76 (110)
T PF00411_consen 3 IHIKSSFNNTIVTLTD-LKGNVLFWSSAGSLGFKGA--RKSTPYAAQQAAEKIAKKAKELGIKTVRVKIKG--FGPGRE- 76 (110)
T ss_dssp EEEEEESSEEEEEEEE-TTSEEEEEEETTTSSTTTT--CGSSHHHHHHHHHHHHHHHHCTTEEEEEEEEES--SSTTHH-
T ss_pred EEEEecCCCEEEEEEC-CCCCEEEEEeccccccccc--cccCHHHHHHHHHHHHHHHHHcCCeEEEEEEcC--CCccHH-
Confidence 6788999999999999 5688899999988888764 356789999999999999999999987752233 234454
Q ss_pred HHHHHHHHCCcEeEeec
Q 029747 171 AVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 171 A~adalRe~GL~f~~~~ 187 (188)
+++.+|...||++...-
T Consensus 77 ~~lk~l~~~gl~I~~I~ 93 (110)
T PF00411_consen 77 AALKALKKSGLKIVSIT 93 (110)
T ss_dssp HHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHhcCCEEEEEE
Confidence 55688899999886543
No 14
>CHL00041 rps11 ribosomal protein S11
Probab=97.41 E-value=0.003 Score=49.41 Aligned_cols=92 Identities=8% Similarity=0.080 Sum_probs=72.8
Q ss_pred eEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHH
Q 029747 90 TLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPRERDKFEGKI 169 (188)
Q Consensus 90 RL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrV 169 (188)
-+.|+-|.+.+.+.|.|. .|.+++.+|.-...+++. .....-||..+++-++++|++.|+..+..--+|. - .||
T Consensus 15 i~hI~~t~NNTiiTlTd~-~G~~l~~~S~G~~gfKg~--rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I~ikG~-G-~Gr- 88 (116)
T CHL00041 15 VIHIQASFNNTIVTVTDV-RGRVISWSSAGACGFKGA--RKGTPFAAQTAAENAIRTVIDQGMKRAEVMIKGP-G-LGR- 88 (116)
T ss_pred EEEEEcccCCEEEEEEcC-CCCEEEEEecCceeeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECC-C-CcH-
Confidence 578899999999999995 577899998887777764 3455789999999999999999999877522442 2 466
Q ss_pred HHHHHHHHHCCcEeEeec
Q 029747 170 RAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 170 kA~adalRe~GL~f~~~~ 187 (188)
++++.+|...||++..--
T Consensus 89 ~~~ir~l~~~glkI~~I~ 106 (116)
T CHL00041 89 DTALRAIRRSGLKLSSIR 106 (116)
T ss_pred HHHHHHHHHCCCEEEEEE
Confidence 677899999999986543
No 15
>KOG0875 consensus 60S ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=97.38 E-value=0.00012 Score=64.48 Aligned_cols=98 Identities=12% Similarity=0.105 Sum_probs=78.6
Q ss_pred CCCceEEEEecCCeEEEEEEEC--CCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHh-cCCCE--------
Q 029747 86 MEPFTLDVFISKRFVSASLTHR--VTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERARE-ADVYT-------- 154 (188)
Q Consensus 86 ~~~pRL~V~kSNkhiyAqVidd--~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~Rake-aGI~~-------- 154 (188)
..++|+.|..+|+.|.+||+-. +.+.++++|.+.|+.-.+......|-.||+.+|.+||.|+++ .|++.
T Consensus 46 t~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s~elpkyg~~~GLtNyaAay~TglLLarR~l~~~gmD~~yeg~~e~ 125 (264)
T KOG0875|consen 46 TPKYRMIVRVINKDIICQIAYATIEGDVIVRAAYAHELPKYGVKVGLTNYAAAYCTGLLLACRLLKRFGMDKIYEGQVEV 125 (264)
T ss_pred CCceEEEEEEechhhHHHHHhheecceEEEEeeccccccccccccccchhHHHHhhHHHHHHHHHHHhCcccccccceee
Confidence 4679999999999999999873 567788999999999888777889999999999999999986 45332
Q ss_pred ------------------EEEecCCCCc--hhhHHHHHHHHHHHCCcEeE
Q 029747 155 ------------------ASYTPRERDK--FEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 155 ------------------vvfdDRgg~k--yhGrVkA~adalRe~GL~f~ 184 (188)
+.+ |-|..+ -..||+..++++.++||.++
T Consensus 126 ~gde~~~e~idgq~~aFt~~L-d~GLaRtttg~kvFGAlkga~dGGL~IP 174 (264)
T KOG0875|consen 126 TGDEYNVESIDGQPGAFTCYL-DAGLARTTTGNKVFGALKGAVDGGLSIP 174 (264)
T ss_pred cCcccccccccCCCCCeEEEe-cccccccCCCceeeeeeehhcccceecC
Confidence 122 333333 24489999999999999876
No 16
>PRK05309 30S ribosomal protein S11; Validated
Probab=97.17 E-value=0.0076 Score=47.97 Aligned_cols=93 Identities=15% Similarity=0.164 Sum_probs=72.2
Q ss_pred ceEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhH
Q 029747 89 FTLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPRERDKFEGK 168 (188)
Q Consensus 89 pRL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGr 168 (188)
-.+.|+-|.+.+.+.|.|. .|.+++.+|.-...+++. ..+..-||..+++.+++.|++.||..+.+--+|. - .|+
T Consensus 18 gi~hI~~t~NNTiitlTd~-~G~~~~~~S~G~~gfKg~--rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG~-G-~Gr 92 (128)
T PRK05309 18 GVAHIHATFNNTIVTITDR-QGNVISWASAGGLGFKGS--RKSTPYAAQVAAEDAAKKAKEHGMKTVEVFVKGP-G-SGR 92 (128)
T ss_pred eEEEEEccCCCEEEEEEcC-CCCEEEEEecCccEeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECC-C-CcH
Confidence 3688999999999999994 677888888776667653 3556779999999999999999999877522342 2 344
Q ss_pred HHHHHHHHHHCCcEeEeec
Q 029747 169 IRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 169 VkA~adalRe~GL~f~~~~ 187 (188)
.+++.+|...||++..--
T Consensus 93 -~~air~L~~~glkI~~I~ 110 (128)
T PRK05309 93 -ESAIRALQAAGLEVTSIK 110 (128)
T ss_pred -HHHHHHHHHCCCEEEEEE
Confidence 677888888999886543
No 17
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=96.70 E-value=0.03 Score=44.05 Aligned_cols=96 Identities=15% Similarity=0.104 Sum_probs=68.2
Q ss_pred EEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCC--CCc---h
Q 029747 91 LDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPRE--RDK---F 165 (188)
Q Consensus 91 L~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRg--g~k---y 165 (188)
+.|+-|-+.+...|.|..+..+++-+|.-..-.++. ..+.--||...++-++++|++.||..|.+--+| +.+ .
T Consensus 5 ~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~kg~--kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~~~ 82 (114)
T TIGR03628 5 AHIYSSFNNTIITITDITGAETIARSSGGMVVKADR--DESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQKSP 82 (114)
T ss_pred EEEEccCCCeEEEEEcCCCCEEEEEecCcceEeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCCCC
Confidence 567888889999999965557787777776666542 233456888899999999999999998762234 222 1
Q ss_pred hhHHHHHHHHHHHCCcEeEeecC
Q 029747 166 EGKIRAVVQSLIDNGIDVKIYLD 188 (188)
Q Consensus 166 hGrVkA~adalRe~GL~f~~~~~ 188 (188)
.--=.+.+.+|...||++..--|
T Consensus 83 G~Gr~~air~l~~~glkI~~I~D 105 (114)
T TIGR03628 83 GPGAQAAIRALARAGLRIGRIED 105 (114)
T ss_pred CCcHHHHHHHHHHCCCEEEEEEE
Confidence 11235677899999999876443
No 18
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=96.54 E-value=0.027 Score=45.38 Aligned_cols=96 Identities=14% Similarity=0.091 Sum_probs=68.2
Q ss_pred eEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCC--CCc---
Q 029747 90 TLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPRE--RDK--- 164 (188)
Q Consensus 90 RL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRg--g~k--- 164 (188)
-+.|+-|-+.+...|.|..+..+++.+|.-..-.++. ..+.-=||...++-++++|++.||+.|.+--+| +..
T Consensus 11 i~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~kg~--kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~Ggn~~~~ 88 (132)
T PRK09607 11 IAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADR--DESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNGQKS 88 (132)
T ss_pred EEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeCCC--ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCcC
Confidence 5778899999999999965446887777766555531 233455888999999999999999998762234 111
Q ss_pred hhhHHHHHHHHHHHCCcEeEeec
Q 029747 165 FEGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 165 yhGrVkA~adalRe~GL~f~~~~ 187 (188)
..--=.+.+.+|...||++..--
T Consensus 89 ~G~Gr~~airal~~~glkI~~I~ 111 (132)
T PRK09607 89 PGPGAQAAIRALARAGLRIGRIE 111 (132)
T ss_pred CCCcHHHHHHHHHHCCCEEEEEE
Confidence 11123567789999999987643
No 19
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=96.07 E-value=0.12 Score=42.57 Aligned_cols=97 Identities=18% Similarity=0.159 Sum_probs=69.4
Q ss_pred eEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecC--CCCchhh
Q 029747 90 TLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPR--ERDKFEG 167 (188)
Q Consensus 90 RL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDR--gg~kyhG 167 (188)
-+.|+-|-+++..+|.|. .|.+++.+|+-...+|+.. ..+.--||...++.+|++|++.||..+..--| |+..-+|
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 VAHIFASFNDTFIHVTDL-SGRETLVRVTGGMKVKADR-DESSPYAAMMAAQDVAARCKELGINALHIKLRATGGVRTKT 107 (149)
T ss_pred EEEEEcccCCeEEEEEcc-cCCEEEEEecCcceecccc-cCCCHHHHHHHHHHHHHHHHHcCCeEEEEEEEecCCCCCCC
Confidence 577888989999999995 5666777777766666432 12334578888999999999999999876222 2222222
Q ss_pred ---HHHHHHHHHHHCCcEeEeecC
Q 029747 168 ---KIRAVVQSLIDNGIDVKIYLD 188 (188)
Q Consensus 168 ---rVkA~adalRe~GL~f~~~~~ 188 (188)
-=.+.+.+|..+||++..--|
T Consensus 108 ~GpGr~~airaL~~~glkI~~I~D 131 (149)
T PTZ00129 108 PGPGAQAALRALARAGLKIGRIED 131 (149)
T ss_pred CCCCHHHHHHHHHHCCCEEEEEEe
Confidence 346778999999999876543
No 20
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=94.37 E-value=0.58 Score=39.54 Aligned_cols=98 Identities=14% Similarity=0.126 Sum_probs=72.7
Q ss_pred cCCCceEEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCc
Q 029747 85 YMEPFTLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPRERDK 164 (188)
Q Consensus 85 ~~~~pRL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~k 164 (188)
+.+-|-..|.-|.++...+|.| ..|+++..+|-----+++. ..+..-||...|--.+.|+++.|+..|-.--+| .
T Consensus 76 f~eiPi~hIraS~NNTivtVtd-~kg~vi~~~ScgteGFrnt--rkgT~iAaQtaavaa~~r~v~~G~~~vrV~VkG--l 150 (190)
T KOG0408|consen 76 FREIPIIHIRASFNNTIVTVTD-VKGEVISWSSCGTEGFRNT--RKGTPIAAQTAAVAAIRRAVDQGMQTVRVRVKG--L 150 (190)
T ss_pred ccccceEEEEecCCCeEEEEEc-cCCcEEEEeeccccccccc--ccCCchhHHHHHHHHHHHHHHhcceEEEEEEec--C
Confidence 5677889999999999999999 6777776666554455543 233455778888888999999999987762233 2
Q ss_pred hhhHHHHHHHHHHHCCcEeEeecC
Q 029747 165 FEGKIRAVVQSLIDNGIDVKIYLD 188 (188)
Q Consensus 165 yhGrVkA~adalRe~GL~f~~~~~ 188 (188)
=-||..| +.+|+-+||.+-+.-|
T Consensus 151 GpGRmsa-~kgl~m~Gl~vvsItD 173 (190)
T KOG0408|consen 151 GPGRMSA-LKGLRMGGLLVVSITD 173 (190)
T ss_pred CccHHHH-HhhhhhcceEEEEeec
Confidence 4577765 5899999999876543
No 21
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=94.27 E-value=0.51 Score=38.03 Aligned_cols=91 Identities=14% Similarity=0.117 Sum_probs=65.2
Q ss_pred EEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHH
Q 029747 91 LDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPRERDKFEGKIR 170 (188)
Q Consensus 91 L~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVk 170 (188)
..|+.|-+.....+.| .+|.++..+|+=-.-+|+.- .+.--||...++.+|+.++|.||..+..-=+| ..--=.
T Consensus 21 ahI~asfNNTivtitD-~~Gn~i~wassG~~gfk~~r--k~tpyAA~~aa~~aa~~a~e~Gi~~v~v~vkg---pG~Gre 94 (129)
T COG0100 21 AHIHASFNNTIVTITD-LTGNVIIWASSGGMGFKGSR--KSTPYAAQLAAEDAAKKAKEHGIKSVEVKVKG---PGPGRE 94 (129)
T ss_pred EEEEcccCCcEEEecC-CCCCEEEEEecCCceEcCCC--CCCHHHHHHHHHHHHHHHHHhCccEEEEEEEC---CCCcHH
Confidence 5677777777778777 67778999999888877542 44455666677999999999999987652233 111235
Q ss_pred HHHHHHHHCCcEeEeec
Q 029747 171 AVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 171 A~adalRe~GL~f~~~~ 187 (188)
|++.+|..+||++..-.
T Consensus 95 aAiraL~~ag~~i~~I~ 111 (129)
T COG0100 95 AAIRALAAAGLKITRIE 111 (129)
T ss_pred HHHHHHHHccceEEEEE
Confidence 66777789999886543
No 22
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=85.69 E-value=12 Score=29.99 Aligned_cols=93 Identities=14% Similarity=0.122 Sum_probs=62.1
Q ss_pred EEEEecCCeEEEEEEECCCCeEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEec--CCCCc---h
Q 029747 91 LDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTP--RERDK---F 165 (188)
Q Consensus 91 L~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdD--Rgg~k---y 165 (188)
..|+-|-+...++|.|-.+..|++-..--- ..|.. ..-++--||.+-....|.+|++.||+.+.+-- .|+-+ .
T Consensus 19 ahi~asfndtfvhitdlsg~eti~rvtggm-kvkad-rdesspyaamlaaqdva~kck~~gi~alh~klratgg~ktktp 96 (139)
T KOG0407|consen 19 AHIFASFNDTFVHVTDLSGKETIVRVTGGM-KVKAD-RDESSPYAAMLAAQDVAAKCKELGITALHIKLRATGGTKTKTP 96 (139)
T ss_pred EEEEeecccceEEEeccCCceEEEEecCCe-EEecc-cccCChHHHHHHHHHHHHHHHhcCeeEEEEEEEecCCcccCCC
Confidence 456777777788888877778887664332 23322 22345667777789999999999999988732 24432 1
Q ss_pred hhHHHHHHHHHHHCCcEeEe
Q 029747 166 EGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 166 hGrVkA~adalRe~GL~f~~ 185 (188)
.---++.+.+|.-+|+.+..
T Consensus 97 gpgaqsalralar~gmrigr 116 (139)
T KOG0407|consen 97 GPGAQSALRALARSGMRIGR 116 (139)
T ss_pred CccHHHHHHHHHHhcceeee
Confidence 22456777888888888754
No 23
>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=72.82 E-value=8.5 Score=34.72 Aligned_cols=47 Identities=15% Similarity=0.271 Sum_probs=33.1
Q ss_pred HHHHHHHHhcCCCEEEEe----------cCCCCch--------hhHHHHHHHHHHHCCcEeEeec
Q 029747 141 RILAERAREADVYTASYT----------PRERDKF--------EGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 141 ~lLA~RakeaGI~~vvfd----------DRgg~ky--------hGrVkA~adalRe~GL~f~~~~ 187 (188)
...|+-|+++|.+-|+++ |.....| .--|+.|++++|+.||+|-+|+
T Consensus 94 dqW~~~ak~aGakY~VlTakHHDGF~LW~S~~t~~~v~~~~~krDiv~El~~A~rk~Glk~G~Y~ 158 (346)
T PF01120_consen 94 DQWAKLAKDAGAKYVVLTAKHHDGFCLWPSKYTDYNVVNSGPKRDIVGELADACRKYGLKFGLYY 158 (346)
T ss_dssp HHHHHHHHHTT-SEEEEEEE-TT--BSS--TT-SSBGGGGGGTS-HHHHHHHHHHHTT-EEEEEE
T ss_pred HHHHHHHHHcCCCEEEeehhhcCccccCCCCCCcccccCCCCCCCHHHHHHHHHHHcCCeEEEEe
Confidence 457889999999999986 1111111 1249999999999999999996
No 24
>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=71.84 E-value=15 Score=35.11 Aligned_cols=56 Identities=13% Similarity=0.087 Sum_probs=45.1
Q ss_pred cCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 128 RSRSDIPACLAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 128 ~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
+..++...+...|..||+++++.||+.|+++..- -.=|--...+++.+.++||.+-
T Consensus 313 G~gt~~~~a~~~g~eIa~~Lk~dgVDAvILtstC-gtCtrcga~m~keiE~~GIPvV 368 (431)
T TIGR01917 313 GNGTAVANSKQFAKEFSKELLAAGVDAVILTSTU-GTCTRCGATMVKEIERAGIPVV 368 (431)
T ss_pred CCCccHHHHHHHHHHHHHHHHHcCCCEEEEcCCC-CcchhHHHHHHHHHHHcCCCEE
Confidence 4567788899999999999999999999996222 2345567888999999998764
No 25
>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=70.74 E-value=8.6 Score=35.60 Aligned_cols=47 Identities=11% Similarity=0.147 Sum_probs=35.8
Q ss_pred HHHHHHHHhcCCCEEEEe----------cCCCCc--------hhhHHHHHHHHHHHCCcEeEeec
Q 029747 141 RILAERAREADVYTASYT----------PRERDK--------FEGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 141 ~lLA~RakeaGI~~vvfd----------DRgg~k--------yhGrVkA~adalRe~GL~f~~~~ 187 (188)
+..|+.++++|.+-++++ |..... ..--|+.+++++|+.||+|-+|.
