Query 003275
Match_columns 834
No_of_seqs 465 out of 4102
Neff 9.7
Searched_HMMs 46136
Date Thu Mar 28 20:24:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003275.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003275hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1054 Glutamate-gated AMPA-t 100.0 9.9E-89 2.2E-93 696.6 43.5 722 2-772 88-846 (897)
2 KOG4440 NMDA selective glutama 100.0 1.8E-78 3.8E-83 623.9 31.4 672 18-771 114-857 (993)
3 KOG1053 Glutamate-gated NMDA-t 100.0 1E-73 2.2E-78 610.3 49.2 690 3-768 99-853 (1258)
4 KOG1052 Glutamate-gated kainat 100.0 1.8E-68 3.9E-73 624.9 53.9 602 120-771 4-624 (656)
5 cd06390 PBP1_iGluR_AMPA_GluR1 100.0 1.1E-43 2.3E-48 382.6 33.3 308 1-330 53-363 (364)
6 cd06392 PBP1_iGluR_delta_1 N-t 100.0 5.8E-43 1.3E-47 376.1 31.7 306 1-331 59-399 (400)
7 cd06387 PBP1_iGluR_AMPA_GluR3 100.0 5.2E-41 1.1E-45 360.3 33.2 309 1-330 60-371 (372)
8 cd06391 PBP1_iGluR_delta_2 N-t 100.0 1.5E-39 3.2E-44 354.1 32.9 313 1-331 59-399 (400)
9 cd06367 PBP1_iGluR_NMDA N-term 100.0 2.6E-39 5.6E-44 353.5 29.8 280 3-326 62-351 (362)
10 cd06389 PBP1_iGluR_AMPA_GluR2 100.0 7.5E-39 1.6E-43 347.8 33.1 311 1-331 54-369 (370)
11 cd06393 PBP1_iGluR_Kainate_Glu 100.0 5.2E-39 1.1E-43 352.8 32.2 304 2-332 70-383 (384)
12 cd06388 PBP1_iGluR_AMPA_GluR4 100.0 9.2E-39 2E-43 346.0 33.4 304 1-331 60-370 (371)
13 cd06365 PBP1_Pheromone_recepto 100.0 7E-39 1.5E-43 359.0 31.7 304 3-327 102-453 (469)
14 cd06380 PBP1_iGluR_AMPA N-term 100.0 3.9E-38 8.5E-43 346.9 34.6 318 1-330 59-381 (382)
15 cd06379 PBP1_iGluR_NMDA_NR1 N- 100.0 3E-38 6.5E-43 346.7 32.5 276 2-327 78-364 (377)
16 cd06374 PBP1_mGluR_groupI Liga 100.0 3.4E-38 7.5E-43 355.2 32.5 310 2-332 115-469 (472)
17 cd06375 PBP1_mGluR_groupII Lig 100.0 5E-38 1.1E-42 350.6 33.4 302 3-326 104-454 (458)
18 cd06376 PBP1_mGluR_groupIII Li 100.0 5.3E-38 1.1E-42 353.2 33.7 304 3-326 102-452 (463)
19 cd06361 PBP1_GPC6A_like Ligand 100.0 9.8E-38 2.1E-42 342.3 32.0 284 3-328 102-395 (403)
20 cd06362 PBP1_mGluR Ligand bind 100.0 1.8E-37 4E-42 349.1 32.9 309 3-331 102-451 (452)
21 cd06364 PBP1_CaSR Ligand-bindi 100.0 5.8E-37 1.3E-41 345.5 33.7 307 3-327 117-494 (510)
22 cd06386 PBP1_NPR_C_like Ligand 100.0 9E-37 1.9E-41 334.9 33.0 296 2-328 65-380 (387)
23 cd06378 PBP1_iGluR_NMDA_NR2 N- 100.0 3.3E-37 7.1E-42 331.5 27.4 285 4-332 62-355 (362)
24 cd06385 PBP1_NPR_A Ligand-bind 100.0 2.4E-35 5.2E-40 327.0 31.7 298 3-328 73-392 (405)
25 cd06371 PBP1_sensory_GC_DEF_li 100.0 6.1E-35 1.3E-39 319.5 32.1 292 2-324 64-369 (382)
26 cd06373 PBP1_NPR_like Ligand b 100.0 3.4E-35 7.5E-40 324.9 30.5 300 2-328 71-390 (396)
27 cd06384 PBP1_NPR_B Ligand-bind 100.0 8.4E-35 1.8E-39 321.5 31.9 298 3-328 72-393 (399)
28 KOG1056 Glutamate-gated metabo 100.0 4E-35 8.7E-40 327.2 29.2 326 4-368 125-494 (878)
29 cd06363 PBP1_Taste_receptor Li 100.0 2.2E-34 4.8E-39 319.1 31.5 285 3-327 106-396 (410)
30 cd06372 PBP1_GC_G_like Ligand- 100.0 6.9E-34 1.5E-38 314.0 32.2 298 3-328 67-387 (391)
31 cd06366 PBP1_GABAb_receptor Li 100.0 6.3E-34 1.4E-38 310.0 29.3 280 3-332 65-348 (350)
32 cd06370 PBP1_Speract_GC_like L 100.0 2.2E-33 4.7E-38 310.5 29.8 293 2-323 67-391 (404)
33 cd06352 PBP1_NPR_GC_like Ligan 100.0 5.9E-33 1.3E-37 307.0 32.6 302 2-329 66-384 (389)
34 PF01094 ANF_receptor: Recepto 100.0 1.6E-33 3.4E-38 307.4 26.7 290 3-314 50-348 (348)
35 cd06394 PBP1_iGluR_Kainate_KA1 100.0 1.4E-33 3E-38 298.2 21.3 263 2-331 63-332 (333)
36 cd06382 PBP1_iGluR_Kainate N-t 100.0 5E-32 1.1E-36 292.0 23.7 260 2-330 61-326 (327)
37 cd06381 PBP1_iGluR_delta_like 100.0 1.7E-30 3.7E-35 280.0 29.9 278 2-331 60-363 (363)
38 cd06383 PBP1_iGluR_AMPA_Like N 100.0 4.8E-31 1.1E-35 284.8 18.9 282 2-305 63-352 (368)
39 cd06368 PBP1_iGluR_non_NMDA_li 100.0 4.9E-30 1.1E-34 276.4 24.8 261 2-330 60-323 (324)
40 cd06342 PBP1_ABC_LIVBP_like Ty 100.0 2.7E-28 5.9E-33 264.3 27.2 267 3-313 65-334 (334)
41 cd06350 PBP1_GPCR_family_C_lik 100.0 3.4E-28 7.3E-33 265.0 25.0 246 3-327 90-340 (348)
42 cd06338 PBP1_ABC_ligand_bindin 100.0 8.3E-28 1.8E-32 261.5 24.4 267 3-313 70-345 (345)
43 PRK15404 leucine ABC transport 100.0 2.1E-27 4.5E-32 258.8 27.4 273 2-318 90-364 (369)
44 cd06345 PBP1_ABC_ligand_bindin 100.0 6.8E-27 1.5E-31 253.9 25.5 259 3-304 66-337 (344)
45 cd06377 PBP1_iGluR_NMDA_NR3 N- 100.0 5.7E-26 1.2E-30 239.8 30.2 280 2-331 79-375 (382)
46 cd06351 PBP1_iGluR_N_LIVBP_lik 100.0 1.6E-26 3.5E-31 249.8 25.5 259 2-326 61-322 (328)
47 cd06346 PBP1_ABC_ligand_bindin 99.9 1.7E-26 3.8E-31 246.8 23.3 243 3-310 66-310 (312)
48 cd06348 PBP1_ABC_ligand_bindin 99.9 9.7E-26 2.1E-30 245.0 26.9 273 3-310 66-343 (344)
49 cd06340 PBP1_ABC_ligand_bindin 99.9 6.4E-26 1.4E-30 246.2 23.8 262 3-306 69-342 (347)
50 cd06344 PBP1_ABC_ligand_bindin 99.9 2.5E-25 5.4E-30 240.3 23.5 260 3-307 65-328 (332)
51 cd06360 PBP1_alkylbenzenes_lik 99.9 9.1E-25 2E-29 236.8 26.8 266 3-308 64-332 (336)
52 cd06327 PBP1_SBP_like_1 Peripl 99.9 6.7E-25 1.4E-29 237.3 23.7 261 3-306 65-330 (334)
53 cd06329 PBP1_SBP_like_3 Peripl 99.9 7.6E-25 1.6E-29 237.4 23.4 258 2-304 64-336 (342)
54 cd06347 PBP1_ABC_ligand_bindin 99.9 3.2E-24 7E-29 232.4 26.9 259 3-306 66-329 (334)
55 cd06359 PBP1_Nba_like Type I p 99.9 3.3E-24 7.1E-29 231.7 25.7 259 3-304 64-325 (333)
56 cd06355 PBP1_FmdD_like Peripla 99.9 4.6E-24 1E-28 231.4 26.8 270 2-314 65-337 (348)
57 COG0683 LivK ABC-type branched 99.9 4E-24 8.7E-29 232.5 25.5 275 2-317 76-356 (366)
58 cd06336 PBP1_ABC_ligand_bindin 99.9 1.4E-24 3E-29 235.8 21.8 262 3-308 70-344 (347)
59 cd06349 PBP1_ABC_ligand_bindin 99.9 1.2E-23 2.6E-28 228.1 27.9 270 2-317 65-339 (340)
60 cd06330 PBP1_Arsenic_SBP_like 99.9 3.7E-24 7.9E-29 232.9 22.8 259 3-300 66-333 (346)
61 cd06343 PBP1_ABC_ligand_bindin 99.9 1.4E-23 3.1E-28 229.7 27.1 277 3-318 73-362 (362)
62 cd06331 PBP1_AmiC_like Type I 99.9 9.9E-24 2.1E-28 228.0 24.8 259 3-304 66-326 (333)
63 cd06328 PBP1_SBP_like_2 Peripl 99.9 2.4E-23 5.3E-28 224.5 25.5 261 3-308 67-331 (333)
64 TIGR03669 urea_ABC_arch urea A 99.9 4.5E-23 9.8E-28 224.1 27.0 278 2-325 66-349 (374)
65 cd06332 PBP1_aromatic_compound 99.9 4.3E-23 9.2E-28 223.5 26.0 261 3-306 64-327 (333)
66 KOG1055 GABA-B ion channel rec 99.9 1.5E-24 3.2E-29 234.4 13.2 304 5-328 114-431 (865)
67 cd06357 PBP1_AmiC Periplasmic 99.9 2.3E-22 4.9E-27 219.1 28.1 279 2-322 65-347 (360)
68 TIGR03407 urea_ABC_UrtA urea A 99.9 1.9E-22 4.2E-27 219.6 26.8 268 2-313 66-337 (359)
69 PF13458 Peripla_BP_6: Peripla 99.9 1.1E-22 2.5E-27 221.1 22.6 270 2-314 67-339 (343)
70 cd06358 PBP1_NHase Type I peri 99.9 4.1E-22 8.8E-27 215.3 25.3 254 3-302 66-324 (333)
71 cd06335 PBP1_ABC_ligand_bindin 99.9 6.4E-22 1.4E-26 214.9 25.6 258 3-299 66-334 (347)
72 cd06356 PBP1_Amide_Urea_BP_lik 99.9 7.2E-22 1.6E-26 213.1 24.9 255 2-301 65-324 (334)
73 cd06337 PBP1_ABC_ligand_bindin 99.9 3.4E-22 7.4E-27 217.6 22.4 267 3-317 68-356 (357)
74 cd06269 PBP1_glutamate_recepto 99.9 2.4E-22 5.1E-27 213.9 20.6 164 3-169 70-234 (298)
75 cd06334 PBP1_ABC_ligand_bindin 99.9 4.4E-21 9.5E-26 207.6 25.5 271 3-300 66-345 (351)
76 PRK10797 glutamate and asparta 99.9 4.3E-21 9.2E-26 202.2 22.9 224 373-719 39-272 (302)
77 PRK09495 glnH glutamine ABC tr 99.9 3.8E-21 8.3E-26 198.1 21.3 219 373-718 24-243 (247)
78 cd06369 PBP1_GC_C_enterotoxin_ 99.9 1.5E-20 3.2E-25 192.9 22.5 274 4-328 81-366 (380)
79 TIGR03863 PQQ_ABC_bind ABC tra 99.9 5.3E-21 1.1E-25 204.8 19.3 245 2-306 57-309 (347)
80 cd06339 PBP1_YraM_LppC_lipopro 99.9 6.1E-21 1.3E-25 205.7 19.7 248 3-303 58-329 (336)
81 PF00497 SBP_bac_3: Bacterial 99.9 6.7E-21 1.5E-25 193.7 17.6 222 376-718 1-224 (225)
82 PRK15010 ABC transporter lysin 99.9 4.8E-20 1E-24 191.3 21.8 223 372-718 24-254 (260)
83 PRK11917 bifunctional adhesin/ 99.9 6.3E-20 1.4E-24 189.4 22.1 219 372-717 36-258 (259)
84 PRK11260 cystine transporter s 99.8 5E-20 1.1E-24 191.9 20.6 222 372-718 39-261 (266)
85 PF13433 Peripla_BP_5: Peripla 99.8 1.3E-19 2.7E-24 187.1 21.6 269 2-327 66-340 (363)
86 PRK15007 putative ABC transpor 99.8 2E-19 4.4E-24 185.1 21.2 217 373-718 20-242 (243)
87 TIGR01096 3A0103s03R lysine-ar 99.8 3.2E-19 7E-24 184.5 21.4 219 374-717 24-250 (250)
88 PRK15437 histidine ABC transpo 99.8 3.4E-19 7.4E-24 184.8 21.0 223 372-718 24-254 (259)
89 cd06326 PBP1_STKc_like Type I 99.8 1.1E-18 2.4E-23 189.1 23.8 255 3-299 67-326 (336)
90 TIGR02995 ectoine_ehuB ectoine 99.8 4.7E-19 1E-23 185.4 19.1 223 372-717 31-260 (275)
91 cd04509 PBP1_ABC_transporter_G 99.8 2E-18 4.3E-23 183.6 19.7 218 4-234 67-290 (299)
92 cd06341 PBP1_ABC_ligand_bindin 99.8 2E-17 4.2E-22 179.6 21.9 248 3-293 66-318 (341)
93 PRK10859 membrane-bound lytic 99.8 7.5E-18 1.6E-22 189.1 19.1 221 372-718 41-266 (482)
94 cd06333 PBP1_ABC-type_HAAT_lik 99.8 6.6E-17 1.4E-21 173.1 22.3 218 3-236 65-293 (312)
95 cd06268 PBP1_ABC_transporter_L 99.7 1.1E-16 2.4E-21 170.1 20.8 220 2-236 64-287 (298)
96 PRK09959 hybrid sensory histid 99.7 2E-16 4.3E-21 200.2 23.9 217 373-718 301-520 (1197)
97 TIGR03870 ABC_MoxJ methanol ox 99.7 1.2E-16 2.7E-21 163.9 18.0 209 375-716 1-241 (246)
98 TIGR02285 conserved hypothetic 99.7 2E-16 4.3E-21 164.9 17.4 230 373-718 17-261 (268)
99 PF00060 Lig_chan: Ligand-gate 99.7 7.9E-19 1.7E-23 165.4 -1.9 107 495-601 1-115 (148)
100 COG0834 HisJ ABC-type amino ac 99.7 1.2E-15 2.6E-20 160.3 20.1 226 372-718 32-264 (275)
101 cd00134 PBPb Bacterial peripla 99.7 2.5E-15 5.5E-20 151.1 20.2 215 376-717 1-218 (218)
102 smart00062 PBPb Bacterial peri 99.7 3.4E-15 7.5E-20 150.1 19.8 216 375-717 1-219 (219)
103 TIGR03871 ABC_peri_MoxJ_2 quin 99.7 3E-15 6.4E-20 152.9 19.3 212 375-717 1-228 (232)
104 PRK09959 hybrid sensory histid 99.7 1.4E-15 3.1E-20 192.3 20.5 222 372-719 54-278 (1197)
105 smart00079 PBPe Eukaryotic hom 99.4 2.4E-12 5.1E-17 118.8 10.9 123 590-718 1-133 (134)
106 COG4623 Predicted soluble lyti 99.3 1.7E-11 3.7E-16 123.0 13.8 220 373-718 22-247 (473)
107 cd01391 Periplasmic_Binding_Pr 99.2 4.5E-10 9.8E-15 116.7 16.6 203 3-234 57-261 (269)
108 TIGR01098 3A0109s03R phosphate 99.0 8.1E-09 1.8E-13 106.9 14.9 199 374-703 32-254 (254)
109 PRK00489 hisG ATP phosphoribos 98.8 3.2E-08 7E-13 103.3 11.8 164 432-718 51-219 (287)
110 PF10613 Lig_chan-Glu_bd: Liga 98.7 8.7E-09 1.9E-13 78.6 3.0 47 395-443 14-65 (65)
111 PF04348 LppC: LppC putative l 98.6 1.9E-06 4.2E-11 97.3 18.9 252 2-312 276-532 (536)
112 TIGR03431 PhnD phosphonate ABC 98.2 2.4E-05 5.2E-10 82.5 14.4 116 590-711 126-257 (288)
113 cd01537 PBP1_Repressors_Sugar_ 97.8 0.00029 6.3E-09 72.9 12.8 153 3-163 54-211 (264)
114 cd06267 PBP1_LacI_sugar_bindin 97.6 0.00053 1.2E-08 71.0 12.6 154 3-164 54-211 (264)
115 cd01536 PBP1_ABC_sugar_binding 97.6 0.002 4.3E-08 66.8 16.0 146 3-155 54-206 (267)
116 PRK11553 alkanesulfonate trans 97.3 0.0024 5.3E-08 68.2 12.9 111 590-706 120-236 (314)
117 PF12974 Phosphonate-bd: ABC t 97.3 0.003 6.4E-08 64.7 12.3 122 589-716 95-230 (243)
118 cd06300 PBP1_ABC_sugar_binding 97.2 0.009 1.9E-07 62.2 15.0 146 3-156 59-210 (272)
119 cd06282 PBP1_GntR_like_2 Ligan 97.1 0.0077 1.7E-07 62.4 13.1 151 3-163 54-209 (266)
120 TIGR01729 taurine_ABC_bnd taur 97.0 0.0089 1.9E-07 63.4 13.7 70 589-665 90-164 (300)
121 COG3107 LppC Putative lipoprot 97.0 0.019 4.2E-07 61.9 14.8 242 2-302 317-585 (604)
122 cd06320 PBP1_allose_binding Pe 96.8 0.034 7.3E-07 58.0 15.9 145 3-155 56-207 (275)
123 cd06323 PBP1_ribose_binding Pe 96.8 0.044 9.6E-07 56.8 15.9 144 3-154 54-205 (268)
124 cd06319 PBP1_ABC_sugar_binding 96.7 0.04 8.7E-07 57.5 15.5 147 3-155 54-210 (277)
125 cd06273 PBP1_GntR_like_1 This 96.6 0.022 4.8E-07 59.1 12.3 133 21-160 71-208 (268)
126 cd06325 PBP1_ABC_uncharacteriz 96.5 0.033 7.1E-07 58.3 12.7 143 3-154 59-208 (281)
127 cd01545 PBP1_SalR Ligand-bindi 96.4 0.041 8.9E-07 57.1 12.9 156 3-165 55-215 (270)
128 cd06301 PBP1_rhizopine_binding 96.3 0.11 2.4E-06 54.0 15.7 156 3-165 55-218 (272)
129 COG3221 PhnD ABC-type phosphat 96.3 0.091 2E-06 54.7 14.3 112 588-705 133-260 (299)
130 PF13379 NMT1_2: NMT1-like fam 96.3 0.016 3.4E-07 59.7 8.6 72 589-665 104-187 (252)
131 cd06317 PBP1_ABC_sugar_binding 96.3 0.092 2E-06 54.6 14.6 149 3-155 55-212 (275)
132 TIGR03427 ABC_peri_uca ABC tra 96.2 0.087 1.9E-06 56.1 14.0 68 591-665 98-170 (328)
133 cd06312 PBP1_ABC_sugar_binding 96.1 0.15 3.4E-06 52.9 15.5 147 3-155 56-208 (271)
134 cd06305 PBP1_methylthioribose_ 96.1 0.13 2.8E-06 53.4 14.5 156 3-165 54-217 (273)
135 cd06298 PBP1_CcpA_like Ligand- 95.9 0.091 2E-06 54.4 12.4 153 3-165 54-213 (268)
136 PF03466 LysR_substrate: LysR 95.7 0.81 1.7E-05 44.7 18.0 182 401-704 19-205 (209)
137 cd06289 PBP1_MalI_like Ligand- 95.7 0.093 2E-06 54.3 11.5 150 3-159 54-207 (268)
138 cd06271 PBP1_AglR_RafR_like Li 95.6 0.15 3.4E-06 52.6 12.9 153 3-163 58-214 (268)
139 cd05466 PBP2_LTTR_substrate Th 95.6 0.92 2E-05 43.3 17.5 70 401-482 13-82 (197)
140 TIGR01728 SsuA_fam ABC transpo 95.4 0.21 4.5E-06 52.4 13.0 71 589-665 91-165 (288)
141 cd06310 PBP1_ABC_sugar_binding 95.4 0.99 2.2E-05 46.7 18.0 154 4-165 57-217 (273)
142 TIGR01481 ccpA catabolite cont 95.3 0.22 4.7E-06 53.5 13.2 132 20-158 130-264 (329)
143 PF09084 NMT1: NMT1/THI5 like; 95.3 0.13 2.8E-06 51.4 10.5 59 589-653 83-145 (216)
144 cd06309 PBP1_YtfQ_like Peripla 95.3 0.71 1.5E-05 47.9 16.6 156 4-164 55-219 (273)
145 TIGR02122 TRAP_TAXI TRAP trans 95.3 0.1 2.2E-06 55.9 10.3 61 589-655 131-197 (320)
146 PRK10653 D-ribose transporter 95.2 0.81 1.8E-05 48.2 16.9 144 4-154 82-231 (295)
147 cd06284 PBP1_LacI_like_6 Ligan 95.2 0.26 5.7E-06 50.9 12.8 147 3-158 54-204 (267)
148 cd08459 PBP2_DntR_NahR_LinR_li 94.9 1.2 2.5E-05 43.3 16.1 70 401-482 13-82 (201)
149 cd06313 PBP1_ABC_sugar_binding 94.9 1.4 2.9E-05 45.8 17.2 145 4-154 55-207 (272)
150 cd08440 PBP2_LTTR_like_4 TThe 94.8 3.2 6.9E-05 39.7 18.8 70 401-482 13-82 (197)
151 PF13407 Peripla_BP_4: Peripla 94.8 0.28 6E-06 50.5 11.5 150 3-157 54-209 (257)
152 cd08442 PBP2_YofA_SoxR_like Th 94.7 3 6.5E-05 39.9 18.2 70 401-482 13-82 (193)
153 cd01575 PBP1_GntR Ligand-bindi 94.6 0.47 1E-05 49.0 12.9 150 3-160 54-207 (268)
154 cd06288 PBP1_sucrose_transcrip 94.6 0.38 8.3E-06 49.7 12.2 134 24-164 74-211 (269)
155 cd06295 PBP1_CelR Ligand bindi 94.5 0.46 9.9E-06 49.4 12.6 136 21-163 80-219 (275)
156 cd08420 PBP2_CysL_like C-termi 94.3 4.4 9.5E-05 38.8 18.6 70 401-482 13-82 (201)
157 cd01540 PBP1_arabinose_binding 94.3 1.9 4.2E-05 45.0 16.8 162 4-165 54-229 (289)
158 cd08468 PBP2_Pa0477 The C-term 94.2 3.7 8E-05 39.9 17.8 73 401-482 13-85 (202)
159 cd08438 PBP2_CidR The C-termin 94.2 4.7 0.0001 38.6 18.5 70 401-482 13-82 (197)
160 cd08412 PBP2_PAO1_like The C-t 94.2 4.2 9E-05 39.0 18.0 71 400-482 12-82 (198)
161 PRK10014 DNA-binding transcrip 94.2 0.66 1.4E-05 50.1 13.3 132 19-157 135-270 (342)
162 cd06299 PBP1_LacI_like_13 Liga 94.2 0.67 1.5E-05 47.7 12.9 152 4-163 55-208 (265)
163 cd06283 PBP1_RegR_EndR_KdgR_li 94.1 0.79 1.7E-05 47.2 13.3 135 22-163 72-211 (267)
164 cd08421 PBP2_LTTR_like_1 The C 94.1 4.1 8.9E-05 39.1 17.8 70 401-482 13-82 (198)
165 cd06278 PBP1_LacI_like_2 Ligan 94.1 0.66 1.4E-05 47.8 12.5 141 3-153 53-197 (266)
166 PRK11151 DNA-binding transcrip 94.0 3.8 8.2E-05 43.3 18.6 70 401-482 104-173 (305)
167 cd06322 PBP1_ABC_sugar_binding 94.0 2.1 4.4E-05 44.2 16.2 143 3-154 54-203 (267)
168 PRK10703 DNA-binding transcrip 94.0 0.66 1.4E-05 50.1 12.9 136 22-163 132-272 (341)
169 cd06274 PBP1_FruR Ligand bindi 94.0 0.99 2.2E-05 46.5 13.7 134 23-163 73-211 (264)
170 cd06275 PBP1_PurR Ligand-bindi 94.0 0.84 1.8E-05 47.1 13.1 134 23-163 74-211 (269)
171 cd06303 PBP1_LuxPQ_Quorum_Sens 93.9 2.2 4.7E-05 44.5 16.2 112 50-165 107-224 (280)
172 cd08418 PBP2_TdcA The C-termin 93.9 5.3 0.00011 38.4 18.1 72 401-482 13-84 (201)
173 cd06294 PBP1_ycjW_transcriptio 93.9 0.73 1.6E-05 47.6 12.5 139 21-165 76-219 (270)
174 cd06307 PBP1_uncharacterized_s 93.9 2.6 5.6E-05 43.7 16.7 154 4-165 58-219 (275)