T Consensus 84 ~~Wa~~~k~AGakY~vlTaKHHDGF~lw~S~~t~~n~~~~~pkrDiv~el~~A~rk~Glk~G~Y~ 148 (384)
T smart00812 84 EEWADLFKKAGAKYVVLTAKHHDGFCLWDSKYSNWNAVDTGPKRDLVGELADAVRKRGLKFGLYH 148 (384)
T ss_pred HHHHHHHHHcCCCeEEeeeeecCCccccCCCCCCCcccCCCCCcchHHHHHHHHHHcCCeEEEEc
Confidence 567899999999999886 111101 12259999999999999999985
No 26
>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=67.22 E-value=21 Score=34.16 Aligned_cols=56 Identities=11% Similarity=0.095 Sum_probs=44.8
Q ss_pred cCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 128 RSRSDIPACLAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 128 ~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
+..++...+...|..||+++++.|++.|+++..- -.-|--....++.+..+||.+-
T Consensus 313 G~gt~~~~a~~~g~eIa~~Lk~dgVDAVILTstC-gtC~r~~a~m~keiE~~GiPvv 368 (431)
T TIGR01918 313 GNGTTVAESKQFAKEFVVELKQGGVDAVILTSTU-GTCTRCGATMVKEIERAGIPVV 368 (431)
T ss_pred CCCchHHHHHHHHHHHHHHHHHcCCCEEEEcCCC-CcchhHHHHHHHHHHHcCCCEE
Confidence 4467778889999999999999999999996222 2345567788899999998764
No 27
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=64.06 E-value=27 Score=23.47 Aligned_cols=42 Identities=19% Similarity=0.233 Sum_probs=30.4
Q ss_pred HHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 140 GRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
-+.+.++|++.|++.+.++|-+ ...|-. .+.+.+++.||++-
T Consensus 17 ~~~~~~~a~~~g~~~v~iTDh~--~~~~~~-~~~~~~~~~gi~~i 58 (67)
T smart00481 17 PEELVKRAKELGLKAIAITDHG--NLFGAV-EFYKAAKKAGIKPI 58 (67)
T ss_pred HHHHHHHHHHcCCCEEEEeeCC--cccCHH-HHHHHHHHcCCeEE
Confidence 3467899999999999997666 344443 45566778888764
No 28
>PF14419 SPOUT_MTase_2: AF2226-like SPOUT RNA Methylase fused to THUMP
Probab=60.95 E-value=26 Score=29.60 Aligned_cols=49 Identities=12% Similarity=0.196 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHC
Q 029747 130 RSDIPACLAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDN 179 (188)
Q Consensus 130 ~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~ 179 (188)
-++..||++.|+-|+..+....+.+.+.. ..+..-.=-+..|+++++++
T Consensus 10 lGd~~a~r~mGerIGRaaQ~FEV~eLiia-p~~~vda~eL~~Fl~gV~~G 58 (173)
T PF14419_consen 10 LGDLKACRKMGERIGRAAQAFEVKELIIA-PKEKVDAYELMEFLRGVREG 58 (173)
T ss_pred cCCHHHHHHHHHHHhHHHhhcchheEEEe-ccCccCHHHHHHHHHHHHHh
Confidence 46899999999999999999999999884 22222223477788888775
No 29
>COG1611 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]
Probab=60.46 E-value=15 Score=31.26 Aligned_cols=41 Identities=27% Similarity=0.262 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 133 IPACLAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 133 ~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
.+.|+.+|+.||++. .++++ |+ ..|-+.|.++++.++|..+
T Consensus 33 ~~~a~~lg~~la~~g------~~V~t--GG--~~GiMea~~~gA~~~gg~~ 73 (205)
T COG1611 33 YELARELGRELAKRG------LLVIT--GG--GPGVMEAVARGALEAGGLV 73 (205)
T ss_pred HHHHHHHHHHHHhCC------cEEEe--CC--chhhhhHHHHHHHHcCCeE
Confidence 466888888888776 67774 65 6899999999999877543
No 30
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=57.17 E-value=27 Score=26.58 Aligned_cols=42 Identities=24% Similarity=0.332 Sum_probs=30.0
Q ss_pred HHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEe
Q 029747 142 ILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 142 lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~ 185 (188)
.+.+.+.+.+|++|++. -...-++.+..+++.+++.|+++++
T Consensus 132 ~l~~~~~~~~id~v~ia--l~~~~~~~i~~ii~~~~~~~v~v~~ 173 (175)
T PF13727_consen 132 DLPELVREHDIDEVIIA--LPWSEEEQIKRIIEELENHGVRVRV 173 (175)
T ss_dssp GHHHHHHHHT--EEEE----TTS-HHHHHHHHHHHHTTT-EEEE
T ss_pred HHHHHHHhCCCCEEEEE--cCccCHHHHHHHHHHHHhCCCEEEE
Confidence 45667778899999984 2345688999999999999999986
No 31
>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=56.01 E-value=33 Score=32.00 Aligned_cols=46 Identities=15% Similarity=0.185 Sum_probs=33.6
Q ss_pred HHHHHHHhcCCCEEEEecCC-----------------CCchhhHHHHHHHHHHHCCcEeEeec
Q 029747 142 ILAERAREADVYTASYTPRE-----------------RDKFEGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 142 lLA~RakeaGI~~vvfdDRg-----------------g~kyhGrVkA~adalRe~GL~f~~~~ 187 (188)
.+|+.+++.|++-++.||-- ..++-+-++++++.+++.|++|.+++
T Consensus 62 ~~a~~~~~~G~e~fviDDGW~~~r~~d~~~~GdW~~~~~kFP~Gl~~l~~~i~~~Gmk~GlW~ 124 (394)
T PF02065_consen 62 ELADAAAELGYEYFVIDDGWFGGRDDDNAGLGDWEPDPKKFPNGLKPLADYIHSLGMKFGLWF 124 (394)
T ss_dssp HHHHHHHHHT-SEEEE-SSSBCTESTTTSTTSBECBBTTTSTTHHHHHHHHHHHTT-EEEEEE
T ss_pred HHHHHHHHhCCEEEEEcCccccccCCCcccCCceeEChhhhCCcHHHHHHHHHHCCCeEEEEe
Confidence 34778899999999996321 12455559999999999999999986
No 32
>PF03646 FlaG: FlaG protein; InterPro: IPR005186 Although these proteins are known to be important for flagellar their exact function is unknown.; PDB: 2HC5_A.
Probab=54.51 E-value=24 Score=26.34 Aligned_cols=41 Identities=10% Similarity=0.009 Sum_probs=30.4
Q ss_pred hhhcccccccCCCceEEEEecCCeEEEEEEECCCCeEEEEE
Q 029747 76 ISFKQRTVAYMEPFTLDVFISKRFVSASLTHRVTSKQVAVA 116 (188)
Q Consensus 76 ~r~rkr~~~~~~~pRL~V~kSNkhiyAqVidd~~g~tVaSA 116 (188)
..+++.+.......++.|+.....++++|+|..+|++|=.-
T Consensus 44 ~~ln~~~~~~~~~l~F~vde~~~~~vVkViD~~T~eVIRqI 84 (107)
T PF03646_consen 44 EKLNEFLQALNTSLRFSVDEESGRVVVKVIDKETGEVIRQI 84 (107)
T ss_dssp HHHHHHHTTSS--EEEEEEEETTEEEEEEEETTT-SEEEEE
T ss_pred HHHHHHHHhcCCceEEEEecCCCcEEEEEEECCCCcEEEeC
Confidence 44555656566778999999999999999999999988443
No 33
>PRK04302 triosephosphate isomerase; Provisional
Probab=52.81 E-value=38 Score=28.38 Aligned_cols=47 Identities=26% Similarity=0.290 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 138 AIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
-.|++.++.++++|++-+...+.....+.+.+..+++.+.+.||..-
T Consensus 72 ~tg~~~~~~l~~~G~~~vii~~ser~~~~~e~~~~v~~a~~~Gl~~I 118 (223)
T PRK04302 72 HTGHILPEAVKDAGAVGTLINHSERRLTLADIEAVVERAKKLGLESV 118 (223)
T ss_pred chhhhHHHHHHHcCCCEEEEeccccccCHHHHHHHHHHHHHCCCeEE
Confidence 56788899999999999998554444677789999999999999764
No 34
>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=50.15 E-value=45 Score=28.61 Aligned_cols=49 Identities=10% Similarity=0.194 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHhcCCCE-EEE-e-cCCCCchhhHHHHHHHHHHHCCcEeEe
Q 029747 137 LAIGRILAERAREADVYT-ASY-T-PRERDKFEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 137 ~~vG~lLA~RakeaGI~~-vvf-d-DRgg~kyhGrVkA~adalRe~GL~f~~ 185 (188)
+.-|+.+++.+.+.|..+ +.| . +........|+..+.+++.++|+.++.
T Consensus 103 ~~a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~~~~ 154 (279)
T PF00532_consen 103 YEAGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLPIDE 154 (279)
T ss_dssp HHHHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSCEEE
T ss_pred hHHHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCCCCc
Confidence 344557777888899998 665 1 111122355899999999999996653
No 35
>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=49.97 E-value=42 Score=27.04 Aligned_cols=45 Identities=13% Similarity=0.106 Sum_probs=30.0
Q ss_pred HHHHHHHHHhcCCCEEEEe--cCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 140 GRILAERAREADVYTASYT--PRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfd--DRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
|+.+++.+.+.|..++.+- +.+......|...|.+++.+.|+++.
T Consensus 104 ~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~~~~ 150 (269)
T cd06288 104 GYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQALAEAGIPFD 150 (269)
T ss_pred HHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHHHHcCCCCC
Confidence 4555555556688888762 12212235699999999999998653
No 36
>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=49.17 E-value=72 Score=25.87 Aligned_cols=55 Identities=13% Similarity=0.301 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHHHHHhc--CCCEEEE-e-cCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 130 RSDIPACLAIGRILAERAREA--DVYTASY-T-PRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 130 ~~n~~AA~~vG~lLA~Rakea--GI~~vvf-d-DRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
..+..+++.+++.|++.+++. |-.++.+ . +.+.....-|...|.+++.+.|+.+.
T Consensus 101 ~d~~~~g~~~~~~l~~~~~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~ 159 (277)
T cd06319 101 SDNYEGAYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCDLA 159 (277)
T ss_pred eccHHHHHHHHHHHHHHHHhhCCCCCcEEEEeccCCCccHHHHHHHHHHHHHhcCCceE
Confidence 356788899999999998875 4556654 1 11112245689999999999998754
No 37
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=46.16 E-value=52 Score=30.81 Aligned_cols=57 Identities=28% Similarity=0.305 Sum_probs=47.6
Q ss_pred CCCHHHHHHHHHH-----------------HHHHHHhcCCCEEEEecCCCCch-hhHHHHHHHHHHHCCcEeEeec
Q 029747 130 RSDIPACLAIGRI-----------------LAERAREADVYTASYTPRERDKF-EGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 130 ~~n~~AA~~vG~l-----------------LA~RakeaGI~~vvfdDRgg~ky-hGrVkA~adalRe~GL~f~~~~ 187 (188)
..|.++|..++++ ||..|.++|++.+-.. .|.... ..++..+++.+++.|+.+.+-.
T Consensus 63 v~~~~~a~al~~I~~~~~iPlvADIHFd~~lAl~a~~~G~~~iRIN-PGNig~~~~~v~~vv~~ak~~~ipIRIGv 137 (360)
T PRK00366 63 VPDMEAAAALPEIKKQLPVPLVADIHFDYRLALAAAEAGADALRIN-PGNIGKRDERVREVVEAAKDYGIPIRIGV 137 (360)
T ss_pred cCCHHHHHhHHHHHHcCCCCEEEecCCCHHHHHHHHHhCCCEEEEC-CCCCCchHHHHHHHHHHHHHCCCCEEEec
Confidence 4688899998875 7889999999999984 566554 7799999999999999887643
No 38
>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=46.03 E-value=57 Score=26.45 Aligned_cols=45 Identities=16% Similarity=0.236 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhcCCCEEEEe--cCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 139 IGRILAERAREADVYTASYT--PRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfd--DRgg~kyhGrVkA~adalRe~GL~f 183 (188)
.|..+++.+.+.|-.++.|- +.+......|+..|.+++.+.|+.+
T Consensus 101 ag~~a~~~L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 147 (265)
T cd06285 101 GGRLATRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEAGIEV 147 (265)
T ss_pred HHHHHHHHHHHCCCccEEEEeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 34444455556688887761 1121224579999999999999875
No 39
>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=45.84 E-value=55 Score=26.36 Aligned_cols=45 Identities=9% Similarity=0.025 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhcCCCEEEEe--cCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 139 IGRILAERAREADVYTASYT--PRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfd--DRgg~kyhGrVkA~adalRe~GL~f 183 (188)
.|+.+++.+.+.|..++.|- +.+......|...|.+++.+.|+++
T Consensus 101 ~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~ 147 (260)
T cd06286 101 AFYEALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTP 147 (260)
T ss_pred HHHHHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCCC
Confidence 34455566666799988761 1122334679999999999999765
No 40
>PF14871 GHL6: Hypothetical glycosyl hydrolase 6
Probab=45.59 E-value=81 Score=24.92 Aligned_cols=48 Identities=19% Similarity=0.324 Sum_probs=35.7
Q ss_pred HHHHHHHHhcCCCEEEEecC--CCCch-------------hhHHHHHHHHHHHCCcEeEeecC
Q 029747 141 RILAERAREADVYTASYTPR--ERDKF-------------EGKIRAVVQSLIDNGIDVKIYLD 188 (188)
Q Consensus 141 ~lLA~RakeaGI~~vvfdDR--gg~ky-------------hGrVkA~adalRe~GL~f~~~~~ 188 (188)
+.+++-+++++++.+++.-+ +++-| ..-+..+++++++.||.+..|+|
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 35678888999998876333 33221 33489999999999999999975
No 41
>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=43.41 E-value=60 Score=26.26 Aligned_cols=45 Identities=16% Similarity=0.107 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhcCCCEEEEecCCC--C-chhhHHHHHHHHHHHCCcEeE
Q 029747 139 IGRILAERAREADVYTASYTPRER--D-KFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfdDRgg--~-kyhGrVkA~adalRe~GL~f~ 184 (188)
.|+.+++.+.++|..++.|- .+. . ....|..+|.+++.+.|+.+.
T Consensus 104 ~~~~a~~~l~~~g~~~i~~i-~~~~~~~~~~~r~~gf~~~~~~~~~~~~ 151 (270)
T cd06296 104 GGLAATEHLLELGHRRIGFI-TGPPDLLCSRARLDGYRAALAEAGIPVD 151 (270)
T ss_pred HHHHHHHHHHHcCCCcEEEE-cCCCcchhHHHHHHHHHHHHHHcCCCCC
Confidence 35555666666788888762 222 2 235689999999999998653
No 42
>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=42.59 E-value=83 Score=25.53 Aligned_cols=48 Identities=10% Similarity=0.004 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHhcCCCEEEE-ecCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 137 LAIGRILAERAREADVYTASY-TPRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 137 ~~vG~lLA~RakeaGI~~vvf-dDRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
+..|+.+++.+.+.|..++.+ ..........|+..|.+++.+.|+.+.
T Consensus 100 ~~~g~~a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~ 148 (263)
T cd06280 100 RAAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAPD 148 (263)
T ss_pred HHHHHHHHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHHHcCCCCC
Confidence 335556666667789888775 222222345689999999999998764
No 43
>PF07713 DUF1604: Protein of unknown function (DUF1604); InterPro: IPR011666 This domain is found at the N terminus of several eukaryotic RNA processing proteins (e.g Q8N3B7 from SWISSPROT).
Probab=41.64 E-value=9.3 Score=28.97 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=15.2
Q ss_pred CCCCCCccccCCcccCCcccccCCC
Q 029747 32 SSLHQGQVLNAPRSFFGVEDFLDDD 56 (188)
Q Consensus 32 ~~~~~g~~~~~~r~~~g~~df~~~~ 56 (188)
+.|.|-+.-.+...--.+|||||++
T Consensus 45 ~~F~SSr~~r~~~~~q~~eDfMDee 69 (87)
T PF07713_consen 45 STFKSSRQNRAKKKQQRPEDFMDEE 69 (87)
T ss_pred cceeehhhhhcccccCChhhccCHH
Confidence 3344444433444477899999965
No 44
>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=41.54 E-value=71 Score=25.88 Aligned_cols=48 Identities=15% Similarity=0.133 Sum_probs=30.4
Q ss_pred CHHHHHHHHHHHHHHHHhcCCCEEEEe--cCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 132 DIPACLAIGRILAERAREADVYTASYT--PRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 132 n~~AA~~vG~lLA~RakeaGI~~vvfd--DRgg~kyhGrVkA~adalRe~GL~f 183 (188)
|..+++.++ +.+.+.|..++.+- +.....-..|..+|.+.+.+.|+.+
T Consensus 100 ~~~~g~~~~----~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 149 (264)
T cd06274 100 NRDGAAELT----RELLAAPPEEVLFLGGLPELSPSRERLAGFRQALADAGLPV 149 (264)
T ss_pred cHHHHHHHH----HHHHHCCCCcEEEEeCCCcccchHHHHHHHHHHHHHcCCCC
Confidence 445555555 44445787777761 1111223569999999999999754
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=41.27 E-value=74 Score=25.92 Aligned_cols=45 Identities=22% Similarity=0.212 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhcCCCEEEEecCCC-C-chhhHHHHHHHHHHHCCcEe
Q 029747 138 AIGRILAERAREADVYTASYTPRER-D-KFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvfdDRgg-~-kyhGrVkA~adalRe~GL~f 183 (188)
..|+.+++.+.+.|...+.|- .+. . ....|..+|.+++.+.|+.+
T Consensus 95 ~~g~~~~~~l~~~g~~~i~~i-~~~~~~~~~~R~~gf~~~~~~~~~~~ 141 (265)
T cd01543 95 AIGRMAAEHFLERGFRHFAFY-GLPGARWSDEREEAFRQLVAEAGYEC 141 (265)
T ss_pred HHHHHHHHHHHHCCCcEEEEE-cCCCCHHHHHHHHHHHHHHHHcCCcc
Confidence 345566677777899998873 222 1 12458999999999999876
No 46
>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=40.84 E-value=77 Score=25.74 Aligned_cols=45 Identities=11% Similarity=0.068 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhcCCCEEEEecCCC---CchhhHHHHHHHHHHHCCcEeE
Q 029747 139 IGRILAERAREADVYTASYTPRER---DKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfdDRgg---~kyhGrVkA~adalRe~GL~f~ 184 (188)
.|+.+++++.++|..++.|- .+. .....|...|.+++.+.|+.+.