175 cd08433 PBP2_Nac The C-teminal 93.8 6.3 0.00014 37.9 18.5 70 401-482 13-82 (198)
176 cd08463 PBP2_DntR_like_4 The C 93.8 5.6 0.00012 38.8 18.1 72 400-482 12-83 (203)
177 cd01542 PBP1_TreR_like Ligand- 93.8 0.78 1.7E-05 47.1 12.4 149 3-164 54-207 (259)
178 PRK12684 transcriptional regul 93.7 3.7 8.1E-05 43.6 17.8 85 373-482 92-176 (313)
179 cd06270 PBP1_GalS_like Ligand 93.7 1.2 2.6E-05 46.0 13.7 131 21-158 71-205 (268)
180 CHL00180 rbcR LysR transcripti 93.7 6 0.00013 41.8 19.3 86 374-482 95-180 (305)
181 cd06272 PBP1_hexuronate_repres 93.6 0.86 1.9E-05 46.9 12.4 133 22-162 68-204 (261)
182 cd06285 PBP1_LacI_like_7 Ligan 93.6 0.91 2E-05 46.8 12.6 135 22-165 72-211 (265)
183 cd06281 PBP1_LacI_like_5 Ligan 93.5 0.77 1.7E-05 47.5 11.8 149 3-160 54-206 (269)
184 PRK12679 cbl transcriptional r 93.5 6.7 0.00015 41.7 19.2 207 374-718 93-306 (316)
185 COG1609 PurR Transcriptional r 93.4 1.2 2.6E-05 47.9 13.3 145 4-158 114-265 (333)
186 cd06308 PBP1_sensor_kinase_lik 93.4 3 6.6E-05 43.0 16.2 138 20-166 73-217 (270)
187 cd06293 PBP1_LacI_like_11 Liga 93.4 1.6 3.4E-05 45.1 14.0 153 3-163 54-210 (269)
188 cd06324 PBP1_ABC_sugar_binding 93.4 1.7 3.7E-05 46.0 14.4 158 4-165 58-238 (305)
189 cd08415 PBP2_LysR_opines_like 93.3 6.3 0.00014 37.7 17.5 71 400-482 12-82 (196)
190 cd06296 PBP1_CatR_like Ligand- 93.3 1 2.2E-05 46.5 12.4 155 3-165 54-214 (270)
191 cd06311 PBP1_ABC_sugar_binding 93.3 3.5 7.5E-05 42.7 16.4 145 4-155 60-210 (274)
192 TIGR02990 ectoine_eutA ectoine 93.3 1.5 3.3E-05 44.1 12.8 132 19-153 62-206 (239)
193 cd06321 PBP1_ABC_sugar_binding 93.2 3.3 7.1E-05 42.8 16.1 147 8-165 62-214 (271)
194 cd01539 PBP1_GGBP Periplasmic 93.2 3.7 8.1E-05 43.3 16.6 153 4-157 57-228 (303)
195 cd01574 PBP1_LacI Ligand-bindi 93.1 1.8 3.9E-05 44.5 13.8 149 3-163 55-207 (264)
196 cd06292 PBP1_LacI_like_10 Liga 93.0 1.7 3.7E-05 44.9 13.5 136 22-163 77-214 (273)
197 PRK11242 DNA-binding transcrip 92.9 8 0.00017 40.6 18.7 83 374-482 91-173 (296)
198 cd08417 PBP2_Nitroaromatics_li 92.8 4.5 9.7E-05 38.9 15.7 70 401-482 13-82 (200)
199 PRK12682 transcriptional regul 92.7 8.3 0.00018 40.8 18.6 84 374-482 93-176 (309)
200 cd08411 PBP2_OxyR The C-termin 92.7 7.6 0.00017 37.3 17.1 70 401-482 14-83 (200)
201 cd06316 PBP1_ABC_sugar_binding 92.6 4.6 9.9E-05 42.4 16.4 157 4-165 56-219 (294)
202 cd08465 PBP2_ToxR The C-termin 92.6 4.5 9.7E-05 39.2 15.3 70 401-482 13-82 (200)
203 cd08462 PBP2_NodD The C-termin 92.5 6.2 0.00013 38.2 16.2 69 401-482 13-81 (200)
204 cd08426 PBP2_LTTR_like_5 The C 92.5 9.7 0.00021 36.5 17.5 70 401-482 13-82 (199)
205 cd08434 PBP2_GltC_like The sub 92.4 10 0.00022 36.0 18.4 70 401-482 13-82 (195)
206 PRK12683 transcriptional regul 92.4 11 0.00023 40.0 18.8 84 374-482 93-176 (309)
207 cd06318 PBP1_ABC_sugar_binding 92.3 6.6 0.00014 40.7 17.1 147 4-155 55-215 (282)
208 cd08413 PBP2_CysB_like The C-t 92.3 9.2 0.0002 36.9 17.1 71 401-482 13-83 (198)
209 cd06297 PBP1_LacI_like_12 Liga 92.2 1.8 3.8E-05 44.8 12.4 135 19-163 69-213 (269)
210 PRK12681 cysB transcriptional 92.2 6.6 0.00014 42.0 17.0 85 373-482 92-176 (324)
211 PRK11303 DNA-binding transcrip 92.2 3.4 7.4E-05 44.1 15.0 130 22-160 135-268 (328)
212 PF00532 Peripla_BP_1: Peripla 92.2 1.4 3.1E-05 45.9 11.5 139 18-163 70-214 (279)
213 cd01544 PBP1_GalR Ligand-bindi 92.1 2.6 5.5E-05 43.6 13.5 135 21-163 67-212 (270)
214 cd06279 PBP1_LacI_like_3 Ligan 92.1 2 4.3E-05 44.9 12.7 154 3-165 55-231 (283)
215 cd06306 PBP1_TorT-like TorT-li 92.1 6.3 0.00014 40.6 16.3 124 22-154 75-207 (268)
216 cd06290 PBP1_LacI_like_9 Ligan 92.0 2.5 5.4E-05 43.5 13.1 126 27-159 76-205 (265)
217 PRK10423 transcriptional repre 91.9 2.3 5E-05 45.4 13.2 130 27-163 135-268 (327)
218 COG2984 ABC-type uncharacteriz 91.9 5.2 0.00011 41.4 14.5 142 5-154 89-240 (322)
219 cd01543 PBP1_XylR Ligand-bindi 91.6 3.6 7.9E-05 42.3 13.9 153 3-165 49-207 (265)
220 cd08460 PBP2_DntR_like_1 The C 91.6 4 8.8E-05 39.4 13.6 70 400-482 12-81 (200)
221 cd08466 PBP2_LeuO The C-termin 91.5 9.4 0.0002 36.6 16.2 70 401-482 13-82 (200)
222 PRK10837 putative DNA-binding 91.5 20 0.00043 37.4 19.8 83 374-482 89-171 (290)
223 PRK10727 DNA-binding transcrip 91.5 2.5 5.4E-05 45.6 12.9 111 52-163 156-270 (343)
224 cd08425 PBP2_CynR The C-termin 91.4 12 0.00026 35.7 16.8 70 401-482 14-83 (197)
225 cd06277 PBP1_LacI_like_1 Ligan 91.4 2.8 6E-05 43.2 12.8 146 3-158 57-205 (268)
226 cd06291 PBP1_Qymf_like Ligand 91.3 3.6 7.8E-05 42.3 13.4 127 23-158 70-201 (265)
227 cd06287 PBP1_LacI_like_8 Ligan 91.2 4.1 8.9E-05 42.1 13.8 134 23-163 74-211 (269)
228 PF07885 Ion_trans_2: Ion chan 91.1 0.22 4.7E-06 40.6 3.2 55 528-582 21-77 (79)
229 cd08464 PBP2_DntR_like_2 The C 90.8 8.8 0.00019 36.8 15.2 70 401-482 13-82 (200)
230 TIGR02424 TF_pcaQ pca operon t 90.8 14 0.00031 38.7 17.7 86 373-482 92-177 (300)
231 cd01541 PBP1_AraR Ligand-bindi 90.7 3.2 6.9E-05 42.9 12.5 135 22-163 77-216 (273)
232 cd01538 PBP1_ABC_xylose_bindin 90.6 10 0.00022 39.6 16.3 147 3-156 54-216 (288)
233 cd06302 PBP1_LsrB_Quorum_Sensi 90.5 14 0.0003 38.8 17.3 145 4-155 56-210 (298)
234 cd08441 PBP2_MetR The C-termin 90.4 17 0.00036 34.9 16.7 69 402-482 14-82 (198)
235 PRK09701 D-allose transporter 90.3 18 0.00039 38.3 18.0 131 22-155 101-241 (311)
236 PRK09526 lacI lac repressor; R 90.3 4.6 0.0001 43.4 13.7 128 26-163 142-273 (342)
237 TIGR00787 dctP tripartite ATP- 90.2 1.1 2.3E-05 46.2 8.2 103 589-703 126-230 (257)
238 cd06354 PBP1_BmpA_PnrA_like Pe 90.2 4.4 9.6E-05 41.8 12.9 144 3-153 56-206 (265)
239 TIGR02417 fruct_sucro_rep D-fr 90.1 4.7 0.0001 43.1 13.5 134 22-165 134-273 (327)
240 cd06314 PBP1_tmGBP Periplasmic 90.0 17 0.00036 37.5 17.2 142 4-155 55-204 (271)
241 cd08467 PBP2_SyrM The C-termin 90.0 17 0.00038 34.9 16.5 71 400-482 12-82 (200)
242 PRK12680 transcriptional regul 89.8 23 0.00049 37.9 18.3 84 374-482 93-176 (327)
243 PRK11480 tauA taurine transpor 89.7 2.5 5.4E-05 45.1 10.7 66 590-662 113-183 (320)
244 cd06286 PBP1_CcpB_like Ligand- 89.7 5.4 0.00012 40.8 13.1 123 30-160 79-205 (260)
245 PF13377 Peripla_BP_3: Peripla 89.6 1.2 2.7E-05 41.6 7.5 98 64-163 1-101 (160)
246 PRK10936 TMAO reductase system 89.6 14 0.00029 39.9 16.5 149 4-164 104-262 (343)
247 cd08461 PBP2_DntR_like_3 The C 89.6 17 0.00037 34.7 16.0 70 401-482 13-82 (198)
248 PF13531 SBP_bac_11: Bacterial 89.4 5.8 0.00013 39.9 12.7 198 399-715 9-226 (230)
249 cd08419 PBP2_CbbR_RubisCO_like 89.3 20 0.00043 34.0 18.6 70 401-482 12-81 (197)
250 cd08444 PBP2_Cbl The C-termina 88.9 23 0.00049 34.1 17.3 72 400-482 12-83 (198)
251 cd08423 PBP2_LTTR_like_6 The C 88.9 22 0.00047 33.9 16.5 73 401-482 13-87 (200)
252 PRK15421 DNA-binding transcrip 88.8 22 0.00049 37.7 17.3 69 402-482 103-171 (317)
253 PRK10401 DNA-binding transcrip 88.7 7.8 0.00017 41.8 14.0 111 52-163 156-270 (346)
254 PF03480 SBP_bac_7: Bacterial 88.7 0.56 1.2E-05 49.2 4.8 90 588-689 125-214 (286)
255 cd08469 PBP2_PnbR The C-termin 88.6 23 0.00049 34.8 16.5 70 401-482 13-82 (221)
256 PRK10341 DNA-binding transcrip 88.6 20 0.00044 37.9 16.9 71 402-482 111-181 (312)
257 PRK14987 gluconate operon tran 88.5 5.9 0.00013 42.4 12.8 134 22-163 136-272 (331)
258 PRK11233 nitrogen assimilation 88.3 19 0.00041 38.0 16.3 70 401-482 105-174 (305)
259 TIGR02955 TMAO_TorT TMAO reduc 88.1 14 0.0003 38.8 15.1 127 27-164 80-215 (295)
260 PRK15395 methyl-galactoside AB 88.0 22 0.00048 38.0 16.8 149 4-154 81-249 (330)
261 TIGR00363 lipoprotein, YaeC fa 88.0 9.5 0.00021 39.0 13.0 121 589-716 106-250 (258)
262 PRK09492 treR trehalose repres 87.9 8 0.00017 41.0 13.3 137 3-154 117-256 (315)
263 cd08443 PBP2_CysB The C-termin 87.7 27 0.00058 33.5 18.4 72 400-482 12-83 (198)
264 cd08456 PBP2_LysR The C-termin 87.4 27 0.00058 33.2 16.9 70 401-482 13-82 (196)
265 PRK11482 putative DNA-binding 87.4 26 0.00057 37.2 16.8 82 373-482 116-197 (317)
266 PRK11074 putative DNA-binding 87.4 29 0.00064 36.4 17.0 85 374-482 92-176 (300)
267 TIGR01256 modA molybdenum ABC 87.0 11 0.00024 37.4 12.8 72 627-704 132-204 (216)
268 PRK11063 metQ DL-methionine tr 86.9 17 0.00037 37.6 14.3 121 589-716 119-263 (271)
269 PRK09791 putative DNA-binding 86.8 29 0.00063 36.4 16.7 86 373-482 94-179 (302)
270 cd06304 PBP1_BmpA_like Peripla 86.7 12 0.00026 38.4 13.3 143 4-153 56-202 (260)
271 cd06280 PBP1_LacI_like_4 Ligan 86.5 12 0.00026 38.3 13.3 129 25-163 74-205 (263)
272 PRK09508 leuO leucine transcri 86.4 15 0.00033 38.9 14.4 70 401-482 125-194 (314)
273 cd08435 PBP2_GbpR The C-termin 86.3 31 0.00067 32.8 18.1 72 401-482 13-84 (201)
274 COG1879 RbsB ABC-type sugar tr 86.1 38 0.00082 36.0 17.3 155 3-163 90-250 (322)
275 PRK09860 putative alcohol dehy 85.9 6.1 0.00013 43.3 11.0 88 61-148 20-109 (383)
276 COG3473 Maleate cis-trans isom 85.4 25 0.00053 34.0 12.8 131 18-151 57-201 (238)
277 cd08414 PBP2_LTTR_aromatics_li 85.4 34 0.00074 32.4 17.9 70 401-482 13-82 (197)
278 PRK10339 DNA-binding transcrip 85.3 10 0.00022 40.4 12.4 131 22-160 130-264 (327)
279 cd08436 PBP2_LTTR_like_3 The C 85.2 34 0.00074 32.3 18.2 71 401-482 13-83 (194)
280 PF03808 Glyco_tran_WecB: Glyc 85.1 13 0.00029 35.4 11.6 99 58-166 35-135 (172)
281 cd08427 PBP2_LTTR_like_2 The C 84.9 35 0.00077 32.2 16.9 72 401-482 13-84 (195)
282 PRK15408 autoinducer 2-binding 84.4 29 0.00064 37.2 15.3 146 3-154 79-233 (336)
283 cd08486 PBP2_CbnR The C-termin 84.4 24 0.00052 33.9 13.7 70 401-482 14-83 (198)
284 COG1454 EutG Alcohol dehydroge 84.3 9.6 0.00021 41.1 11.2 91 61-151 18-110 (377)
285 cd08449 PBP2_XapR The C-termin 84.2 39 0.00084 32.0 18.4 72 401-482 13-84 (197)
286 cd08429 PBP2_NhaR The C-termin 84.1 43 0.00092 32.5 17.4 71 401-480 13-83 (204)
287 PRK11013 DNA-binding transcrip 84.1 60 0.0013 34.2 17.6 70 401-482 107-176 (309)
288 cd08448 PBP2_LTTR_aromatics_li 83.8 39 0.00086 31.9 17.5 70 401-482 13-82 (197)
289 PRK15454 ethanol dehydrogenase 83.2 5.1 0.00011 44.0 8.9 88 61-148 38-127 (395)
290 PF03401 TctC: Tripartite tric 83.1 31 0.00067 35.7 14.3 122 589-715 88-241 (274)
291 cd08457 PBP2_OccR The C-termin 82.9 44 0.00096 31.7 18.2 70 401-482 13-82 (196)
292 PF12727 PBP_like: PBP superfa 82.8 18 0.0004 35.2 11.7 102 589-701 81-190 (193)
293 TIGR03339 phn_lysR aminoethylp 82.6 62 0.0013 33.3 17.9 69 402-482 98-166 (279)
294 cd08437 PBP2_MleR The substrat 82.3 47 0.001 31.6 18.2 72 401-482 13-84 (198)
295 COG1638 DctP TRAP-type C4-dica 81.5 12 0.00025 40.0 10.5 213 404-706 47-264 (332)
296 cd08416 PBP2_MdcR The C-termin 81.5 49 0.0011 31.4 16.8 72 401-482 13-84 (199)
297 cd08458 PBP2_NocR The C-termin 81.3 51 0.0011 31.4 17.7 70 401-482 13-82 (196)
298 cd08192 Fe-ADH7 Iron-containin 81.2 13 0.00027 40.7 11.1 89 61-149 13-103 (370)
299 TIGR02634 xylF D-xylose ABC tr 81.2 61 0.0013 34.0 16.1 132 17-155 68-209 (302)
300 PRK10094 DNA-binding transcrip 81.2 77 0.0017 33.4 17.3 70 403-482 108-177 (308)
301 COG1910 Periplasmic molybdate- 81.1 15 0.00031 35.8 9.8 108 589-708 87-202 (223)
302 COG0715 TauA ABC-type nitrate/ 81.0 7.5 0.00016 41.7 9.2 71 588-665 125-201 (335)
303 TIGR02405 trehalos_R_Ecol treh 80.9 27 0.00059 36.8 13.4 118 25-154 133-253 (311)
304 cd08190 HOT Hydroxyacid-oxoaci 80.9 7.4 0.00016 43.1 9.2 87 61-147 12-100 (414)
305 PRK10624 L-1,2-propanediol oxi 80.6 7.7 0.00017 42.5 9.2 87 61-147 19-107 (382)
306 PF00465 Fe-ADH: Iron-containi 80.5 7 0.00015 42.6 8.8 89 61-151 12-102 (366)
307 cd06533 Glyco_transf_WecG_TagA 80.0 24 0.00052 33.6 11.2 99 57-165 32-132 (171)
308 PRK11041 DNA-binding transcrip 79.7 12 0.00026 39.5 10.2 112 52-164 132-247 (309)
309 cd08193 HVD 5-hydroxyvalerate 79.6 8.6 0.00019 42.1 9.1 89 61-149 15-105 (376)
310 PRK09861 cytoplasmic membrane 79.4 58 0.0013 33.6 14.6 123 588-716 119-264 (272)
311 cd08445 PBP2_BenM_CatM_CatR Th 79.4 60 0.0013 31.1 17.5 70 401-482 14-83 (203)
312 PRK11062 nhaR transcriptional 79.3 63 0.0014 33.8 15.4 85 374-481 93-177 (296)
313 cd08551 Fe-ADH iron-containing 79.2 9.8 0.00021 41.5 9.4 90 61-150 12-103 (370)
314 cd08189 Fe-ADH5 Iron-containin 79.0 16 0.00036 39.8 11.0 90 61-150 15-106 (374)
315 cd08194 Fe-ADH6 Iron-containin 77.7 11 0.00024 41.1 9.3 87 61-147 12-100 (375)
316 COG0725 ModA ABC-type molybdat 77.7 62 0.0014 33.1 14.0 69 405-482 46-120 (258)
317 cd08430 PBP2_IlvY The C-termin 77.4 66 0.0014 30.4 18.4 72 400-482 12-83 (199)
318 TIGR02638 lactal_redase lactal 76.5 12 0.00025 41.1 9.0 88 61-148 18-107 (379)
319 PF13407 Peripla_BP_4: Peripla 75.9 6.8 0.00015 40.0 6.7 78 75-154 1-81 (257)
320 TIGR02637 RhaS rhamnose ABC tr 75.9 1.1E+02 0.0023 32.1 16.9 137 11-155 64-210 (302)
321 PRK10355 xylF D-xylose transpo 74.6 1E+02 0.0022 32.9 15.6 137 19-164 97-243 (330)
322 cd08188 Fe-ADH4 Iron-containin 74.5 16 0.00034 40.0 9.3 88 61-148 17-106 (377)
323 cd08185 Fe-ADH1 Iron-containin 74.0 16 0.00034 40.1 9.2 88 61-149 15-105 (380)
324 PF00625 Guanylate_kin: Guanyl 72.8 52 0.0011 31.6 11.7 129 3-151 2-134 (183)
325 KOG1419 Voltage-gated K+ chann 72.8 6.2 0.00013 43.5 5.3 89 496-584 234-324 (654)
326 cd08451 PBP2_BudR The C-termin 72.0 90 0.0019 29.4 18.4 70 402-482 15-84 (199)
327 cd08181 PPD-like 1,3-propanedi 71.8 19 0.00042 39.0 9.2 86 61-147 15-103 (357)
328 PRK03635 chromosome replicatio 71.7 1.2E+02 0.0025 31.7 15.0 82 374-482 90-171 (294)
329 cd08453 PBP2_IlvR The C-termin 71.7 93 0.002 29.5 18.2 73 401-482 13-85 (200)
330 PF13685 Fe-ADH_2: Iron-contai 71.5 23 0.00051 35.9 9.0 98 62-165 9-108 (250)
331 PRK11716 DNA-binding transcrip 70.8 1.3E+02 0.0027 30.7 15.6 71 401-482 80-150 (269)
332 KOG3857 Alcohol dehydrogenase, 70.5 31 0.00068 35.9 9.4 96 44-139 38-137 (465)
333 cd08170 GlyDH Glycerol dehydro 70.4 15 0.00033 39.7 8.0 84 61-147 12-97 (351)
334 cd08176 LPO Lactadehyde:propan 70.3 18 0.0004 39.5 8.7 87 61-147 17-105 (377)
335 TIGR00696 wecB_tagA_cpsF bacte 70.1 71 0.0015 30.6 11.5 87 57-151 34-122 (177)
336 cd08191 HHD 6-hydroxyhexanoate 69.5 24 0.00053 38.7 9.4 89 61-150 12-102 (386)
337 cd08450 PBP2_HcaR The C-termin 69.0 1E+02 0.0022 29.0 17.7 70 401-482 13-82 (196)
338 PF04392 ABC_sub_bind: ABC tra 68.4 62 0.0013 33.9 11.9 118 14-139 68-194 (294)
339 PF01634 HisG: ATP phosphoribo 68.2 14 0.0003 34.7 6.0 102 590-704 57-160 (163)
340 PF14503 YhfZ_C: YhfZ C-termin 67.3 24 0.00052 35.1 7.8 103 601-717 114-224 (232)
341 PLN02245 ATP phosphoribosyl tr 66.8 45 0.00098 36.1 10.2 104 590-703 178-294 (403)
342 cd08485 PBP2_ClcR The C-termin 66.6 1.2E+02 0.0026 28.8 17.6 70 401-482 14-83 (198)
343 PRK03601 transcriptional regul 66.5 1.6E+02 0.0035 30.3 15.2 84 373-482 88-171 (275)
344 cd08187 BDH Butanol dehydrogen 66.2 26 0.00056 38.4 8.8 87 61-148 18-107 (382)
345 cd08446 PBP2_Chlorocatechol Th 66.2 1.2E+02 0.0026 28.6 17.8 70 401-482 14-83 (198)
346 cd08182 HEPD Hydroxyethylphosp 66.1 28 0.00061 37.9 9.0 86 61-149 12-99 (367)
347 cd08431 PBP2_HupR The C-termin 66.1 1.2E+02 0.0026 28.6 15.5 71 401-482 13-83 (195)
348 cd07766 DHQ_Fe-ADH Dehydroquin 65.6 76 0.0016 33.9 12.2 100 61-165 12-113 (332)
349 cd06305 PBP1_methylthioribose_ 64.5 27 0.00059 35.8 8.3 77 75-154 2-81 (273)
350 PLN03192 Voltage-dependent pot 64.4 4.7 0.0001 49.3 2.8 55 530-584 249-305 (823)
351 cd08186 Fe-ADH8 Iron-containin 63.9 32 0.00069 37.7 9.0 89 61-149 12-106 (383)
352 cd08171 GlyDH-like2 Glycerol d 63.9 27 0.00059 37.6 8.3 86 61-148 12-99 (345)
353 PF07302 AroM: AroM protein; 63.9 50 0.0011 32.6 9.2 115 24-150 83-201 (221)
354 cd06276 PBP1_FucR_like Ligand- 63.8 76 0.0017 32.1 11.3 122 20-160 68-192 (247)
355 cd01537 PBP1_Repressors_Sugar_ 63.8 24 0.00052 35.7 7.7 77 75-154 2-80 (264)
356 PRK13583 hisG ATP phosphoribos 63.1 72 0.0016 31.8 10.2 92 590-691 110-212 (228)
357 cd06301 PBP1_rhizopine_binding 62.2 28 0.0006 35.7 7.9 78 74-154 1-82 (272)
358 cd06267 PBP1_LacI_sugar_bindin 62.1 31 0.00067 34.9 8.2 76 75-154 2-79 (264)
359 cd08432 PBP2_GcdR_TrpI_HvrB_Am 62.0 1.1E+02 0.0023 28.7 11.6 66 401-481 13-78 (194)
360 PRK14498 putative molybdopteri 61.9 83 0.0018 37.2 12.5 67 70-139 184-262 (633)
361 cd06353 PBP1_BmpA_Med_like Per 61.3 58 0.0013 33.4 9.8 85 74-166 1-89 (258)
362 PRK03692 putative UDP-N-acetyl 61.0 83 0.0018 31.9 10.5 89 56-151 90-179 (243)
363 PRK11119 proX glycine betaine 60.9 65 0.0014 34.4 10.3 63 370-455 25-88 (331)
364 PRK09423 gldA glycerol dehydro 60.5 30 0.00066 37.6 8.0 97 61-165 19-117 (366)
365 cd08452 PBP2_AlsR The C-termin 59.3 1.6E+02 0.0035 27.8 18.0 70 401-482 13-82 (197)
366 cd08428 PBP2_IciA_ArgP The C-t 59.3 1.6E+02 0.0034 27.7 16.5 66 403-481 15-80 (195)
367 PRK10677 modA molybdate transp 59.0 81 0.0017 32.3 10.4 71 403-482 41-117 (257)
368 PRK09906 DNA-binding transcrip 58.7 2.3E+02 0.005 29.4 18.0 70 401-482 103-172 (296)
369 cd06306 PBP1_TorT-like TorT-li 58.5 35 0.00075 35.0 7.8 79 75-154 2-82 (268)
370 cd08183 Fe-ADH2 Iron-containin 57.4 48 0.001 36.2 8.9 83 61-148 12-96 (374)
371 PRK10537 voltage-gated potassi 57.3 8.8 0.00019 42.0 3.1 54 527-580 164-219 (393)
372 cd06289 PBP1_MalI_like Ligand- 57.2 44 0.00095 34.0 8.3 77 75-154 2-80 (268)
373 PF04273 DUF442: Putative phos 56.8 1.3E+02 0.0029 26.1 10.6 83 67-149 23-106 (110)
374 TIGR00035 asp_race aspartate r 56.7 21 0.00045 35.9 5.5 40 62-104 107-146 (229)
375 cd06282 PBP1_GntR_like_2 Ligan 56.6 48 0.001 33.7 8.5 77 75-154 2-80 (266)
376 cd06353 PBP1_BmpA_Med_like Per 56.4 81 0.0018 32.3 10.0 143 2-153 55-200 (258)
377 TIGR00070 hisG ATP phosphoribo 55.6 44 0.00095 32.0 7.1 76 590-678 100-175 (182)
378 cd01538 PBP1_ABC_xylose_bindin 55.2 56 0.0012 33.9 8.8 77 75-154 2-81 (288)
379 cd06277 PBP1_LacI_like_1 Ligan 54.9 61 0.0013 33.1 9.0 75 75-154 2-81 (268)
380 PF14981 FAM165: FAM165 family 54.8 28 0.0006 24.3 3.9 33 738-770 3-35 (51)
381 PRK09756 PTS system N-acetylga 54.7 69 0.0015 30.0 8.1 80 59-147 17-97 (158)
382 TIGR00854 pts-sorbose PTS syst 54.3 62 0.0013 30.0 7.7 80 60-147 14-93 (151)
383 PF01102 Glycophorin_A: Glycop 54.3 22 0.00048 31.4 4.4 30 742-771 65-94 (122)
384 cd08550 GlyDH-like Glycerol_de 54.2 48 0.001 35.8 8.1 84 61-147 12-97 (349)
385 cd06303 PBP1_LuxPQ_Quorum_Sens 54.0 37 0.0008 35.1 7.1 79 75-153 2-84 (280)
386 cd06322 PBP1_ABC_sugar_binding 54.0 52 0.0011 33.5 8.2 77 75-154 2-81 (267)
387 cd00001 PTS_IIB_man PTS_IIB, P 53.9 63 0.0014 30.0 7.7 81 60-148 13-93 (151)
388 cd08422 PBP2_CrgA_like The C-t 53.8 78 0.0017 29.7 9.1 66 401-481 14-79 (197)
389 PF03830 PTSIIB_sorb: PTS syst 52.8 25 0.00055 32.6 4.9 81 60-148 14-94 (151)
390 cd01391 Periplasmic_Binding_Pr 52.6 49 0.0011 33.1 7.8 77 75-154 2-83 (269)
391 PRK15408 autoinducer 2-binding 52.4 69 0.0015 34.4 9.0 82 71-154 22-106 (336)
392 PRK09986 DNA-binding transcrip 52.4 2.8E+02 0.0062 28.6 18.0 85 374-482 97-181 (294)
393 cd01536 PBP1_ABC_sugar_binding 52.0 58 0.0013 33.0 8.2 77 74-153 1-80 (267)
394 cd06310 PBP1_ABC_sugar_binding 51.8 53 0.0012 33.6 7.9 80 74-154 1-83 (273)
395 PRK11425 PTS system N-acetylga 51.0 78 0.0017 29.6 7.9 80 59-147 15-94 (157)
396 cd06318 PBP1_ABC_sugar_binding 50.9 56 0.0012 33.7 7.9 77 75-154 2-81 (282)
397 cd06312 PBP1_ABC_sugar_binding 50.7 57 0.0012 33.4 7.9 79 74-154 1-83 (271)
398 cd06299 PBP1_LacI_like_13 Liga 50.4 74 0.0016 32.3 8.7 76 75-154 2-79 (265)
399 cd08178 AAD_C C-terminal alcoh 50.4 61 0.0013 35.7 8.3 79 70-148 19-99 (398)
400 PRK14737 gmk guanylate kinase; 49.8 2E+02 0.0044 27.6 11.0 128 3-153 4-138 (186)
401 PRK00945 acetyl-CoA decarbonyl 49.2 83 0.0018 29.8 7.7 113 3-126 35-168 (171)
402 PRK07377 hypothetical protein; 48.6 43 0.00094 31.6 5.6 62 373-451 74-135 (184)
403 PRK11139 DNA-binding transcrip 48.4 3.3E+02 0.0072 28.2 14.0 63 404-481 110-172 (297)
404 PRK13348 chromosome replicatio 48.4 3.3E+02 0.0072 28.2 15.2 65 405-482 107-171 (294)
405 PRK01686 hisG ATP phosphoribos 47.9 2.8E+02 0.0061 27.5 11.5 92 601-704 115-208 (215)
406 cd06167 LabA_like LabA_like pr 47.4 2.2E+02 0.0048 25.9 11.8 92 62-154 28-124 (149)
407 cd06281 PBP1_LacI_like_5 Ligan 47.2 88 0.0019 31.9 8.7 76 75-153 2-79 (269)
408 PRK00002 aroB 3-dehydroquinate 46.9 1.6E+02 0.0035 31.8 10.8 101 61-165 20-127 (358)
409 TIGR03298 argP transcriptional 46.6 3.5E+02 0.0076 27.9 15.6 65 404-481 106-170 (292)
410 cd08175 G1PDH Glycerol-1-phosp 46.2 79 0.0017 34.1 8.3 98 61-165 12-113 (348)
411 PRK10200 putative racemase; Pr 46.2 88 0.0019 31.4 8.0 71 4-103 75-146 (230)
412 PF13380 CoA_binding_2: CoA bi 46.1 29 0.00063 30.5 4.1 86 73-165 1-88 (116)
413 cd01324 cbb3_Oxidase_CcoQ Cyto 45.5 18 0.00038 26.1 2.1 29 496-524 11-39 (48)
414 cd01545 PBP1_SalR Ligand-bindi 45.4 88 0.0019 31.8 8.3 78 75-154 2-81 (270)
415 cd06317 PBP1_ABC_sugar_binding 45.0 85 0.0018 32.0 8.2 77 75-154 2-82 (275)
416 TIGR00315 cdhB CO dehydrogenas 44.9 1.1E+02 0.0025 28.6 7.9 115 3-126 28-160 (162)
417 PRK10014 DNA-binding transcrip 44.7 1.2E+02 0.0025 32.4 9.4 79 73-154 65-145 (342)
418 TIGR00249 sixA phosphohistidin 44.5 1.3E+02 0.0029 27.8 8.4 98 52-150 23-120 (152)
419 TIGR03414 ABC_choline_bnd chol 44.4 2.2E+02 0.0048 29.7 11.0 40 404-452 24-63 (290)
420 COG3340 PepE Peptidase E [Amin 43.6 2E+02 0.0044 28.2 9.4 85 60-154 21-107 (224)
421 PRK11303 DNA-binding transcrip 43.1 1.3E+02 0.0029 31.7 9.5 80 72-154 61-142 (328)
422 PRK10936 TMAO reductase system 42.9 1E+02 0.0023 33.0 8.7 81 72-154 46-129 (343)
423 cd06320 PBP1_allose_binding Pe 42.9 87 0.0019 32.1 7.8 79 75-154 2-83 (275)
424 KOG3713 Voltage-gated K+ chann 42.7 28 0.0006 38.3 3.9 62 507-572 357-420 (477)
425 cd01540 PBP1_arabinose_binding 42.5 83 0.0018 32.5 7.7 76 75-154 2-80 (289)
426 cd06295 PBP1_CelR Ligand bindi 42.4 1.3E+02 0.0028 30.8 9.0 78 71-154 2-88 (275)
427 cd06270 PBP1_GalS_like Ligand 42.3 1.2E+02 0.0027 30.8 8.8 76 75-154 2-79 (268)
428 cd02071 MM_CoA_mut_B12_BD meth 42.3 2E+02 0.0044 25.3 9.0 62 87-154 14-79 (122)
429 cd08197 DOIS 2-deoxy-scyllo-in 42.2 2.5E+02 0.0055 30.3 11.3 100 62-165 13-119 (355)
430 PF08374 Protocadherin: Protoc 42.1 39 0.00084 32.8 4.3 36 735-770 31-66 (221)
431 cd06315 PBP1_ABC_sugar_binding 41.4 1.3E+02 0.0028 31.1 8.8 79 73-154 1-82 (280)
432 cd06296 PBP1_CatR_like Ligand- 41.4 1.2E+02 0.0025 30.9 8.5 76 75-154 2-79 (270)
433 PF02608 Bmp: Basic membrane p 41.2 1.4E+02 0.0031 31.4 9.2 88 73-167 2-94 (306)
434 PRK10355 xylF D-xylose transpo 41.2 1.2E+02 0.0026 32.4 8.7 80 72-154 25-107 (330)
435 cd06319 PBP1_ABC_sugar_binding 40.5 99 0.0021 31.6 7.8 77 75-154 2-81 (277)
436 COG3181 Uncharacterized protei 40.5 3.4E+02 0.0074 28.7 11.3 124 587-715 130-284 (319)
437 cd06300 PBP1_ABC_sugar_binding 40.5 1.1E+02 0.0023 31.3 8.1 80 74-154 1-86 (272)
438 cd01542 PBP1_TreR_like Ligand- 40.5 1.3E+02 0.0027 30.4 8.5 75 75-153 2-78 (259)
439 PRK10653 D-ribose transporter 40.3 1.2E+02 0.0025 31.7 8.4 80 72-154 26-108 (295)
440 PF00072 Response_reg: Respons 40.1 1.9E+02 0.0041 24.4 8.4 74 77-164 2-78 (112)
441 PF15179 Myc_target_1: Myc tar 40.1 41 0.00089 31.5 4.0 38 733-770 13-51 (197)
442 COG0134 TrpC Indole-3-glycerol 40.0 54 0.0012 33.1 5.2 88 61-156 69-159 (254)
443 PF01745 IPT: Isopentenyl tran 39.7 21 0.00046 34.9 2.3 31 4-34 2-32 (233)
444 PRK09189 uroporphyrinogen-III 39.6 98 0.0021 31.2 7.4 89 57-151 101-191 (240)
445 cd08481 PBP2_GcdR_like The C-t 39.5 3E+02 0.0064 25.6 10.7 64 403-481 15-78 (194)
446 cd06302 PBP1_LsrB_Quorum_Sensi 39.5 1.1E+02 0.0023 32.1 7.9 78 75-154 2-82 (298)
447 PRK05452 anaerobic nitric oxid 39.4 4.2E+02 0.0092 30.0 13.0 140 8-167 198-348 (479)
448 cd08177 MAR Maleylacetate redu 39.4 82 0.0018 33.8 7.1 97 61-165 12-110 (337)
449 cd06273 PBP1_GntR_like_1 This 39.0 1.4E+02 0.003 30.3 8.6 76 75-154 2-79 (268)
450 cd06315 PBP1_ABC_sugar_binding 39.0 4.4E+02 0.0096 26.9 15.6 132 22-157 75-216 (280)
451 PRK09701 D-allose transporter 38.7 1.4E+02 0.003 31.5 8.7 85 69-154 21-108 (311)
452 cd06323 PBP1_ribose_binding Pe 38.3 1.1E+02 0.0024 31.0 7.7 77 75-154 2-81 (268)
453 cd06285 PBP1_LacI_like_7 Ligan 38.3 1.5E+02 0.0033 29.9 8.8 76 75-154 2-79 (265)
454 cd08180 PDD 1,3-propanediol de 38.2 77 0.0017 33.9 6.6 78 68-146 18-97 (332)
455 cd08179 NADPH_BDH NADPH-depend 38.2 75 0.0016 34.7 6.7 79 70-148 21-102 (375)
456 COG0563 Adk Adenylate kinase a 38.1 74 0.0016 30.5 5.8 28 6-33 3-30 (178)
457 cd06278 PBP1_LacI_like_2 Ligan 37.9 1.4E+02 0.003 30.2 8.4 75 75-154 2-78 (266)
458 cd08549 G1PDH_related Glycerol 37.8 1.4E+02 0.003 31.9 8.5 98 61-165 12-113 (332)
459 PRK10481 hypothetical protein; 37.7 3.1E+02 0.0068 27.3 10.1 75 64-142 120-195 (224)
460 TIGR02667 moaB_proteo molybden 37.6 1.5E+02 0.0032 27.9 7.6 65 72-138 4-72 (163)
461 PF02602 HEM4: Uroporphyrinoge 37.6 61 0.0013 32.4 5.5 92 53-151 97-189 (231)
462 cd01539 PBP1_GGBP Periplasmic 37.5 1.3E+02 0.0029 31.4 8.3 77 75-154 2-83 (303)
463 cd08184 Fe-ADH3 Iron-containin 37.3 1.5E+02 0.0034 31.8 8.7 84 61-148 12-102 (347)
464 TIGR02417 fruct_sucro_rep D-fr 37.3 1.4E+02 0.0031 31.5 8.6 80 72-154 60-141 (327)
465 COG2358 Imp TRAP-type uncharac 37.0 1.2E+02 0.0025 32.1 7.3 78 589-674 127-214 (321)
466 cd06274 PBP1_FruR Ligand bindi 36.9 1.5E+02 0.0033 29.9 8.6 76 75-154 2-79 (264)
467 cd01575 PBP1_GntR Ligand-bindi 36.5 1.4E+02 0.0031 30.1 8.3 76 75-154 2-79 (268)
468 cd06321 PBP1_ABC_sugar_binding 36.5 1.3E+02 0.0029 30.5 8.1 77 75-154 2-83 (271)
469 cd06271 PBP1_AglR_RafR_like Li 36.4 1.4E+02 0.003 30.2 8.1 76 75-154 2-83 (268)
470 cd06324 PBP1_ABC_sugar_binding 36.1 1.3E+02 0.0028 31.6 7.9 77 75-154 2-83 (305)
471 PRK13957 indole-3-glycerol-pho 35.8 2.4E+02 0.0053 28.5 9.2 88 61-156 64-154 (247)
472 cd06283 PBP1_RegR_EndR_KdgR_li 35.4 1.7E+02 0.0038 29.5 8.7 76 75-154 2-79 (267)
473 cd08173 Gro1PDH Sn-glycerol-1- 34.9 1.4E+02 0.003 32.0 8.0 95 62-165 14-111 (339)
474 cd00338 Ser_Recombinase Serine 34.2 3.4E+02 0.0073 24.1 10.8 75 55-153 15-95 (137)
475 cd06316 PBP1_ABC_sugar_binding 34.1 1.3E+02 0.0029 31.1 7.7 79 74-154 1-82 (294)
476 TIGR02637 RhaS rhamnose ABC tr 33.5 1.4E+02 0.0029 31.2 7.6 77 76-154 2-82 (302)
477 PF04971 Lysis_S: Lysis protei 33.4 48 0.001 25.6 2.8 32 743-774 33-64 (68)
478 cd06298 PBP1_CcpA_like Ligand- 33.4 1.7E+02 0.0037 29.6 8.2 75 75-153 2-78 (268)
479 PLN02727 NAD kinase 33.4 3.1E+02 0.0068 33.3 10.7 108 39-150 253-362 (986)
480 TIGR02976 phageshock_pspB phag 33.3 25 0.00055 28.0 1.4 18 754-771 13-30 (75)
481 cd06294 PBP1_ycjW_transcriptio 33.2 1.8E+02 0.0039 29.4 8.4 69 82-154 16-84 (270)
482 cd08472 PBP2_CrgA_like_3 The C 33.2 4.1E+02 0.0088 24.8 11.0 66 401-481 14-79 (202)
483 PF02310 B12-binding: B12 bind 33.2 1.3E+02 0.0028 26.3 6.2 72 60-139 17-89 (121)
484 cd08439 PBP2_LrhA_like The C-t 32.7 1.3E+02 0.0028 28.1 6.8 68 401-482 13-80 (185)
485 PF00218 IGPS: Indole-3-glycer 32.6 2E+02 0.0044 29.3 8.1 89 60-156 70-161 (254)
486 cd00886 MogA_MoaB MogA_MoaB fa 32.6 1.8E+02 0.0039 26.9 7.3 63 74-138 2-70 (152)
487 cd08169 DHQ-like Dehydroquinat 32.5 4.1E+02 0.0088 28.6 11.0 101 61-165 12-118 (344)
488 PF13671 AAA_33: AAA domain; P 32.5 37 0.0008 30.8 2.7 32 5-36 1-32 (143)
489 cd03174 DRE_TIM_metallolyase D 32.4 1.9E+02 0.0042 29.5 8.4 37 2-38 6-42 (265)
490 PF12273 RCR: Chitin synthesis 32.3 45 0.00098 30.0 3.1 27 743-769 3-29 (130)
491 PF05545 FixQ: Cbb3-type cytoc 32.3 30 0.00065 25.0 1.6 30 496-525 10-39 (49)
492 PRK00843 egsA NAD(P)-dependent 32.2 2.8E+02 0.006 29.9 9.7 96 61-165 22-120 (350)
493 cd03364 TOPRIM_DnaG_primases T 32.1 74 0.0016 25.5 4.1 40 64-104 36-75 (79)
494 cd07939 DRE_TIM_NifV Streptomy 32.1 5.6E+02 0.012 26.1 12.2 25 11-35 16-40 (259)
495 PRK12595 bifunctional 3-deoxy- 31.9 6E+02 0.013 27.5 12.0 70 4-79 118-190 (360)
496 PRK00865 glutamate racemase; P 31.8 2.6E+02 0.0056 28.7 9.0 31 3-33 66-96 (261)
497 PRK13010 purU formyltetrahydro 31.8 6.2E+02 0.013 26.4 14.4 91 4-100 10-118 (289)
498 cd06292 PBP1_LacI_like_10 Liga 31.6 2.2E+02 0.0048 28.9 8.7 77 75-154 2-84 (273)
499 PRK14987 gluconate operon tran 31.6 2.1E+02 0.0045 30.3 8.8 78 73-154 64-143 (331)
500 PLN02428 lipoic acid synthase 31.6 3.4E+02 0.0074 29.1 9.9 115 46-163 121-256 (349)
No 1
>KOG1054 consensus Glutamate-gated AMPA-type ion channel receptor subunit GluR2 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=9.9e-89 Score=696.62 Aligned_cols=722 Identities=20% Similarity=0.335 Sum_probs=592.8
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
.+||.||+|-+.-.....+..+|+.+++|+|+++. |. +...++.+++.|+-. .++++++.||+|.+++.+| |
T Consensus 88 s~Gv~Aifg~yd~ks~~~ltsfc~aLh~~~vtpsf--p~--~~~~~Fviq~RP~l~---~al~s~i~hy~W~~fv~ly-D 159 (897)
T KOG1054|consen 88 SRGVYAIFGFYDKKSVNTLTSFCGALHVSFVTPSF--PT--DGDNQFVIQMRPALK---GALLSLIDHYKWEKFVYLY-D 159 (897)
T ss_pred hhhHhhheecccccchhhhhhhccceeeeeecccC--Cc--CCCceEEEEeCchHH---HHHHHHHHhcccceEEEEE-c
Confidence 46899999999999999999999999999999755 32 234467888888654 8999999999999999999 7
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
.+.|...++.+.+.+.+++..|.....-.. .+..+++.+++.+...+.+.|++.|..+....++.++.+.+-...+|++
T Consensus 160 ~~rg~s~Lqai~~~a~~~nw~VtA~~v~~~-~d~~~yr~~f~~l~~r~e~rv~iDce~~~~~~il~q~i~~~k~~~~YHY 238 (897)
T KOG1054|consen 160 TDRGLSILQAIMEAAAQNNWQVTAINVGNI-NDVKEYRMLFEMLDRRQENRVLIDCESERRNRILLQVIELGKHVKGYHY 238 (897)
T ss_pred ccchHHHHHHHHHHHHhcCceEEEEEcCCc-ccHHHHHHHHHHHhccccceEEEEcccHHHHHHHHHHHHHhhhccceEE
Confidence 778999999999999999999987655443 3456699999999999999999999999999999999998888899999
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhc---CCCCCCCccchhHHHhhHHHHHHHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKY---KENSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~---~~~~~~~~~~~~~~~YDav~~la~A 238 (834)
+..+..-...|. ........++.+++...-+++..++|.++|++.-. ++.+..++.+.++.+|||+.+.++|
T Consensus 239 vlaNl~f~d~dl-----~~f~~g~aNitgFqivn~~~~~~~k~~~~~~~l~~~~~~g~~~~~~k~tsAlthDailV~~ea 313 (897)
T KOG1054|consen 239 VLANLGFTDIDL-----ERFQHGGANITGFQIVNKNNPMVKKFIQRWKELDEREYPGASNDPIKYTSALTHDAILVMAEA 313 (897)
T ss_pred EEeeCCCchhhH-----HHHhcCCcceeEEEEecCCChHHHHHHHHHhhhcccccCCCCCCCcchhhhhhhhHHHHHHHH
Confidence 997632221111 23444556789999999999999999999987543 3444467788899999999999999
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeeccce
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGGTGS 318 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~~~~ 318 (834)
+..+.++..++..+ +.+|+++ -.+..+|.+|..+-++++++.++|+||+|+||..|.|.+...+|+++..++.
T Consensus 314 f~~~~~q~~~~~rR------G~~GD~~-an~~~p~~qG~~I~ralk~v~~eGLTGniqFd~~G~R~Nyt~~i~elk~~~~ 386 (897)
T KOG1054|consen 314 FRSLRRQRIDISRR------GNAGDCL-ANPAVPWEQGIDIERALKQVQVEGLTGNIQFDKYGRRTNYTIDIVELKSNGS 386 (897)
T ss_pred HHHHHHhhhchhcc------CCCcccc-CCCCCchhcchhHHHHHHheeecccccceeecccCccccceEEEEEeccCCc
Confidence 99988775444322 2244432 2347799999999999999999999999999999999999999999999999
Q ss_pred EEEEEecCCCCcccccccccccCCCCCCCCCccceeeecCCccccCcccccCCCCCceEEEecCccccccceecc---CC
Q 003275 319 RRIGYWSNYSGLSVVAPEILYTKPPNSSSNRHLYSVIWPGEITATPRGWVFPNNGMPLRIAVPNRVSYNEFVAKD---KS 395 (834)
Q Consensus 319 ~~vG~w~~~~gl~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~pr~~~~~~~g~~lrv~~~~~~~~~p~~~~~---~~ 395 (834)
+++|+|....|+....... ..+ +... ..+.++..|.+....||..+.... .+
T Consensus 387 rk~~~W~e~~~fv~~~t~a-~~~--~d~~----------------------~~~n~tvvvttiL~spyvm~kkn~~~~eg 441 (897)
T KOG1054|consen 387 RKVGYWNEGEGFVPGSTVA-QSR--NDQA----------------------SKENRTVVVTTILESPYVMLKKNHEQLEG 441 (897)
T ss_pred ceeeeecccCceeeccccc-ccc--cccc----------------------ccccceEEEEEecCCchhHHHhhHHHhcC
Confidence 9999999998865332210 000 0000 011233444443333443332221 26
Q ss_pred CCceeeeeHHHHHHHHHhCCCCcCEEEEe---cCCCCCCCC-hHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeee
Q 003275 396 PPGVKGYCIDVFEAAVNLLPYPVPHNYIM---YGNGKRNPI-YNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYME 471 (834)
Q Consensus 396 ~~~~~G~~~dll~~l~~~l~~~~~~~~~~---~~~~~~n~s-~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~ 471 (834)
+.++.|||+||+.+||++.++++++..+. +|..+..++ |+||++.|..|++|+++++++||..|++.+|||.|++.