T Consensus 103 ~~~~~~~~L~~~G~~~i~~i-~~~~~~~~~~~R~~Gf~~a~~~~~~~~~ 150 (269)
T cd06293 103 GGRLATRHLARAGHRRIAFV-GGPDALISARERYAGYREALAEAHIPEV 150 (269)
T ss_pred HHHHHHHHHHHCCCceEEEE-ecCcccccHHHHHHHHHHHHHHcCCCCC
Confidence 34445555566799888762 221 1224689999999999998653
No 47
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=40.53 E-value=78 Score=26.68 Aligned_cols=44 Identities=5% Similarity=0.070 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhcCCCEEEEecCCC---CchhhHHHHHHHHHHHCCcEe
Q 029747 139 IGRILAERAREADVYTASYTPRER---DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfdDRgg---~kyhGrVkA~adalRe~GL~f 183 (188)
-|+.+++.+.+.|..++.|= .+. .....|...|.+++.+.|+.+
T Consensus 161 ~~~~a~~~L~~~G~~~I~~i-~~~~~~~~~~~R~~Gf~~al~~~~~~~ 207 (327)
T PRK10423 161 GGDLATQYLIDKGYTRIACI-TGPLDKTPARLRLEGYRAAMKRAGLNI 207 (327)
T ss_pred HHHHHHHHHHHcCCCeEEEE-eCCccccchHHHHHHHHHHHHHcCCCC
Confidence 35666677777899998761 222 223569999999999999865
No 48
>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=40.41 E-value=63 Score=25.35 Aligned_cols=46 Identities=22% Similarity=0.361 Sum_probs=32.9
Q ss_pred HHHHHHHHHhcCCCEEEEecCCCCch-hhHHHHHHHHHHHCCcEeEee
Q 029747 140 GRILAERAREADVYTASYTPRERDKF-EGKIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfdDRgg~ky-hGrVkA~adalRe~GL~f~~~ 186 (188)
..+|.+-|.+.||+.|+++ +..-.+ ..+..++.+.+.+.||.+..+
T Consensus 77 ~~~l~~l~~~~~~~~V~~~-~~~~~~~~~rd~~v~~~l~~~~i~~~~~ 123 (165)
T PF00875_consen 77 EEVLPELAKEYGATAVYFN-EEYTPYERRRDERVRKALKKHGIKVHTF 123 (165)
T ss_dssp HHHHHHHHHHHTESEEEEE----SHHHHHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHhcCcCeeEec-cccCHHHHHHHHHHHHHHHhcceEEEEE
Confidence 3455666778899999994 543332 457889999999999999765
No 49
>COG3669 Alpha-L-fucosidase [Carbohydrate transport and metabolism]
Probab=39.88 E-value=66 Score=30.78 Aligned_cols=46 Identities=15% Similarity=0.150 Sum_probs=33.6
Q ss_pred HHHHHHHhcCCCEEEEe---------------cCCCCchhh---HHHHHHHHHHHCCcEeEeec
Q 029747 142 ILAERAREADVYTASYT---------------PRERDKFEG---KIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 142 lLA~RakeaGI~~vvfd---------------DRgg~kyhG---rVkA~adalRe~GL~f~~~~ 187 (188)
-.|+-.||+|.+.|+.- +-+..+..+ -|..+++++|+.||.|.+|+
T Consensus 58 eWar~fK~aGAKyvilvakHHDGFaLw~t~ys~wnsvk~GpKrDlvgela~Avr~qGL~FGvy~ 121 (430)
T COG3669 58 EWARLFKEAGAKYVILVAKHHDGFALWPTDYSVWNSVKRGPKRDLVGELAKAVREQGLRFGVYL 121 (430)
T ss_pred HHHHHHHHcCCcEEEEeeeecCCeeecccccccccccccCCcccHHHHHHHHHHHcCCeeeEee
Confidence 45788899999987652 111122233 39999999999999999997
No 50
>PLN03231 putative alpha-galactosidase; Provisional
Probab=39.70 E-value=70 Score=29.73 Aligned_cols=57 Identities=9% Similarity=0.058 Sum_probs=42.0
Q ss_pred CHHHHHHHHHHHHHHHHhcCCCEEEEecCCC------------------------------Cchhh-----HHHHHHHHH
Q 029747 132 DIPACLAIGRILAERAREADVYTASYTPRER------------------------------DKFEG-----KIRAVVQSL 176 (188)
Q Consensus 132 n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg------------------------------~kyhG-----rVkA~adal 176 (188)
|.+.......++++-++++|.+-|+.||--- .++-. -++++++-+
T Consensus 16 ~E~~i~~~Ad~v~~gL~~~GY~Yv~iDd~W~~~~~~g~~~~~~~~~~~~~~d~~G~l~pd~~rFPs~~~~~G~k~lADyv 95 (357)
T PLN03231 16 SEEQFLENAKIVSETLKPHGYEYVVIDYLWYRKLKHGWFKTSAKSPGYDLIDKWGRPLPDPKRWPSTTGGKGFAPIAAKV 95 (357)
T ss_pred CHHHHHHHHHHHHcchHHhCCEEEEECCcccccccccccccccccccccccCCCCCcccCcccCCCCccccCcHHHHHHH
Confidence 4455555667788999999999999952211 11111 399999999
Q ss_pred HHCCcEeEeecC
Q 029747 177 IDNGIDVKIYLD 188 (188)
Q Consensus 177 Re~GL~f~~~~~ 188 (188)
-+-||+|.+|.+
T Consensus 96 Hs~GLKfGIY~~ 107 (357)
T PLN03231 96 HALGLKLGIHVM 107 (357)
T ss_pred HhCCcceEEEec
Confidence 999999999975
No 51
>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=39.23 E-value=68 Score=25.95 Aligned_cols=37 Identities=11% Similarity=0.185 Sum_probs=25.0
Q ss_pred HHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEe
Q 029747 144 AERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 144 A~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~ 185 (188)
+.....+||++|+| .. .+... .+..+-++++||++.-
T Consensus 101 a~ai~~agI~~Vvy-~~-~~~~~---~~~~~~l~~~gi~v~~ 137 (151)
T TIGR02571 101 TKSIIQAGIKKIYY-AQ-DYHNH---PYAIELFEQAGVELKK 137 (151)
T ss_pred HHHHHHhCCCEEEE-cc-CCCCc---HHHHHHHHHCCCEEEE
Confidence 33445689999999 32 22222 2457899999999873
No 52
>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=38.78 E-value=88 Score=24.63 Aligned_cols=44 Identities=11% Similarity=0.153 Sum_probs=29.0
Q ss_pred HHHHHHHHHhcCCCEEEE-ecCCC-CchhhHHHHHHHHHHHCCcEe
Q 029747 140 GRILAERAREADVYTASY-TPRER-DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvf-dDRgg-~kyhGrVkA~adalRe~GL~f 183 (188)
|+.+++.+.+.|..++.+ ..... .-...+...|.+.+.+.|+++
T Consensus 104 g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~~~ 149 (264)
T cd06267 104 AYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAGIPL 149 (264)
T ss_pred HHHHHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHHHcCCCC
Confidence 555556666668877765 21222 234568999999999999654
No 53
>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=38.68 E-value=74 Score=29.66 Aligned_cols=56 Identities=25% Similarity=0.244 Sum_probs=48.1
Q ss_pred CCCHHHHHHHHHH-----------------HHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEee
Q 029747 130 RSDIPACLAIGRI-----------------LAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 130 ~~n~~AA~~vG~l-----------------LA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~~ 186 (188)
..|.++|..++++ +|..|.++|++++-. -.|..-...++..+++.+++.|+.+.+-
T Consensus 55 vp~~~~A~al~~I~~~~~iPlVADIHFd~~lAl~a~~~g~dkiRI-NPGNig~~e~v~~vv~~ak~~~ipIRIG 127 (346)
T TIGR00612 55 VPDRESAAAFEAIKEGTNVPLVADIHFDYRLAALAMAKGVAKVRI-NPGNIGFRERVRDVVEKARDHGKAMRIG 127 (346)
T ss_pred CCCHHHHHhHHHHHhCCCCCEEEeeCCCcHHHHHHHHhccCeEEE-CCCCCCCHHHHHHHHHHHHHCCCCEEEe
Confidence 4678889988865 889999999999999 4677777889999999999999988764
No 54
>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=38.56 E-value=1.6e+02 Score=22.12 Aligned_cols=48 Identities=21% Similarity=0.254 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEe
Q 029747 136 CLAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 136 A~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~ 185 (188)
+-.||+-+|++..+.|-..|++..|+ .-..+...+++.+.+.|.++.+
T Consensus 9 ~~giG~~~a~~l~~~g~~~v~~~~r~--~~~~~~~~l~~~l~~~~~~~~~ 56 (167)
T PF00106_consen 9 SSGIGRALARALARRGARVVILTSRS--EDSEGAQELIQELKAPGAKITF 56 (167)
T ss_dssp TSHHHHHHHHHHHHTTTEEEEEEESS--CHHHHHHHHHHHHHHTTSEEEE
T ss_pred CCHHHHHHHHHHHhcCceEEEEeeec--cccccccccccccccccccccc
Confidence 44689999999999988888875444 3356788888888888766554
No 55
>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=38.37 E-value=1.1e+02 Score=24.62 Aligned_cols=46 Identities=17% Similarity=0.071 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhcCCCEEEEe-cCCC-CchhhHHHHHHHHHHHCCcEeE
Q 029747 139 IGRILAERAREADVYTASYT-PRER-DKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfd-DRgg-~kyhGrVkA~adalRe~GL~f~ 184 (188)
.|+.+++.+.+.|..++.|- .... .....|...|.+++.+.|+.+.
T Consensus 103 ~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~ 150 (264)
T cd01574 103 GARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALEAAGIAPP 150 (264)
T ss_pred HHHHHHHHHHHCCCCEEEEEecCCccchHHHHHHHHHHHHHHCCCCcc
Confidence 34455555555788887762 1112 1224688999999999998654
No 56
>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=38.27 E-value=98 Score=24.98 Aligned_cols=48 Identities=13% Similarity=0.187 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHhcCCCEEEEe--cCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 137 LAIGRILAERAREADVYTASYT--PRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 137 ~~vG~lLA~RakeaGI~~vvfd--DRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
+..|+.+++.+.+.|..++.|- ..+.....-|...|.+++.+.|+++.
T Consensus 102 ~~~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~ 151 (269)
T cd06275 102 EEGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPVN 151 (269)
T ss_pred HHHHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCCCC
Confidence 3445556666667798888761 11222235589999999999998764
No 57
>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=38.03 E-value=94 Score=25.32 Aligned_cols=47 Identities=13% Similarity=0.192 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHhcCCCEEEEe-cCCCCc-hhhHHHHHHHHHHHCCcEe
Q 029747 137 LAIGRILAERAREADVYTASYT-PRERDK-FEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 137 ~~vG~lLA~RakeaGI~~vvfd-DRgg~k-yhGrVkA~adalRe~GL~f 183 (188)
+..|+.+|+.+.+.|..++.|- +..... -..|..+|.+++.+.|+.+
T Consensus 110 ~~~g~~~a~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~ 158 (275)
T cd06295 110 VGGGRLATEHLLARGRRRIAFLGGPQDMPEGEERLEGYREALAEAGLPL 158 (275)
T ss_pred HHHHHHHHHHHHHCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHcCCCC
Confidence 3455666666777888888762 111212 2468999999999999653
No 58
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=37.88 E-value=85 Score=26.75 Aligned_cols=47 Identities=17% Similarity=0.228 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHhcCCCEEEEe--cCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 138 AIGRILAERAREADVYTASYT--PRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvfd--DRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
..|+.+++.+.+.|-.++.|= +.+....+.|..+|.+++.+.|+++.
T Consensus 164 ~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~~~ 212 (341)
T PRK10703 164 EGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVP 212 (341)
T ss_pred HHHHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHHHHHHHcCCCCC
Confidence 346666677777888887761 11222345689999999999998763
No 59
>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=37.83 E-value=88 Score=25.77 Aligned_cols=48 Identities=10% Similarity=-0.056 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHh--cCCCEEEEe-cCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 137 LAIGRILAERARE--ADVYTASYT-PRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 137 ~~vG~lLA~Rake--aGI~~vvfd-DRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
+..|+.+++.+.+ .|..++.|= .........|...|.+++++.|+.+.
T Consensus 100 ~~~~~~a~~~L~~~~~G~~~Ia~i~~~~~~~~~~R~~gf~~~l~~~g~~~~ 150 (247)
T cd06276 100 EKAIYNALQEGLEKLKKYKKLILVFPNKTAIPKEIKRGFERFCKDYNIETE 150 (247)
T ss_pred HHHHHHHHHHHHHHhcCCCEEEEEecCccHhHHHHHHHHHHHHHHcCCCcc
Confidence 3445566777777 899998761 11112335689999999999999753
No 60
>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=37.74 E-value=69 Score=24.34 Aligned_cols=37 Identities=14% Similarity=0.177 Sum_probs=25.5
Q ss_pred HHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 142 ILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 142 lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
-+.+.|.++|+..++|. .+ ..-..+.+.++++||.+-
T Consensus 70 ~~v~~~~~~g~~~v~~~-~g-----~~~~~~~~~a~~~gi~vi 106 (116)
T PF13380_consen 70 EIVDEAAALGVKAVWLQ-PG-----AESEELIEAAREAGIRVI 106 (116)
T ss_dssp HHHHHHHHHT-SEEEE--TT-----S--HHHHHHHHHTT-EEE
T ss_pred HHHHHHHHcCCCEEEEE-cc-----hHHHHHHHHHHHcCCEEE
Confidence 34567788899999994 34 677889999999999863
No 61
>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=37.63 E-value=86 Score=25.09 Aligned_cols=46 Identities=11% Similarity=0.056 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHhcCCCEEEEecCCC---C-chhhHHHHHHHHHHHCCcEe
Q 029747 137 LAIGRILAERAREADVYTASYTPRER---D-KFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 137 ~~vG~lLA~RakeaGI~~vvfdDRgg---~-kyhGrVkA~adalRe~GL~f 183 (188)
+..|+.+++.+.+.|..++.| =.+. . ..+.|..+|.+.+.+.|+++
T Consensus 101 ~~~g~~~~~~l~~~g~~~i~~-i~~~~~~~~~~~~r~~gf~~~l~~~~~~~ 150 (266)
T cd06282 101 RAAARDVAQALAALGHRRIAM-LAGRLAASDRARQRYAGYRAAMRAAGLAP 150 (266)
T ss_pred HHHHHHHHHHHHHcCcccEEE-eccccccCchHHHHHHHHHHHHHHcCCCC
Confidence 445555666666678888776 2221 1 23568999999999999864
No 62
>PLN02229 alpha-galactosidase
Probab=36.49 E-value=1.1e+02 Score=29.21 Aligned_cols=57 Identities=11% Similarity=0.173 Sum_probs=41.3
Q ss_pred CHHHHHHHHH-HHHHHHHhcCCCEEEEecCC--------C------CchhhHHHHHHHHHHHCCcEeEeecC
Q 029747 132 DIPACLAIGR-ILAERAREADVYTASYTPRE--------R------DKFEGKIRAVVQSLIDNGIDVKIYLD 188 (188)
Q Consensus 132 n~~AA~~vG~-lLA~RakeaGI~~vvfdDRg--------g------~kyhGrVkA~adalRe~GL~f~~~~~ 188 (188)
|-+....+.. +++.-++++|++-|+.||-- | .++-.-+++++|-+.+.||+|.+|.|
T Consensus 78 ~E~~i~~~ad~~v~~Gl~~~Gy~yv~iDDgW~~~~rd~~G~l~~d~~rFP~G~k~ladyiH~~GlKfGIy~d 149 (427)
T PLN02229 78 NETVIKETADALVSTGLADLGYIHVNIDDCWSNLKRDSKGQLVPDPKTFPSGIKLLADYVHSKGLKLGIYSD 149 (427)
T ss_pred CHHHHHHHHHHHHHhHHHhCCCEEEEEcCCcCCCCcCCCCCEEEChhhcCCcHHHHHHHHHHCCCceEEecc
Confidence 4455555555 45677789999999996411 1 12333399999999999999999986
No 63
>PRK09492 treR trehalose repressor; Provisional
Probab=36.37 E-value=1.1e+02 Score=25.67 Aligned_cols=43 Identities=14% Similarity=0.111 Sum_probs=30.4
Q ss_pred HHHHHHHHhcCCCEEEEecCCC--C--chhhHHHHHHHHHHHCCcEeE
Q 029747 141 RILAERAREADVYTASYTPRER--D--KFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 141 ~lLA~RakeaGI~~vvfdDRgg--~--kyhGrVkA~adalRe~GL~f~ 184 (188)
+.+++.+.+.|..++.|- .+. . ....|...|.+++.+.|+.+.
T Consensus 164 ~~a~~~L~~~G~~~I~~i-~~~~~~~~~~~~R~~Gf~~al~~~g~~~~ 210 (315)
T PRK09492 164 KLLMQRLYDQGHRHISYL-GVDHSDVTTGKRRHQAYLAFCKQHKLTPV 210 (315)
T ss_pred HHHHHHHHHcCCCeEEEE-cCCcccchhHHHHHHHHHHHHHHcCCCce
Confidence 445555667899998872 222 1 125799999999999999754
No 64
>PF09666 Sororin: Sororin protein; InterPro: IPR018605 Sororin is an essential, cell cycle-dependent mediator of sister chromatid cohesion []. The protein is nuclear in interphase cells, dispersed from the chromatin in mitosis, and interacts with the cohesin complex [].
Probab=35.71 E-value=14 Score=30.88 Aligned_cols=15 Identities=40% Similarity=0.886 Sum_probs=12.6
Q ss_pred CCcccCCcccccCCC
Q 029747 42 APRSFFGVEDFLDDD 56 (188)
Q Consensus 42 ~~r~~~g~~df~~~~ 56 (188)
.-|++||-|||++.+
T Consensus 100 ~r~nLFGFE~~L~~e 114 (162)
T PF09666_consen 100 GRRNLFGFEEFLAPE 114 (162)
T ss_pred ccccccchhhhccch
Confidence 458999999999954
No 65
>PHA02588 cd deoxycytidylate deaminase; Provisional
Probab=35.09 E-value=86 Score=25.76 Aligned_cols=39 Identities=18% Similarity=0.186 Sum_probs=25.1
Q ss_pred HHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEee
Q 029747 144 AERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 144 A~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~~ 186 (188)
+.....+||.+|+|. .......+ --++-|+++||++..+
T Consensus 115 a~aI~~~gI~rVvy~-~~~~~~~~---~~~~~L~~~Gi~v~~~ 153 (168)
T PHA02588 115 AKAIAQSGIKKLVYC-EKYDRNGP---GWDDILRKSGIEVIQI 153 (168)
T ss_pred HHHHHHhCCCEEEEe-eccCCCcH---HHHHHHHHCCCEEEEe
Confidence 344456899999983 22111222 2478899999998753
No 66
>cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=34.83 E-value=1.1e+02 Score=25.39 Aligned_cols=47 Identities=17% Similarity=0.186 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhcCCCEEEEe--cCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 138 AIGRILAERAREADVYTASYT--PRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvfd--DRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
..|..+++.+.+.|..++.|= +........|..+|.+++++.|+...
T Consensus 104 ~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~~~~ 152 (269)
T cd06287 104 ATARMLLEHLRAQGARQIALIVGSARRNSYLEAEAAYRAFAAEHGMPPV 152 (269)
T ss_pred HHHHHHHHHHHHcCCCcEEEEeCCcccccHHHHHHHHHHHHHHcCCCcc
Confidence 446777788888899888761 11112335589999999999998653
No 67
>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=34.26 E-value=1.3e+02 Score=26.38 Aligned_cols=40 Identities=15% Similarity=0.227 Sum_probs=29.6
Q ss_pred HHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 145 ERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 145 ~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
.-+++.|+..+.|.+.+|-++-.-++|+++++-++|+.++
T Consensus 142 aml~dmG~~SiKffPm~Gl~~leE~~avAkA~a~~g~~lE 181 (218)
T PF07071_consen 142 AMLKDMGGSSIKFFPMGGLKHLEELKAVAKACARNGFTLE 181 (218)
T ss_dssp HHHHHTT--EEEE---TTTTTHHHHHHHHHHHHHCT-EEE
T ss_pred HHHHHcCCCeeeEeecCCcccHHHHHHHHHHHHHcCceeC
Confidence 3467899999997788999999999999999999998774
No 68
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=34.26 E-value=1.4e+02 Score=25.19 Aligned_cols=44 Identities=16% Similarity=0.049 Sum_probs=31.1
Q ss_pred HHHHHHHHHhcCCCEEEEecCCC---CchhhHHHHHHHHHHHCCcEeE
Q 029747 140 GRILAERAREADVYTASYTPRER---DKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfdDRgg---~kyhGrVkA~adalRe~GL~f~ 184 (188)
|..+++.+.+.|..++.|- .+. .....|...|.+++.+.|+.+.
T Consensus 167 ~~~a~~~L~~~G~r~I~~i-~~~~~~~~~~~R~~Gf~~al~~~g~~~~ 213 (328)
T PRK11303 167 AEMLAESLLKFPAESILLL-GALPELSVSFEREQGFRQALKDDPREVH 213 (328)
T ss_pred HHHHHHHHHHCCCCeEEEE-eCccccccHHHHHHHHHHHHHHcCCCce
Confidence 4556677777898888762 222 2235689999999999998654
No 69
>COG1472 BglX Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]
Probab=34.25 E-value=96 Score=28.93 Aligned_cols=57 Identities=21% Similarity=0.344 Sum_probs=41.1
Q ss_pred hhcCCCCHHHHHHHHHHHHHHHHhcCCCEE-------EEecCCC---Cc-hhh-------HHHHHHHHHHHCCcE
Q 029747 126 VLRSRSDIPACLAIGRILAERAREADVYTA-------SYTPRER---DK-FEG-------KIRAVVQSLIDNGID 182 (188)
Q Consensus 126 ~L~s~~n~~AA~~vG~lLA~RakeaGI~~v-------vfdDRgg---~k-yhG-------rVkA~adalRe~GL~ 182 (188)
.+..+-|.+.++.+|+++|+-+.+.||+-. ..+++++ .. |+. -..|++++++.+|+.
T Consensus 88 alaa~~~~~la~~~g~~~A~Elra~Gin~~fAPvlDv~~~p~~~ri~ersfgeDP~lv~~l~~a~i~Glq~~gv~ 162 (397)
T COG1472 88 ALAATWDPELARKVGRVIAKELRALGINLDFAPVLDVARDPRWGRIGERSFGEDPELVALLAAAFIKGLQGAGVA 162 (397)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHcCCCccccceeecccCCCcCccccccCCCCHHHHHHHHHHHHHHHhhCCce
Confidence 456677899999999999999999999841 1212222 22 332 367899999998874
No 70
>PF02811 PHP: PHP domain; InterPro: IPR004013 The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. This family is often associated with an N-terminal region IPR003141 from INTERPRO.; GO: 0003824 catalytic activity; PDB: 2WJE_A 3QY8_A 2WJD_A 2WJF_A 1PB0_B 1M68_A 1M65_A 3E38_B 2W9M_A 3E0F_A ....
Probab=34.22 E-value=1.2e+02 Score=22.93 Aligned_cols=40 Identities=23% Similarity=0.311 Sum_probs=30.0
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEe
Q 029747 143 LAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~ 185 (188)
+.++|++.|++.+.++|-+ .+.| +..+.+.+.+.||++-.
T Consensus 21 ~v~~A~~~Gl~~i~iTDH~--~~~~-~~~~~~~~~~~~i~vi~ 60 (175)
T PF02811_consen 21 YVEQAKEKGLDAIAITDHN--NFAG-YPDFYKEAKKKGIKVIP 60 (175)
T ss_dssp HHHHHHHTTESEEEEEEET--TTTT-HHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHcCCCEEEEcCCc--cccc-chHHHHHHHhcCCceEE
Confidence 4599999999999997663 2334 66777778888887654
No 71
>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
Probab=33.89 E-value=1.7e+02 Score=24.54 Aligned_cols=41 Identities=20% Similarity=0.109 Sum_probs=31.7
Q ss_pred HHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEe
Q 029747 144 AERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 144 A~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~ 185 (188)
|+-+.+.||.--+. =-..++-..++..+++.+++.|+++-+
T Consensus 22 a~~L~~fgi~ye~~-VvSAHRTPe~m~~ya~~a~~~g~~viI 62 (162)
T COG0041 22 AEILEEFGVPYEVR-VVSAHRTPEKMFEYAEEAEERGVKVII 62 (162)
T ss_pred HHHHHHcCCCeEEE-EEeccCCHHHHHHHHHHHHHCCCeEEE
Confidence 55566789974333 146788999999999999999998754
No 72
>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=33.70 E-value=1.2e+02 Score=24.37 Aligned_cols=46 Identities=15% Similarity=0.255 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhcCCCEEEE-ecCCC-CchhhHHHHHHHHHHHCCcEe
Q 029747 138 AIGRILAERAREADVYTASY-TPRER-DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvf-dDRgg-~kyhGrVkA~adalRe~GL~f 183 (188)
..|+.+++.+.+.|..++.+ .+... ..-..|...|.+++.+.|+.+
T Consensus 102 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~ 149 (268)
T cd01575 102 EAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDP 149 (268)
T ss_pred HHHHHHHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCCC
Confidence 44555666666778877765 21221 233568999999999999754
No 73
>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=33.58 E-value=98 Score=24.78 Aligned_cols=46 Identities=13% Similarity=0.172 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhcCCCEEEE-ecCCCC-chhhHHHHHHHHHHHCCcEe
Q 029747 138 AIGRILAERAREADVYTASY-TPRERD-KFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvf-dDRgg~-kyhGrVkA~adalRe~GL~f 183 (188)
..|+.+++.+.+.|..++.| ...... -...|...|.+++.+.|+++
T Consensus 101 ~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~~~~~~~~~ 148 (267)
T cd06284 101 AAARLAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAEAGLPA 148 (267)
T ss_pred HHHHHHHHHHHHcCCceEEEEcCCccchhHHHHHHHHHHHHHHcCCCC
Confidence 34455555666678888776 211122 23558999999999999754
No 74
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=33.50 E-value=65 Score=29.69 Aligned_cols=39 Identities=18% Similarity=0.422 Sum_probs=29.6
Q ss_pred HHHHHHhcCCCEEEE-ecCCCCchhhHH--HHHHHHHHHCCcEeE
Q 029747 143 LAERAREADVYTASY-TPRERDKFEGKI--RAVVQSLIDNGIDVK 184 (188)
Q Consensus 143 LA~RakeaGI~~vvf-dDRgg~kyhGrV--kA~adalRe~GL~f~ 184 (188)
.|+...++||.+|++ +|.+. +|+. +.+.+-|+++||++.
T Consensus 58 cad~ii~~gi~rVVi~~D~d~---~G~~~~~~~~~~L~~aGi~V~ 99 (360)
T PRK14719 58 IADDLIAENISEVILLTDFDR---AGRVYAKNIMEEFQSRGIKVN 99 (360)
T ss_pred HHHHHHHcCCCEEEEEECCCC---CCCccchHHHHHHHHCCCEEE
Confidence 678888899999986 23332 6665 457889999999984
No 75
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=33.20 E-value=1.3e+02 Score=24.43 Aligned_cols=44 Identities=16% Similarity=0.185 Sum_probs=29.6
Q ss_pred HHHHHHHHHhcCCCEEEE-ecCCC-CchhhHHHHHHHHHHHCCcEe
Q 029747 140 GRILAERAREADVYTASY-TPRER-DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvf-dDRgg-~kyhGrVkA~adalRe~GL~f 183 (188)
|+.+++.+.+.|-.++.| ..... ..-.-|...|.+.+++.|+.+
T Consensus 104 ~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 149 (268)
T cd06270 104 GYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEAGIAL 149 (268)
T ss_pred HHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 555566666678888776 11111 223468999999999999875
No 76
>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=33.18 E-value=1.1e+02 Score=24.38 Aligned_cols=46 Identities=13% Similarity=0.099 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhcCCCEEEE-ecCCC-Cc-hhhHHHHHHHHHHHCCcEe
Q 029747 138 AIGRILAERAREADVYTASY-TPRER-DK-FEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvf-dDRgg-~k-yhGrVkA~adalRe~GL~f 183 (188)
..|+.+|+.+.+.|..++.+ ..... .. .+.|...|.+.+.+.|+.+
T Consensus 102 ~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~~~~~~~~ 150 (267)
T cd06283 102 EAAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEALAEHGIGV 150 (267)
T ss_pred HHHHHHHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHHHHcCCCC
Confidence 34677777777889888775 11111 12 2479999999999999643
No 77
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=32.93 E-value=1.1e+02 Score=26.11 Aligned_cols=43 Identities=12% Similarity=0.210 Sum_probs=30.8
Q ss_pred HHHHHHHHHhcCCCEEEEecCCC---CchhhHHHHHHHHHHHCCcEe
Q 029747 140 GRILAERAREADVYTASYTPRER---DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfdDRgg---~kyhGrVkA~adalRe~GL~f 183 (188)
|+.+++.+.+.|..++.|- .+. .....|...|.+++.+.|+.+
T Consensus 164 ~~~a~~~L~~~G~~~I~~i-~~~~~~~~~~~R~~Gf~~al~~~gi~~ 209 (343)
T PRK10727 164 AWLATRHLIQQGHTRIGYL-CSNHSISDAEDRLQGYYDALAESGIPA 209 (343)
T ss_pred HHHHHHHHHHCCCccEEEE-eCCccccchHHHHHHHHHHHHHCCCCC
Confidence 4556666677898887762 222 224569999999999999865
No 78
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=32.54 E-value=95 Score=25.67 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 133 IPACLAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 133 ~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
.++|..+|+.||++ | ..+++ |+ -..|-+.|++++++++|=.+
T Consensus 18 ~~~A~~lG~~la~~----g-~~lV~---GG-g~~GlM~a~a~ga~~~gG~v 59 (178)
T TIGR00730 18 KELAAELGAYLAGQ----G-WGLVY---GG-GRVGLMGAIADAAMENGGTA 59 (178)
T ss_pred HHHHHHHHHHHHHC----C-CEEEE---CC-ChHhHHHHHHHHHHhcCCeE
Confidence 46788888888875 4 34455 33 25789999999999987643
No 79
>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=32.48 E-value=1.1e+02 Score=24.59 Aligned_cols=47 Identities=13% Similarity=0.145 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhcCCCEEEEecCCC--Cc--hhhHHHHHHHHHHHCCcEeE
Q 029747 137 LAIGRILAERAREADVYTASYTPRER--DK--FEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 137 ~~vG~lLA~RakeaGI~~vvfdDRgg--~k--yhGrVkA~adalRe~GL~f~ 184 (188)
+..|+.+++.+.+.|..++.|= .+. .. -..|...|.+++.+.|+.+.
T Consensus 101 ~~~~~~~~~~l~~~g~~~i~~i-~~~~~~~~~~~~r~~gf~~~l~~~~~~~~ 151 (268)
T cd06273 101 REAGRLAARHLIALGHRRIAMI-FGPTQGNDRARARRAGVRAALAEAGLELP 151 (268)
T ss_pred HHHHHHHHHHHHHCCCCeEEEE-eccccCCccHHHHHHHHHHHHHHcCCCCC
Confidence 4445555666666788888762 221 11 12489999999999997643
No 80
>PRK13125 trpA tryptophan synthase subunit alpha; Provisional
Probab=32.40 E-value=1.4e+02 Score=25.49 Aligned_cols=44 Identities=9% Similarity=0.198 Sum_probs=31.6
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEeec
Q 029747 143 LAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~~~ 187 (188)
+++.+.++|++.+.+- --.+........+++.+++.|++.-+.+
T Consensus 93 ~i~~~~~~Gadgvii~-dlp~e~~~~~~~~~~~~~~~Gl~~~~~v 136 (244)
T PRK13125 93 FLNMARDVGADGVLFP-DLLIDYPDDLEKYVEIIKNKGLKPVFFT 136 (244)
T ss_pred HHHHHHHcCCCEEEEC-CCCCCcHHHHHHHHHHHHHcCCCEEEEE
Confidence 4777888999998882 2222334567788899999999876654
No 81
>PRK07738 flagellar protein FlaG; Provisional
Probab=32.18 E-value=72 Score=25.22 Aligned_cols=38 Identities=3% Similarity=-0.021 Sum_probs=31.7
Q ss_pred hhhcccccccCCCceEEEEecCCeEEEEEEECCCCeEE
Q 029747 76 ISFKQRTVAYMEPFTLDVFISKRFVSASLTHRVTSKQV 113 (188)
Q Consensus 76 ~r~rkr~~~~~~~pRL~V~kSNkhiyAqVidd~~g~tV 113 (188)
..+++.+.......+..|+.....++++|+|..+|.+|
T Consensus 53 eklN~~l~~~~~~L~F~vdeet~~~vVkVvD~~T~EVI 90 (117)
T PRK07738 53 DGMNELLEPSQTSLKFELHEKLNEYYVQVVDERTNEVI 90 (117)
T ss_pred HHHHHHHHhcCCceEEEEecCCCcEEEEEEECCCCeee
Confidence 45566666667788999999999999999999999877
No 82
>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=32.07 E-value=1.9e+02 Score=23.33 Aligned_cols=50 Identities=18% Similarity=0.240 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEeec
Q 029747 135 ACLAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 135 AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~~~ 187 (188)
.|..+...+.+.|.+.+. .++|+ +...-......+++.++++|-.+.++.
T Consensus 77 ~a~~~~~~~~~~a~~~~~-nii~E--~tl~~~~~~~~~~~~~k~~GY~v~l~~ 126 (199)
T PF06414_consen 77 EASRLAEKLIEYAIENRY-NIIFE--GTLSNPSKLRKLIREAKAAGYKVELYY 126 (199)
T ss_dssp HHHHHHHHHHHHHHHCT---EEEE----TTSSHHHHHHHHHHHCTT-EEEEEE
T ss_pred HHHHHHHHHHHHHHHcCC-CEEEe--cCCCChhHHHHHHHHHHcCCceEEEEE
Confidence 355566667778888887 55674 334444566669999999999988763
No 83
>COG3345 GalA Alpha-galactosidase [Carbohydrate transport and metabolism]
Probab=31.71 E-value=61 Score=32.50 Aligned_cols=45 Identities=20% Similarity=0.263 Sum_probs=36.1
Q ss_pred HHHHHHHhcCCCEEEEecCCCC------------------chhhHHHHHHHHHHHCCcEeEeec
Q 029747 142 ILAERAREADVYTASYTPRERD------------------KFEGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 142 lLA~RakeaGI~~vvfdDRgg~------------------kyhGrVkA~adalRe~GL~f~~~~ 187 (188)
.+++-|++.|++-+++| .|-+ ++.+-|..++++++|.|++|.+.+
T Consensus 313 e~vk~akk~gvE~FvlD-DGwfg~rndd~~slGDWlv~seKfPsgiE~li~~I~e~Gl~fGIWl 375 (687)
T COG3345 313 ENVKEAKKFGVELFVLD-DGWFGGRNDDLKSLGDWLVNSEKFPSGIEELIEAIAENGLIFGIWL 375 (687)
T ss_pred HHHHHHhhcCeEEEEEc-cccccccCcchhhhhceecchhhccccHHHHHHHHHHcCCccceee
Confidence 35677888899999885 4443 566779999999999999998865
No 84
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=31.31 E-value=1.4e+02 Score=25.44 Aligned_cols=44 Identities=9% Similarity=0.179 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhcCCCEEEEecCCCC---chhhHHHHHHHHHHHCCcEe
Q 029747 139 IGRILAERAREADVYTASYTPRERD---KFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfdDRgg~---kyhGrVkA~adalRe~GL~f 183 (188)
.|+.+++.+.+.|-.++.|- .+.. ....|...|.+++.+.|+.+
T Consensus 169 ~~~~a~~~L~~~G~~~I~~i-~g~~~~~~~~~R~~Gf~~al~~~g~~~ 215 (342)
T PRK10014 169 AAQLLTEHLIRNGHQRIAWL-GGQSSSLTRAERVGGYCATLLKFGLPF 215 (342)
T ss_pred HHHHHHHHHHHCCCCEEEEE-cCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 34445555566788888772 2221 23569999999999999865
No 85
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=31.16 E-value=1.5e+02 Score=24.15 Aligned_cols=43 Identities=7% Similarity=-0.048 Sum_probs=29.5
Q ss_pred HHHHHHHHHhcCCCEEEEecCCCC---chhhHHHHHHHHHHHCCcEe
Q 029747 140 GRILAERAREADVYTASYTPRERD---KFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfdDRgg~---kyhGrVkA~adalRe~GL~f 183 (188)
|+.+++.+.+.|..++.| =.+.. ....|+..|.+++.+.|+++
T Consensus 104 g~~a~~~l~~~G~~~i~~-l~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 149 (269)
T cd06281 104 MRQAVEYLISLGHRRIAL-VGGGSNTRPGRERLEGYKAAFAAAGLPP 149 (269)
T ss_pred HHHHHHHHHHCCCcEEEE-ecCccccccHHHHHHHHHHHHHHcCCCC
Confidence 455566666679888876 22322 22458899999999999864
No 86
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=31.12 E-value=1.5e+02 Score=23.85 Aligned_cols=45 Identities=7% Similarity=0.025 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhcCCCEEEEe-cCCC-C-chhhHHHHHHHHHHHCCcEe
Q 029747 139 IGRILAERAREADVYTASYT-PRER-D-KFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfd-DRgg-~-kyhGrVkA~adalRe~GL~f 183 (188)
.|+.+++.+.+.|-.++.+= .... . --+.|...|.+.+.+.|+++
T Consensus 103 ~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~gf~~~~~~~~~~~ 150 (268)
T cd06298 103 AAFEATELLIKNGHKKIAFISGPLEDSINGDERLAGYKEALSEANIEF 150 (268)
T ss_pred HHHHHHHHHHHcCCceEEEEeCCcccccchhHHHHHHHHHHHHcCCCC
Confidence 34444555555788877761 1111 1 23568999999999999865
No 87
>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=30.96 E-value=1.6e+02 Score=23.59 Aligned_cols=48 Identities=13% Similarity=0.156 Sum_probs=29.9
Q ss_pred CHHHHHHHHHHHHHHHHhcCCCEEEEe--cCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 132 DIPACLAIGRILAERAREADVYTASYT--PRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 132 n~~AA~~vG~lLA~RakeaGI~~vvfd--DRgg~kyhGrVkA~adalRe~GL~f 183 (188)
+..+++.+++ .+.+.|..++.+= +.+...-..|...|.+.+.+.|+++
T Consensus 99 ~~~~g~~~~~----~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 148 (266)
T cd06278 99 NYEAGRLAAE----LLLAKGCRRIAFIGGPADTSTSRERERGFRDALAAAGVPV 148 (266)
T ss_pred hHHHHHHHHH----HHHHCCCceEEEEcCCCcccchHHHHHHHHHHHHHcCCCh
Confidence 4555555544 4445688887761 1121223458899999999999864
No 88
>PRK12744 short chain dehydrogenase; Provisional
Probab=30.86 E-value=1.8e+02 Score=23.78 Aligned_cols=45 Identities=9% Similarity=0.145 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 138 AIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
-||.-+|+.+.+.|..-+++ ++...........+++.+...|.++
T Consensus 19 gIG~~~a~~l~~~G~~vv~i-~~~~~~~~~~~~~~~~~l~~~~~~~ 63 (257)
T PRK12744 19 NLGGLIARDLAAQGAKAVAI-HYNSAASKADAEETVAAVKAAGAKA 63 (257)
T ss_pred hHHHHHHHHHHHCCCcEEEE-ecCCccchHHHHHHHHHHHHhCCcE
Confidence 58888888888888876666 2333333445555566655545433
No 89
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=30.63 E-value=1.1e+02 Score=24.57 Aligned_cols=46 Identities=15% Similarity=0.134 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhcCCCEEEE-ecCCCCc-hhhHHHHHHHHHHHCCcE
Q 029747 137 LAIGRILAERAREADVYTASY-TPRERDK-FEGKIRAVVQSLIDNGID 182 (188)
Q Consensus 137 ~~vG~lLA~RakeaGI~~vvf-dDRgg~k-yhGrVkA~adalRe~GL~ 182 (188)
+..|+.+++.+.+.|..++.+ ....... -+-|...|.+++++.|+.
T Consensus 107 ~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~ 154 (270)
T cd06294 107 IQAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALEDHGIP 154 (270)
T ss_pred HHHHHHHHHHHHHcCCccEEEecCCcccHHHHHHHHHHHHHHHHcCCC
Confidence 344555556666668888765 2122222 245899999999999974
No 90
>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=30.58 E-value=1.5e+02 Score=23.84 Aligned_cols=47 Identities=9% Similarity=0.171 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhcCCCEEEE-ecCCCCc-hhhHHHHHHHHHHHCCcEe
Q 029747 137 LAIGRILAERAREADVYTASY-TPRERDK-FEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 137 ~~vG~lLA~RakeaGI~~vvf-dDRgg~k-yhGrVkA~adalRe~GL~f 183 (188)
+..|+.+++.+.+.|-.++.+ .....+. -..|...|.+++.+.|+.+
T Consensus 103 ~~~g~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 151 (270)
T cd01545 103 RAAAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALAEAGLPL 151 (270)
T ss_pred HHHHHHHHHHHHHCCCceEEEEeCCCCchhHHHHHHHHHHHHHHcCCCC
Confidence 345566666666778888765 2122222 2357899999999999876
No 91
>PLN02808 alpha-galactosidase
Probab=30.55 E-value=1.2e+02 Score=28.47 Aligned_cols=58 Identities=12% Similarity=0.127 Sum_probs=41.3
Q ss_pred CCHHHHHHHHHHH-HHHHHhcCCCEEEEecCCC--------------CchhhHHHHHHHHHHHCCcEeEeecC
Q 029747 131 SDIPACLAIGRIL-AERAREADVYTASYTPRER--------------DKFEGKIRAVVQSLIDNGIDVKIYLD 188 (188)
Q Consensus 131 ~n~~AA~~vG~lL-A~RakeaGI~~vvfdDRgg--------------~kyhGrVkA~adalRe~GL~f~~~~~ 188 (188)
-|-.-...+...| +.-++++|.+-|+.||--- .++-.-++++++-+.+.||+|.+|.|
T Consensus 46 i~e~~i~~~a~~mv~~Gl~~~Gy~yv~iDd~W~~~~rd~~G~~~~d~~rFP~G~~~lad~iH~~GlkfGiy~~ 118 (386)
T PLN02808 46 INETLIKQTADAMVSSGLAALGYKYINLDDCWAELKRDSQGNLVPKASTFPSGIKALADYVHSKGLKLGIYSD 118 (386)
T ss_pred CCHHHHHHHHHHHHHcchHHhCCEEEEEcCCcCCCCcCCCCCEeeChhhcCccHHHHHHHHHHCCCceEEEec
Confidence 4555566666554 4557789999999963211 12323499999999999999999986
No 92
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=30.34 E-value=1.3e+02 Score=26.67 Aligned_cols=44 Identities=9% Similarity=0.097 Sum_probs=33.9
Q ss_pred HHHHHHHHHHhcCCCEEEEecCCC---CchhhHHHHHHHHHHHCCcEe
Q 029747 139 IGRILAERAREADVYTASYTPRER---DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfdDRgg---~kyhGrVkA~adalRe~GL~f 183 (188)
-|+.+++.+.++|..++.| --+. .....|...|.+++.+.|+.+
T Consensus 162 ~~~~a~~~L~~~G~~~i~~-i~~~~~~~~~~~R~~Gf~~al~~~~~~~ 208 (333)
T COG1609 162 GAYLATEHLIELGHRRIAF-IGGPLDSSASRERLEGYRAALREAGLPI 208 (333)
T ss_pred HHHHHHHHHHHCCCceEEE-EeCCCccccHhHHHHHHHHHHHHCCCCC
Confidence 3566777788899998887 2333 344779999999999999986
No 93
>PRK12738 kbaY tagatose-bisphosphate aldolase; Reviewed
Probab=30.07 E-value=1.5e+02 Score=26.59 Aligned_cols=45 Identities=18% Similarity=0.048 Sum_probs=35.9
Q ss_pred HHHHHHHHhcCCCEEEEecCCCCchhh---HHHHHHHHHHHCCcEeEee
Q 029747 141 RILAERAREADVYTASYTPRERDKFEG---KIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 141 ~lLA~RakeaGI~~vvfdDRgg~kyhG---rVkA~adalRe~GL~f~~~ 186 (188)
.....+|.++|.+.|.| |-....|.. ..+.+++-+...|+.++--
T Consensus 87 ~e~i~~ai~~GFtSVM~-DgS~lp~eeNi~~T~evv~~Ah~~gv~VEaE 134 (286)
T PRK12738 87 LDDIRRKVHAGVRSAMI-DGSHFPFAENVKLVKSVVDFCHSQDCSVEAE 134 (286)
T ss_pred HHHHHHHHHcCCCeEee-cCCCCCHHHHHHHHHHHHHHHHHcCCeEEEE
Confidence 34577899999999999 677777776 5677888888889888654
No 94
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=29.88 E-value=1.5e+02 Score=24.62 Aligned_cols=50 Identities=18% Similarity=0.178 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCEEEEe-cCCCCc-hhhHHHHHHHHHHHCCcEeE
Q 029747 131 SDIPACLAIGRILAERAREADVYTASYT-PRERDK-FEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 131 ~n~~AA~~vG~lLA~RakeaGI~~vvfd-DRgg~k-yhGrVkA~adalRe~GL~f~ 184 (188)
.|..+++. +++.+.+.|..++.|- ...... -..|...|.+++++.|+.+.