T Consensus 442 n~ryEGyCvdLa~~iAkhi~~~Y~l~iv~dgkyGardaD~k~WnGMvGeLv~grAdiavApLTIt~~REeviDFSKPfMs 521 (897)
T KOG1054|consen 442 NERYEGYCVDLAAEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMS 521 (897)
T ss_pred CcccceeHHHHHHHHHHhcCceEEEEEecCCcccccCCCcccccchhHHHhcCccceEEeeeeeehhhhhhhccccchhh
Confidence 78999999999999999999874444443 233335566 99999999999999999999999999999999999999
Q ss_pred ceEEEEEecCC-CCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCC-------------CCcchhhHHH
Q 003275 472 SGLVVVAPVQK-LKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGP-------------PSQQLVTIFW 537 (834)
Q Consensus 472 ~~~~~vv~~~~-~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~-------------~~~~~~~~~~ 537 (834)
.|+.+|++++. ..++.+.|+.|+..++|+|++..++-+++++++..|.++.||+-. ...++.+++|
T Consensus 522 lGISIMIKKPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~Ee~~rg~~t~~~~~NeFgifNsLW 601 (897)
T KOG1054|consen 522 LGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFERGRFTPSDPPNEFGIFNSLW 601 (897)
T ss_pred cCeEEEEeCcccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEeccCchheeccccccCCCCCCCCCccchhhHHHH
Confidence 99999999987 678999999999999999999999999999999999988765321 2356899999
Q ss_pred HHHHHhhccCCC-cccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCC-CeeEeeCchhhHH
Q 003275 538 FSFSTMFFSHRE-NTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTE-PIGVQDGSFAWNY 615 (834)
Q Consensus 538 ~~~~~l~~~~~~-~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~-~v~~~~~s~~~~~ 615 (834)
|+++++++|+-. .|||.++|++..+||||+|||+++|||||++|||+.++.+||+|.|||.+|.+ ..|+..+....+|
T Consensus 602 FsLgAFMQQG~DI~PRslSGRIvggvWWFFTlIIiSSYTANLAAFLTvErMvsPIESaEDLAkQteIaYGt~~~GSTkeF 681 (897)
T KOG1054|consen 602 FSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEF 681 (897)
T ss_pred HHHHHHHhcCCCCCccccccceeccchhhhhhhhhhhhhhHHHHHHhHHhhcCcchhHHHHhhcceeeeeecCCCchHHH
Confidence 999999999855 89999999999999999999999999999999999999999999999998876 3677777777777
Q ss_pred HHhhhcccccce----------EecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCcccccceEEE
Q 003275 616 LVDELKIAESRL----------VKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQEFTKSGWGFA 685 (834)
Q Consensus 616 l~~~~~~~~~~~----------~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~ 685 (834)
+++..-.--.++ +-..+..|.++.+++. .+.+|++.+...-+|..++.+|+-..|+..+.+.+||+|
T Consensus 682 Fr~Skiavy~kMW~yM~SaepsVFv~t~aeGv~rVRks---KGkyAfLLEsTmNey~eqRkPCDTMKVGgNLds~GYGiA 758 (897)
T KOG1054|consen 682 FRRSKIAVYEKMWTYMKSAEPSVFVRTTAEGVARVRKS---KGKYAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIA 758 (897)
T ss_pred HhhhhHHHHHHHHHHHhcCCcceeeehhhhHHHHHHhc---CCceEeehHhhhhhhhhccCCccceecccccCCcceeec
Confidence 754210000111 2246788999999874 677899999888888887778999999999999999999
Q ss_pred EcCCCcchHHHHHHHHhhhccccHHHHHHhhcC-CCCCCCCCCCCCCCCCcccccchhHHHHHHHHHHHHHHHHHHHHHH
Q 003275 686 FQRDSPLAIDLSTAILQLSENGDLQKIHNKWLT-YNECSMDLSPADGGGSRLSLKSFWGLFLICGIACFLALIFFFCRVC 764 (834)
Q Consensus 686 ~~k~spl~~~~~~~i~~l~e~G~~~~i~~kw~~-~~~c~~~~~~~~~~~~~l~l~~~~g~f~il~~g~~lal~vf~~e~~ 764 (834)
.||||.|+..+|.+++.|.|.|+++++++|||. ++.|........+....|+|.+++|+||||..|++||+++.++|+|
T Consensus 759 Tp~Gsslr~~vNLAvLkL~E~G~LdKLkNKWWYDkGeC~sg~~ds~~ktsaLsLSnVAGvFYIL~gGl~laMlvALiEF~ 838 (897)
T KOG1054|consen 759 TPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGSGGGDSKDKTSALSLSNVAGVFYILVGGLGLAMLVALIEFC 838 (897)
T ss_pred CCCCcccccchhhhhhhhcccchHHHhhhhhcccccccCCCCCCCCcchhhcchhhccceeeeehhhHHHHHHHHHHHHH
Confidence 999999999999999999999999999999998 8999987766655678999999999999999999999999999999
Q ss_pred HHhhccCC
Q 003275 765 GQFRRFGS 772 (834)
Q Consensus 765 ~~~~~~~~ 772 (834)
|+.+...+
T Consensus 839 yksr~Eak 846 (897)
T KOG1054|consen 839 YKSRAEAK 846 (897)
T ss_pred HHhhHHHH
Confidence 98876543
No 2
>KOG4440 consensus NMDA selective glutamate-gated ion channel receptor subunit GRIN1 [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1.8e-78 Score=623.93 Aligned_cols=672 Identities=24% Similarity=0.410 Sum_probs=563.6
Q ss_pred HHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHH
Q 003275 18 HVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDAL 96 (834)
Q Consensus 18 ~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l 96 (834)
.+++-.+.-+++|++.....+..+++ .-++.|+|++|+.++|+..-..++.+|.|++|+++.+||.-|+.....++..+
T Consensus 114 ~~vSYT~gFY~iPV~G~~~Rda~fSdKnIh~sFlRtvpPyshqa~VwleMl~~~~y~~vi~l~s~d~~gra~~~r~qt~~ 193 (993)
T KOG4440|consen 114 TPVSYTAGFYRIPVLGLTTRDAIFSDKNIHLSFLRTVPPYSHQASVWLEMLRVYSYNHVILLVSDDHEGRAAQKRLQTLL 193 (993)
T ss_pred ccceeeccceeeeeeeeeehhhhhccCceeeeEeecCCCccchhHHHHHHHHHhhcceEEEEEcccccchhHHhHHHHHH
Confidence 34455678899999999999999999 56899999999999999999999999999999999999998988888888888
Q ss_pred hcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEEeCCCcccCCCCCC
Q 003275 97 SKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIATDWLPSVLDSTEP 176 (834)
Q Consensus 97 ~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~~~~~~~~~~~~~~ 176 (834)
++...++.....+.++. .+++..|-.+|..++||+++..+.+++..+++.|.+++|++.|||||++......
T Consensus 194 e~~~~~~e~v~~f~p~~--~~~t~~l~~~k~~~~rv~~~~as~dDA~~ifr~Ag~lnmTG~G~VWiV~E~a~~~------ 265 (993)
T KOG4440|consen 194 EERESKAEKVLQFDPGT--KNVTALLMEAKELEARVIILSASEDDAATIFRAAGMLNMTGSGYVWIVGERAISG------ 265 (993)
T ss_pred HHHhhhhhhheecCccc--chHHHHHhhhhhhhheeEEeecccchHHHHHHhhhhhcccCceEEEEEecccccc------
Confidence 87777766666676654 7899999999999999999999999999999999999999999999998643221
Q ss_pred CChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCC
Q 003275 177 VDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPK 256 (834)
Q Consensus 177 ~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~ 256 (834)
....+|++|++.-...+ ..+..-|+|.++|.|+++++.+..-.
T Consensus 266 -----nn~PdG~LGlqL~~~~~-------------------------~~~hirDsv~vlasAv~e~~~~e~I~------- 308 (993)
T KOG4440|consen 266 -----NNLPDGILGLQLINGKN-------------------------ESAHIRDSVGVLASAVHELLEKENIT------- 308 (993)
T ss_pred -----CCCCCceeeeEeecCcc-------------------------ccceehhhHHHHHHHHHHHHhhccCC-------
Confidence 13467999987743211 12346799999999999998753321
Q ss_pred CCCCCCCCccCCCccccCchHHHHHHHHhc-ccccceeeEEEccCCCCCCCcEEEEEe-eccceEEEEEecCCCCccccc
Q 003275 257 LHDTNGSMLNLSSLRVFDGGQQFLQTLLRM-NFTGLSGEIRFDADKNLVNPAYDVLNI-GGTGSRRIGYWSNYSGLSVVA 334 (834)
Q Consensus 257 ~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~-~f~g~tG~i~Fd~~g~~~~~~~~I~~~-~~~~~~~vG~w~~~~gl~~~~ 334 (834)
..+..||++..+|..|..|.+.+... .-.|.||++.||++||+....|+|+|+ ++.....+|.|+.. .+.
T Consensus 309 ----~~P~~c~d~~~~w~~g~~l~~~l~s~~~~~g~TgrV~Fnd~gdRi~a~YdiiN~hq~rk~Vg~~~yd~~---r~~- 380 (993)
T KOG4440|consen 309 ----DPPRGCVDNTNIWKTGPLLKRVLMSSKYADGVTGRVEFNDDGDRIFANYDIINLHQNRKLVGVGIYDGT---RVI- 380 (993)
T ss_pred ----CCCCcccCccchhcccHHHHHHHhhhcccCCcceeEEEcCCCceeeccceeEehhhhhhhhhhccccce---eec-
Confidence 12345778888999999999888764 567999999999999999999999999 45555566666432 222
Q ss_pred ccccccCCCCCCCCCccceeeecCCccccCcccccCCCCCceEEEecCccccccceeccC--------------------
Q 003275 335 PEILYTKPPNSSSNRHLYSVIWPGEITATPRGWVFPNNGMPLRIAVPNRVSYNEFVAKDK-------------------- 394 (834)
Q Consensus 335 ~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~pr~~~~~~~g~~lrv~~~~~~~~~p~~~~~~-------------------- 394 (834)
.+-+.|+|||+-++.|++..+| ++|||.+.+.+| |+|...
T Consensus 381 --------------~nd~~IiWpGg~~~KP~gi~~p---thLrivTi~~~P---FVYv~p~~sd~~c~eef~~~~d~~~k 440 (993)
T KOG4440|consen 381 --------------PNDRKIIWPGGETEKPRGIQMP---THLRIVTIHQEP---FVYVKPTLSDGTCKEEFTVNGDPVKK 440 (993)
T ss_pred --------------cCCceeecCCCCcCCCcccccc---ceeEEEEeccCC---eEEEecCCCCcchhhhccccCCcccc
Confidence 1236899999999999999988 579999977754 444320
Q ss_pred -----------------CCCceeeeeHHHHHHHHHhCCCCcCEEEEecCC-CC----------CCCChHHHHHHHHhCcc
Q 003275 395 -----------------SPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGN-GK----------RNPIYNDIVQQVALNKF 446 (834)
Q Consensus 395 -----------------~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~-~~----------~n~s~~~~~~~l~~g~~ 446 (834)
..-|+.|||||++..+++.+||+++..+++.|. +. ....|+|++++|..|++
T Consensus 441 ~~c~gpn~s~p~s~~~t~~fCC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~A 520 (993)
T KOG4440|consen 441 VICTGPNDSSPGSPRHTVPFCCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQA 520 (993)
T ss_pred eeecCCCCCCCCCcccCcchhhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeecccccccceehhhhhhhhCCcc
Confidence 023678999999999999999997777777331 11 12369999999999999
Q ss_pred cEEeeeeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCC-CC
Q 003275 447 DAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNE-FR 525 (834)
Q Consensus 447 D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~-~~ 525 (834)
||++++++|+++|.++++||.||...|+.++.++..+.+....|++||+..+|++++++..+++++++++++.++.+ |.
T Consensus 521 DMivaplTINpERa~yieFskPfkYqGitILeKk~~r~Stl~SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPFgRFk 600 (993)
T KOG4440|consen 521 DMIVAPLTINPERAQYIEFSKPFKYQGITILEKKEIRRSTLDSFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPFGRFK 600 (993)
T ss_pred ceEeeceeeChhhhhheeccCcccccceEEEeeCCCCCchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999987643 22
Q ss_pred -------CCCCcchhhHHHHHHHHhhccC--CCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhh
Q 003275 526 -------GPPSQQLVTIFWFSFSTMFFSH--RENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDS 596 (834)
Q Consensus 526 -------~~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~d 596 (834)
.....+++..+||+|+.|+..+ ...|+|.+.|++-++|.=|++|+.++|||||++||...+.+..++++.|
T Consensus 601 ~~ds~~~ee~alnlssAmWF~WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTANLAAFLVLdrPe~~ltGinD 680 (993)
T KOG4440|consen 601 VNDSEEEEEDALNLSSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLDRPEERLTGIND 680 (993)
T ss_pred eccCccchhhhcchhhhHHHHhHhhhccccCCCCCcchhHHHHHHHHhhhheeeehhhhhhhhhheeecCccccccCCCC
Confidence 1234569999999999999886 4589999999999999999999999999999999999999999999998
Q ss_pred hhcCC----CCeeEeeCchhhHHHHhhhcccc--cce--EecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCc
Q 003275 597 LISST----EPIGVQDGSFAWNYLVDELKIAE--SRL--VKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNC 668 (834)
Q Consensus 597 L~~~~----~~v~~~~~s~~~~~l~~~~~~~~--~~~--~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~ 668 (834)
-.-.+ ...+...+|....|++++..... .++ ..|.+.+|.++++++ |+.+|++.|..-++|..++ +|
T Consensus 681 pRLRNps~nf~~aTVk~SsVd~YFrRqVELS~MyR~ME~hNy~~A~eAiq~v~~----gkL~AFIWDS~rLEfEAs~-~C 755 (993)
T KOG4440|consen 681 PRLRNPSDNFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRD----GKLHAFIWDSARLEFEASQ-KC 755 (993)
T ss_pred ccccCcccceeEEEecCccHHHHHHHHhHHHHHHHhhhhcchhhHHHHHHHHHc----CceeEEEeecceeeehhhc-cc
Confidence 44222 35778889999999976443221 111 236788899999999 9999999999999999888 99
Q ss_pred cEEEeCCcccccceEEEEcCCCcchHHHHHHHHhhhccccHHHHHHhhcC---CCCCCCCCCCCCCCCCcccccchhHHH
Q 003275 669 EFRTVGQEFTKSGWGFAFQRDSPLAIDLSTAILQLSENGDLQKIHNKWLT---YNECSMDLSPADGGGSRLSLKSFWGLF 745 (834)
Q Consensus 669 ~l~~v~~~~~~~~~~~~~~k~spl~~~~~~~i~~l~e~G~~~~i~~kw~~---~~~c~~~~~~~~~~~~~l~l~~~~g~f 745 (834)
++...|+.|..++||+.++|+||+.+.+..+|+++.|+|.|+++.++|.. +..|..... .+..|++++++|+|
T Consensus 756 eLvT~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~~hEsGfMEkLDk~Wi~~Ggpq~c~~~~k----~PatLgl~NMagvF 831 (993)
T KOG4440|consen 756 ELVTTGELFGRSGYGIGLQKDSPWTQNVTLAILKSHESGFMEKLDKTWIRYGGPQECDSRSK----APATLGLENMAGVF 831 (993)
T ss_pred ceEeccccccccccccccccCCCCcchhhHHHHHhhhcchHHHHHHHHHhcCCcchhhhhcc----CcccccccccccEE
Confidence 99999999999999999999999999999999999999999999999997 355554333 67899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccC
Q 003275 746 LICGIACFLALIFFFCRVCGQFRRFG 771 (834)
Q Consensus 746 ~il~~g~~lal~vf~~e~~~~~~~~~ 771 (834)
++.+.|++++++..++|+.|++++..
T Consensus 832 iLV~~Gia~GifLifiEv~Ykrh~~~ 857 (993)
T KOG4440|consen 832 ILVAGGIAAGIFLIFIEVAYKRHKDA 857 (993)
T ss_pred EEEecchhheeeEEEEeehhhhhhhh
Confidence 99999999999988999999887653
No 3
>KOG1053 consensus Glutamate-gated NMDA-type ion channel receptor subunit GRIN2A and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1e-73 Score=610.30 Aligned_cols=690 Identities=21% Similarity=0.395 Sum_probs=534.4
Q ss_pred CCcEEEECCCChh---hHHHHHHhhccCCccEEecccCCCC-CCCCC-CCceEEccCChHHHHHHHHHHHHHcCCeEEEE
Q 003275 3 NEVVAAIGPQSSG---IAHVISHVVNELNVPLLSFGATDPT-LTSLQ-YPYFLRTTQSDYYQMHAVADLVEYYGWREVIA 77 (834)
Q Consensus 3 ~~V~aiiGp~~S~---~~~~~~~~~~~~~vP~Is~~at~~~-ls~~~-~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~i 77 (834)
.+|.+|+=--.|. ++..+--+....+||+|+..+.+.. ++++. ...|+++.++-.+|++++.++++.|+|..+++
T Consensus 99 ~~V~glvf~d~s~~~avaq~LDfiSs~t~iPIisi~gg~a~~~~~kd~gs~flQlg~Sieqqa~Vml~iL~~ydW~~Fs~ 178 (1258)
T KOG1053|consen 99 ARVHGLVFEDDSDTEAVAQILDFISSQTHIPIISIHGGAAMVLTPKDLGSTFLQLGPSIEQQAQVMLKILEEYDWYNFSL 178 (1258)
T ss_pred cceeEEEeecCccchHHHHHHHHHHHhcCCcEEEEecCccceecCCCCcceEEEeCCcHHHHHHHHHHHHHHcCcceeEE
Confidence 3566655443443 3334444677889999998775544 44432 35799999999999999999999999999999
Q ss_pred EEEcCCcccchHHHHHHHHhcC--CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 78 IFVDDDYGRNGISVLGDALSKK--RAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 78 I~~d~~~g~~~~~~l~~~l~~~--g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
|...-+.-+..+..+++..... |.++.......+.. ++.......++++-++.||+++|+.+++..||+.|.++||+
T Consensus 179 vtt~~pg~~~f~~~ir~~~d~s~vgwe~i~v~~l~~s~-~d~~a~~q~qLkki~a~VillyC~~eea~~IF~~A~q~Gl~ 257 (1258)
T KOG1053|consen 179 VTTQFPGNRTFVSLIRQTNDNSHVGWEMINVLTLDPST-DDLLAKLQAQLKKIQAPVILLYCSREEAERIFEEAEQAGLT 257 (1258)
T ss_pred EEeecCchHHHHHHHHHhhhhccccceeeeeeecCCCC-CchHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHHhcCCc
Confidence 9988887777888888877654 66666555555443 23334444556666689999999999999999999999999
Q ss_pred CCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHH
Q 003275 156 AGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLV 235 (834)
Q Consensus 156 ~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~l 235 (834)
+++|+||++...... +. ..-+...|++.+... .|+ ..+..++-|+|-++
T Consensus 258 g~~y~Wi~pqlv~g~-~~------~pa~~P~GLisv~~~------------~w~------------~~l~~rVrdgvaiv 306 (1258)
T KOG1053|consen 258 GPGYVWIVPQLVEGL-EP------RPAEFPLGLISVSYD------------TWR------------YSLEARVRDGVAIV 306 (1258)
T ss_pred CCceEEEeehhccCC-CC------CCccCccceeeeecc------------chh------------hhHHHHHhhhHHHH
Confidence 999999996533321 11 111344576665442 232 12355788999999
Q ss_pred HHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEee-
Q 003275 236 AHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIG- 314 (834)
Q Consensus 236 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~- 314 (834)
|.|...++...+.+.-. +.++. -........++.|...|.|++|+| ++++|+++|-.+++...++...
T Consensus 307 a~aa~s~~~~~~~lp~~---~~~C~------~~~~~~~~~~~~l~r~l~NvT~~g--~~lsf~~~g~~v~p~lvvI~l~~ 375 (1258)
T KOG1053|consen 307 ARAASSMLRIHGFLPEP---KMDCR------EQEETRLTSGETLHRFLANVTWDG--RDLSFNEDGYLVHPNLVVIDLNR 375 (1258)
T ss_pred HHHHHHHHhhcccCCCc---ccccc------cccCccccchhhhhhhhheeeecc--cceeecCCceeeccceEEEecCC
Confidence 99999998776553211 11111 111112335899999999999999 7899999998888888877664
Q ss_pred ccceEEEEEecCCCCcccccccccccCCCCCCCCCccceeeecCCccccCcccccCCCCCceEEEecCccccccceeccC
Q 003275 315 GTGSRRIGYWSNYSGLSVVAPEILYTKPPNSSSNRHLYSVIWPGEITATPRGWVFPNNGMPLRIAVPNRVSYNEFVAKDK 394 (834)
Q Consensus 315 ~~~~~~vG~w~~~~gl~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~pr~~~~~~~g~~lrv~~~~~~~~~p~~~~~~ 394 (834)
+..|.+||.|.+.. |.| +-.+||--.. ...+.| ...+|+|.+.++.||..-...|.
T Consensus 376 ~r~We~VG~We~~~-L~M-------------------~y~vWPr~~~---~~q~~~-d~~HL~VvTLeE~PFVive~vDP 431 (1258)
T KOG1053|consen 376 DRTWERVGSWENGT-LVM-------------------KYPVWPRYHK---FLQPVP-DKLHLTVVTLEERPFVIVEDVDP 431 (1258)
T ss_pred CcchheeceecCCe-EEE-------------------eccccccccC---ccCCCC-CcceeEEEEeccCCeEEEecCCC
Confidence 46799999998765 332 3455662111 111111 22466666666544332111110
Q ss_pred -----------------------------CCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCC----CCCChHHHHHHH
Q 003275 395 -----------------------------SPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGK----RNPIYNDIVQQV 441 (834)
Q Consensus 395 -----------------------------~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~----~n~s~~~~~~~l 441 (834)
-+.|++||||||++.|++.+||+ |.++..+||+ .|+.|+||+++|
T Consensus 432 ~t~~C~~ntvpc~s~~~~t~ss~~~~~~tvKkCCkGfCIDiLkKlA~~v~Ft--YDLYlVtnGKhGkk~ng~WnGmIGev 509 (1258)
T KOG1053|consen 432 LTQTCVRNTVPCRSQLNSTFSSGDEANRTVKKCCKGFCIDILKKLARDVKFT--YDLYLVTNGKHGKKINGVWNGMIGEV 509 (1258)
T ss_pred CcCcCCCCCCcchhhhhhccCCCccCCchHHhhhhhhhHHHHHHHHhhcCcc--eEEEEecCCcccceecCcchhhHHHH
Confidence 14579999999999999999999 5555555554 689999999999
Q ss_pred HhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhh-hheeeccc
Q 003275 442 ALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAV-VWILEHRF 520 (834)
Q Consensus 442 ~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v-~~~~~~~~ 520 (834)
..+++||+++.++|+.+|.+.+|||.||.++++.+||...+...+..+||.||++.+|+.+++++++++.+ ++++|+.+
T Consensus 510 ~~~rA~MAVgSltINeeRSevVDFSvPFveTgIsVmV~rsngtvspsAFLePfs~svWVmmFVm~livaai~vFlFEy~S 589 (1258)
T KOG1053|consen 510 VYQRADMAVGSLTINEERSEVVDFSVPFVETGISVMVARSNGTVSPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFS 589 (1258)
T ss_pred HhhhhheeeeeeEechhhhccccccccccccceEEEEEecCCccCchhhcCCcchHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 99999999999999999999999999999999999999999888999999999999999999988877655 56888886
Q ss_pred CCCC---------CCCCCcchhhHHHHHHHHhhccC--CCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeeccc
Q 003275 521 NNEF---------RGPPSQQLVTIFWFSFSTMFFSH--RENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTS 589 (834)
Q Consensus 521 ~~~~---------~~~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~ 589 (834)
+-.+ .+.+.+.++.++|..|+.+|... -++|+.+.+|+++.+|.||++|+.++|||||+++|....+..