T Consensus 135 Dn~~~g~~----a~~~l~~~G~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~ 186 (309)
T PRK11041 135 DNLTAAFE----AVNYLHELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGITVD 186 (309)
T ss_pred CcHHHHHH----HHHHHHHcCCceEEEEeCCccccchHHHHHHHHHHHHHcCCCCC
Confidence 34455554 4444455688887761 112222 24589999999999998753
No 95
>PLN02692 alpha-galactosidase
Probab=29.33 E-value=1.2e+02 Score=28.75 Aligned_cols=57 Identities=14% Similarity=0.198 Sum_probs=40.1
Q ss_pred CHHHHHHHHH-HHHHHHHhcCCCEEEEecCC--------------CCchhhHHHHHHHHHHHCCcEeEeecC
Q 029747 132 DIPACLAIGR-ILAERAREADVYTASYTPRE--------------RDKFEGKIRAVVQSLIDNGIDVKIYLD 188 (188)
Q Consensus 132 n~~AA~~vG~-lLA~RakeaGI~~vvfdDRg--------------g~kyhGrVkA~adalRe~GL~f~~~~~ 188 (188)
|-+....+.. +.+.-.+++|.+-|+.||-- ..++-.-+++++|-+.+.||+|.+|.|
T Consensus 71 ~E~~i~~~ad~~~~~gl~~~Gy~yv~iDDgW~~~~rd~~G~~~~d~~kFP~G~k~ladyiH~~GLKfGIy~d 142 (412)
T PLN02692 71 DEKMIKETADALVSTGLSKLGYTYVNIDDCWAEIARDEKGNLVPKKSTFPSGIKALADYVHSKGLKLGIYSD 142 (412)
T ss_pred CHHHHHHHHHHHHhccchhcCcEEEEEcCCcCCCCCCCCCCeeeChhhcCCcHHHHHHHHHHCCCceEEEec
Confidence 4444555554 34455678999999996421 123434499999999999999999985
No 96
>COG2131 ComEB Deoxycytidylate deaminase [Nucleotide transport and metabolism]
Probab=28.75 E-value=1.2e+02 Score=25.35 Aligned_cols=41 Identities=20% Similarity=0.143 Sum_probs=29.9
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEe
Q 029747 143 LAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~ 185 (188)
.|+...++||++|++ ...|.-+-......+.+.++|+++..
T Consensus 110 Cak~Ii~aGIk~Vvy--~~~Y~~~~~~~~s~~l~~~agv~~~~ 150 (164)
T COG2131 110 CAKLIIQAGIKEVVY--AEPYPTETVAPYSQELLEEAGVKVRQ 150 (164)
T ss_pred HHHHHHHhCceEEEe--ecCCCcchhhHHHHHHHHhCCceEEe
Confidence 455566799999999 34444444667788889999998864
No 97
>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=28.74 E-value=2.5e+02 Score=22.82 Aligned_cols=54 Identities=9% Similarity=0.079 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCCEEEE-e-cCCCCchhhHHHHHHHHHHHC-CcEeEe
Q 029747 130 RSDIPACLAIGRILAERAREADVYTASY-T-PRERDKFEGKIRAVVQSLIDN-GIDVKI 185 (188)
Q Consensus 130 ~~n~~AA~~vG~lLA~RakeaGI~~vvf-d-DRgg~kyhGrVkA~adalRe~-GL~f~~ 185 (188)
..+..+++.+++.|+++. .|-.++.+ . +.....-..|.++|.+.+.+. |+++..
T Consensus 102 ~d~~~~g~~~~~~l~~~~--~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~ 158 (275)
T cd06320 102 TDNKANGVRGAEWIIDKL--AEGGKVAIIEGKAGAFAAEQRTEGFTEAIKKASGIEVVA 158 (275)
T ss_pred cCcHHHHHHHHHHHHHHh--CCCceEEEEeCCCCCccHHHHHHHHHHHHhhCCCcEEEE
Confidence 345566666666666553 25556554 1 122222356899999999999 998643
No 98
>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=28.36 E-value=1.3e+02 Score=24.27 Aligned_cols=46 Identities=11% Similarity=0.139 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhcCCCEEEE-ecCCC-CchhhHHHHHHHHHHHCCcEe
Q 029747 138 AIGRILAERAREADVYTASY-TPRER-DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvf-dDRgg-~kyhGrVkA~adalRe~GL~f 183 (188)
..|+.+++.+.+.|..++.+ ..... ....-|..+|.+++.+.|+.+
T Consensus 97 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 144 (261)
T cd06272 97 KAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDENGISI 144 (261)
T ss_pred HHHHHHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHHHcCCCC
Confidence 34556666666778888776 11111 233558999999999999743
No 99
>PRK12827 short chain dehydrogenase; Provisional
Probab=28.29 E-value=2.1e+02 Score=22.73 Aligned_cols=44 Identities=16% Similarity=0.082 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCc
Q 029747 137 LAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGI 181 (188)
Q Consensus 137 ~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL 181 (188)
--||..||+.+.+.|..-+.+ ++....-......+.+.+.+.|-
T Consensus 16 g~iG~~la~~l~~~g~~v~~~-~~~~~~~~~~~~~~~~~~~~~~~ 59 (249)
T PRK12827 16 GGLGRAIAVRLAADGADVIVL-DIHPMRGRAEADAVAAGIEAAGG 59 (249)
T ss_pred ChHHHHHHHHHHHCCCeEEEE-cCcccccHHHHHHHHHHHHhcCC
Confidence 457888888888888765555 44433333445555555544443
No 100
>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=28.19 E-value=1e+02 Score=27.00 Aligned_cols=57 Identities=25% Similarity=0.354 Sum_probs=39.6
Q ss_pred cCCCCHHHHHHHHHHHHHHHHhcCCCEEE-------EecCCC--C-chh------h-HHHHHHHHHHHCCcEeE
Q 029747 128 RSRSDIPACLAIGRILAERAREADVYTAS-------YTPRER--D-KFE------G-KIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 128 ~s~~n~~AA~~vG~lLA~RakeaGI~~vv-------fdDRgg--~-kyh------G-rVkA~adalRe~GL~f~ 184 (188)
..+.|.+.++..|..+|+-+...||+-.. .+++++ . -|+ + -..|++++++++||---
T Consensus 79 ~at~d~~~a~~~g~~~a~el~~~Gin~~~aPv~Dv~~~p~~~~~~rsfgeDp~~v~~~~~a~v~G~q~~gv~~~ 152 (299)
T PF00933_consen 79 AATWDPELAYEVGRIIARELRALGINVNFAPVVDVNRNPRWGRGERSFGEDPDLVAEMARAFVRGLQGAGVAAT 152 (299)
T ss_dssp HHHTCHHHHHHHHHHHHHHHHHTT-SEEEEEB----SSTTSTTGGGSS-SSHHHHHHHHHHHHHHHHCTTSEEE
T ss_pred hhhccchHHHHHHHHHHHHHHHhhhccccccceeeeeeccccccccccchhHHHHHHHHHHHhccccccccccc
Confidence 45679999999999999999999998622 122222 0 111 1 26799999999998643
No 101
>COG1683 Uncharacterized conserved protein [Function unknown]
Probab=28.12 E-value=1.5e+02 Score=24.76 Aligned_cols=56 Identities=25% Similarity=0.364 Sum_probs=39.4
Q ss_pred CCCHHHHHHHH-HHHHHHHHhcCCCEEEEecCCC---------CchhhHH----HHHHHHHHHCCcEeEe
Q 029747 130 RSDIPACLAIG-RILAERAREADVYTASYTPRER---------DKFEGKI----RAVVQSLIDNGIDVKI 185 (188)
Q Consensus 130 ~~n~~AA~~vG-~lLA~RakeaGI~~vvfdDRgg---------~kyhGrV----kA~adalRe~GL~f~~ 185 (188)
..|+.++..-| +...+.+++.+|..+++-++.+ +.+.|+. --++..|.++|+.+.+
T Consensus 77 g~DVTe~~~~~a~~~L~~a~~~~~~~aILk~kSPSCG~~~vydg~f~G~~~~G~Gvtaa~L~e~~~~v~~ 146 (156)
T COG1683 77 GRDVTEAFLSGAERTLALAKEAGIDGAILKEKSPSCGSGFVYDGSFSGKRIAGSGVTAAALMENGIEVPS 146 (156)
T ss_pred cchHHHHHHHHHHHHHHHhhhcCCcEEEEecCCCCCCceeeEeeccCCccccCccHHHHHHHHhCCcccc
Confidence 45777777776 6677788889999988854543 2344543 3477889999988764
No 102
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=28.09 E-value=2.3e+02 Score=22.93 Aligned_cols=50 Identities=14% Similarity=0.116 Sum_probs=31.9
Q ss_pred CHHHHHHHHHHHHHHHHhcCCCEEEEecCCCC---chhhHHHHHHHHHHHC-CcEeE
Q 029747 132 DIPACLAIGRILAERAREADVYTASYTPRERD---KFEGKIRAVVQSLIDN-GIDVK 184 (188)
Q Consensus 132 n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~---kyhGrVkA~adalRe~-GL~f~ 184 (188)
+..+++.+++.|++++ .|..++.| -.+.. .-.-|..+|.+++.+. |+.+.
T Consensus 105 ~~~~~~~~~~~l~~~~--~g~~~i~~-i~~~~~~~~~~~r~~gf~~a~~~~~~~~~~ 158 (273)
T cd06310 105 NVAAGKLAAEALAELL--GKKGKVAV-ISFVPGSSTTDQREEGFLEGLKEYPGIEIV 158 (273)
T ss_pred hHHHHHHHHHHHHHHc--CCCceEEE-EeCCCCCccHHHHHHHHHHHHHhCCCcEEE
Confidence 4455566666666553 36778776 22322 1244889999999999 98764
No 103
>PF07355 GRDB: Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); InterPro: IPR022787 This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon. ; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=28.05 E-value=1e+02 Score=28.82 Aligned_cols=31 Identities=16% Similarity=0.203 Sum_probs=27.6
Q ss_pred cCCCCHHHHHHHHHHHHHHHHhcCCCEEEEe
Q 029747 128 RSRSDIPACLAIGRILAERAREADVYTASYT 158 (188)
Q Consensus 128 ~s~~n~~AA~~vG~lLA~RakeaGI~~vvfd 158 (188)
+..+++.-++..|.-||+.+++.||+.|+++
T Consensus 317 G~gt~~~~~~~~g~eIa~~Lk~dgVDAVILT 347 (349)
T PF07355_consen 317 GNGTAVANAKRFGPEIAKELKEDGVDAVILT 347 (349)
T ss_pred CCCccHHHHHHHHHHHHHHHHHcCCCEEEEe
Confidence 4467788899999999999999999999985
No 104
>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=27.99 E-value=2e+02 Score=23.62 Aligned_cols=54 Identities=13% Similarity=0.123 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCC--CEEEE-e--cCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 130 RSDIPACLAIGRILAERAREADV--YTASY-T--PRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 130 ~~n~~AA~~vG~lLA~RakeaGI--~~vvf-d--DRgg~kyhGrVkA~adalRe~GL~f 183 (188)
..+..+++..|+.|++.+.+.|. .++.+ . +.....-..|+..+.+++.+.|+..
T Consensus 105 ~d~~~~g~~~~~~l~~~~~~~g~~~~~i~~i~~~~~~~~~~~~R~~G~~~~l~~~~~~~ 163 (289)
T cd01540 105 MSATKIGEQVGEAIADEMKKRGWDPKEVGALRITYDELDTAKPRTDGALEALKAPGFPE 163 (289)
T ss_pred CCHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecCCCCcchhhHHHHHHHHHhcCCCCc
Confidence 45788889999999998888786 44432 1 1121233569999999999999863
No 105
>PRK07523 gluconate 5-dehydrogenase; Provisional
Probab=27.81 E-value=2.1e+02 Score=23.30 Aligned_cols=43 Identities=28% Similarity=0.323 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 136 CLAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 136 A~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
+.-||..+|+++.+.|..-+.. +|.. .+..++.+.+++.|.++
T Consensus 19 ~g~iG~~ia~~l~~~G~~V~~~-~r~~----~~~~~~~~~i~~~~~~~ 61 (255)
T PRK07523 19 SQGIGYALAEGLAQAGAEVILN-GRDP----AKLAAAAESLKGQGLSA 61 (255)
T ss_pred cchHHHHHHHHHHHcCCEEEEE-eCCH----HHHHHHHHHHHhcCceE
Confidence 3468999999999999754444 5653 34556666666666444
No 106
>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=27.79 E-value=1.7e+02 Score=23.49 Aligned_cols=48 Identities=6% Similarity=0.057 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCEEEEecCCC---CchhhHHHHHHHHHHHCCcEe
Q 029747 131 SDIPACLAIGRILAERAREADVYTASYTPRER---DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 131 ~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg---~kyhGrVkA~adalRe~GL~f 183 (188)
.+.++++.++ +.+.++|..++.| -.+. ..-..|..+|.+.+.+.|+.+
T Consensus 98 d~~~a~~~~~----~~l~~~g~~~i~~-i~~~~~~~~~~~r~~gf~~~~~~~~~~~ 148 (265)
T cd06290 98 DNFQGGYLAT----QHLIDLGHRRIAH-ITGPRGHIDARDRLAGYRKALEEAGLEV 148 (265)
T ss_pred CcHHHHHHHH----HHHHHCCCCeEEE-EeCccccchhhHHHHHHHHHHHHcCCCC
Confidence 3555555554 4455568888776 1221 222458999999999999865
No 107
>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=27.75 E-value=91 Score=21.05 Aligned_cols=43 Identities=26% Similarity=0.310 Sum_probs=28.4
Q ss_pred HHHHHHHHHhcC--CCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEe
Q 029747 140 GRILAERAREAD--VYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 140 G~lLA~RakeaG--I~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~ 185 (188)
|.-+.+-|+++| |.++.++ .+ ....++..+.+.+.+.|+.+..
T Consensus 4 G~~~V~eaL~~~~~i~~l~~~-~~--~~~~~~~~i~~~~~~~~i~v~~ 48 (76)
T PF08032_consen 4 GRHAVEEALKSGPRIKKLFVT-EE--KADKRIKEILKLAKKKGIPVYE 48 (76)
T ss_dssp SHHHHHHHHHCTGGEEEEEEE-TT-----CCTHHHHHHHHHCT-EEEE
T ss_pred EHHHHHHHHcCCCCccEEEEE-cC--ccchhHHHHHHHHHHcCCeEEE
Confidence 445566677777 7788884 34 4455678889999999988764
No 108
>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=27.72 E-value=1.5e+02 Score=23.65 Aligned_cols=46 Identities=13% Similarity=0.069 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhcCCCEEEEe-cCCCC-chhhHHHHHHHHHHHCCcEe
Q 029747 138 AIGRILAERAREADVYTASYT-PRERD-KFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvfd-DRgg~-kyhGrVkA~adalRe~GL~f 183 (188)
..|+.+++.+.+.|..++.+- ..... ....|...|.+++.+.|+.+
T Consensus 106 ~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 153 (268)
T cd06271 106 AAAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEAGLPL 153 (268)
T ss_pred HHHHHHHHHHHHcCCCcEEEecCccccchHHHHHHHHHHHHHHhCCCC
Confidence 345555666666788887761 11111 22458999999999999864
No 109
>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=27.65 E-value=1.8e+02 Score=25.99 Aligned_cols=43 Identities=16% Similarity=0.056 Sum_probs=34.7
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhh---HHHHHHHHHHHCCcEeEee
Q 029747 143 LAERAREADVYTASYTPRERDKFEG---KIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhG---rVkA~adalRe~GL~f~~~ 186 (188)
..++|.++|.+.|.| |-+...|.. ..+.+++-+...|+.++--
T Consensus 87 ~i~~ai~~GFtSVM~-DgS~lp~eeNi~~T~~vv~~Ah~~gv~VEaE 132 (282)
T TIGR01858 87 DIRQKVHAGVRSAMI-DGSHFPFAQNVKLVKEVVDFCHRQDCSVEAE 132 (282)
T ss_pred HHHHHHHcCCCEEee-cCCCCCHHHHHHHHHHHHHHHHHcCCeEEEE
Confidence 358999999999999 677777766 5677888888899988754
No 110
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=27.46 E-value=1.6e+02 Score=24.82 Aligned_cols=44 Identities=9% Similarity=0.038 Sum_probs=31.3
Q ss_pred HHHHHHHHHhcCCCEEEEecCCCC--c--hhhHHHHHHHHHHHCCcEeE
Q 029747 140 GRILAERAREADVYTASYTPRERD--K--FEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfdDRgg~--k--yhGrVkA~adalRe~GL~f~ 184 (188)
|+.+++.+.+.|..++.| -.+.. . ...|...|.+++.+.|+.+.
T Consensus 164 ~~~a~~~L~~~G~~~I~~-i~g~~~~~~~~~~R~~Gf~~~l~~~g~~~~ 211 (329)
T TIGR01481 164 TKEAVGELIAKGHKSIAF-VGGPLSDSINGEDRLEGYKEALNKAGIQFG 211 (329)
T ss_pred HHHHHHHHHHCCCCeEEE-EecCcccccchHHHHHHHHHHHHHcCCCCC
Confidence 556666677789998876 22221 1 25689999999999998753
No 111
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=27.43 E-value=1.8e+02 Score=25.20 Aligned_cols=44 Identities=34% Similarity=0.389 Sum_probs=34.9
Q ss_pred HHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEe
Q 029747 140 GRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~ 185 (188)
...|++.|.++|+..++. ..+... -|-+..+.+.+.+.|+++.+
T Consensus 65 ~~~l~~~~~e~g~kavIv-p~~~~~-~g~~~~lk~~~e~~gi~~~~ 108 (217)
T PF02593_consen 65 TYELPEIAKEAGVKAVIV-PSESPK-PGLRRQLKKQLEEFGIEVEF 108 (217)
T ss_pred HHHHHHHHHHcCCCEEEE-ecCCCc-cchHHHHHHHHHhcCceeec
Confidence 356788899999999988 454444 78899999999999987753
No 112
>PLN00125 Succinyl-CoA ligase [GDP-forming] subunit alpha
Probab=27.34 E-value=1.4e+02 Score=26.90 Aligned_cols=40 Identities=13% Similarity=-0.052 Sum_probs=31.4
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 143 LAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
..+.|.++||..++. -..++...|....+.+.+|+.|+.+
T Consensus 85 al~e~~~~Gvk~~vI-isaGf~e~g~~~~~~~~ar~~girv 124 (300)
T PLN00125 85 AILEAMEAELDLVVC-ITEGIPQHDMVRVKAALNRQSKTRL 124 (300)
T ss_pred HHHHHHHcCCCEEEE-ECCCCCcccHHHHHHHHHhhcCCEE
Confidence 345688999998876 4688888886677777789999865
No 113
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=27.29 E-value=1.7e+02 Score=23.67 Aligned_cols=45 Identities=18% Similarity=0.211 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhcCCCEEEEecCCCC---chhhHHHHHHHHHHHCCcEeE
Q 029747 139 IGRILAERAREADVYTASYTPRERD---KFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfdDRgg~---kyhGrVkA~adalRe~GL~f~ 184 (188)
.|+.+++.+.+.|-.++.+- .+.. ...-|...|.+++.+.|+++.
T Consensus 105 ~~~~a~~~l~~~g~~~i~~i-~~~~~~~~~~~R~~gf~~~~~~~~~~~~ 152 (268)
T cd06277 105 GAYAATEYLIEKGHRKIGFV-GDPLYSPSFEERYEGYKKALLDHGIPFN 152 (268)
T ss_pred HHHHHHHHHHHCCCCcEEEE-CCCCCCcchHHHHHHHHHHHHHcCCCCC
Confidence 35556666677788887762 2221 234588999999999998753
No 114
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=27.23 E-value=2e+02 Score=24.48 Aligned_cols=43 Identities=16% Similarity=0.193 Sum_probs=29.1
Q ss_pred HHHHHHHHHhcCCCEEEEe-cCCCCchhhHHHHHHHHHHHCCcE
Q 029747 140 GRILAERAREADVYTASYT-PRERDKFEGKIRAVVQSLIDNGID 182 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfd-DRgg~kyhGrVkA~adalRe~GL~ 182 (188)
|+.+++.+.+.|..++.|- .........|...|.+++.+.|+.