T Consensus 590 Pvgyn~~l~~gkkpggp~FtigkaiwllwaLvFnnsVpv~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d 669 (1258)
T KOG1053|consen 590 PVGYNRNLANGKKPGGPSFTIGKAIWLLWALVFNNSVPVENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYD 669 (1258)
T ss_pred cccccccccCCCCCCCcceehhhHHHHHHHHHhCCCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Confidence 5433 22346789999999999999774 679999999999999999999999999999999999999999
Q ss_pred CCCChhhhhcCC-------CCeeEeeCchhhHHHHhhhcccccceEec--CCHHHHHHHHhcCCCCCceEEEEechhhHH
Q 003275 590 QIEGIDSLISST-------EPIGVQDGSFAWNYLVDELKIAESRLVKL--KNMEEYSIALARGPKGGGVAAIVDELPYIE 660 (834)
Q Consensus 590 ~i~s~~dL~~~~-------~~v~~~~~s~~~~~l~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~ 660 (834)
++.++.|=.-+. .++|...++..++++++.+..-.+.++.| ...++.++.|++ |+.||+|.|...++
T Consensus 670 ~vSGlsD~KfqrP~dq~PpFRFGTVpngSTE~niR~Nyp~MHeYM~kyNq~~v~dal~sLK~----gKLDAFIyDaAVLn 745 (1258)
T KOG1053|consen 670 TVSGLSDPKFQRPHDQYPPFRFGTVPNGSTERNIRSNYPEMHEYMVKYNQPGVEDALESLKN----GKLDAFIYDAAVLN 745 (1258)
T ss_pred hccccCcccccCccccCCCcccccCCCCchhhhHHhccHHHHHHHHHhccCchHHHHHHHhc----ccchhHHHHHHHHH
Confidence 999999855332 35788777777887766443222444444 477899999999 99999999999999
Q ss_pred HHhhc-CCccEEEeC--CcccccceEEEEcCCCcchHHHHHHHHhhhccccHHHHHHhhcCCCCCCCCCCCCCCCCCccc
Q 003275 661 LFMSK-TNCEFRTVG--QEFTKSGWGFAFQRDSPLAIDLSTAILQLSENGDLQKIHNKWLTYNECSMDLSPADGGGSRLS 737 (834)
Q Consensus 661 ~~~~~-~~~~l~~v~--~~~~~~~~~~~~~k~spl~~~~~~~i~~l~e~G~~~~i~~kw~~~~~c~~~~~~~~~~~~~l~ 737 (834)
|+..+ +.|++..+| ..|...+||+++|||||++..||.+|+++...|.++++++.|+. +.|.++..+. .+.+|+
T Consensus 746 Y~agkDegCKLvTIGsgKvFAttGYGIal~k~Spwkr~IdlallQy~gdGeme~Le~~Wlt-gic~n~k~ev--mSsqLd 822 (1258)
T KOG1053|consen 746 YMAGKDEGCKLVTIGSGKVFATTGYGIALPKNSPWKRQIDLALLQYLGDGEMEMLETLWLT-GICHNSKNEV--MSSQLD 822 (1258)
T ss_pred HhhccCCCceEEEecCCceeeecceeeecCCCCcchhhHHHHHHHHhccchHHHHHHHHhh-cccccchhhh--hhcccC
Confidence 99865 469999998 89999999999999999999999999999999999999999998 6777666665 789999
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 003275 738 LKSFWGLFLICGIACFLALIFFFCRVCGQFR 768 (834)
Q Consensus 738 l~~~~g~f~il~~g~~lal~vf~~e~~~~~~ 768 (834)
+++|+|+|++|++|+++|+++|+.|.+++.+
T Consensus 823 IdnmaGvFymL~~amgLSllvfi~EHlvYw~ 853 (1258)
T KOG1053|consen 823 IDNMAGVFYMLAVAMGLSLLVFIWEHLVYWK 853 (1258)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999765543
No 4
>KOG1052 consensus Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1.8e-68 Score=624.93 Aligned_cols=602 Identities=36% Similarity=0.614 Sum_probs=512.9
Q ss_pred HHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCCh
Q 003275 120 SLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTD 199 (834)
Q Consensus 120 ~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~ 199 (834)
.++.+++....+++++++.+..+..++.+|.+.||+..+|+|+.+++.....+.... ....+.++|+++.+.+.|.+.
T Consensus 4 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~a~~~~~~~~~~~~i~t~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~s~ 81 (656)
T KOG1052|consen 4 KLLLKLKAMRTRVFVLHMFPILALAIFSQAEELGMMQFGYVWILTNLLTDALDLDEL--YSLIDVMNGVLGLRGHIPRSE 81 (656)
T ss_pred hHHHHhhccCceEEEEeCCHHHHHHHHHHHHHhCccccCeEEEEEecchhhhccccc--ccchhheeeEEeeccCCCccH
Confidence 456667778899999999999999999999999999999999999987776665432 345577889999999999999
Q ss_pred hHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHH
Q 003275 200 LKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQF 279 (834)
Q Consensus 200 ~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l 279 (834)
..++|..+|+.. ....+.++.++||+++++|.|+++... .... ...|...+.|.++..+
T Consensus 82 ~~~~~~~~~~~~------~~~~~~~~~~~~D~~~~~a~~~~~~~~-~~~~--------------~~~~~~~~~~~~~~~~ 140 (656)
T KOG1052|consen 82 LLQNFVTRWQTS------NVELLVYALWAYDAIQALARAVESLLN-IGNL--------------SLSCGRNNSWLDALGV 140 (656)
T ss_pred HHHHHHHHHhhc------cccccchhhHHHHHHHHHHHHHHHhhc-CCCC--------------ceecCCCCcccchhHH
Confidence 999999999764 234677899999999999999999764 1221 1233333456678888
Q ss_pred HHHHHhcccc---cceeeEEEccCCCCCCCcEEEEEeeccceEEEEEecCCCCcccccccccccCCCCCCCCCccceeee
Q 003275 280 LQTLLRMNFT---GLSGEIRFDADKNLVNPAYDVLNIGGTGSRRIGYWSNYSGLSVVAPEILYTKPPNSSSNRHLYSVIW 356 (834)
Q Consensus 280 ~~~l~~~~f~---g~tG~i~Fd~~g~~~~~~~~I~~~~~~~~~~vG~w~~~~gl~~~~~~~~~~~~~~~~~~~~l~~i~W 356 (834)
.+.++..... |.+|.+.++.++.+....|+|+|+.+.+.+.||.|++..| .++.|
T Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~n~~~~~~~~ig~W~~~~~----------------------~~i~~ 198 (656)
T KOG1052|consen 141 FNFGKKLLVVNLSGVTGQFQFFRGGLLEYFKYEILNLNGSGERRIGYWYPRGG----------------------ENISW 198 (656)
T ss_pred HHHHHhhhhhccccceeEEEecCCCccccceEEEEEecCcCceeEEEecCCCC----------------------ceeec
Confidence 8888876654 4567888888888999999999999999999999998764 46899
Q ss_pred cCCccccCcccccCCCCCceEEEecCccccccceecc--C-CCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCC--CC
Q 003275 357 PGEITATPRGWVFPNNGMPLRIAVPNRVSYNEFVAKD--K-SPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGK--RN 431 (834)
Q Consensus 357 pg~~~~~pr~~~~~~~g~~lrv~~~~~~~~~p~~~~~--~-~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~--~n 431 (834)
||.....|++|.++.+|++|||+++..+||..++... . ++..+.|+|+||++++++.+||+++++.++.+.|. ++
T Consensus 199 ~~~~~~~~~~~~~~~~~~~l~v~~~~~~P~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~g~~~~~ 278 (656)
T KOG1052|consen 199 PGKDYFVPKGWFFPTNGKPLRVGVVTEPPFVDLVEDLAILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGSGSRDPN 278 (656)
T ss_pred cCCcccCcCCccccCCCceEEEEEeccCCceeeeecccccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCCCCCCCC
Confidence 9999999999999999999999999888877666542 1 35689999999999999999999888888876544 45
Q ss_pred CChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHh
Q 003275 432 PIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGA 511 (834)
Q Consensus 432 ~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~ 511 (834)
|+|+|++++|.+|++|++ ++++++++|.+++|||.||++.++++++++++.....|.|++||++++|++++++++++++
T Consensus 279 g~~~g~v~~l~~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~~~~fl~Pf~~~vW~~i~~~~l~~~~ 357 (656)
T KOG1052|consen 279 GNWDGLVGQLVDGEADVG-ADITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSKLWNFLAPFSPEVWLLILASLLLVGL 357 (656)
T ss_pred CChhHHHHHHhcCccccc-cceEEeecccccEEeccceEeccEEEEEEecCCcccceEEecCCcHHHHHHHHHHHHHHHH
Confidence 799999999999999999 9999999999999999999999999999999865559999999999999999999999999
Q ss_pred hhheeecccCCCCCCCC-----CcchhhHHHHHHHHhhccC-CCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEe
Q 003275 512 VVWILEHRFNNEFRGPP-----SQQLVTIFWFSFSTMFFSH-RENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQ 585 (834)
Q Consensus 512 v~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~l~~~~-~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~ 585 (834)
++|+++|+.+.++ ..+ .....+++|+++++++.++ .+.|++.++|+++++||++++|++++|||+|+|+||++
T Consensus 358 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~ 436 (656)
T KOG1052|consen 358 LLWILERLSPYEL-PPRQIVTSLFSLLNCLWLTVGSLLQQGSDEIPRSLSTRLLLGAWWLFVLILISSYTANLTAFLTVP 436 (656)
T ss_pred HHHHHhccccccC-CccccceeEeecccchhhhhHHHhccCCCccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 9999999999888 222 1124557899999888886 56999999999999999999999999999999999999
Q ss_pred ecccCCCChhhhhc-CCCCeeEeeCchhhHHHHhh---hccccc-ceEecCCHHHHHHHHhcCCCCCceEEEEechhhHH
Q 003275 586 QLTSQIEGIDSLIS-STEPIGVQDGSFAWNYLVDE---LKIAES-RLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIE 660 (834)
Q Consensus 586 ~~~~~i~s~~dL~~-~~~~v~~~~~s~~~~~l~~~---~~~~~~-~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~ 660 (834)
+..++|++++||.+ ++.++|+..+++...++.+. .....+ ..+.+.+.+|+.+++++|.. |+++++.++.++..
T Consensus 437 ~~~~~i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~-~~~~~~~~~~~~~~ 515 (656)
T KOG1052|consen 437 RLRSPIDSLDDLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQRSVPLASPEEGVERVRKGPS-GGYAFASDELYLAY 515 (656)
T ss_pred ccCCcccCHHHHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccCCCccCCCHHHHHHHHHcCCC-CceEEEeccHHHHH
Confidence 99999999999995 77889999999999999765 333334 67788999999999999544 46666666666666
Q ss_pred HHhhcCCccEEEeCCcccccceEEEEcCCCcchHHHHHHHHhhhccccHHHHHHhhcCCCCCCCCCCCCCCCCCcccccc
Q 003275 661 LFMSKTNCEFRTVGQEFTKSGWGFAFQRDSPLAIDLSTAILQLSENGDLQKIHNKWLTYNECSMDLSPADGGGSRLSLKS 740 (834)
Q Consensus 661 ~~~~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~~~~~i~~l~e~G~~~~i~~kw~~~~~c~~~~~~~~~~~~~l~l~~ 740 (834)
+..+++.|+++.+++.+...+++ ++||||||++.+|++|+++.|.|.++++++||+....|........ ....|++++
T Consensus 516 ~~~~~~~c~~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e~g~l~~~~~kw~~~~~~~~~~~~~~-~~~~l~~~~ 593 (656)
T KOG1052|consen 516 LFLRDEICDLTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQETGILQKLKRKWFSKKPCLPKCSQTE-KTKALDLES 593 (656)
T ss_pred HHhhcCCCceEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhccccHHHHHHHHhccCCCCCCCCCCcc-cccccchhh
Confidence 66665569999999999999999 9999999999999999999999999999999999544422222221 467899999
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 003275 741 FWGLFLICGIACFLALIFFFCRVCGQFRRFG 771 (834)
Q Consensus 741 ~~g~f~il~~g~~lal~vf~~e~~~~~~~~~ 771 (834)
++|+|+++++|+++|+++|++|++|++++..
T Consensus 594 ~~g~F~i~~~g~~lal~vfi~E~~~~~~~~~ 624 (656)
T KOG1052|consen 594 FWGLFLILLVGYLLALLVFILELLYSRRRTL 624 (656)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 9999999999999999999999999988875
No 5
>cd06390 PBP1_iGluR_AMPA_GluR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=1.1e-43 Score=382.56 Aligned_cols=308 Identities=17% Similarity=0.262 Sum_probs=258.8
Q ss_pred CCCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 1 MENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 1 ~~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
|++||+|||||.++.++..++.+|+..+||+|+++. |..+ ..+|++++.|+ ++.|+++++++|||++|++||+
T Consensus 53 ~~~gV~AI~Gp~s~~~a~~v~sic~~~~vP~i~~~~--~~~~--~~~~~i~~~P~---~~~Ai~diI~~~~W~~v~iIYd 125 (364)
T cd06390 53 FSKGVYAIFGFYDRKTVNMLTSFCGALHVCFITPSF--PVDT--SNQFVLQLRPE---LQDALISVIEHYKWQKFVYIYD 125 (364)
T ss_pred hhcCceEEEccCChhHHHHHHHhhcCCCCCceecCC--CCCC--CCceEEEeChh---HHHHHHHHHHHcCCcEEEEEEe
Confidence 468999999999999999999999999999999754 4333 33568999997 8999999999999999999995
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
++||...++.|.+++++.|++|.....++. +..+++.+|++|+.+++|+||++|+++.+..+++++.+.+|+..+|+
T Consensus 126 -~d~g~~~lq~l~~~~~~~~~~I~~~~~~~~--~~~d~~~~L~~ik~~~~rvIVl~~~~~~~~~~L~~a~~~~~~~~gy~ 202 (364)
T cd06390 126 -ADRGLSVLQKVLDTAAEKNWQVTAVNILTT--TEEGYRKLFQDLDKKKERLIVVDCESERLNAILNQIIKLEKNGIGYH 202 (364)
T ss_pred -CCccHHHHHHHHHhhhccCceeeEEEeecC--ChHHHHHHHHhccccCCeEEEEECCHHHHHHHHHHHHHhhccCCceE
Confidence 459999999999999999999998777663 35799999999999999999999999999999999999999999999
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcC---CCCCCCccchhHHHhhHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYK---ENSPSGFNSYALYAYDSVWLVAH 237 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~---~~~~~~~~~~~~~~YDav~~la~ 237 (834)
||+|+......+. ......++|++|++.+.|+++..++|..+|++.... +.....++.+++++|||||++|+
T Consensus 203 wI~t~l~~~~~~~-----~~~~~~~~nitg~r~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~l~yDaV~~~A~ 277 (364)
T cd06390 203 YILANLGFMDIDL-----TKFRESGANVTGFQLVNYTDTTVSRIMQQWKNFDARDLPRVDWKRPKYTSALTYDGVRVMAE 277 (364)
T ss_pred EEecCCCcccccH-----HHHhcCCcCceEEEEecCCCHHHHHHHHHHHhhccccCCCCCcCCcchHHHHHHHHHHHHHH
Confidence 9999822211111 345568899999999999999999999999876541 22233578899999999999999
Q ss_pred HHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeeccc
Q 003275 238 ALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGGTG 317 (834)
Q Consensus 238 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~~~ 317 (834)
|++++..++..+++..+ +..|......+|..|..|+++|++++|+|+||+++||++|++.+..|+|+|+.+.|
T Consensus 278 A~~~l~~~~~~~~~~~~-------~~~C~~~~~~~w~~G~~l~~~i~~~~f~GlTG~i~F~~~G~r~~~~~~I~~~~~~g 350 (364)
T cd06390 278 AFQNLRKQRIDISRRGN-------AGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDG 350 (364)
T ss_pred HHHHHHHcCCCcccCCC-------CCCCCCCCCCCCccHHHHHHHHHhhcccccccceeeCCCCCcccceEEEEEecCCc
Confidence 99998655443322111 11222223457999999999999999999999999999999999999999999999
Q ss_pred eEEEEEecCCCCc
Q 003275 318 SRRIGYWSNYSGL 330 (834)
Q Consensus 318 ~~~vG~w~~~~gl 330 (834)
+++||+|++..||
T Consensus 351 ~~~vG~W~~~~g~ 363 (364)
T cd06390 351 IRKIGYWNEDEKL 363 (364)
T ss_pred ceEEEEECCCCCc
Confidence 9999999998876
No 6
>cd06392 PBP1_iGluR_delta_1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 may be closer related to non-NMDA receptors. In contrast to GluRdelta2, GluRdel
Probab=100.00 E-value=5.8e-43 Score=376.13 Aligned_cols=306 Identities=20% Similarity=0.317 Sum_probs=246.7
Q ss_pred CCCCcEEEECCCChhhHHHHHHhhccCCccEEeccc-----------CCCCCCCCCCCceEEccCChHHHHHHHHHHHHH
Q 003275 1 MENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGA-----------TDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEY 69 (834)
Q Consensus 1 ~~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~a-----------t~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~ 69 (834)
|++||+|||||.++.++..++++|++++||+|++++ ++|.++..+||+++|+. ..+..|+++++++
T Consensus 59 ~~~gV~AI~Gp~s~~~a~~v~sic~~l~VP~is~~~~~~~~~~~~~~~~p~~~~~~~~~~lrp~---~~~~~Ai~dlV~~ 135 (400)
T cd06392 59 MTQGILALVTSTGCASANALQSLTDAMHIPHLFVQRNSGGSPRTACHLNPSPEGEEYTLAARPP---VRLNDVMLKLVTE 135 (400)
T ss_pred HhcCeEEEECCCchhHHHHHHHHhccCcCCcEeecccccccccccccCCCCcCcCceeEEecCc---hHHHHHHHHHHHh
Confidence 468999999999999999999999999999999866 45666667778777774 3567899999999
Q ss_pred cCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeec-------CCCCCChHHHHHHHHHhhcCCceEEEEEeChhhH
Q 003275 70 YGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAP-------FSPGASRSAINSLLVGANLMESRVFVVHVNPDTG 142 (834)
Q Consensus 70 ~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~-------~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~ 142 (834)
|+|++|++|| |++||...++.|.+++.+.+.+|.++.. +++.. .+.....|.+++.++ ++|||+|+++.+
T Consensus 136 ~~W~~v~~iY-D~d~gl~~lq~L~~~~~~~~~~I~~~~v~~~~~~~~~~~l-~~~~~~~L~~~~~~~-r~iVv~~s~~~~ 212 (400)
T cd06392 136 LRWQKFIVFY-DSEYDIRGLQSFLDQASRLGLDVSLQKVDRNISRVFTNLF-TTMKTEELNRYRDTL-RRAILLLSPRGA 212 (400)
T ss_pred CCCcEEEEEE-ECcccHHHHHHHHHHHhhcCceEEEEEcccCcchhhhhHH-HHHHHhhhhhccccc-eEEEEEcCcHHH
Confidence 9999999999 8999999999999999999999987662 22221 234456666666666 899999999999
Q ss_pred HHHHHHHHhCCCCCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceE----EEecCCCChhHHHHH----HHHHhhhcC
Q 003275 143 LTIFSVAKSLGMTAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVA----LRHHTPDTDLKKNFI----SRWKNLKYK 214 (834)
Q Consensus 143 ~~i~~~a~~~g~~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~----~~~~~~~~~~~~~F~----~~~~~~~~~ 214 (834)
..++++|.++||+..+|+||++++.....+. .+.++|.++ ++.+.|.+....+|. .+|++....
T Consensus 213 ~~il~qA~~lgM~~~~y~wI~t~~~~~~~dl--------~~~~~g~~~niT~~r~~~~~~~~~~~~~~~~~~r~~~~~~~ 284 (400)
T cd06392 213 QTFINEAVETNLASKDSHWVFVNEEISDTEI--------LELVHSALGRMTVIRQIFPLSKDNNQRCIRNNHRISSLLCD 284 (400)
T ss_pred HHHHHHHHHhCcccCCeEEEEecCCcccccH--------HHHhcccccceeeEEEecCCcHHHHHHHHHHHHHHHhhhcc
Confidence 9999999999999999999999987654333 344555554 999988877666664 677644421
Q ss_pred C--CCCCCccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccC--CCccccCchHHHHHHHHhccccc
Q 003275 215 E--NSPSGFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNL--SSLRVFDGGQQFLQTLLRMNFTG 290 (834)
Q Consensus 215 ~--~~~~~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~g~~l~~~l~~~~f~g 290 (834)
. .....++++++++|||||++|+|+++++...... ...+ ++| .+.++|+.|..|+++|++++|+|
T Consensus 285 ~~~~~~~~l~~~aalayDaV~~~A~Al~~ll~~~~~~---------~~~~--l~C~~~~~~~w~~G~~ll~~ik~v~f~G 353 (400)
T cd06392 285 PQEGYLQMLQVSNLYLYDSVLMLANAFHRKLEDRKWH---------SMAS--LNCIRKSTKPWNGGRSMLETIKKGHITG 353 (400)
T ss_pred cccccccccchhHHHHHHHHHHHHHHHHHHhhccccC---------CCCC--CccCCCCCCCCCChHHHHHHHHhCCCcc
Confidence 1 1111478899999999999999999876432221 1122 344 56789999999999999999999
Q ss_pred ceeeEEEccCCCCCCCcEEEEEe-----eccceEEEEEecCCCCcc
Q 003275 291 LSGEIRFDADKNLVNPAYDVLNI-----GGTGSRRIGYWSNYSGLS 331 (834)
Q Consensus 291 ~tG~i~Fd~~g~~~~~~~~I~~~-----~~~~~~~vG~w~~~~gl~ 331 (834)
+||+|+||++|++.++.|+|+|+ .|.|.++||+|++.+||+
T Consensus 354 LTG~I~F~~~G~r~~~~ldIi~l~~~~~~g~g~~~iG~W~~~~gl~ 399 (400)
T cd06392 354 LTGVMEFKEDGANPHVQFEILGTSYSETFGKDVRRLATWDSEKGLN 399 (400)
T ss_pred CccceeECCCCCCcCCceEEEeccccccCCCCceEeEEecCCCCCC
Confidence 99999999999999999999994 477799999999999875
No 7
>cd06387 PBP1_iGluR_AMPA_GluR3 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=5.2e-41 Score=360.32 Aligned_cols=309 Identities=15% Similarity=0.261 Sum_probs=254.6
Q ss_pred CCCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 1 MENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 1 ~~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
|++||.||+||.++..+.++..+|+..+||+|.+... .+...+|.+++.|+ +..|+++++++|+|++|++||
T Consensus 60 ~~~GV~AIfGp~~~~s~~~v~s~c~~~~iP~i~~~~~----~~~~~~~~l~l~P~---l~~Ai~diI~~~~Wr~~~~iY- 131 (372)
T cd06387 60 FSRGVYAIFGFYDQMSMNTLTSFCGALHTSFITPSFP----TDADVQFVIQMRPA---LKGAILSLLAHYKWEKFVYLY- 131 (372)
T ss_pred hhcccEEEEecCCHhHHHHHHHhhccccCCeeeeCCC----CCCCCceEEEEChh---HHHHHHHHHHhcCCCEEEEEe-
Confidence 4679999999999999999999999999999987332 12334778899998 689999999999999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|+++|...++.|.++++..+..|......+.. ...+++..+++|++++.++|||+|+++.+..|+++|.++||+..+|+
T Consensus 132 d~d~gl~~Lq~L~~~~~~~~~~V~~~~v~~~~-~~~~~~~~l~el~~~~~r~iIld~s~~~~~~il~~a~e~gM~~~~y~ 210 (372)
T cd06387 132 DTERGFSILQAIMEAAVQNNWQVTARSVGNIK-DVQEFRRIIEEMDRRQEKRYLIDCEVERINTILEQVVILGKHSRGYH 210 (372)
T ss_pred cCchhHHHHHHHHHhhccCCceEEEEEeccCC-chHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHcCccccceE
Confidence 77899999999999999999999877655533 34689999999999999999999999999999999999999999999
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcC---CCCCCCccchhHHHhhHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYK---ENSPSGFNSYALYAYDSVWLVAH 237 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~---~~~~~~~~~~~~~~YDav~~la~ 237 (834)
||+++......+. .+......+++|++.+.|+++..++|.++|++.... +....+++.+++++|||||++|+
T Consensus 211 ~ilt~ld~~~~dl-----~~~~~g~~NItg~rl~~~~~~~~~~f~~~w~~~~~~~~~~~~~~~l~~~~al~yDaV~~~A~ 285 (372)
T cd06387 211 YMLANLGFTDISL-----ERVMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEAKNSPLKYTSALTHDAILVIAE 285 (372)
T ss_pred EEEecCCcccccH-----HHhccCCcceeEEEEecCCCchHHHHHHHHHhCCcccCCCCCCCCcchHHHHHHHHHHHHHH
Confidence 9999743332222 122222233999999999999999999999876542 22233567899999999999999
Q ss_pred HHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeeccc
Q 003275 238 ALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGGTG 317 (834)
Q Consensus 238 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~~~ 317 (834)
|++++......++.. ..+..|.-....+|..|..|+++|++++|+|+||+|+||++|+|.+..|+|+|+.+.|
T Consensus 286 A~~~l~~~~~~~~~~-------~~~~~C~~~~~~~W~~G~~l~~~ik~v~~~GLTG~i~F~~~G~R~~~~ldIinl~~~g 358 (372)
T cd06387 286 AFRYLRRQRVDVSRR-------GSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTNYTIDVYEMKPSG 358 (372)
T ss_pred HHHHHHhcCCCcccC-------CCCCCcCCCCCCCccchHHHHHHHHhcccCCCccceeeCCCCCcccceEEEEEecCCC
Confidence 999986543332111 0111222223568999999999999999999999999999999999999999999999
Q ss_pred eEEEEEecCCCCc
Q 003275 318 SRRIGYWSNYSGL 330 (834)
Q Consensus 318 ~~~vG~w~~~~gl 330 (834)
+++||+|++..|+
T Consensus 359 ~~kIG~W~~~~g~ 371 (372)
T cd06387 359 SRKAGYWNEYERF 371 (372)
T ss_pred ceeEEEECCCCCc
Confidence 9999999999886
No 8
>cd06391 PBP1_iGluR_delta_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related to non-NMDA receptors. GluRdelta2 was shown to function as a
Probab=100.00 E-value=1.5e-39 Score=354.12 Aligned_cols=313 Identities=19% Similarity=0.316 Sum_probs=249.2
Q ss_pred CCCCcEEEECCCChhhHHHHHHhhccCCccEEec----ccCC-----CCCCC--CCCCceEEccCChHHHHHHHHHHHHH
Q 003275 1 MENEVVAAIGPQSSGIAHVISHVVNELNVPLLSF----GATD-----PTLTS--LQYPYFLRTTQSDYYQMHAVADLVEY 69 (834)
Q Consensus 1 ~~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~----~at~-----~~ls~--~~~p~~~r~~ps~~~q~~aia~ll~~ 69 (834)
++++|.|||||.++..+..++.+|+.++||+|++ ++++ |.+++ .+||+++| |+ ..|+.|+++++++
T Consensus 59 ~~~gv~ai~Gp~~~~~~~~v~~~~~~~~vP~i~~~~~~~~t~~~~~~~~~~~~~~~y~~~~r--p~-~~~~~ai~~li~~ 135 (400)
T cd06391 59 MNQGILALVSSIGCTSAGSLQSLADAMHIPHLFIQRSTAGTPRSSCGLTRSNRNDDYTLSVR--PP-VYLNDVILRVVTE 135 (400)
T ss_pred HhCCeEEEECCCcchHHHHHHHHhccCcCCeEEeecccccCccccCCCCCCCCcccceEEec--Ch-HHHHHHHHHHHHH
Confidence 3578999999999999999999999999999984 4433 34443 56888888 43 6788999999999
Q ss_pred cCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCCh---HHHHH-HHHHhhc--CCceEEEEEeChhhHH
Q 003275 70 YGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASR---SAINS-LLVGANL--MESRVFVVHVNPDTGL 143 (834)
Q Consensus 70 ~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~---~~~~~-~l~~l~~--~~~~vivl~~~~~~~~ 143 (834)
|+|++++++ .|++||...++.|.+++++.|+||..... ....++ ..+.. .+.+|++ .+.++||++|+++.+.
T Consensus 136 f~W~~v~i~-~d~~~~~~~l~~l~~~~~~~~i~I~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~rviVl~~~~~~~~ 213 (400)
T cd06391 136 YAWQKFIIF-YDTDYDIRGIQEFLDKVSQQGMDVALQKV-ENNINKMITGLFRTMRIEELNRYRDTLRRAILVMNPATAK 213 (400)
T ss_pred cCCcEEEEE-EeCCccHHHHHHHHHHHHHcCCeEEEEec-CcchhhhhHHHHHHHHHHHHHhhcccccEEEEECCcHHHH
Confidence 999998865 57788999999999999999999997442 211110 12222 4455654 5679999999999999
Q ss_pred HHHHHHHhCCCCCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCC-----CC-
Q 003275 144 TIFSVAKSLGMTAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKE-----NS- 217 (834)
Q Consensus 144 ~i~~~a~~~g~~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~-----~~- 217 (834)
.+|++|+++||++.+|+||++++....++.. +...+.+.|+.+++++.|.+....+|..+|..++... ..
T Consensus 214 ~ll~~a~~~gm~~~~y~wi~t~~~~~~~dl~----~~~~~~~~~v~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~ 289 (400)
T cd06391 214 SFITEVVETNLVAFDCHWIIINEEISDMDVQ----ELVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISSSLCDPKDPF 289 (400)
T ss_pred HHHHHHHHcCCCCCCeEEEEeCccccccccc----hHHhcccceEEEeccCCchHHHHHHHHHHHhhhccccccCccccc
Confidence 9999999999999999999999988887763 2334567888999999998888999999998765311 11
Q ss_pred CCCccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEE
Q 003275 218 PSGFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRF 297 (834)
Q Consensus 218 ~~~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~F 297 (834)
...++.+++++|||||++|+|++++........ .....|...+..+|..|..|+++|++++|+|+||+|+|
T Consensus 290 ~~~~~~~~alayDaV~~~A~A~~~l~~~~~~~~---------~~~~~c~~~~~~~w~~G~~ll~~i~~~~f~GlTG~i~f 360 (400)
T cd06391 290 AQMMEISNLYIYDTVLLLANAFHKKLEDRKWHS---------MASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEF 360 (400)
T ss_pred cccccchhhHHHHHHHHHHHHHHHHHhhccccC---------CCCcccccCCCCCCCChHHHHHHHHhcCcccceeceEE
Confidence 113678999999999999999998753322211 11112333346689999999999999999999999999
Q ss_pred ccCCCCCCCcEEEEEee-----ccceEEEEEecCCCCcc
Q 003275 298 DADKNLVNPAYDVLNIG-----GTGSRRIGYWSNYSGLS 331 (834)
Q Consensus 298 d~~g~~~~~~~~I~~~~-----~~~~~~vG~w~~~~gl~ 331 (834)
+++|+|.++.|+|+|+. +.|.++||+|++..||+
T Consensus 361 ~~~g~r~~~~~dIin~~~~~~~~~g~rkiG~Ws~~~gl~ 399 (400)
T cd06391 361 NENGGNPNVHFEILGTNYGEDLGRGVRKLGCWNPITGLN 399 (400)
T ss_pred CCCCCccCCceEEEEeeccccCCCcceEEEEEcCCcCCC
Confidence 99999999999999996 88999999999999864
No 9
>cd06367 PBP1_iGluR_NMDA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits
Probab=100.00 E-value=2.6e-39 Score=353.51 Aligned_cols=280 Identities=21% Similarity=0.324 Sum_probs=240.4
Q ss_pred CCcEEEECCCChhh---HHHHHHhhccCCccEEecccCCCCC-CC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEE
Q 003275 3 NEVVAAIGPQSSGI---AHVISHVVNELNVPLLSFGATDPTL-TS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIA 77 (834)
Q Consensus 3 ~~V~aiiGp~~S~~---~~~~~~~~~~~~vP~Is~~at~~~l-s~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~i 77 (834)
++|.+|+||.+|.. +.+++++++.++||+|+++++++.+ ++ .+||||||+.|++..|+.++++++++|+|++|++
T Consensus 62 ~~v~~iig~~~s~~~~~~~~~~~v~~~~~iP~Is~~~~~~~~~s~~~~~~~~~R~~p~~~~~~~ai~~ll~~~~w~~vai 141 (362)
T cd06367 62 QVVAGVVFSDPTDEEAVAQILDFTSAQTRIPVVGISGRESIFMSDKNIHSLFLQTGPSLEQQADVMLEILEEYDWHQFSV 141 (362)
T ss_pred cceEEEEecCCCCccchhhhhhhhhhhhcCcEEEeeccccccccCCCcccceEeecCcHHHHHHHHHHHHHHcCCeEEEE
Confidence 57999999999998 9999999999999999999999998 76 6799999999999999999999999999999999
Q ss_pred EEEcCCcccchHHHHHHHHhcCCcE--EEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 78 IFVDDDYGRNGISVLGDALSKKRAK--ISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 78 I~~d~~~g~~~~~~l~~~l~~~g~~--I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
||.+++||++..+.+++.+++.|+| ++....++... ..++..++.++++.++|+||++|+..++..++++|.++||+
T Consensus 142 i~~~~~~g~~~~~~l~~~l~~~g~~~~i~~~~~~~~~~-~~~~~~~l~~l~~~~~~vivl~~~~~~~~~il~~a~~~g~~ 220 (362)
T cd06367 142 VTSRDPGYRDFLDRVETTLEESFVGWEFQLVLTLDLSD-DDGDARLLRQLKKLESRVILLYCSKEEAERIFEAAASLGLT 220 (362)
T ss_pred EEEcCcccHHHHHHHHHHHHhcccceeeeeeEEeccCC-CcchHHHHHHHHhcCCcEEEEeCCHHHHHHHHHHHHHcCCC
Confidence 9999999999999999999999999 77666666442 23788999999999999999999999999999999999999
Q ss_pred CCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHH
Q 003275 156 AGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLV 235 (834)
Q Consensus 156 ~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~l 235 (834)
+++|+||.++.+..... ...+...|++++++..+ ..+.+++||||+++
T Consensus 221 ~~~~~wI~~~~~~~~~~-------~~~~~~~G~~g~~~~~~-------------------------~~~~~~~~Dav~~~ 268 (362)
T cd06367 221 GPGYVWIVGELALGSGL-------APEGLPVGLLGVGLDTW-------------------------YSLEARVRDAVAIV 268 (362)
T ss_pred CCCcEEEECcccccccC-------CccCCCCeeEEEEeccc-------------------------ccHHHHHHHHHHHH
Confidence 99999999998764211 11255679999987532 23577899999999
Q ss_pred HHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCcc--ccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEe
Q 003275 236 AHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLR--VFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNI 313 (834)
Q Consensus 236 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~ 313 (834)
|+|+++++.+.+... .....|.... .|.+|..|+++|++++|.|++|+|+||++|++.++.|+|+|+
T Consensus 269 a~Al~~~~~~~~~~~-----------~~~~~C~~~~~~~~~~g~~l~~~l~~~~f~G~tg~v~F~~~G~~~~~~~~I~~l 337 (362)
T cd06367 269 ARAAESLLRDKGALP-----------EPPVNCYDTANKRESSGQYLARFLMNVTFDGETGDVSFNEDGYLSNPKLVIINL 337 (362)
T ss_pred HHHHHHHHHhcCCCC-----------CCCCCcCCCCCCCCCchHHHHHHHhcccccCCCCceeECCCcccccceEEEEEe
Confidence 999999986533221 1112344432 278899999999999999999999999999998899999999
Q ss_pred e-ccceEEEEEecC
Q 003275 314 G-GTGSRRIGYWSN 326 (834)
Q Consensus 314 ~-~~~~~~vG~w~~ 326 (834)
+ +.++++||.|++
T Consensus 338 ~~~~~~~~VG~W~~ 351 (362)
T cd06367 338 RRNRKWERVGSWEN 351 (362)
T ss_pred cCCCcceEEEEEcC
Confidence 9 789999999975
No 10
>cd06389 PBP1_iGluR_AMPA_GluR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=7.5e-39 Score=347.77 Aligned_cols=311 Identities=19% Similarity=0.294 Sum_probs=251.3
Q ss_pred CCCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 1 MENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 1 ~~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
|++||+|||||.+|..+.+++++|+.++||+|+++++. +..++|.+++.|+ ...++++++++|+|++|++||+
T Consensus 54 ~~~GV~AI~Gp~ss~~~~~v~~i~~~~~IP~I~~~~~~----~~~~~f~~~~~p~---~~~ai~d~i~~~~wk~vailYd 126 (370)
T cd06389 54 FSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPT----DGTHPFVIQMRPD---LKGALLSLIEYYQWDKFAYLYD 126 (370)
T ss_pred hhcCcEEEEecCCHHHHHHHHHhhccCCCCeeeecCCC----CCCCceEEEecch---hhhHHHHHHHhcCCcEEEEEec
Confidence 46899999999999999999999999999999986552 3467888898887 4789999999999999999996
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeee--cCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKA--PFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~--~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
++||...++.|.+.+++.|++|+... .+.......|++.+|++|+++++|+||++|+++++..++++|+++||+.++
T Consensus 127 -sd~gl~~lq~l~~~~~~~g~~V~~~~~~~i~~~~~~~d~~~~L~~ik~~~~~~Iil~~~~~~~~~il~qa~~~gm~~~~ 205 (370)
T cd06389 127 -SDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDRKDEAYRSLFQDLENKKERRVILDCERDKVNDIVDQVITIGKHVKG 205 (370)
T ss_pred -CchHHHHHHHHHHhhccCCceEEEEEeecCCCccchHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHhCccccc
Confidence 66999999999999999998877443 222223456999999999999999999999999999999999999999999
Q ss_pred eEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhc---CCCCCCCccchhHHHhhHHHHH
Q 003275 159 YVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKY---KENSPSGFNSYALYAYDSVWLV 235 (834)
Q Consensus 159 ~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~---~~~~~~~~~~~~~~~YDav~~l 235 (834)
|+||+++......+.. .....-.++.+++...++.+..++|.++|++... ++.....++.+++++||||+++
T Consensus 206 y~~il~~~~~~~~~l~-----~~~~~~~nitg~~~~~~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~aAl~yDAV~v~ 280 (370)
T cd06389 206 YHYIIANLGFTDGDLS-----KIQFGGANVSGFQIVDYDDPLVSKFIQRWSTLEEKEYPGAHTKTIKYTSALTYDAVQVM 280 (370)
T ss_pred eEEEEccCCccccchh-----hhccCCcceEEEEEecCCCchHHHHHHHHHhcCccccCCCCCcCcchHHHHHHHHHHHH
Confidence 9999986422221210 1112234678888888889999999999986322 1112245788999999999999
Q ss_pred HHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeec
Q 003275 236 AHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGG 315 (834)
Q Consensus 236 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~ 315 (834)
|+|++++......+... ..+..|.-....+|.+|..|+++|++++|+|+||+++||++|++.+..++|+++++
T Consensus 281 a~A~~~l~~~~~~~~~~-------~~~~~C~~~~~~~w~~G~~i~~~l~~~~~~GlTG~i~Fd~~G~r~~~~~~ii~l~~ 353 (370)
T cd06389 281 TEAFRNLRKQRIEISRR-------GNAGDCLANPAVPWGQGVEIERALKQVQVEGLTGNIKFDQNGKRINYTINVMELKS 353 (370)
T ss_pred HHHHHHHHHcCCCcccC-------CCCCCcCCCCCCCCCCcHHHHHHHHhcccCccccceEeCCCCccccceEEEEEecC
Confidence 99999985543222110 01112222335689999999999999999999999999999999988999999999
Q ss_pred cceEEEEEecCCCCcc
Q 003275 316 TGSRRIGYWSNYSGLS 331 (834)
Q Consensus 316 ~~~~~vG~w~~~~gl~ 331 (834)
+|+++||+|++..||.
T Consensus 354 ~g~~kvG~W~~~~~~~ 369 (370)
T cd06389 354 NGPRKIGYWSEVDKMV 369 (370)
T ss_pred CcceEEEEEcCCCCcc
Confidence 9999999999998875
No 11
>cd06393 PBP1_iGluR_Kainate_GluR5_7 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated
Probab=100.00 E-value=5.2e-39 Score=352.84 Aligned_cols=304 Identities=19% Similarity=0.294 Sum_probs=252.4
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
.++|+|||||.+|..+.+++++++.++||+|++++++|.+++. .+|++|+.|++..+..++++++++|+|++|++||++
T Consensus 70 ~~~V~AiiGp~~S~~~~av~~i~~~~~iP~Is~~~t~~~lt~~-~~~~~~~~~~~~~~~~a~~~~~~~~~wk~vaily~~ 148 (384)
T cd06393 70 ALGVVAIFGPSQGSCTNAVQSICNALEVPHIQLRWKHHPLDNK-DTFYVNLYPDYASLSHAILDLVQYLKWRSATVVYDD 148 (384)
T ss_pred ccCcEEEECCCChHHHHHHHHHHhccCCCeEeccCCCcccCcc-ceeEEEeccCHHHHHHHHHHHHHHcCCcEEEEEEeC
Confidence 3689999999999999999999999999999999999988864 357888889998999999999999999999999976
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
++ |...++.|.+++++.|++|+.. .++. ++.|++.+|++|++.++++||++++..++..++++|+++||+.+.|+|
T Consensus 149 ~~-g~~~l~~~~~~~~~~g~~v~~~-~~~~--~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~~~~ 224 (384)
T cd06393 149 ST-GLIRLQELIMAPSRYNIRLKIR-QLPT--DSDDARPLLKEMKRGREFRIIFDCSHQMAAQILKQAMAMGMMTEYYHF 224 (384)
T ss_pred ch-hHHHHHHHHHhhhccCceEEEE-ECCC--CchHHHHHHHHHhhcCceEEEEECCHHHHHHHHHHHHHhccccCceEE
Confidence 54 6666778888889999999863 3553 348999999999999999999999999999999999999999999999
Q ss_pred EEeCCCcccCCCCCCCChhhHhhccc--ceEEEecCCCChhHHHHHHHHHhh-hcCCC------CCCCccchhHHHhhHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQG--VVALRHHTPDTDLKKNFISRWKNL-KYKEN------SPSGFNSYALYAYDSV 232 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~G--v~~~~~~~~~~~~~~~F~~~~~~~-~~~~~------~~~~~~~~~~~~YDav 232 (834)
+.++.....++. ... ..+| +++++...++++..++|.++|+++ +.... ....++.+++++||||
T Consensus 225 ~~~~~~~~~~~~-----~~~--~~~~~~it~~~~~~~~~~~~~~f~~~~~~~~~~~~p~~~~~~~~~~~~~~aal~yDav 297 (384)
T cd06393 225 IFTTLDLYALDL-----EPY--RYSGVNLTGFRILNVDNPHVSSIVEKWSMERLQAAPKPETGLLDGVMMTDAALLYDAV 297 (384)
T ss_pred EEccCccccccc-----hhh--hcCcceEEEEEecCCCcHHHHHHHHHHHhhhhccccccccccccccccchhHHhhhhH
Confidence 987753332222 111 1234 578888888899999999999854 43110 0112367899999999
Q ss_pred HHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEcc-CCCCCCCcEEEE
Q 003275 233 WLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDA-DKNLVNPAYDVL 311 (834)
Q Consensus 233 ~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~-~g~~~~~~~~I~ 311 (834)
+++|+|++++.... ...+.|....+|..|.+|+++|++++|+|+||+++||+ +|.|.+..++|+
T Consensus 298 ~~~a~A~~~~~~~~---------------~~~~~c~~~~~w~~G~~i~~~l~~~~~~GltG~i~Fd~~~g~r~~~~~~i~ 362 (384)
T cd06393 298 HMVSVCYQRAPQMT---------------VNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDII 362 (384)
T ss_pred HHHHHHHhhhhhcC---------------CCCCCCCCCCCCcccHHHHHHHhheeecccccceEecCCCCeeeeeEEEEE
Confidence 99999999753210 12235666779999999999999999999999999986 678899999999
Q ss_pred EeeccceEEEEEecCCCCccc
Q 003275 312 NIGGTGSRRIGYWSNYSGLSV 332 (834)
Q Consensus 312 ~~~~~~~~~vG~w~~~~gl~~ 332 (834)
|+.+.++++||+|++..||++
T Consensus 363 ~~~~~g~~~vg~W~~~~g~~~ 383 (384)
T cd06393 363 SLKEDGLEKVGVWNPNTGLNI 383 (384)
T ss_pred EecCCcceeeEEEcCCCCcCC
Confidence 999999999999999999863
No 12
>cd06388 PBP1_iGluR_AMPA_GluR4 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=9.2e-39 Score=346.01 Aligned_cols=304 Identities=21% Similarity=0.328 Sum_probs=245.3
Q ss_pred CCCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 1 MENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 1 ~~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
|++||+|||||.+|..+.+++++|+..+||+|+++++ +...+.|.+++.|+ +..++++++++|+|++|++||+
T Consensus 60 ~~~gV~AI~Gp~ss~~~~~v~~i~~~~~IP~I~~~~~----~~~~~~f~i~~~p~---~~~a~~~~i~~~~wk~vaiiYd 132 (371)
T cd06388 60 YSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFP----TEGESQFVLQLRPS---LRGALLSLLDHYEWNRFVFLYD 132 (371)
T ss_pred HhCCceEEEecCCHHHHHHHHHHhhCCCCCeeecCcc----ccCCCceEEEeChh---hhhHHHHHHHhcCceEEEEEec
Confidence 4689999999999999999999999999999997653 12334444455555 4578888999999999999994
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
+++|...++.|.+++++.|++|+.....+.+ +.|++.+|.+|+.+++++||++|+++.+..|+++|+++||+.++|+
T Consensus 133 -~~~~~~~lq~l~~~~~~~g~~v~~~~~~~~~--~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~y~ 209 (371)
T cd06388 133 -TDRGYSILQAIMEKAGQNGWQVSAICVENFN--DASYRRLLEDLDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYH 209 (371)
T ss_pred -CCccHHHHHHHHHhhHhcCCeeeeEEeccCC--cHHHHHHHHHhcccccEEEEEECCHHHHHHHHHHHHhcCccccceE
Confidence 4456677999999999999999876655433 4699999999999999999999999999999999999999999999
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhccc---ceEEEecCCCChhHHHHHHHHHhhhcCC--CCCCCccchhHHHhhHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQG---VVALRHHTPDTDLKKNFISRWKNLKYKE--NSPSGFNSYALYAYDSVWLV 235 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~G---v~~~~~~~~~~~~~~~F~~~~~~~~~~~--~~~~~~~~~~~~~YDav~~l 235 (834)
||+++..... ....+...| +.+++...++.+..++|.++|++.+... +.+..++.+++++||||+++
T Consensus 210 ~il~~~~~~~--------~~l~~~~~g~~nitg~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~aAl~YDaV~l~ 281 (371)
T cd06388 210 YIIANLGFKD--------ISLERFMHGGANVTGFQLVDFNTPMVTKLMQRWKKLDQREYPGSESPPKYTSALTYDGVLVM 281 (371)
T ss_pred EEEccCcccc--------ccHHHHhccCCceEEEEeecCCChhHHHHHHHHHhcCccccCCCCCCccchHHHHHHHHHHH
Confidence 9998642111 122233334 8899998888899999999998765421 11135788999999999999
Q ss_pred HHHHHHHHhcCCCccccCCCCCCCCCCCCccC--CCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEe
Q 003275 236 AHALDALLNEGGKFTFSNDPKLHDTNGSMLNL--SSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNI 313 (834)
Q Consensus 236 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~ 313 (834)
|+|++++.......+. .+....| ....+|..|..|+++|++++|+|+||+++||++|++.+..++|+++
T Consensus 282 a~A~~~l~~~~~~~~~---------~~~~~~C~~~~~~~w~~G~~i~~~lk~~~~~GlTG~i~Fd~~G~r~~~~l~Ii~l 352 (371)
T cd06388 282 AEAFRNLRRQKIDISR---------RGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNIQFDHYGRRVNYTMDVFEL 352 (371)
T ss_pred HHHHHHHHhcCCCccc---------CCCCCCcCCCCCCCCcccHHHHHHHHhcCcCCCccceeECCCCCcccceEEEEEc
Confidence 9999997543221100 1111233 4466899999999999999999999999999999999889999999
Q ss_pred eccceEEEEEecCCCCcc
Q 003275 314 GGTGSRRIGYWSNYSGLS 331 (834)
Q Consensus 314 ~~~~~~~vG~w~~~~gl~ 331 (834)
.+.|+++||+|++..||+
T Consensus 353 ~~~g~~kvG~W~~~~g~~ 370 (371)
T cd06388 353 KSNGPRKIGYWNDMDKLV 370 (371)
T ss_pred cCCCceEEEEEcCCCCcc
Confidence 999999999999999875
No 13
>cd06365 PBP1_Pheromone_receptor Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptor, the GABAb receptor, the calcium-sensing receptor (CaSR), the T1R taste receptor, and a small group of uncharacterized orphan receptors.
Probab=100.00 E-value=7e-39 Score=358.96 Aligned_cols=304 Identities=20% Similarity=0.297 Sum_probs=246.1
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|+|||||.+|..+.+++++++.++||+|||+++++.+++ .+||||||+.|+|..|+.|+++++++|+|++|++|+.|
T Consensus 102 ~~vvavIG~~~S~~s~~va~i~~~~~IP~Is~~sts~~lsd~~~yp~ffRt~psd~~q~~ai~~li~~f~W~~Vaiv~~d 181 (469)
T cd06365 102 RKSVAVIGGPSWALSATIATLLGLYKFPQLTYGPFDPLLSDRVQFPSLYQMAPKDTSLPLGMVSLMLHFSWTWVGLVISD 181 (469)
T ss_pred CceEEEEcCCccHHHHHHHHHhhhhcccceeeccCCccccchhhCCcceEecCCchhHHHHHHHHHHhcCCeEEEEEEec
Confidence 57999999999999999999999999999999999999997 67999999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCCh--HHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASR--SAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~--~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
++||...++.|.+++++.|+||++.+.++....+ .++...+.+|+++++||||++++.+++..++.++.+.+. .++
T Consensus 182 ~~yg~~~~~~~~~~~~~~gi~I~~~~~i~~~~~~~~~~~~~~l~~i~~~~arvIvl~~~~~~~~~l~~~~~~~~~--~~~ 259 (469)
T cd06365 182 DDRGEQFLSDLREEMQRNGICLAFVEKIPVNMQLYLTRAEKYYNQIMTSSAKVIIIYGDTDSLLEVSFRLWQYLL--IGK 259 (469)
T ss_pred ChhHHHHHHHHHHHHHHCCeEEEEEEEecCCchhhHHHHHHHHHHhhcCCCeEEEEEcCcHHHHHHHHHHHHhcc--Cce
Confidence 9999999999999999999999999988866432 488999999999999999999998888776666665443 569
Q ss_pred EEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHH---------------HHhhhcCC---------
Q 003275 160 VWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISR---------------WKNLKYKE--------- 215 (834)
Q Consensus 160 vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~---------------~~~~~~~~--------- 215 (834)
+||.+++|....... ....+.++|++++.++.+..+++++|.++ |+..|.+.
T Consensus 260 ~wi~s~~w~~~~~~~----~~~~~~~~G~lg~~~~~~~~~~f~~fl~~l~~~~~~~npw~~efwe~~f~c~~~~~~~~~~ 335 (469)
T cd06365 260 VWITTSQWDVTTSPK----DFTLNSFHGTLIFSHHHSEIPGFKDFLQTVNPSKYPEDIFLEKLWWIYFNCSLSKSSCKTL 335 (469)
T ss_pred EEEeecccccccccc----ccccceeeEEEEEEeccCcCcchHHHhhccCcccCCCccHHHhhHhHhcCcccCcCCcccc
Confidence 999998875433221 23447799999999998887877776644 55544311
Q ss_pred -----CCCC----------CccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHH
Q 003275 216 -----NSPS----------GFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFL 280 (834)
Q Consensus 216 -----~~~~----------~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~ 280 (834)
+... .....+.++||||+++|+|||+++.++... ....+|.. ... ++.+|+
T Consensus 336 ~~c~~~~~~~~~~~~~~~~~~~~~~~~v~dAVya~AhALh~~l~c~~~~------------~~~~~~~~-~~~-~~~~l~ 401 (469)
T cd06365 336 KNCLSNASLEWLPLHYFDMAMSEESYNVYNAVYAVAHALHEMLLQQVET------------QSENNGKR-LIF-LPWQLH 401 (469)
T ss_pred CCCCCCccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHhhccC------------CCcCCCCC-CCc-cHHHHH
Confidence 0000 013356789999999999999999764421 00112222 223 588999
Q ss_pred HHHHhcccccceee-EEEccCCCCCCCcEEEEEeec--c---ceEEEEEecCC
Q 003275 281 QTLLRMNFTGLSGE-IRFDADKNLVNPAYDVLNIGG--T---GSRRIGYWSNY 327 (834)
Q Consensus 281 ~~l~~~~f~g~tG~-i~Fd~~g~~~~~~~~I~~~~~--~---~~~~vG~w~~~ 327 (834)
++|++++|.|.+|. |.||+|||+ ...|+|+|++. + ..++||.|++.