T Consensus 168 ~~~a~~~L~~~Gh~~I~~i~~~~~~~~~~R~~Gf~~al~~~g~~ 211 (331)
T PRK14987 168 ARQMTTAIIARGHRHIAYLGARLDERTIIKQKGYEQAMLDAGLV 211 (331)
T ss_pred HHHHHHHHHHCCCceEEEEcCCCcccHHHHHHHHHHHHHHcCCC
Confidence 4555566667898888772 111122345899999999999983
No 115
>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=27.19 E-value=1.9e+02 Score=20.44 Aligned_cols=36 Identities=14% Similarity=0.224 Sum_probs=26.5
Q ss_pred hcCCCEEEEecCCCCch------------hhHHHHHHHHHHHCCcEeEe
Q 029747 149 EADVYTASYTPRERDKF------------EGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 149 eaGI~~vvfdDRgg~ky------------hGrVkA~adalRe~GL~f~~ 185 (188)
.++|..+.+ ++....+ ...+..+.+.|++.|+.+..
T Consensus 24 ~anI~~~~y-~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~ 71 (85)
T cd04906 24 PRNITEFNY-RYADEKDAHIFVGVSVANGAEELAELLEDLKSAGYEVVD 71 (85)
T ss_pred CCceeEEEE-EccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEE
Confidence 689998888 4532111 35688999999999998864
No 116
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=26.93 E-value=1.5e+02 Score=27.93 Aligned_cols=56 Identities=30% Similarity=0.375 Sum_probs=44.7
Q ss_pred CCCHHHHHHHHHH-----------------HHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEee
Q 029747 130 RSDIPACLAIGRI-----------------LAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 130 ~~n~~AA~~vG~l-----------------LA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~~ 186 (188)
..+.++|..+-++ ||..+.+.|+.++-. -.|..-..-+++.+++.+++.|+.+.+-
T Consensus 57 v~~~e~A~A~~~Ik~~~~vPLVaDiHf~~rla~~~~~~g~~k~RI-NPGNig~~~~v~~vVe~Ak~~g~piRIG 129 (361)
T COG0821 57 VPDMEAAEALKEIKQRLNVPLVADIHFDYRLALEAAECGVDKVRI-NPGNIGFKDRVREVVEAAKDKGIPIRIG 129 (361)
T ss_pred cCCHHHHHHHHHHHHhCCCCEEEEeeccHHHHHHhhhcCcceEEE-CCcccCcHHHHHHHHHHHHHcCCCEEEe
Confidence 4567777776654 777888999999888 4676667779999999999999988764
No 117
>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=26.90 E-value=1.7e+02 Score=27.34 Aligned_cols=48 Identities=15% Similarity=0.100 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhcCCCEEEEecCCCCch-hhHHHHHHHHHHHCCcEeEeec
Q 029747 139 IGRILAERAREADVYTASYTPRERDKF-EGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvfdDRgg~ky-hGrVkA~adalRe~GL~f~~~~ 187 (188)
.-.+|.+-+.+-+|+.|.+ .+....| .-+-.++.+.+.+.||++..+-
T Consensus 75 ~~~~l~~l~~~~~i~~v~~-~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~ 123 (475)
T TIGR02766 75 TVAALLDCVRSTGATRLFF-NHLYDPVSLVRDHRAKEVLTAQGISVQSFN 123 (475)
T ss_pred HHHHHHHHHHHcCCCEEEE-ecccCHHHHHHHHHHHHHHHHcCCEEEEec
Confidence 3456777778999999999 4554333 3367788888999999987653
No 118
>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=26.53 E-value=2.8e+02 Score=21.19 Aligned_cols=47 Identities=17% Similarity=0.135 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHhcCCCEEEE-ecCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 138 AIGRILAERAREADVYTASY-TPRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvf-dDRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
..|+.+++.+.+.|..++.+ .+........++.++.+++.+.|+++.
T Consensus 110 ~~~~~~~~~l~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (269)
T cd01391 110 QAGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAGIEVV 157 (269)
T ss_pred HHHHHHHHHHHHhCCceEEEEecCCcchhhHHHHHHHHHHHhcCcEEE
Confidence 44666666666777777664 112213456789999999999996653
No 119
>PLN02899 alpha-galactosidase
Probab=26.21 E-value=1.3e+02 Score=30.29 Aligned_cols=58 Identities=10% Similarity=0.022 Sum_probs=43.9
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCEEEEecCCC---------------------------Cchhh-----HHHHHHHHHHH
Q 029747 131 SDIPACLAIGRILAERAREADVYTASYTPRER---------------------------DKFEG-----KIRAVVQSLID 178 (188)
Q Consensus 131 ~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg---------------------------~kyhG-----rVkA~adalRe 178 (188)
-|-+.....+..+++.++++|.+-|+.||--. .++-. -+++++|-+-+
T Consensus 45 I~E~~i~~~Ad~vs~GLk~~GY~YVnIDDcW~~~~~~g~~~~s~g~~~~D~~GrLvPDp~RFPSs~~g~GmK~LADYVHs 124 (633)
T PLN02899 45 VSEEEFLQNAEIVSQRLLPFGYEYVVVDYLWYRKKVEGAYVDSLGFDVIDEWGRPIPDPGRWPSSRGGKGFTEVAEKVHA 124 (633)
T ss_pred CCHHHHHHHHHHHHcchHhhCCeEEEEccccccccccccccccccccccCCCCCCccCcccCCCCccCCCcHHHHHHHHh
Confidence 45555666667789999999999999864321 12221 38999999999
Q ss_pred CCcEeEeecC
Q 029747 179 NGIDVKIYLD 188 (188)
Q Consensus 179 ~GL~f~~~~~ 188 (188)
-||+|.+|+|
T Consensus 125 kGLKFGIY~~ 134 (633)
T PLN02899 125 MGLKFGIHVM 134 (633)
T ss_pred CCcceEEEec
Confidence 9999999975
No 120
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=25.90 E-value=1.4e+02 Score=24.34 Aligned_cols=42 Identities=14% Similarity=0.120 Sum_probs=32.6
Q ss_pred HHHHHHHHhcCCCEE----------EEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 141 RILAERAREADVYTA----------SYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 141 ~lLA~RakeaGI~~v----------vfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
-.++.+|+..|++-| .| +.|.++-.-|+..+.+.|.|-||+=
T Consensus 43 ~~fvl~Al~~GaDGV~v~GC~~geCHy-~~GN~ka~rR~~~lke~l~elgie~ 94 (132)
T COG1908 43 PEFVLKALRKGADGVLVAGCKIGECHY-ISGNYKAKRRMELLKELLKELGIEP 94 (132)
T ss_pred HHHHHHHHHcCCCeEEEecccccceee-eccchHHHHHHHHHHHHHHHhCCCc
Confidence 346678888888765 45 5777777889999999999999863
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=25.62 E-value=2.2e+02 Score=23.02 Aligned_cols=48 Identities=13% Similarity=0.035 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCEEEEecCCC---CchhhHHHHHHHHHHHCCcEe
Q 029747 131 SDIPACLAIGRILAERAREADVYTASYTPRER---DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 131 ~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg---~kyhGrVkA~adalRe~GL~f 183 (188)
.|..+++.++ +.+.++|-.++.| =.+. ..-..|...|.+++.+.|+.+
T Consensus 105 d~~~~~~~~~----~~l~~~g~~~i~~-i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 155 (273)
T cd06292 105 DDALAMRLAV----RHLVALGHRRIGF-ASGPGRTVPRRRKIAGFRAALEEAGLEP 155 (273)
T ss_pred CcHHHHHHHH----HHHHHCCCceEEE-EeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 3455555544 4445568888876 1222 112468999999999999754
No 122
>PRK07710 acetolactate synthase catalytic subunit; Reviewed
Probab=25.23 E-value=1.6e+02 Score=28.08 Aligned_cols=41 Identities=20% Similarity=0.131 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 138 AIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
.++..|++++++.||+.|.- .-++.+..|.+++.+.||.+-
T Consensus 17 ~~~~~i~~~L~~~Gv~~vFg------~pG~~~~~l~~al~~~~i~~i 57 (571)
T PRK07710 17 TGAQMLIEALEKEGVEVIFG------YPGGAVLPLYDALYDCGIPHI 57 (571)
T ss_pred hHHHHHHHHHHHcCCCEEEe------CCCcchHHHHHHHHhcCCcEE
Confidence 56899999999999999765 134678889999988888764
No 123
>cd00946 FBP_aldolase_IIA Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is homodimeric and used in gluconeogenesis and glycolysis. 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=25.20 E-value=3.4e+02 Score=25.14 Aligned_cols=54 Identities=6% Similarity=0.035 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhh---HHHHHHHHHHHCCcEeEeec
Q 029747 133 IPACLAIGRILAERAREADVYTASYTPRERDKFEG---KIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 133 ~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhG---rVkA~adalRe~GL~f~~~~ 187 (188)
.+.+..-+.-...+|.+.|.+.|.| |-....|.. ..+.+++-+...|+.++.-|
T Consensus 105 ~~~~~~a~~~~~~~a~~~GftSVMi-DgS~lp~eENI~~TkevVe~Ah~~gvsVEaEl 161 (345)
T cd00946 105 FDGLLEADEEYFKQHGEPLFSSHML-DLSEEPLEENIEICKKYLERMAKINMWLEMEI 161 (345)
T ss_pred hHHHHHHHHHHHHHhccCCCceEEe-eCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEe
Confidence 5667777777788999999999999 677777765 56778888889999887543
No 124
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=25.19 E-value=1.9e+02 Score=23.45 Aligned_cols=44 Identities=11% Similarity=0.039 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhcCCCEEEE-ecCCCCchhhHHHHHHHHHHHCCcE
Q 029747 139 IGRILAERAREADVYTASY-TPRERDKFEGKIRAVVQSLIDNGID 182 (188)
Q Consensus 139 vG~lLA~RakeaGI~~vvf-dDRgg~kyhGrVkA~adalRe~GL~ 182 (188)
.|+.+++.+.+.|..++.+ ........+-|...|.+++.+.|+.
T Consensus 108 ~g~~~~~~l~~~G~~~i~~l~~~~~~~~~~r~~g~~~~l~~~~~~ 152 (273)
T cd01541 108 GGYKATEYLIELGHRKIAGIFKADDLQGVKRMKGFIKAYREHGIP 152 (273)
T ss_pred HHHHHHHHHHHcCCcCEEEecCCCcccHHHHHHHHHHHHHHcCCC
Confidence 3444445555568777754 1111122356899999999999974
No 125
>PRK12737 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=25.10 E-value=2.1e+02 Score=25.59 Aligned_cols=44 Identities=16% Similarity=0.111 Sum_probs=34.9
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhh---HHHHHHHHHHHCCcEeEeec
Q 029747 143 LAERAREADVYTASYTPRERDKFEG---KIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhG---rVkA~adalRe~GL~f~~~~ 187 (188)
..++|.++|.+.|.| |-+...|.. ..+.+++-+...|+.++--|
T Consensus 89 ~i~~ai~~GftSVMi-DgS~lp~eeNi~~T~~vv~~Ah~~gvsVEaEl 135 (284)
T PRK12737 89 DIKKKVRAGIRSVMI-DGSHLSFEENIAIVKEVVEFCHRYDASVEAEL 135 (284)
T ss_pred HHHHHHHcCCCeEEe-cCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEE
Confidence 458999999999999 576666765 56778888899999887543
No 126
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=24.87 E-value=1.7e+02 Score=25.33 Aligned_cols=41 Identities=32% Similarity=0.302 Sum_probs=31.7
Q ss_pred HHHHHhcCCCEEEEecCCCCc-hhhHHHHHHHHHHHCCcEeEe
Q 029747 144 AERAREADVYTASYTPRERDK-FEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 144 A~RakeaGI~~vvfdDRgg~k-yhGrVkA~adalRe~GL~f~~ 185 (188)
.+||+++||...++ ++..+. ...-=.++++.+.+.+.++-+
T Consensus 43 lerA~~~gIpt~~~-~~k~~~~r~~~d~~l~~~l~~~~~dlvv 84 (200)
T COG0299 43 LERAAKAGIPTVVL-DRKEFPSREAFDRALVEALDEYGPDLVV 84 (200)
T ss_pred HHHHHHcCCCEEEe-ccccCCCHHHHHHHHHHHHHhcCCCEEE
Confidence 58999999999999 576644 222457889999999988765
No 127
>PLN02591 tryptophan synthase
Probab=24.80 E-value=2.3e+02 Score=24.82 Aligned_cols=43 Identities=19% Similarity=0.170 Sum_probs=33.9
Q ss_pred HHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEeec
Q 029747 141 RILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 141 ~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~~~ 187 (188)
+-+.++|+++|++-+++ +. .-..-...+.+.+++.||++-+.+
T Consensus 96 ~~F~~~~~~aGv~Gvii-pD---LP~ee~~~~~~~~~~~gl~~I~lv 138 (250)
T PLN02591 96 DKFMATIKEAGVHGLVV-PD---LPLEETEALRAEAAKNGIELVLLT 138 (250)
T ss_pred HHHHHHHHHcCCCEEEe-CC---CCHHHHHHHHHHHHHcCCeEEEEe
Confidence 55789999999999998 32 334778888999999999886643
No 128
>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=24.32 E-value=2.1e+02 Score=23.00 Aligned_cols=44 Identities=11% Similarity=0.055 Sum_probs=29.3
Q ss_pred HHHHHHHHHhcCCCEEEE-ecC-CCCchhhHHHHHHHHHHHCCcEe
Q 029747 140 GRILAERAREADVYTASY-TPR-ERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvf-dDR-gg~kyhGrVkA~adalRe~GL~f 183 (188)
+..+++.+.+.|..++.| ... .......|+.+|.+++.+.|+++
T Consensus 104 ~~~~~~~l~~~g~~~I~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 149 (265)
T cd06299 104 MTEAVSLLVALGHKKIGYISGPQDTSTGRERLEAFRQACASLGLEV 149 (265)
T ss_pred HHHHHHHHHHcCCCcEEEEeCCCCcccHHHHHHHHHHHHHHCCCCC
Confidence 445556666778888776 111 11223568999999999999754
No 129
>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=24.20 E-value=2.2e+02 Score=22.87 Aligned_cols=47 Identities=19% Similarity=0.240 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhcCCCEEEEe-cCCC--CchhhHHHHHHHHHHHCCcEeE
Q 029747 138 AIGRILAERAREADVYTASYT-PRER--DKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvfd-DRgg--~kyhGrVkA~adalRe~GL~f~ 184 (188)
..|+.+++.+.+.|..++.+- .... .....|...|.+.+.+.|+++.
T Consensus 98 ~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~ 147 (265)
T cd06291 98 EGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLEVR 147 (265)
T ss_pred HHHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHHHcCCCCC
Confidence 344555555566788887752 1111 1234689999999999998753
No 130
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=24.16 E-value=3.2e+02 Score=22.10 Aligned_cols=52 Identities=8% Similarity=-0.044 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCEEEEe--cCCCCchhhHHHHHHHHHHHC-CcEeE
Q 029747 131 SDIPACLAIGRILAERAREADVYTASYT--PRERDKFEGKIRAVVQSLIDN-GIDVK 184 (188)
Q Consensus 131 ~n~~AA~~vG~lLA~RakeaGI~~vvfd--DRgg~kyhGrVkA~adalRe~-GL~f~ 184 (188)
.+..+++.+++.|.+.+ .|-.++.+- +.....-..|...|.+++.+. |+++.
T Consensus 103 d~~~~g~~~~~~l~~~~--~g~~~i~~l~~~~~~~~~~~R~~g~~~~l~~~~~~~~~ 157 (270)
T cd06308 103 DNYEIGRQAGEYIANLL--PGKGNILEIWGLEGSSPAIERHDGFKEALSKYPKIKIV 157 (270)
T ss_pred CcHHHHHHHHHHHHHHc--CCCceEEEEECCCCCchHHHHHHHHHHHHHHCCCCEEE
Confidence 45566666666665543 367777651 111122356899999999999 98754
No 131
>cd07939 DRE_TIM_NifV Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain. FrbC (NifV) of Streptomyces rubellomurinus catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate and CoA, a reaction similar to one catalyzed by homocitrate synthase. The gene encoding FrbC is one of several genes required for the biosynthesis of FR900098, a potent antimalarial antibiotic. This protein is also required for assembly of the nitrogenase MoFe complex but its exact role is unknown. This family also includes the NifV proteins of Heliobacterium chlorum and Gluconacetobacter diazotrophicus, which appear to be orthologous to FrbC. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarbox
Probab=24.11 E-value=2.3e+02 Score=24.20 Aligned_cols=69 Identities=14% Similarity=0.106 Sum_probs=38.2
Q ss_pred eEEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecCCCC-chhhHHHHHHHHHHHCCcE
Q 029747 111 KQVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPRERD-KFEGKIRAVVQSLIDNGID 182 (188)
Q Consensus 111 ~tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~-kyhGrVkA~adalRe~GL~ 182 (188)
.+-+..++.+..++..+. .+.+.+..--..+++.|++.|+. +.|...... ---..+..+++.+.+.|.+
T Consensus 85 ~i~i~~~~s~~~~~~~~~--~~~~~~~~~~~~~i~~a~~~G~~-v~~~~~~~~~~~~~~~~~~~~~~~~~G~~ 154 (259)
T cd07939 85 AVHISIPVSDIHLAHKLG--KDRAWVLDQLRRLVGRAKDRGLF-VSVGAEDASRADPDFLIEFAEVAQEAGAD 154 (259)
T ss_pred EEEEEEecCHHHHHHHhC--CCHHHHHHHHHHHHHHHHHCCCe-EEEeeccCCCCCHHHHHHHHHHHHHCCCC
Confidence 344555666666655443 23444444445567777777863 443211122 2245677777777777765
No 132
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=23.91 E-value=3.1e+02 Score=22.07 Aligned_cols=51 Identities=12% Similarity=0.145 Sum_probs=31.5
Q ss_pred CHHHHHHHHHHHHHHHHhcCCCEEEE-ecCCCCchhhHHHHHHHHHHHC-CcEeE
Q 029747 132 DIPACLAIGRILAERAREADVYTASY-TPRERDKFEGKIRAVVQSLIDN-GIDVK 184 (188)
Q Consensus 132 n~~AA~~vG~lLA~RakeaGI~~vvf-dDRgg~kyhGrVkA~adalRe~-GL~f~ 184 (188)
+..+++..++.|++++ .|-.++.+ .......-..|.++|.+++.+. |+++.
T Consensus 103 ~~~~g~~~~~~l~~~~--~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~~~~ 155 (267)
T cd06322 103 NYAGGVLAGELAAKVL--NGKGQVAIIDYPTVQSVVDRVRGFKEALADYPNIKIV 155 (267)
T ss_pred hHHHHHHHHHHHHHHh--CCCceEEEEecCCCccHHHHHHHHHHHHHhCCCcEEE
Confidence 4555666666666553 36666654 2112222345899999999999 98753
No 133
>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=23.88 E-value=2.3e+02 Score=23.93 Aligned_cols=43 Identities=16% Similarity=0.145 Sum_probs=31.8
Q ss_pred HHHHHHHHHhcCCCEEEEecCCC---CchhhHHHHHHHHHHHCCcEe
Q 029747 140 GRILAERAREADVYTASYTPRER---DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfdDRgg---~kyhGrVkA~adalRe~GL~f 183 (188)
|..+++.+.+.|..++.|- .+. .....|..+|.+++.+.|+..