T Consensus 402 ~~l~~v~F~~~~g~~v~Fd~nGd~-~~~YdI~n~q~~~~~~~~~~~VG~~~~~ 453 (469)
T cd06365 402 SFLKNIQFKNPAGDEVNLNQKRKL-DTEYDILNYWNFPQGLGLKVKVGEFSPQ 453 (469)
T ss_pred HHHHhccccCCCCCEEEecCCCCc-CceeeEEEEEECCCCCEEEEEEEEEeCC
Confidence 99999999999995 999999996 57999999972 2 36899999753
No 14
>cd06380 PBP1_iGluR_AMPA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, a member of the glutamate-receptor ion channels (iGluRs). AMPA receptors are the major mediators of excitatory synaptic transmission in the central nervous system. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excita
Probab=100.00 E-value=3.9e-38 Score=346.90 Aligned_cols=318 Identities=21% Similarity=0.328 Sum_probs=251.8
Q ss_pred CCCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 1 MENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 1 ~~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
++++|+|||||.+|..+.+++++++.++||+|+++++.+.++ ..++|+||+.|+. ..++++++++++|++|++||+
T Consensus 59 l~~~V~aiiGp~~s~~~~~~~~~~~~~~iP~i~~~~~~~~l~-~~~~~~fr~~p~~---~~a~~~~~~~~~wk~vaii~~ 134 (382)
T cd06380 59 LSRGVFAIFGSYDKSSVNTLTSYSDALHVPFITPSFPTNDLD-DGNQFVLQMRPSL---IQALVDLIEHYGWRKVVYLYD 134 (382)
T ss_pred HhcCcEEEEecCcHHHHHHHHHHHhcCCCCeEecCCCcccCC-CCCcEEEEeccch---hHHHHHHHHhcCCeEEEEEEC
Confidence 356899999999999999999999999999999999988885 4679999998863 358899999999999999997
Q ss_pred cCCcccchHHHHHHHHhcCC--cEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 81 DDDYGRNGISVLGDALSKKR--AKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g--~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
+++ |...++.+.+.+++.| +.|.... +....+..|++.+|.+|+++++|+||++++.+++..++++|+++||+.++
T Consensus 135 ~~~-~~~~~~~~~~~~~~~g~~i~v~~~~-~~~~~~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~i~~qa~~~gm~~~~ 212 (382)
T cd06380 135 SDR-GLLRLQQLLDYLREKDNKWQVTARR-VDNVTDEEEFLRLLEDLDRRKEKRIVLDCESERLNKILEQIVDVGKNRKG 212 (382)
T ss_pred CCc-chHHHHHHHHHHhccCCceEEEEEE-ecCCCcHHHHHHHHHHhhcccceEEEEECCHHHHHHHHHHHHHhhhcccc
Confidence 665 6677888999999988 6665432 22222347999999999999999999999999999999999999999999
Q ss_pred eEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcC---CCCCCCccchhHHHhhHHHHH
Q 003275 159 YVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYK---ENSPSGFNSYALYAYDSVWLV 235 (834)
Q Consensus 159 ~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~---~~~~~~~~~~~~~~YDav~~l 235 (834)
|+||.+++.....+. ........++.+++...+..+..++|.++|++.+.. ......++.+++++||||+++
T Consensus 213 y~~i~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~aYDav~~~ 287 (382)
T cd06380 213 YHYILANLGFDDIDL-----SKFLFGGVNITGFQLVDNTNPTVQKFLQRWKKLDPREWPGAGTSPIKYTAALAHDAVLVM 287 (382)
T ss_pred eEEEEccCCcccccH-----HHhccCceeeEEEeccCCCCHHHHHHHHHHHhcCccccCcCCcCCcchHHHHHHHHHHHH
Confidence 999998754433322 011122234677777777788999999999988731 112234677999999999999
Q ss_pred HHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeec
Q 003275 236 AHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGG 315 (834)
Q Consensus 236 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~ 315 (834)
|+|++++...+++..+..... ....+..|.....++|.+|.+|+++|++++|+|++|+++||++|++.+..++|+++++
T Consensus 288 a~Al~~~~~~~~~~~~~~~~~-~~~~~~~C~~~~~~~~~~g~~i~~~l~~~~~~G~tG~i~Fd~~G~~~~~~~~i~~~~~ 366 (382)
T cd06380 288 AEAFRSLRRQRGSGRHRIDIS-RRGNGGDCLANPAVPWEHGIDIERALKKVQFEGLTGNVQFDEFGQRTNYTLDVVELKT 366 (382)
T ss_pred HHHHHHHHHhccccccccccc-cCCCCCcCCCCCCCCccchHHHHHHHHhcccCCcccceEECCCCCcccccEEEEEecC
Confidence 999999876543211110000 0112223333455679999999999999999999999999999999889999999999
Q ss_pred cceEEEEEecCCCCc
Q 003275 316 TGSRRIGYWSNYSGL 330 (834)
Q Consensus 316 ~~~~~vG~w~~~~gl 330 (834)
++.++||+|++..||
T Consensus 367 ~~~~~vg~w~~~~g~ 381 (382)
T cd06380 367 RGLRKVGYWNEDDGL 381 (382)
T ss_pred CCceEEEEECCCcCc
Confidence 999999999998875
No 15
>cd06379 PBP1_iGluR_NMDA_NR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore
Probab=100.00 E-value=3e-38 Score=346.69 Aligned_cols=276 Identities=23% Similarity=0.367 Sum_probs=234.8
Q ss_pred CCCcEEEEC-CC-Chh---hHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEE
Q 003275 2 ENEVVAAIG-PQ-SSG---IAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREV 75 (834)
Q Consensus 2 ~~~V~aiiG-p~-~S~---~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v 75 (834)
+++|+|||| +. +|. .+.+++.+++.++||+|+++++++.+++ ..|||+||+.|++..|+.++++++++++|++|
T Consensus 78 ~~~V~aii~~~~~ss~~~~~~~~v~~~~~~~~iP~Is~~a~~~~ls~~~~~~~~~R~~psd~~~~~a~~~~l~~~~w~~v 157 (377)
T cd06379 78 SNQVYAVIVSHPPTSNDHLTPTSVSYTAGFYRIPVVGISTRDSIFSDKNIHLSFLRTVPPYSHQADVWLEMLRSFKWNKV 157 (377)
T ss_pred hcceEEEEEeCCCCCcccccHHHHHHHhhCCCCcEEecccCCccccCccccccEEEecCCHHHHHHHHHHHHHHcCCeEE
Confidence 468999973 33 443 4777888999999999999999999987 46999999999999999999999999999999
Q ss_pred EEEEEcCCcccchHHHHHHHHhcCCc----EEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHh
Q 003275 76 IAIFVDDDYGRNGISVLGDALSKKRA----KISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKS 151 (834)
Q Consensus 76 ~iI~~d~~~g~~~~~~l~~~l~~~g~----~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~ 151 (834)
++||++++||....+.|.+++++.|+ +|+..+.++. +..+++.++.+|++.++|+||++++.+++..++++|.+
T Consensus 158 aii~~~~~~g~~~~~~~~~~~~~~g~~~~~~v~~~~~~~~--~~~d~~~~l~~ik~~~~~vIvl~~~~~~~~~l~~qa~~ 235 (377)
T cd06379 158 ILLVSDDHEGRAAQKRFETLLEEREIEFKIKVEKVVEFEP--GEKNVTSLLQEAKELTSRVILLSASEDDAAVIYRNAGM 235 (377)
T ss_pred EEEEEcCcchhHHHHHHHHHHHhcCCccceeeeEEEecCC--chhhHHHHHHHHhhcCCeEEEEEcCHHHHHHHHHHHHH
Confidence 99999999999999999999999999 8888777764 34789999999999999999999999999999999999
Q ss_pred CCCCCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhH
Q 003275 152 LGMTAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDS 231 (834)
Q Consensus 152 ~g~~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDa 231 (834)
+||++.+|+||.++.+... .+...|++++++..+ ..+++++|||
T Consensus 236 ~g~~~~~~~wi~t~~~~~~-----------~~~~~g~~g~~~~~~-------------------------~~~~~~~yDA 279 (377)
T cd06379 236 LNMTGEGYVWIVSEQAGAA-----------RNAPDGVLGLQLING-------------------------KNESSHIRDA 279 (377)
T ss_pred cCCCCCCEEEEEecccccc-----------ccCCCceEEEEECCC-------------------------CCHHHHHHHH
Confidence 9999999999999876321 134579999987542 1246789999
Q ss_pred HHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCc-cccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEE
Q 003275 232 VWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSL-RVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDV 310 (834)
Q Consensus 232 v~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I 310 (834)
||++|+|++++++... .+ .....|... .+|.+|..|+++|++++|+|++|+|+||++|++....|+|
T Consensus 280 V~~~A~Al~~~~~~~~-~~-----------~~~~~c~~~~~~~~~g~~l~~~l~~v~f~G~tg~i~Fd~~Gd~~~~~~~I 347 (377)
T cd06379 280 VAVLASAIQELFEKEN-IT-----------EPPRECVGNTVIWETGPLFKRALMSSKYPGETGRVEFNDDGDRKFANYDI 347 (377)
T ss_pred HHHHHHHHHHHHcCCC-CC-----------CCCccccCCCCCCcchHHHHHHHHhCCcCCccCceEECCCCCccCccEEE
Confidence 9999999999875211 10 001122222 3588999999999999999999999999999998899999
Q ss_pred EEeeccceEEEEEecCC
Q 003275 311 LNIGGTGSRRIGYWSNY 327 (834)
Q Consensus 311 ~~~~~~~~~~vG~w~~~ 327 (834)
+|+++.++++||+|++.
T Consensus 348 ~~~~~~~~~~VG~w~~~ 364 (377)
T cd06379 348 MNIQNRKLVQVGLYNGD 364 (377)
T ss_pred EEecCCCceEeeEEcCc
Confidence 99999999999999864
No 16
>cd06374 PBP1_mGluR_groupI Ligand binding domain of the group I metabotropic glutamate receptor. Ligand binding domain of the group I metabotropic glutamate receptor, a family containing mGlu1R and mGlu5R, all of which stimulate phospholipase C (PLC) hydrolysis. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes.
Probab=100.00 E-value=3.4e-38 Score=355.21 Aligned_cols=310 Identities=22% Similarity=0.370 Sum_probs=249.0
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
+++|+|||||.+|..+.+++++++.++||+|+++++++.+++ ..||||||+.|+|..|+.++++++++|+|++|++||+
T Consensus 115 ~~~V~aiiGp~~S~~~~ava~~~~~~~iP~Is~~ats~~ls~~~~~p~~fRt~p~d~~~~~al~~l~~~~~W~~Vaii~~ 194 (472)
T cd06374 115 KKPIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSIDLSDKTLFKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHT 194 (472)
T ss_pred CCCeEEEECCCcchHHHHHHHHhhhhcccccccccCchhhcccccCCceEEcCCChHHHHHHHHHHHHHCCCcEEEEEEe
Confidence 358999999999999999999999999999999999999998 5799999999999999999999999999999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
|++||+...+.|.+.+++.|+||++.+.++...+..+++.++.+|++++ ++||++++....+..++++|+++||. .+
T Consensus 195 ~~~yg~~~~~~~~~~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~lk~~~~da~vvv~~~~~~~~~~~l~~a~~~g~~-~~ 273 (472)
T cd06374 195 EGNYGESGMEAFKELAAHEGLCIAHSDKIYSNAGEQSFDRLLRKLRSRLPKARVVVCFCEGMTVRGLLMAMRRLGVG-GE 273 (472)
T ss_pred cchHHHHHHHHHHHHHHHCCeeEEEEEEecCCCchHHHHHHHHHHHhcCCCcEEEEEEechHHHHHHHHHHHHhcCC-Cc
Confidence 9999999999999999999999999888865555689999999999754 55666667788899999999999996 56
Q ss_pred eEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHH---------------HHHHHhhhcCCC-----C-
Q 003275 159 YVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNF---------------ISRWKNLKYKEN-----S- 217 (834)
Q Consensus 159 ~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F---------------~~~~~~~~~~~~-----~- 217 (834)
++||.+++|....... ....+.++|++++.++.+..+++++| .+.|+..+.+.. .
T Consensus 274 ~~wi~s~~~~~~~~~~----~~~~~~~~G~l~~~~~~~~~~~F~~~l~~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~ 349 (472)
T cd06374 274 FQLIGSDGWADRDDVV----EGYEEEAEGGITIKLQSPEVPSFDDYYLKLRPETNTRNPWFREFWQHRFQCRLPGHPQEN 349 (472)
T ss_pred eEEEEecccccchHhh----hcchhhhheeEEEEecCCCCccHHHHHHhCCcccCCCChHHHHHHHHhcCCCcCCccCcC
Confidence 8999998776431111 12346689999998887776666654 456766654210 0
Q ss_pred -C----------C----CccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHH
Q 003275 218 -P----------S----GFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQT 282 (834)
Q Consensus 218 -~----------~----~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~ 282 (834)
. . ....++.++|||||++|+|||+++.+.... ....|.... ..+|.+|+++
T Consensus 350 ~~~~~~c~~~~~~~~~~~~~~~~~~vyDAVyaiA~ALh~~~~~~~~~-------------~~~~c~~~~-~~~~~~l~~~ 415 (472)
T cd06374 350 PNYIKICTGNESLDEQYVQDSKMGFVINAIYAMAHGLHNMHQDLCPG-------------HVGLCDAMK-PIDGRKLLEY 415 (472)
T ss_pred CccCCCCCCcccccccccccceeHHHHHHHHHHHHHHHHHHHhhCCC-------------CCCCCcCCC-CCCHHHHHHH
Confidence 0 0 012456689999999999999998643211 011233222 2369999999
Q ss_pred HHhccccccee-eEEEccCCCCCCCcEEEEEeec-----cceEEEEEecCCCCccc
Q 003275 283 LLRMNFTGLSG-EIRFDADKNLVNPAYDVLNIGG-----TGSRRIGYWSNYSGLSV 332 (834)
Q Consensus 283 l~~~~f~g~tG-~i~Fd~~g~~~~~~~~I~~~~~-----~~~~~vG~w~~~~gl~~ 332 (834)
|++++|+|++| +|.||++|++. ..|+|+|++. .++++||+|++ .+|.+
T Consensus 416 l~~v~F~g~tG~~v~Fd~~G~~~-~~ydI~n~~~~~~~~~~~~~VG~w~~-~~l~~ 469 (472)
T cd06374 416 LLKTSFSGVSGEEVYFDENGDSP-GRYDIMNLQYTEDLRFDYINVGSWHE-GDLGI 469 (472)
T ss_pred HHhCcccCCCCCeEEEcCCCCCC-CceEEEEEEECCCCCEEEEEEEEEeC-Ccccc
Confidence 99999999999 69999999975 6899999984 25799999974 35553
No 17
>cd06375 PBP1_mGluR_groupII Ligand binding domain of the group II metabotropic glutamate receptor. Ligand binding domain of the group II metabotropic glutamate receptor, a family that contains mGlu2R and mGlu3R, all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes
Probab=100.00 E-value=5e-38 Score=350.56 Aligned_cols=302 Identities=20% Similarity=0.393 Sum_probs=248.0
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|+|||||.+|..+.+++++++.++||+||+++++|.|++ .+||||||+.|+|..|+.|+++++++|||++|++||.|
T Consensus 104 ~~V~aVIG~~~S~~s~ava~~~~~~~IP~Is~~sts~~Ls~~~~~~~ffRt~psd~~qa~ai~~ll~~~~W~~Vaii~~~ 183 (458)
T cd06375 104 LAIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASE 183 (458)
T ss_pred CCeEEEEcCCCchHHHHHHHHhhhccccceeeccCChhhcccccCCCeEEecCCcHHHHHHHHHHHHHCCCeEEEEEEeC
Confidence 47999999999999999999999999999999999999998 67999999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc-CCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANL-MESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~-~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
++||+..++.|.+++++.|+||+..+.++...+..++..++++|++ .++||||+.++..++..++++|.++|+. ++
T Consensus 184 ~~yG~~~~~~~~~~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~l~~~~~a~vVvl~~~~~~~~~ll~~a~~~g~~---~~ 260 (458)
T cd06375 184 GDYGETGIEAFEQEARLRNICIATSEKVGRSADRKSYDSVIRKLLQKPNARVVVLFTRSEDARELLAAAKRLNAS---FT 260 (458)
T ss_pred chHHHHHHHHHHHHHHHCCeeEEEEEEecCCCCHHHHHHHHHHHhccCCCEEEEEecChHHHHHHHHHHHHcCCc---EE
Confidence 9999999999999999999999998888766566899999999875 6899999999999999999999999985 79
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHH---------------HHHHhhhcCCCC--------
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFI---------------SRWKNLKYKENS-------- 217 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~---------------~~~~~~~~~~~~-------- 217 (834)
||.+++|....... ....+.++|++++.+.....+++++|+ +.|+..|.+...
T Consensus 261 wigs~~~~~~~~~~----~~~~~~~~G~i~~~~~~~~i~~f~~yl~~l~p~~~~~n~w~~e~w~~~f~c~~~~~~~~~~~ 336 (458)
T cd06375 261 WVASDGWGAQESIV----KGSEDVAEGAITIELASHPIPDFDRYFQSLTPETNTRNPWFKDFWEQKFQCSLQNRDCANTT 336 (458)
T ss_pred EEEeccccccchhh----hccchhhceEEEEEeccccchhHHHHHHhCCcCcCCCCcHHHHHHHHHcCCCCCCCCccCCC
Confidence 99999876321111 112356899999998876666665554 457666651100
Q ss_pred -----C------CCccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHH-HHHHh
Q 003275 218 -----P------SGFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFL-QTLLR 285 (834)
Q Consensus 218 -----~------~~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~-~~l~~ 285 (834)
. .....+..++||||+++|||||+++.+.... ....|.....+ ++.+|+ +.|++
T Consensus 337 C~~~~~~~~~~~~~~~~~~~~v~~AVyA~AhaLh~~l~~~c~~-------------~~~~c~~~~~~-~~~~l~~~~L~~ 402 (458)
T cd06375 337 TNDKERLLDKVNYEQESKIMFVVNAVYAMAHALHNMQRDLCPN-------------TTKLCDAMKPL-DGKKLYKEYLLN 402 (458)
T ss_pred CCchhcccccCcccccchHHHHHHHHHHHHHHHHHHHHhcCCC-------------CCCCCCCCCCC-CHHHHHHHHHHh
Confidence 0 0123468889999999999999998653321 01134444445 588999 59999
Q ss_pred cccc-----ccee-eEEEccCCCCCCCcEEEEEeec--cc----eEEEEEecC
Q 003275 286 MNFT-----GLSG-EIRFDADKNLVNPAYDVLNIGG--TG----SRRIGYWSN 326 (834)
Q Consensus 286 ~~f~-----g~tG-~i~Fd~~g~~~~~~~~I~~~~~--~~----~~~vG~w~~ 326 (834)
++|. |.+| +|.||++|+. ...|+|+|++. ++ .++||.|+.
T Consensus 403 v~F~~~~~~~~~g~~v~Fd~nGd~-~~~YdI~n~q~~~~~~~~~~~~VG~w~~ 454 (458)
T cd06375 403 VSFTAPFRPDLADSEVKFDSQGDG-LGRYNIFNYQRTGNSYGYRYVGVGAWAN 454 (458)
T ss_pred ccccccccCCCCCCeeEECCCCCC-CcceEEEEEEEcCCCCcEEEEEEEEEec
Confidence 9999 9998 5999999995 57899999983 22 579999964
No 18
>cd06376 PBP1_mGluR_groupIII Ligand-binding domain of the group III metabotropic glutamate receptor. Ligand-binding domain of the group III metabotropic glutamate receptor, a family which contains mGlu4R, mGluR6R, mGluR7, and mGluR8; all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes.
Probab=100.00 E-value=5.3e-38 Score=353.17 Aligned_cols=304 Identities=18% Similarity=0.368 Sum_probs=247.2
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|+|||||.+|..+.+++++++.++||+|++++++|.+++ .+||||||+.|+|..|+.|+++++++|+|++|++||.|
T Consensus 102 ~~V~aviG~~~S~~t~ava~i~~~~~iP~Is~~ats~~ls~~~~~~~ffR~~p~d~~~~~ai~~~i~~~~w~~Vaii~~~ 181 (463)
T cd06376 102 EKVVGVIGASASSVSIMVANILRLFQIPQISYASTAPELSDDRRYDFFSRVVPPDSFQAQAMVDIVKALGWNYVSTLASE 181 (463)
T ss_pred CCeEEEECCCCchHHHHHHHHhccccCcccccccCChhhcccccCCceEEccCCHHHHHHHHHHHHHHcCCeEEEEEEeC
Confidence 58999999999999999999999999999999999999987 67999999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHhhc-CCceEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 82 DDYGRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGANL-MESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~-~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
++||...++.|.+++++. |+||.....++...+..|+..++++|++ .++|+||+.++..++..++++|+++|+++ .|
T Consensus 182 ~~yg~~~~~~~~~~~~~~g~~~v~~~~~i~~~~~~~d~~~~l~~ik~~~~~~vIvl~~~~~~~~~ll~~a~~~~~~g-~~ 260 (463)
T cd06376 182 GNYGESGVEAFTQISREAGGVCIAQSIKIPREPRPGEFDKIIKRLLETPNARAVIIFANEDDIRRVLEAAKRANQVG-HF 260 (463)
T ss_pred ChHHHHHHHHHHHHHHHcCCceEEEEEecCCCCCHHHHHHHHHHHhccCCCeEEEEecChHHHHHHHHHHHhcCCcC-ce
Confidence 999999999999999987 5788776666655566899999999986 69999999999999999999999999875 59
Q ss_pred EEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHH---------------HHHHhhhcCCCC----C--
Q 003275 160 VWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFI---------------SRWKNLKYKENS----P-- 218 (834)
Q Consensus 160 vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~---------------~~~~~~~~~~~~----~-- 218 (834)
+||.++++........ ...+.+.|++++.+.....+++++|. +.|+..|.+... +
T Consensus 261 ~wig~d~~~~~~~~~~----~~~~~~~G~~~~~~~~~~~~~F~~~~~~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~~ 336 (463)
T cd06376 261 LWVGSDSWGAKISPIL----QQEDVAEGAITILPKRASIEGFDAYFTSRTLENNRRNVWFAEFWEENFNCKLTISGSKKE 336 (463)
T ss_pred EEEEeccccccccccc----cCcceeeeEEEEEeccccchhHHHHHHhCCcccCCCCcHHHHHHHHhCCCcccCCCCccc
Confidence 9999998764332211 11256889999988766666555544 467765542100 0
Q ss_pred -----------------CCccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHH
Q 003275 219 -----------------SGFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQ 281 (834)
Q Consensus 219 -----------------~~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~ 281 (834)
......++++|||||++|+|||+++.+.... ....|.... |.+|.+|++
T Consensus 337 ~~~~~C~~~~~~~~~~~~~~~~~~~~v~dAVyaiA~ALh~l~~~~c~~-------------~~~~C~~~~-~~~~~~l~~ 402 (463)
T cd06376 337 DTDRKCTGQERIGRDSTYEQEGKVQFVIDAVYAMAHALHSMHKDLCPG-------------YTGVCPEME-PADGKKLLK 402 (463)
T ss_pred cccCcCcchhhccccCcccccchhHHHHHHHHHHHHHHHHHHHhhCCC-------------CCCCCccCC-CCCHHHHHH
Confidence 0012267899999999999999998653211 011233322 457999999
Q ss_pred HHHhccccccee-eEEEccCCCCCCCcEEEEEeec-----cceEEEEEecC
Q 003275 282 TLLRMNFTGLSG-EIRFDADKNLVNPAYDVLNIGG-----TGSRRIGYWSN 326 (834)
Q Consensus 282 ~l~~~~f~g~tG-~i~Fd~~g~~~~~~~~I~~~~~-----~~~~~vG~w~~ 326 (834)
+|++++|+|++| +|.||++|++. ..|+|+|++. .+.++||.|++
T Consensus 403 ~L~~v~F~g~tg~~v~Fd~~G~~~-~~Ydi~n~q~~~~~~~~~~~VG~w~~ 452 (463)
T cd06376 403 YIRAVNFNGSAGTPVMFNENGDAP-GRYDIFQYQITNTSSPGYRLIGQWTD 452 (463)
T ss_pred HHHhCCccCCCCCeEEeCCCCCCC-CceEEEEEEecCCCceeEEEEEEECC
Confidence 999999999999 69999999964 6899999982 35889999975
No 19
>cd06361 PBP1_GPC6A_like Ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor. This family includes the ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor, and its fish homolog, the 5.24 chemoreceptor. GPRC6A is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses.