T Consensus 166 ~~~~~~~L~~~G~~~I~~i-~~~~~~~~~~~R~~Gf~~al~~~~~~~ 211 (327)
T TIGR02417 166 AAELIERLLSQHADEFWYL-GAQPELSVSRDRLAGFRQALKQATLEV 211 (327)
T ss_pred HHHHHHHHHHCCCCeEEEE-eCcccchhHHHHHHHHHHHHHHcCCCh
Confidence 5667777888999888762 222 224569999999999999863
No 134
>PF14488 DUF4434: Domain of unknown function (DUF4434)
Probab=23.87 E-value=2.4e+02 Score=22.99 Aligned_cols=44 Identities=9% Similarity=0.045 Sum_probs=31.2
Q ss_pred HHHHHHhcCCCEEEEecCCC----Cch--hh-----------HHHHHHHHHHHCCcEeEeec
Q 029747 143 LAERAREADVYTASYTPRER----DKF--EG-----------KIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg----~ky--hG-----------rVkA~adalRe~GL~f~~~~ 187 (188)
+-+-.++.||+.|++. +.+ .-| .+ -|.++++++.+.|++|-+-|
T Consensus 25 ~~~~m~~~GidtlIlq-~~~~~~~~~yps~~~~~~~~~~~~d~l~~~L~~A~~~Gmkv~~Gl 85 (166)
T PF14488_consen 25 EFRAMKAIGIDTLILQ-WTGYGGFAFYPSKLSPGGFYMPPVDLLEMILDAADKYGMKVFVGL 85 (166)
T ss_pred HHHHHHHcCCcEEEEE-EeecCCcccCCccccCccccCCcccHHHHHHHHHHHcCCEEEEeC
Confidence 3456778999999873 222 112 22 68999999999999987644
No 135
>cd07940 DRE_TIM_IPMS 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain. 2-isopropylmalate synthase (IPMS) catalyzes an aldol-type condensation of acetyl-CoA and 2-oxoisovalerate yielding 2-isopropylmalate and CoA, the first committed step in leucine biosynthesis. This family includes the Arabidopsis thaliana IPMS1 and IPMS2 proteins, the Glycine max GmN56 protein, and the Brassica insularis BatIMS protein. This family also includes a group of archeal IPMS-like proteins represented by the Methanocaldococcus jannaschii AksA protein. AksA catalyzes the condensation of alpha-ketoglutarate and acetyl-CoA to form trans-homoaconitate, one of 13 steps in the conversion of alpha-ketoglutarate and acetylCoA to alpha-ketosuberate, a precursor to coenzyme B and biotin. AksA also catalyzes the condensation of alpha-ketoadipate or alpha-ketopimelate with acetylCoA to form, respectively, the (R)-homocitrate homologs (R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and (R)-2-h
Probab=23.62 E-value=2.3e+02 Score=24.36 Aligned_cols=49 Identities=14% Similarity=0.132 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHhcCCCEEEEecCCCC-chhhHHHHHHHHHHHCCcE
Q 029747 133 IPACLAIGRILAERAREADVYTASYTPRERD-KFEGKIRAVVQSLIDNGID 182 (188)
Q Consensus 133 ~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~-kyhGrVkA~adalRe~GL~ 182 (188)
.+.+.....-+++.|++.|+. |.|...... ---..+..+++.+.+.|++
T Consensus 109 ~~~~~~~~~~~i~~a~~~G~~-v~~~~~~~~~~~~~~~~~~~~~~~~~G~~ 158 (268)
T cd07940 109 REEVLERAVEAVEYAKSHGLD-VEFSAEDATRTDLDFLIEVVEAAIEAGAT 158 (268)
T ss_pred HHHHHHHHHHHHHHHHHcCCe-EEEeeecCCCCCHHHHHHHHHHHHHcCCC
Confidence 333334444445555555543 333211111 1233455555555555544
No 136
>COG0007 CysG Uroporphyrinogen-III methylase [Coenzyme metabolism]
Probab=23.59 E-value=1.6e+02 Score=26.02 Aligned_cols=46 Identities=24% Similarity=0.403 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhcCCCEEEEecCCCCch-hhHHHHHHHHHHHCCcEeEee
Q 029747 138 AIGRILAERAREADVYTASYTPRERDKF-EGKIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvfdDRgg~ky-hGrVkA~adalRe~GL~f~~~ 186 (188)
.|-++|-+.|.+ |-.-|-+ .+|..| .||...=++.+.+.||.|.+-
T Consensus 69 eIn~~lv~~a~~-G~~VVRL--KgGDP~iFGRggEE~~~l~~~gI~~eVV 115 (244)
T COG0007 69 EINALLVELARE-GKRVVRL--KGGDPYIFGRGGEEIEALAEAGIEFEVV 115 (244)
T ss_pred HHHHHHHHHHhc-CCeEEEe--cCCCCCeecCcHHHHHHHHHcCCceEEe
Confidence 666778888877 7333445 677665 999999999999999999873
No 137
>PRK09195 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=23.14 E-value=2.5e+02 Score=25.15 Aligned_cols=44 Identities=11% Similarity=0.003 Sum_probs=34.2
Q ss_pred HHHHHHHhcCCCEEEEecCCCCchhh---HHHHHHHHHHHCCcEeEee
Q 029747 142 ILAERAREADVYTASYTPRERDKFEG---KIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 142 lLA~RakeaGI~~vvfdDRgg~kyhG---rVkA~adalRe~GL~f~~~ 186 (188)
-..++|.++|.+.|.| |-+...|.. ..+.+++-+...|+.++--
T Consensus 88 e~i~~Ai~~GftSVM~-DgS~l~~eeNi~~T~~vv~~Ah~~gv~VEaE 134 (284)
T PRK09195 88 DDIAQKVRSGVRSVMI-DGSHLPFAQNISLVKEVVDFCHRFDVSVEAE 134 (284)
T ss_pred HHHHHHHHcCCCEEEe-CCCCCCHHHHHHHHHHHHHHHHHcCCEEEEE
Confidence 3478899999999999 577666766 5667888888889887643
No 138
>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=23.07 E-value=2.4e+02 Score=22.03 Aligned_cols=43 Identities=12% Similarity=0.135 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHhcCCCEEEE-ecCCC-CchhhHHHHHHHHHHHCC
Q 029747 138 AIGRILAERAREADVYTASY-TPRER-DKFEGKIRAVVQSLIDNG 180 (188)
Q Consensus 138 ~vG~lLA~RakeaGI~~vvf-dDRgg-~kyhGrVkA~adalRe~G 180 (188)
..|..+++.+.+.|..++.+ ..... .-...+...|.+++.+.|
T Consensus 104 ~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~ 148 (264)
T cd01537 104 QAGYLAGEHLAEKGHRRIALLAGPLGSSTARERVAGFKDALKEAG 148 (264)
T ss_pred HHHHHHHHHHHHhcCCcEEEEECCCCCCcHHHHHHHHHHHHHHcC
Confidence 57778888888888888765 11222 233568999999999988
No 139
>PRK05835 fructose-bisphosphate aldolase; Provisional
Probab=23.00 E-value=2.5e+02 Score=25.53 Aligned_cols=44 Identities=23% Similarity=0.253 Sum_probs=34.5
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhh---HHHHHHHHHHHCCcEeEeec
Q 029747 143 LAERAREADVYTASYTPRERDKFEG---KIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhG---rVkA~adalRe~GL~f~~~~ 187 (188)
..++|.++|.+.|.| |-+...|.. ..+.+++-+...|+.++--|
T Consensus 89 ~i~~ai~~GftSVM~-DgS~l~~eeNi~~T~~vve~Ah~~gv~VEaEl 135 (307)
T PRK05835 89 SCEKAVKAGFTSVMI-DASHHAFEENLELTSKVVKMAHNAGVSVEAEL 135 (307)
T ss_pred HHHHHHHcCCCEEEE-eCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEe
Confidence 356799999999999 566666655 56788899999999887543
No 140
>PRK08610 fructose-bisphosphate aldolase; Reviewed
Probab=22.93 E-value=2.6e+02 Score=25.12 Aligned_cols=42 Identities=19% Similarity=0.272 Sum_probs=33.6
Q ss_pred HHHHHhcCCCEEEEecCCCCchhh---HHHHHHHHHHHCCcEeEee
Q 029747 144 AERAREADVYTASYTPRERDKFEG---KIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 144 A~RakeaGI~~vvfdDRgg~kyhG---rVkA~adalRe~GL~f~~~ 186 (188)
.++|.++|.+.|.| |-+...|.. ..+.+++-+...|+.++--
T Consensus 93 i~~ai~~GftSVM~-DgS~l~~eeNi~~T~~vve~Ah~~gv~VEaE 137 (286)
T PRK08610 93 CKEAIDAGFTSVMI-DASHSPFEENVATTKKVVEYAHEKGVSVEAE 137 (286)
T ss_pred HHHHHHcCCCEEEE-eCCCCCHHHHHHHHHHHHHHHHHcCCEEEEE
Confidence 46799999999999 677777766 5677888888899888653
No 141
>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=22.42 E-value=1.9e+02 Score=27.14 Aligned_cols=55 Identities=27% Similarity=0.254 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHH----------------------HHHHHhcCCCEEEEecCCCC--------ch-hhHHHHHHHHHHH
Q 029747 130 RSDIPACLAIGRIL----------------------AERAREADVYTASYTPRERD--------KF-EGKIRAVVQSLID 178 (188)
Q Consensus 130 ~~n~~AA~~vG~lL----------------------A~RakeaGI~~vvfdDRgg~--------ky-hGrVkA~adalRe 178 (188)
..|.++|..++++- |..|.+. +.++-.. .|.. .. ..+++.+++.++|
T Consensus 52 vp~~~~a~al~~I~~~l~~~g~~iPlVADIHFd~~lAl~a~~~-v~kiRIN-PGNi~~~~~~~~g~~~~~~~~vv~~ake 129 (359)
T PF04551_consen 52 VPDMEAAEALKEIKKRLRALGSPIPLVADIHFDYRLALEAIEA-VDKIRIN-PGNIVDEFQEELGSIREKVKEVVEAAKE 129 (359)
T ss_dssp E-SHHHHHHHHHHHHHHHCTT-SS-EEEEESTTCHHHHHHHHC--SEEEE--TTTSS----SS-SS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHhhccCCCCCCeeeecCCCHHHHHHHHHH-hCeEEEC-CCcccccccccccchHHHHHHHHHHHHH
Confidence 35778888888664 4467778 8998884 5655 33 7899999999999
Q ss_pred CCcEeEee
Q 029747 179 NGIDVKIY 186 (188)
Q Consensus 179 ~GL~f~~~ 186 (188)
.|+-+.+-
T Consensus 130 ~~ipIRIG 137 (359)
T PF04551_consen 130 RGIPIRIG 137 (359)
T ss_dssp HT-EEEEE
T ss_pred CCCCEEEe
Confidence 99988764
No 142
>CHL00200 trpA tryptophan synthase alpha subunit; Provisional
Probab=22.34 E-value=2.3e+02 Score=24.88 Aligned_cols=42 Identities=7% Similarity=-0.048 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEee
Q 029747 141 RILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 141 ~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~~ 186 (188)
+-+.+.|+++|++-+.+. -- -..-..-+.+.+++.||.+-..
T Consensus 109 e~F~~~~~~aGvdgviip-DL---P~ee~~~~~~~~~~~gi~~I~l 150 (263)
T CHL00200 109 NKFIKKISQAGVKGLIIP-DL---PYEESDYLISVCNLYNIELILL 150 (263)
T ss_pred HHHHHHHHHcCCeEEEec-CC---CHHHHHHHHHHHHHcCCCEEEE
Confidence 447889999999999983 22 2355778889999999987654
No 143
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate
Probab=22.21 E-value=3.8e+02 Score=22.06 Aligned_cols=51 Identities=2% Similarity=-0.063 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCEEEE-ecCCCCchhhHHHHHHHHHHHC-CcEe
Q 029747 131 SDIPACLAIGRILAERAREADVYTASY-TPRERDKFEGKIRAVVQSLIDN-GIDV 183 (188)
Q Consensus 131 ~n~~AA~~vG~lLA~RakeaGI~~vvf-dDRgg~kyhGrVkA~adalRe~-GL~f 183 (188)
.|..+++.+++.|++.+ .|-.++.| ........+.|...|.+++.+. |++.
T Consensus 112 d~~~~g~~~~~~L~~~~--~g~~~i~~l~~~~~~~~~~R~~gf~~al~~~~~~~~ 164 (280)
T cd06303 112 DHAAGARLLADYFIKRY--PNHARYAMLYFSPGYISTARGDTFIDCVHARNNWTL 164 (280)
T ss_pred CHHHHHHHHHHHHHHhc--CCCcEEEEEECCCCcchhHHHHHHHHHHHhCCCceE
Confidence 44555555555554432 57677665 1111233467999999999998 8764
No 144
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=22.17 E-value=3.6e+02 Score=21.82 Aligned_cols=52 Identities=8% Similarity=-0.080 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCEEEEe--cCCCCchhhHHHHHHHHHHHCC-cEeE
Q 029747 131 SDIPACLAIGRILAERAREADVYTASYT--PRERDKFEGKIRAVVQSLIDNG-IDVK 184 (188)
Q Consensus 131 ~n~~AA~~vG~lLA~RakeaGI~~vvfd--DRgg~kyhGrVkA~adalRe~G-L~f~ 184 (188)
.|..+++..++.|.+++ .|..++.+- +.+......|...|.+++.+.| +.+.
T Consensus 106 d~~~~g~~~~~~l~~~~--~g~~~i~~i~~~~~~~~~~~R~~g~~~a~~~~~~~~~~ 160 (272)
T cd06300 106 DQAEFGKQGAEWLVKEL--GGKGNVLVVRGLAGHPVDEDRYAGAKEVLKEYPGIKIV 160 (272)
T ss_pred CHHHHHHHHHHHHHHHc--CCCceEEEEECCCCCcchHHHHHHHHHHHHHCCCcEEE
Confidence 44555566665555543 266666541 1111223568999999999998 8754
No 145
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=22.15 E-value=1.7e+02 Score=23.97 Aligned_cols=50 Identities=22% Similarity=0.133 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCCEEEE-e-cCCCC------chhhHHHHHHHHHHHCCcEeE
Q 029747 130 RSDIPACLAIGRILAERAREADVYTASY-T-PRERD------KFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 130 ~~n~~AA~~vG~lLA~RakeaGI~~vvf-d-DRgg~------kyhGrVkA~adalRe~GL~f~ 184 (188)
..|..+++..++.|.++ ..++.| . +.... ....|...|.+++.+.|++++
T Consensus 96 ~d~~~~g~~a~~~L~~~-----~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~~~~~~~g~~~~ 153 (269)
T cd06297 96 LDNRLGGRLAGAYLADF-----PGRIGAITVEEEPDRAFRRTVFAERRAGFQQALKDAGRPFS 153 (269)
T ss_pred ECcHHHHHHHHHHHHHh-----CCceEEEeCccccccccccccHHHHHHHHHHHHHHcCCCCC
Confidence 45777777777777776 233333 1 11112 235689999999999999764
No 146
>PRK07709 fructose-bisphosphate aldolase; Provisional
Probab=22.12 E-value=2.7e+02 Score=24.89 Aligned_cols=43 Identities=19% Similarity=0.220 Sum_probs=33.8
Q ss_pred HHHHHhcCCCEEEEecCCCCchhh---HHHHHHHHHHHCCcEeEeec
Q 029747 144 AERAREADVYTASYTPRERDKFEG---KIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 144 A~RakeaGI~~vvfdDRgg~kyhG---rVkA~adalRe~GL~f~~~~ 187 (188)
..+|+++|.+.|.| |-+...|.. ..+.+++-+...|+.++--|
T Consensus 93 i~~ai~~GftSVM~-DgS~lp~eeNi~~Trevv~~Ah~~gv~VEaEl 138 (285)
T PRK07709 93 CKEAIDAGFTSVMI-DASHHPFEENVETTKKVVEYAHARNVSVEAEL 138 (285)
T ss_pred HHHHHHcCCCEEEE-eCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEE
Confidence 44899999999999 566666765 56778888899999887543
No 147
>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=22.07 E-value=2.7e+02 Score=24.86 Aligned_cols=44 Identities=27% Similarity=0.274 Sum_probs=34.2
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhh---HHHHHHHHHHHCCcEeEeec
Q 029747 143 LAERAREADVYTASYTPRERDKFEG---KIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhG---rVkA~adalRe~GL~f~~~~ 187 (188)
...+|.++|.+.|.| |-+...+.. ..+.+++-++..|+.++.-|
T Consensus 84 ~i~~ai~~GftSVMi-D~S~l~~eeNi~~t~~vv~~ah~~gv~VEaEl 130 (276)
T cd00947 84 LIKRAIRAGFSSVMI-DGSHLPFEENVAKTKEVVELAHAYGVSVEAEL 130 (276)
T ss_pred HHHHHHHhCCCEEEe-CCCCCCHHHHHHHHHHHHHHHHHcCCeEEEEE
Confidence 346888999999999 677766765 56778888899999887543
No 148
>PRK11858 aksA trans-homoaconitate synthase; Reviewed
Probab=22.07 E-value=2.3e+02 Score=25.97 Aligned_cols=66 Identities=17% Similarity=0.161 Sum_probs=26.4
Q ss_pred EEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEEEEecC-CCCchhhHHHHHHHHHHHCCcE
Q 029747 114 AVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTASYTPR-ERDKFEGKIRAVVQSLIDNGID 182 (188)
Q Consensus 114 aSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~vvfdDR-gg~kyhGrVkA~adalRe~GL~ 182 (188)
+..++.+.-++..++ .+.+.+...-....+.|++.|+. |.|... .+..-...+..+++.+.+.|.+
T Consensus 94 i~~~~Sd~h~~~~~~--~s~~~~l~~~~~~v~~a~~~G~~-v~~~~ed~~r~~~~~l~~~~~~~~~~Ga~ 160 (378)
T PRK11858 94 IFIATSDIHIKHKLK--KTREEVLERMVEAVEYAKDHGLY-VSFSAEDASRTDLDFLIEFAKAAEEAGAD 160 (378)
T ss_pred EEEcCCHHHHHHHhC--CCHHHHHHHHHHHHHHHHHCCCe-EEEEeccCCCCCHHHHHHHHHHHHhCCCC
Confidence 344444443333322 22333333334444455555543 222111 1111234455555555555543
No 149
>PRK12452 cardiolipin synthetase; Reviewed
Probab=22.03 E-value=2.8e+02 Score=26.59 Aligned_cols=48 Identities=17% Similarity=0.263 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHhcCCC-EEEEecCCCCchhhHHHHHHHHHHHCCcEeEeec
Q 029747 136 CLAIGRILAERAREADVY-TASYTPRERDKFEGKIRAVVQSLIDNGIDVKIYL 187 (188)
Q Consensus 136 A~~vG~lLA~RakeaGI~-~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~~~ 187 (188)
...+-..|.++|+ .||+ .+.+|+-|.... -..+.+.|+++|+++..+.
T Consensus 179 g~~i~~aL~~aa~-rGV~VRiL~D~~Gs~~~---~~~~~~~L~~aGi~v~~f~ 227 (509)
T PRK12452 179 GTKVRDALIKKAK-DGVIVRFLYDGLGSNTL---RRRFLQPMKEAGIEIVEFD 227 (509)
T ss_pred HHHHHHHHHHHHH-CCCEEEEEEECCCCCCC---CHHHHHHHHhCCeEEEEec
Confidence 4455566666554 7998 677865554321 2457788999999998653
No 150
>PRK08452 flagellar protein FlaG; Provisional
Probab=21.40 E-value=1.3e+02 Score=23.97 Aligned_cols=38 Identities=5% Similarity=-0.063 Sum_probs=29.4
Q ss_pred hhhcccccccCCCceEEEEecCCeEEEEEEECCCCeEE
Q 029747 76 ISFKQRTVAYMEPFTLDVFISKRFVSASLTHRVTSKQV 113 (188)
Q Consensus 76 ~r~rkr~~~~~~~pRL~V~kSNkhiyAqVidd~~g~tV 113 (188)
..+++.+.......+..++..-.-++++|+|..+|++|
T Consensus 60 e~lN~~~~~~~~~L~F~~de~~~~~vVkVvD~~T~eVI 97 (124)
T PRK08452 60 EKLNEEMKRLDTNIRFGYNDKIKGLVVSVKEANGGKVI 97 (124)
T ss_pred HHHHHHHHhhCCceEEEEcCCCCcEEEEEEECCCCcee
Confidence 34445555556677888888888999999999999877
No 151
>PRK08195 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated
Probab=21.37 E-value=2.5e+02 Score=25.49 Aligned_cols=42 Identities=12% Similarity=0.060 Sum_probs=33.8
Q ss_pred HHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHC---CcEeEe
Q 029747 144 AERAREADVYTASYTPRERDKFEGKIRAVVQSLIDN---GIDVKI 185 (188)
Q Consensus 144 A~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~---GL~f~~ 185 (188)
++++.+.|++.+.+-|..|...--.|..++..+++. ++.+.+
T Consensus 150 a~~~~~~Ga~~i~i~DT~G~~~P~~v~~~v~~l~~~l~~~i~ig~ 194 (337)
T PRK08195 150 AKLMESYGAQCVYVVDSAGALLPEDVRDRVRALRAALKPDTQVGF 194 (337)
T ss_pred HHHHHhCCCCEEEeCCCCCCCCHHHHHHHHHHHHHhcCCCCeEEE
Confidence 677778899999887888888888888888888875 465544
No 152
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=21.36 E-value=2.7e+02 Score=23.87 Aligned_cols=48 Identities=10% Similarity=0.077 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCCEEEEecCCC---CchhhHHHHHHHHHHHCCcEe
Q 029747 131 SDIPACLAIGRILAERAREADVYTASYTPRER---DKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 131 ~n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg---~kyhGrVkA~adalRe~GL~f 183 (188)
.|..+++..++ .+.+.|..++.|- .+. .....|+..|.+++.+.|+.+
T Consensus 159 D~~~~~~~a~~----~L~~~G~~~I~~i-~~~~~~~~~~~R~~Gf~~al~~~gi~~ 209 (346)
T PRK10401 159 DNVSGARMATR----MLLNNGHQRIGYL-SSSHGIEDDAMRRAGWMSALKEQGIIP 209 (346)
T ss_pred CcHHHHHHHHH----HHHHCCCCeEEEE-eCCCcCcchHHHHHHHHHHHHHcCCCC
Confidence 34555544444 4456788887651 222 223569999999999999864
No 153
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=21.35 E-value=2.6e+02 Score=21.86 Aligned_cols=12 Identities=8% Similarity=-0.000 Sum_probs=5.3
Q ss_pred HHHHHHHHhcCC
Q 029747 141 RILAERAREADV 152 (188)
Q Consensus 141 ~lLA~RakeaGI 152 (188)
+.+.+.++++|.
T Consensus 71 ~~~~~~L~~~g~ 82 (132)
T TIGR00640 71 PALRKELDKLGR 82 (132)
T ss_pred HHHHHHHHhcCC
Confidence 334444444444
No 154
>PRK13111 trpA tryptophan synthase subunit alpha; Provisional
Probab=21.32 E-value=2.7e+02 Score=24.40 Aligned_cols=42 Identities=19% Similarity=0.165 Sum_probs=31.8
Q ss_pred HHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEee
Q 029747 141 RILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 141 ~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~~ 186 (188)
+-+.+.|+++|++-+.+ +. .-..-...+.+.+++.||++-+.
T Consensus 107 e~f~~~~~~aGvdGvii-pD---Lp~ee~~~~~~~~~~~gl~~I~l 148 (258)
T PRK13111 107 ERFAADAAEAGVDGLII-PD---LPPEEAEELRAAAKKHGLDLIFL 148 (258)
T ss_pred HHHHHHHHHcCCcEEEE-CC---CCHHHHHHHHHHHHHcCCcEEEE
Confidence 35788999999999888 32 22367888889999999887653
No 155
>cd07945 DRE_TIM_CMS Leptospira interrogans citramalate synthase (CMS) and related proteins, N-terminal catalytic TIM barrel domain. Citramalate synthase (CMS) catalyzes the conversion of pyruvate and acetyl-CoA to (R)-citramalate in the first dedicated step of the citramalate pathway. Citramalate is only found in Leptospira interrogans and a few other microorganisms. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center con
Probab=21.23 E-value=2.6e+02 Score=24.56 Aligned_cols=69 Identities=16% Similarity=0.005 Sum_probs=32.0
Q ss_pred EEEEEecchhhhhhhhcCCCCHHHHHHHHHHHHHHHHhcCCCEE-EEecCC-CCc-hhhHHHHHHHHHHHCCcE
Q 029747 112 QVAVAGTNSKDIKAVLRSRSDIPACLAIGRILAERAREADVYTA-SYTPRE-RDK-FEGKIRAVVQSLIDNGID 182 (188)
Q Consensus 112 tVaSAST~Ek~ik~~L~s~~n~~AA~~vG~lLA~RakeaGI~~v-vfdDRg-g~k-yhGrVkA~adalRe~GL~ 182 (188)
+-+..++.+.-++..+. .+.+-+...-..+.+.|++.|+.-. .+.|-+ +++ -...+..+++.+.+.|.+
T Consensus 91 i~i~~~~S~~h~~~~~~--~t~~e~l~~~~~~i~~a~~~G~~v~~~~~d~~~~~r~~~~~~~~~~~~~~~~G~~ 162 (280)
T cd07945 91 LNLLTKGSLKHCTEQLR--KTPEEHFADIREVIEYAIKNGIEVNIYLEDWSNGMRDSPDYVFQLVDFLSDLPIK 162 (280)
T ss_pred EEEEEeCCHHHHHHHHC--cCHHHHHHHHHHHHHHHHhCCCEEEEEEEeCCCCCcCCHHHHHHHHHHHHHcCCC
Confidence 33444555544443332 2344444444455666666665421 122211 111 234566666666666655
No 156
>smart00822 PKS_KR This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group.
Probab=20.94 E-value=3.4e+02 Score=19.72 Aligned_cols=47 Identities=17% Similarity=0.102 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeE
Q 029747 137 LAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 137 ~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~ 184 (188)
--+|.-+++.+.+.|...++...|....-. .....++.+.+.|.++.
T Consensus 10 ~~iG~~~~~~l~~~g~~~v~~~~r~~~~~~-~~~~~~~~~~~~~~~~~ 56 (180)
T smart00822 10 GGLGLELARWLAERGARHLVLLSRSGPDAP-GAAELLAELEALGAEVT 56 (180)
T ss_pred ChHHHHHHHHHHHhhCCeEEEEeCCCCCCc-cHHHHHHHHHhcCCeEE
Confidence 358888888888888876665345432221 12223455555665554
No 157
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=20.89 E-value=3.2e+02 Score=19.50 Aligned_cols=34 Identities=12% Similarity=0.047 Sum_probs=25.6
Q ss_pred ceEEEEecCCeEEEEEEECCCCeEEEEEecchhhhh
Q 029747 89 FTLDVFISKRFVSASLTHRVTSKQVAVAGTNSKDIK 124 (188)
Q Consensus 89 pRL~V~kSNkhiyAqVidd~~g~tVaSAST~Ek~ik 124 (188)
|-|.+...+-..++.|.. +|+++++....+.+++
T Consensus 39 pgl~~r~~~p~~t~~IF~--sGki~itGaks~~~~~ 72 (86)
T PF00352_consen 39 PGLIYRLRNPKATVLIFS--SGKIVITGAKSEEEAK 72 (86)
T ss_dssp SSEEEEETTTTEEEEEET--TSEEEEEEESSHHHHH
T ss_pred CeEEEeecCCcEEEEEEc--CCEEEEEecCCHHHHH
Confidence 567777777777777776 8999988876666654
No 158
>cd07937 DRE_TIM_PC_TC_5S Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain. This family includes the carboxyltransferase domains of pyruvate carboxylase (PC) and the transcarboxylase (TC) 5S subunit. Transcarboxylase 5S is a cobalt-dependent metalloenzyme subunit of the biotin-dependent transcarboxylase multienzyme complex. Transcarboxylase 5S transfers carbon dioxide from the 1.3S biotin to pyruvate in the second of two carboxylation reactions catalyzed by TC. The first reaction involves the transfer of carbon dioxide from methylmalonyl-CoA to the 1.3S biotin, and is catalyzed by the 12S subunit. These two steps allow a carboxylate group to be transferred from oxaloacetate to propionyl-CoA to yield pyruvate and methylmalonyl-CoA. The catalytic domain of transcarboxylase 5S has a canonical TIM-barrel fold with a large C-terminal extension that forms a funnel leading to the active site. Transcarboxylase 5S forms a homodimer and there are six dimers per complex
Probab=20.89 E-value=2.7e+02 Score=24.22 Aligned_cols=43 Identities=12% Similarity=0.110 Sum_probs=33.6
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHC-CcEeEe
Q 029747 143 LAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDN-GIDVKI 185 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~-GL~f~~ 185 (188)
+++.+.+.|++.+.+-|.-|......+..++..+++. ++.+.+
T Consensus 154 ~~~~~~~~Ga~~i~l~DT~G~~~P~~v~~lv~~l~~~~~~~l~~ 197 (275)
T cd07937 154 LAKELEDMGADSICIKDMAGLLTPYAAYELVKALKKEVGLPIHL 197 (275)
T ss_pred HHHHHHHcCCCEEEEcCCCCCCCHHHHHHHHHHHHHhCCCeEEE
Confidence 4667788899999987788888888888888888875 555443
No 159
>cd06413 GH25_muramidase_1 Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain. Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.
Probab=20.81 E-value=2.5e+02 Score=22.74 Aligned_cols=39 Identities=18% Similarity=0.191 Sum_probs=24.8
Q ss_pred HhcCCCEEEEecCCC-CchhhHHHHHHHHHHHCCcEeEee
Q 029747 148 READVYTASYTPRER-DKFEGKIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 148 keaGI~~vvfdDRgg-~kyhGrVkA~adalRe~GL~f~~~ 186 (188)
+..||..|+.--..| .-...+-..-++.++++||.+.+|
T Consensus 21 k~~gi~fviiKateG~~~~D~~~~~~~~~a~~~Gl~vG~Y 60 (191)
T cd06413 21 RAQGVSFAYIKATEGGDHVDKRFAENWRGARAAGLPRGAY 60 (191)
T ss_pred HhCCCcEEEEEEcCCCCccCHHHHHHHHHHHHcCCceEEE
Confidence 457888777611122 223446666777888888888777
No 160
>cd07938 DRE_TIM_HMGL 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain. 3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate, one of the terminal steps in ketone body generation and leucine degradation, and is a key enzyme in the pathway that supplies metabolic fuel to extrahepatic tissues. Mutations in HMGL cause a human autosomal recessive disorder called primary metabolic aciduria that affects ketogenesis and leucine catabolism and can be fatal due to an inability to tolerate hypoglycemia. HMGL has a TIM barrel domain with a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. The cleavage of HMG-CoA requires the presence of a divalent cation like Mg2+ or Mn2+, and the reaction is thought to involve general acid/base catalysis. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropy
Probab=20.70 E-value=2.6e+02 Score=24.42 Aligned_cols=36 Identities=14% Similarity=0.177 Sum_probs=19.5
Q ss_pred HHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHC
Q 029747 144 AERAREADVYTASYTPRERDKFEGKIRAVVQSLIDN 179 (188)
Q Consensus 144 A~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~ 179 (188)
++.+.+.|++.+.+-|..|...--.+..+++.+++.
T Consensus 155 ~~~~~~~Ga~~i~l~DT~G~~~P~~v~~lv~~l~~~ 190 (274)
T cd07938 155 AERLLDLGCDEISLGDTIGVATPAQVRRLLEAVLER 190 (274)
T ss_pred HHHHHHcCCCEEEECCCCCccCHHHHHHHHHHHHHH
Confidence 344445566665554555555555555555555554
No 161
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff.
Probab=20.62 E-value=2.2e+02 Score=26.68 Aligned_cols=40 Identities=20% Similarity=0.109 Sum_probs=30.2
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhh-----HHHHHHHHHHHCCcEe
Q 029747 143 LAERAREADVYTASYTPRERDKFEG-----KIRAVVQSLIDNGIDV 183 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhG-----rVkA~adalRe~GL~f 183 (188)
+.+.|.++||..+++ -.+++...| .-..+.+.++++|+.+
T Consensus 80 ~l~e~~~~gv~~~vi-~s~gf~e~g~~g~~~~~~l~~~a~~~girv 124 (447)
T TIGR02717 80 VVEECGEKGVKGAVV-ITAGFKEVGEEGAELEQELVEIARKYGMRL 124 (447)
T ss_pred HHHHHHhcCCCEEEE-ECCCccccCcchHHHHHHHHHHHHHcCCEE
Confidence 356688899999886 356666544 2478999999999975
No 162
>PRK05692 hydroxymethylglutaryl-CoA lyase; Provisional
Probab=20.55 E-value=2.5e+02 Score=24.76 Aligned_cols=15 Identities=20% Similarity=0.251 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHCCcE
Q 029747 168 KIRAVVQSLIDNGID 182 (188)
Q Consensus 168 rVkA~adalRe~GL~ 182 (188)
.+..+++.+.+.|.+
T Consensus 156 ~~~~~~~~~~~~G~d 170 (287)
T PRK05692 156 AVADVAERLFALGCY 170 (287)
T ss_pred HHHHHHHHHHHcCCc
Confidence 455555555555554
No 163
>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=20.54 E-value=3.1e+02 Score=19.62 Aligned_cols=43 Identities=16% Similarity=0.177 Sum_probs=30.0
Q ss_pred HHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEe
Q 029747 141 RILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKI 185 (188)
Q Consensus 141 ~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~ 185 (188)
.-++..|+++|+ .|.. +.=.-.--.-...+++.+++.|+.+-+
T Consensus 76 ~~~~~~~l~~g~-~v~~-EKP~~~~~~~~~~l~~~a~~~~~~~~V 118 (120)
T PF01408_consen 76 AEIAKKALEAGK-HVLV-EKPLALTLEEAEELVEAAKEKGVKVMV 118 (120)
T ss_dssp HHHHHHHHHTTS-EEEE-ESSSSSSHHHHHHHHHHHHHHTSCEEE
T ss_pred HHHHHHHHHcCC-EEEE-EcCCcCCHHHHHHHHHHHHHhCCEEEE
Confidence 346788888998 6666 333334455688888889998887654
No 164
>TIGR03581 EF_0839 conserved hypothetical protein EF_0839/AHA_3917. Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.
Probab=20.48 E-value=2.3e+02 Score=25.20 Aligned_cols=39 Identities=13% Similarity=0.133 Sum_probs=33.5
Q ss_pred HHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 145 ERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 145 ~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
.-+++.|...+.|.+.+|-++-.-.+|+++++-+.|+-+
T Consensus 142 aml~dmG~~SiKffPM~Gl~~leE~~avA~aca~~g~~l 180 (236)
T TIGR03581 142 AMLKDMGGSSVKFFPMGGLKHLEEYAAVAKACAKHGFYL 180 (236)
T ss_pred HHHHHcCCCeeeEeecCCcccHHHHHHHHHHHHHcCCcc
Confidence 346778999998768899999999999999999999764
No 165
>PF01346 FKBP_N: Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; InterPro: IPR000774 Peptidyl-prolyl cis-trans isomerase (PPIase) catalyses the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides [, ]. This alpha helical domain is found at the N terminus of proteins belonging to the FKBP-type peptidyl-prolyl cis-trans isomerase(IPR001179 from INTERPRO) family. Peptidyl-prolyl cis-trans isomerase has been shown to accelerate the refolding of several proteins in vitro [, , ]; the FKPB-type enzymes probably act in the folding of extracytoplasmic proteins.; GO: 0006457 protein folding; PDB: 1FD9_A 2VCD_A 3OE2_A 2UZ5_A 3B09_A 1Q6H_B 1Q6I_B 1Q6U_A.
Probab=20.41 E-value=1e+02 Score=23.17 Aligned_cols=25 Identities=8% Similarity=0.167 Sum_probs=20.8
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCCE
Q 029747 130 RSDIPACLAIGRILAERAREADVYT 154 (188)
Q Consensus 130 ~~n~~AA~~vG~lLA~RakeaGI~~ 154 (188)
+..-..+|.+|..++......+...
T Consensus 20 ~~~~k~SYalG~~iG~~l~~~~~~~ 44 (124)
T PF01346_consen 20 TDEDKLSYALGVQIGQQLKQQGFEQ 44 (124)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHCHCC
T ss_pred CHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 4456789999999999999887766
No 166
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=20.33 E-value=3.7e+02 Score=21.86 Aligned_cols=52 Identities=15% Similarity=0.250 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHHHHHHHhcCCCEEEEecC-CCCchhhHHHHHHHHHHHCCcEeE
Q 029747 132 DIPACLAIGRILAERAREADVYTASYTPR-ERDKFEGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 132 n~~AA~~vG~lLA~RakeaGI~~vvfdDR-gg~kyhGrVkA~adalRe~GL~f~ 184 (188)
|..+++..++.|.++. ..|.+.+.|... ......-|..+|.+++.+.|+.+.
T Consensus 102 ~~~~g~~a~~~l~~~~-~~g~~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~ 154 (271)
T cd06314 102 NYAAGRTAGEIMKKAL-PGGGKVAIFVGSLGADNAKERIQGIKDAIKDSKIEIV 154 (271)
T ss_pred hHHHHHHHHHHHHHHc-CCCCEEEEEecCCCCCCHHHHHHHHHHHHhcCCcEEE
Confidence 4455555555554442 125555555211 112235699999999999998754
No 167
>PF00857 Isochorismatase: Isochorismatase family; InterPro: IPR000868 This is a family of hydrolase enzymes. Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate (3.3.2.1 from EC).; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1XN4_A 3KL2_F 1YZV_A 3IRV_A 1IM5_A 1ILW_A 3PL1_A 1NF9_A 1NF8_A 1X9G_A ....
Probab=20.28 E-value=1.8e+02 Score=22.51 Aligned_cols=46 Identities=22% Similarity=0.154 Sum_probs=34.0
Q ss_pred HHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEeEeecC
Q 029747 140 GRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDVKIYLD 188 (188)
Q Consensus 140 G~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f~~~~~ 188 (188)
+.-|.+.+++.||+.+++ .|..-++=|.+-+..+.+.|..+-+.-|
T Consensus 100 ~t~L~~~L~~~gi~~vil---~G~~t~~CV~~Ta~~a~~~g~~v~v~~D 145 (174)
T PF00857_consen 100 GTDLDEILRKRGIDTVIL---CGVATDVCVLATARDAFDRGYRVIVVED 145 (174)
T ss_dssp TSSHHHHHHHTTESEEEE---EEESTTTHHHHHHHHHHHTT-EEEEEEE
T ss_pred cccccccccccccceEEE---cccccCcEEehhHHHHHHCCCEEEEECh
Confidence 445677778889999888 3556777888888888888988876543
No 168
>PRK07998 gatY putative fructose-1,6-bisphosphate aldolase; Reviewed
Probab=20.13 E-value=3.2e+02 Score=24.52 Aligned_cols=43 Identities=16% Similarity=0.072 Sum_probs=33.2
Q ss_pred HHHHHHhcCCCEEEEecCCCCchhh---HHHHHHHHHHHCCcEeEee
Q 029747 143 LAERAREADVYTASYTPRERDKFEG---KIRAVVQSLIDNGIDVKIY 186 (188)
Q Consensus 143 LA~RakeaGI~~vvfdDRgg~kyhG---rVkA~adalRe~GL~f~~~ 186 (188)
..++|.++|.+.|.| |-....+.. ..+.+++-+...|+.++.-
T Consensus 89 ~i~~Ai~~GftSVM~-DgS~l~~eeNi~~T~~vve~Ah~~gv~VEaE 134 (283)
T PRK07998 89 DVKQAVRAGFTSVMI-DGAALPFEENIAFTKEAVDFAKSYGVPVEAE 134 (283)
T ss_pred HHHHHHHcCCCEEEE-eCCCCCHHHHHHHHHHHHHHHHHcCCEEEEE
Confidence 345788999999999 576666654 5778888889999887643
No 169
>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=20.02 E-value=3.2e+02 Score=22.94 Aligned_cols=48 Identities=10% Similarity=0.092 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHhcCCCEEEEecCCCCch-hhHHHHHHHHHHHCCcEeE
Q 029747 136 CLAIGRILAERAREADVYTASYTPRERDKF-EGKIRAVVQSLIDNGIDVK 184 (188)
Q Consensus 136 A~~vG~lLA~RakeaGI~~vvfdDRgg~ky-hGrVkA~adalRe~GL~f~ 184 (188)
....+..+++.+++.|.+++.+- .....| ..+..+|.+++.+.|+++.
T Consensus 120 ~~~~~~~~~~~l~~~g~~~v~~l-~~~~~~~~~~~~~~~~~~~~~G~~~~ 168 (336)
T cd06326 120 YADEIAAIVRHLVTLGLKRIAVF-YQDDAFGKDGLAGVEKALAARGLKPV 168 (336)
T ss_pred hHHHHHHHHHHHHHhCCceEEEE-EecCcchHHHHHHHHHHHHHcCCCeE
Confidence 33455667777778899887651 112222 5689999999999998753
No 170
>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=20.01 E-value=3.5e+02 Score=21.77 Aligned_cols=42 Identities=19% Similarity=0.108 Sum_probs=30.5
Q ss_pred CHHHHHHHHHHHHHHHHhcCCCEEEEecCCCCchhhHHHHHHHHHHHCCcEe
Q 029747 132 DIPACLAIGRILAERAREADVYTASYTPRERDKFEGKIRAVVQSLIDNGIDV 183 (188)
Q Consensus 132 n~~AA~~vG~lLA~RakeaGI~~vvfdDRgg~kyhGrVkA~adalRe~GL~f 183 (188)
-.++|..+|+.||+ .|+ .+++ |+ ..|-..++++++.++|-.+
T Consensus 16 ~~~~A~~lg~~La~----~g~-~lv~---Gg--~~GlM~a~a~ga~~~gg~v 57 (159)
T TIGR00725 16 LYEIAYRLGKELAK----KGH-ILIN---GG--RTGVMEAVSKGAREAGGLV 57 (159)
T ss_pred HHHHHHHHHHHHHH----CCC-EEEc---CC--chhHHHHHHHHHHHCCCeE
Confidence 35678888888876 476 4444 55 4499999999999888543
Done!