Probab=100.00 E-value=9.8e-38 Score=342.30 Aligned_cols=284 Identities=25% Similarity=0.337 Sum_probs=238.2
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|+|||||.+|..+.+++++++.++||+|||++++|.|++ .+||||||+.|+|..|+.++++++++|||++|++|++|
T Consensus 102 ~~V~aVIG~~~S~~s~ava~v~~~~~IP~IS~~ats~~Ls~~~~~~~ffRt~p~D~~qa~ai~~li~~~~w~~Vaii~~~ 181 (403)
T cd06361 102 PRIKAVIGAGYSEISMAVSRMLNLQLIPQVSYASTAEILSDKIRFPSFLRTVPSDFYQTKAMAHLIKKSGWNWVGIIITD 181 (403)
T ss_pred CCeEEEECCCcchHHHHHHHHhccCCcceEecCcCCcccCCcccCCCeeECCCchHhHHHHHHHHHHHcCCcEEEEEEec
Confidence 58999999999999999999999999999999999999997 68999999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCCh-----HHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASR-----SAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~-----~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
++||+...+.|.+++++.|+||+..+.++...++ .+++.+++.++.+++||||+.++..++..++++|+++|+
T Consensus 182 d~yG~~~~~~f~~~~~~~GicIa~~e~~~~~~~~~~~~~~~~~~~~~~ik~~~a~vVvv~~~~~~~~~l~~~a~~~g~-- 259 (403)
T cd06361 182 DDYGRSALETFIIQAEANGVCIAFKEILPASLSDNTKLNRIIRTTEKIIEENKVNVIVVFARQFHVFLLFNKAIERNI-- 259 (403)
T ss_pred CchHHHHHHHHHHHHHHCCeEEEEEEEecCccCcchhHHHHHHHHHHHHhcCCCeEEEEEeChHHHHHHHHHHHHhCC--
Confidence 9999999999999999999999999988765322 455666677889999999999999999999999999998
Q ss_pred CCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHH
Q 003275 157 GSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVA 236 (834)
Q Consensus 157 ~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la 236 (834)
+++||.+++|........ ....+.+.|++++.+..+..+ .|.+.+++.+ ..++||||+++|
T Consensus 260 -~~~wigs~~w~~~~~~~~---~~~~~~~~g~ig~~~~~~~~~---~F~~~~~~~~------------~~~v~~AVyaiA 320 (403)
T cd06361 260 -NKVWIASDNWSTAKKILT---DPNVKKIGKVVGFTFKSGNIS---SFHQFLKNLL------------IHSIQLAVFALA 320 (403)
T ss_pred -CeEEEEECcccCcccccc---CCcccccceEEEEEecCCccc---hHHHHHHHhh------------HHHHHHHHHHHH
Confidence 589999998865332221 112356789999988765544 4555555543 346899999999
Q ss_pred HHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeecc
Q 003275 237 HALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGGT 316 (834)
Q Consensus 237 ~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~~ 316 (834)
+|||+++.+. .|...... ++.+|+++|++++|+|++|++.||++|+. ...|+|+|++++
T Consensus 321 ~Al~~~~~~~-------------------~c~~~~~~-~~~~l~~~L~~~~f~g~~~~v~Fd~~gd~-~~~y~I~~~~~~ 379 (403)
T cd06361 321 HAIRDLCQER-------------------QCQNPNAF-QPWELLGQLKNVTFEDGGNMYHFDANGDL-NLGYDVVLWKED 379 (403)
T ss_pred HHHHHhccCC-------------------CCCCCCCc-CHHHHHHHHheeEEecCCceEEECCCCCC-CcceEEEEeEec
Confidence 9999964321 12222122 58999999999999999889999999996 688999999864
Q ss_pred c----eEEEEEecCCC
Q 003275 317 G----SRRIGYWSNYS 328 (834)
Q Consensus 317 ~----~~~vG~w~~~~ 328 (834)
+ +++||.|++.+
T Consensus 380 ~~~~~~~~vg~~~~~~ 395 (403)
T cd06361 380 NGHMTVTIMAEYDPQN 395 (403)
T ss_pred CCcEEEEEEEEEeCCC
Confidence 3 68999999876
No 20
>cd06362 PBP1_mGluR Ligand binding domain of the metabotropic glutamate receptors (mGluR). Ligand binding domain of the metabotropic glutamate receptors (mGluR), which are members of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses. mGluRs bind to glutamate and function as an excitatory neurotransmitter; they are involved in learning, memory, anxiety, and the perception of pain. Eight subtypes of mGluRs have been cloned so far, and are classified into three groups according to their sequence similarities, transduction mechanisms, and pharmacological profiles. Group I is composed of mGlu1R and mGlu5R that both stimulate PLC hydrolysis. Group II includes mGlu2R and mGlu3R, which inhibit adenylyl cyclase, as do mGlu4R, mGlu6R, mGlu7R, and mGlu8R, which form group III.
Probab=100.00 E-value=1.8e-37 Score=349.11 Aligned_cols=309 Identities=22% Similarity=0.385 Sum_probs=251.4
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|+|||||.+|.++.+++++++.+++|+|+++++++.+++ .+||||||+.|++..|+.++++++++|+|++|++|+.|
T Consensus 102 ~~v~aviG~~~S~~~~av~~~~~~~~ip~Is~~sts~~ls~~~~~~~~fR~~p~d~~~~~a~~~~l~~~~w~~vaii~~~ 181 (452)
T cd06362 102 KPVAGVIGASYSSVSIQVANLLRLFKIPQISYASTSPELSDKTRYDYFSRTVPPDSFQAQAMVDIVKAFNWTYVSTVASE 181 (452)
T ss_pred CCeEEEECCCCCchHHHHHHHhccccCcccccccCchhhccccccCCEEEecCChHHHHHHHHHHHHHCCCcEEEEEEeC
Confidence 58999999999999999999999999999999999999987 67999999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc-CCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANL-MESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~-~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
++||....+.|.+.+++.|+||+..+.++...+..+++.++.+|++ .++|+||+.+...++..++++|++.|++ ..++
T Consensus 182 ~~~G~~~~~~~~~~~~~~gi~i~~~~~~~~~~~~~d~~~~l~~l~~~~~a~viil~~~~~~~~~~~~~a~~~g~~-~~~~ 260 (452)
T cd06362 182 GNYGEKGIEAFEKLAAERGICIAGSEKIPSSATEEEFDNIIRKLLSKPNARVVVLFCREDDIRGLLAAAKRLNAE-GHFQ 260 (452)
T ss_pred CHHHHHHHHHHHHHHHHCCeeEEEEEEcCCCCCHHHHHHHHHHHhhcCCCeEEEEEcChHHHHHHHHHHHHcCCc-CceE
Confidence 9999999999999999999999998888765556899999999987 5799999999999999999999999997 5689
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHH---------------HHHHHHhhhcCC----CC----
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKN---------------FISRWKNLKYKE----NS---- 217 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~---------------F~~~~~~~~~~~----~~---- 217 (834)
||.++++....... ....+..+|++++.+.....+.+++ |.+.|+..+.+. ..
T Consensus 261 ~i~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~i~~f~~~l~~l~~~~~~~~~~~~~~w~~~~~c~~~~~~~~~~~ 336 (452)
T cd06362 261 WIASDGWGARNSVV----EGLEDVAEGAITIELQSAEVPGFDEYFLSLTPENNSRNPWFREFWEQKFNCKLTGNGSTKDN 336 (452)
T ss_pred EEEeccccccchhh----cccccccceEEEEEecccccccHHHHhhhCCcCcCCCChHHHHHHHHhcCCCcCCCCccccC
Confidence 99998775432111 1233668899888776655444433 334455444310 00
Q ss_pred -----------CCCccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhc
Q 003275 218 -----------PSGFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRM 286 (834)
Q Consensus 218 -----------~~~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~ 286 (834)
......+++++|||||++|+|||+++.++.... . ..|.... +.+|.+|+++|+++
T Consensus 337 ~~c~~~~~~~~~~~~~~~~~~vyDAV~a~A~AL~~~l~~~~~~~------------~-~~c~~~~-~~~~~~l~~~l~~v 402 (452)
T cd06362 337 TCCTERILLLSNYEQESKVQFVIDAVYAMAHALHNMHRDLCPGT------------T-GLCDAMK-PIDGRKLLFYLRNV 402 (452)
T ss_pred CCCccccccccccccccchhHHHHHHHHHHHHHHHHHHhhCCCC------------C-CCCcCcc-CCCHHHHHHHHHhC
Confidence 012345788999999999999999986532210 0 1133222 45799999999999
Q ss_pred cccccee-eEEEccCCCCCCCcEEEEEeec----cceEEEEEecCCCCcc
Q 003275 287 NFTGLSG-EIRFDADKNLVNPAYDVLNIGG----TGSRRIGYWSNYSGLS 331 (834)
Q Consensus 287 ~f~g~tG-~i~Fd~~g~~~~~~~~I~~~~~----~~~~~vG~w~~~~gl~ 331 (834)
+|+|++| +|+||++|++. ..|+|+|++. .++++||+|++..||+
T Consensus 403 ~f~g~tg~~v~Fd~~G~~~-~~y~I~~~~~~~~~~~~~~VG~w~~~~~~~ 451 (452)
T cd06362 403 SFSGLAGGPVRFDANGDGP-GRYDIFNYQRTNGKYDYVKVGSWKGELSLN 451 (452)
T ss_pred CcCCCCCceEEECCCCCCC-CceEEEEEEEcCCceEEEEEEEEecccccC
Confidence 9999998 79999999975 6999999983 3589999999887654
No 21
>cd06364 PBP1_CaSR Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. CaSR provides feedback control of extracellular calcium homeostasis by responding sensitively to acute fluctuations in extracellular ionized Ca2+ concentration. This ligand-binding domain has homology to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). CaSR is widely expressed in mammalian tissues and is active in tissues that are not directly involved in extracellular calcium homeostasis. Moreover, CaSR responds to aromatic, aliphatic, and polar amino acids, but not to positively charged or branched chain amino acids, which suggests that changes in plasma amino acid levels are likely to modulate whole body calci
Probab=100.00 E-value=5.8e-37 Score=345.48 Aligned_cols=307 Identities=22% Similarity=0.363 Sum_probs=247.7
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
.+|+|||||.+|.++.+++++++.++||+||++++++.+++ .+||||||+.|+|..|+.++++++++|||++|++|+.|
T Consensus 117 ~~v~aVIG~~sS~~s~ava~~~~~~~IP~IS~~sss~~ls~~~~yp~ffRt~psd~~q~~Ai~~l~~~f~wk~VaiI~~d 196 (510)
T cd06364 117 PSTIAVVGATGSGVSTAVANLLGLFYIPQVSYASSSRLLSNKNQFKSFLRTIPNDEHQATAMADIIEYFRWNWVGTIAAD 196 (510)
T ss_pred CceEEEECCCchhHHHHHHHHhccccccccccccCCcccCCccccCCeeEcCCChHHHHHHHHHHHHHcCCeEEEEEEec
Confidence 35789999999999999999999999999999999999998 67999999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
++||+...+.|.+++++.|+||+..+.++...+..++.+++.+|+++++||||+.+...++..++++|+++|+. +++|
T Consensus 197 d~yG~~~~~~~~~~~~~~Gi~I~~~~~i~~~~~~~d~~~~l~klk~~~a~vVvl~~~~~~~~~ll~qa~~~g~~--~~iw 274 (510)
T cd06364 197 DDYGRPGIEKFREEAEERDICIDFSELISQYSDEEEIQRVVEVIQNSTAKVIVVFSSGPDLEPLIKEIVRRNIT--GKIW 274 (510)
T ss_pred CcchHHHHHHHHHHHHHCCcEEEEEEEeCCCCCHHHHHHHHHHHHhcCCeEEEEEeCcHHHHHHHHHHHHhCCC--CcEE
Confidence 99999999999999999999999988777544568999999999999999999999999999999999999985 4799
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHH---------------HHHHhhhcCC-----CC----
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFI---------------SRWKNLKYKE-----NS---- 217 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~---------------~~~~~~~~~~-----~~---- 217 (834)
|.+++|....... ++...+.+.|++++.+.....+++++|+ +.|+..|.+. ..
T Consensus 275 I~s~~w~~~~~~~---~~~~~~~~gg~lg~~~~~~~i~~f~~~l~~l~p~~~~~~~~~~~~we~~f~c~~~~~~~~~~~~ 351 (510)
T cd06364 275 LASEAWASSSLIA---MPEYFDVMGGTIGFALKAGQIPGFREFLQKVHPKKSSHNGFAKEFWEETFNCYLEDSPKNALPV 351 (510)
T ss_pred EEEchhhcccccc---cCCccceeeEEEEEEECCCcCccHHHHHHhCCcccCCCChHHHHHHHHhcCCCCCCCccccccc
Confidence 9998775432221 1234577899999988765555444433 4466555411 00
Q ss_pred --------------------C-C-----------------CccchhHHHhhHHHHHHHHHHHHHhcCCC-ccccCCCCCC
Q 003275 218 --------------------P-S-----------------GFNSYALYAYDSVWLVAHALDALLNEGGK-FTFSNDPKLH 258 (834)
Q Consensus 218 --------------------~-~-----------------~~~~~~~~~YDav~~la~Al~~~~~~~~~-~~~~~~~~~~ 258 (834)
. . ....+..++|||||++|||||+++.+... ..++
T Consensus 352 ~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~v~~AVyAvAhaLh~~~~c~~~~~~~~------ 425 (510)
T cd06364 352 DTFLGHEESGDDSENGSTAFRPLCTGDENIASVETPYLDYTHLRISYNVYLAVYSIAHALQDIYTCTPGKGLFT------ 425 (510)
T ss_pred ccccccccccccccccccccCCCCCChhhhcccCCccccccchhhHHHHHHHHHHHHHHHHHHhcCCCCCCCcc------
Confidence 0 0 01234677999999999999999876422 1110
Q ss_pred CCCCCCccCCCccccCchHHHHHHHHhccccccee-eEEEccCCCCCCCcEEEEEeec---cc---eEEEEEecCC
Q 003275 259 DTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSG-EIRFDADKNLVNPAYDVLNIGG---TG---SRRIGYWSNY 327 (834)
Q Consensus 259 ~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG-~i~Fd~~g~~~~~~~~I~~~~~---~~---~~~vG~w~~~ 327 (834)
...|...... ++.+|+++|++++|+|.+| ++.||++|+. ...|+|+||+. ++ .++||.|++.
T Consensus 426 -----~~~c~~~~~~-~~~~l~~~L~~v~F~~~~g~~v~Fd~~Gd~-~~~YdI~n~q~~~~~~~~~~v~VG~~~~~ 494 (510)
T cd06364 426 -----NGSCADIKKV-EAWQVLKHLRHLNFTDNMGEQVRFDEGGDL-VGNYSIINWHLSPEDGSVVFKEVGYYNVY 494 (510)
T ss_pred -----CCCCCCCCCC-CHHHHHHHHHhcEEecCCCCEEEEecCCCC-ccceeEEEeeecCCCCcEEEEEEEEEcCC
Confidence 1124443334 4889999999999999998 5999999996 57999999983 22 5799999864
No 22
>cd06386 PBP1_NPR_C_like Ligand-binding domain of type C natriuretic peptide receptor. Ligand-binding domain of type C natriuretic peptide receptor (NPR-C). NPR-C is found in atrial, mesentery, placenta, lung, kidney, venous tissue, aortic smooth muscle, and aortic endothelial cells. The affinity of NPR-C for natriuretic peptides is ANPCNPBNP. The extracellular domain of NPR-C is about 30% identical to NPR-A and NPR-B. However, unlike the cyclase-linked receptors, it contains only 37 intracellular amino acids and no guanylyl cyclase activity. Major function of NPR-C is to clear natriuretic peptides from the circulation or extracellular surroundings through constitutive receptor-mediated internalization and degradation.
Probab=100.00 E-value=9e-37 Score=334.91 Aligned_cols=296 Identities=20% Similarity=0.289 Sum_probs=243.9
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC--CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS--LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIF 79 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~--~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~ 79 (834)
+++|.|||||.||..+.+++++++.++||+|+++++++.+++ ..|||+||+.|++..++.++++++++|+|++|++||
T Consensus 65 ~~~v~aiiGp~~s~~~~~va~ia~~~~iP~Is~~a~~~~~s~~~~~yp~~~R~~p~~~~~~~a~~~ll~~~~W~~vaiiy 144 (387)
T cd06386 65 ARKPDLILGPVCEYAAAPVARLASHWNIPMISAGALAAGFSHKKSEYSHLTRVAPSYVKMGETFSALFERFHWRSALLVY 144 (387)
T ss_pred hhCCCEEECCCCccHHHHHHHHHHhCCCcEEccccCchhhccCcccCCeeEEecCchHHHHHHHHHHHHhCCCeEEEEEE
Confidence 358999999999999999999999999999999999999986 358999999999999999999999999999999999
Q ss_pred EcCCcccch---HHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 80 VDDDYGRNG---ISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 80 ~d~~~g~~~---~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
++++||+.. ++.|.+++++.|++|+.....+. .+.++..+|.++++.+ |+||++++.+.+..++++|+++||++
T Consensus 145 ~~~~~~~~~~~~~~~l~~~~~~~gi~v~~~~~~~~--~~~d~~~~l~~ik~~~-rvii~~~~~~~~~~ll~~A~~~gm~~ 221 (387)
T cd06386 145 EDDKQERNCYFTLEGVHHVFQEEGYHMSIYPFDET--KDLDLDEIIRAIQASE-RVVIMCAGADTIRSIMLAAHRRGLTS 221 (387)
T ss_pred EcCCCCccceehHHHHHHHHHhcCceEEEEecCCC--CcccHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCC
Confidence 999999886 89999999999999987665542 3468999999999887 99999999999999999999999999
Q ss_pred CCeEEEEeCCCc-ccCCC-----CCCCC---hhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCC---CCCCCccch
Q 003275 157 GSYVWIATDWLP-SVLDS-----TEPVD---IDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKE---NSPSGFNSY 224 (834)
Q Consensus 157 ~~~vwi~~~~~~-~~~~~-----~~~~~---~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~---~~~~~~~~~ 224 (834)
.+|+||..+... ..... ....+ ....+.++|+.+++++ .+++++|.+++++++... .....++.+
T Consensus 222 ~~yv~i~~d~~~~~~~~~~~w~~~~~~~~~~~~a~~~~~~v~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~ 298 (387)
T cd06386 222 GDYIFFNIELFNSSSYGDGSWKRGDKHDFEAKQAYSSLNTVTLLRTV---KPEFEKFSMEVKSSVEKAGDLNDCDYVNMF 298 (387)
T ss_pred CCEEEEEEecccccccCCCCCccCCCcCHHHHHHHHhheEEeccCCC---ChHHHHHHHHHHHHHHhCCCCcccccchHH
Confidence 999999998663 11110 01122 1233455566555544 567888999988554311 111235688
Q ss_pred hHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCC
Q 003275 225 ALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLV 304 (834)
Q Consensus 225 ~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~ 304 (834)
++++||||+++|+|+++++..++. +.+|..|.++|++++|+|++|++.||++|++.
T Consensus 299 aa~~yDav~l~A~Al~~~~~~g~~------------------------~~~g~~l~~~l~~~~f~G~tG~v~~d~~g~r~ 354 (387)
T cd06386 299 VEGFHDAILLYALALHEVLKNGYS------------------------KKDGTKITQRMWNRTFEGIAGQVSIDANGDRY 354 (387)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCCC------------------------CCCHHHHHHHHhCCceeeccccEEECCCCCcc
Confidence 999999999999999998754321 34799999999999999999999999999985
Q ss_pred CCcEEEEEeec---cceEEEEEecCCC
Q 003275 305 NPAYDVLNIGG---TGSRRIGYWSNYS 328 (834)
Q Consensus 305 ~~~~~I~~~~~---~~~~~vG~w~~~~ 328 (834)
..|.|+.+++ ++++.||.|...+
T Consensus 355 -~~~~v~~~~~~~~~~~~~~~~~~~~~ 380 (387)
T cd06386 355 -GDFSVIAMTDVEAGTYEVVGNYFGKN 380 (387)
T ss_pred -ccEEEEEccCCCCccEEEEeEEcccc
Confidence 6999999964 5689999997543
No 23
>cd06378 PBP1_iGluR_NMDA_NR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=100.00 E-value=3.3e-37 Score=331.50 Aligned_cols=285 Identities=16% Similarity=0.244 Sum_probs=226.5
Q ss_pred CcEEEE-CCCChh--hHHHHHHhhccCCccEEecccCCC-CCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEE
Q 003275 4 EVVAAI-GPQSSG--IAHVISHVVNELNVPLLSFGATDP-TLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAI 78 (834)
Q Consensus 4 ~V~aii-Gp~~S~--~~~~~~~~~~~~~vP~Is~~at~~-~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI 78 (834)
+|+||| ||.++. .+..++.++++++||+|+++++++ .+++ .++|||+|+.|++..|+.||++++++|+|++|++|
T Consensus 62 ~V~aiIfgp~~~~~~~a~~~s~~~~~~~vP~is~~~~s~~~ls~~~~~p~flr~~Psd~~q~~Ai~~Ii~~f~W~~v~iV 141 (362)
T cd06378 62 KVHGVVFEDDTDQEAVAQILDFISAQTFLPILGIHGGSSMIMAAKDSGSTFLQFGPSIEQQAAVMLKIMEEYDWHAFSVV 141 (362)
T ss_pred ceEEEEecCCCCccccchhhhhhhhceeccEEEecccccccccCCCCCceEEEeCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence 699755 999997 567888899999999999987765 5566 67999999999999999999999999999999999
Q ss_pred EEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCC-hHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCC
Q 003275 79 FVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGAS-RSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 79 ~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~-~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~ 157 (834)
|++++.+..+.+.+++.++..++|+.....++...+ +..+..++.+++..++||||++|+.+.+..++++|+++||+++
T Consensus 142 ~~~~~g~~~~~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~lk~~~arViVl~~s~~~a~~if~~A~~~gm~g~ 221 (362)
T cd06378 142 TSRFPGYDDFVSAVRTTVDNSFVGWELQSVLTLDMSDDDGDARTQRQLKKLESQVILLYCSKEEAEYIFRAARSAGLTGP 221 (362)
T ss_pred EEcCCCHHHHHHHHHHHHhhcccceeEEEEEeeccCCCcchHHHHHHHHhcCCCEEEEECCHHHHHHHHHHHHHcCCcCC
Confidence 999887777888888887776676654444443322 2347889999999999999999999999999999999999999
Q ss_pred CeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHH
Q 003275 158 SYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAH 237 (834)
Q Consensus 158 ~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~ 237 (834)
+|+||++++.....+.. ..+...|++++.. ++|++. +.+..||||+++|+
T Consensus 222 ~yvWI~t~~~~~~~~~~------~~~~~~G~i~v~~------------~~w~~~------------~~a~~~DaV~vva~ 271 (362)
T cd06378 222 GYVWIVPSLVLGNTDLG------PSEFPVGLISVSY------------DGWRYS------------LRARVRDGVAIIAT 271 (362)
T ss_pred CeEEEecccccCCCccc------cccCCcceEeecc------------cccccc------------HHHHHHHHHHHHHH
Confidence 99999999876553221 0134577777653 234321 25578999999999
Q ss_pred HHHHHHhcCCCccccCCCCCCCCCCCCccCCC-cc-ccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeec
Q 003275 238 ALDALLNEGGKFTFSNDPKLHDTNGSMLNLSS-LR-VFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGG 315 (834)
Q Consensus 238 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~ 315 (834)
|++.++++.+.++. ...+|.. .. +|..|..|+++|++++|+|+ +++||++|++.++.|+|+|+++
T Consensus 272 Al~~l~~~~~~~~~-----------~~~~C~~~~~~~~~~G~~l~~~l~~v~~~G~--~i~F~~~G~r~~~~ldIinl~~ 338 (362)
T cd06378 272 GASAMLRQHGFIPE-----------AKGSCYGQAEKRDLPPNTLHRYMMNVTWEGR--DLSFTEDGYLVNPKLVVISLNK 338 (362)
T ss_pred HHHHHHhccCCCCC-----------CCCCcCCCCCCCCCchHHHHHHhhcceECCC--ceeECCCCeEccceEEEEEecC
Confidence 99998765444321 1112322 22 48899999999999999997 9999999999999999999996
Q ss_pred -cceEEEEEecCCCCccc
Q 003275 316 -TGSRRIGYWSNYSGLSV 332 (834)
Q Consensus 316 -~~~~~vG~w~~~~gl~~ 332 (834)
.+|++||+|+++ +|.+
T Consensus 339 ~~g~~kVG~W~~~-~L~~ 355 (362)
T cd06378 339 ERVWEEVGKWENG-SLRL 355 (362)
T ss_pred CCCceEEEEEcCC-eEEE
Confidence 599999999844 3443
No 24
>cd06385 PBP1_NPR_A Ligand-binding domain of type A natriuretic peptide receptor. Ligand-binding domain of type A natriuretic peptide receptor (NPR-A). NPR-A is one of three known single membrane-spanning natriuretic peptide receptors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. In mammals there are three natriuretic peptides: ANP, BNP, and CNP. NPR-A is highly expressed in kidney, adrenal, terminal ileum, adipose, aortic, and lung tissues. The rank order of NPR-A activation by natriuretic peptides is ANPBNPCNP. Single allele-inactivating mutations in the promoter of human NPR-A are associated with hypertension and heart failure.
Probab=100.00 E-value=2.4e-35 Score=326.98 Aligned_cols=298 Identities=21% Similarity=0.254 Sum_probs=245.0
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEE-EEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIA-IFV 80 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~i-I~~ 80 (834)
++|.|||||.||..+.+++++++.++||+||++++++.+++ .+|||+||+.|++..++.++++++++|+|+++++ +|.
T Consensus 73 ~~v~aiiGp~~S~~~~~va~~a~~~~iP~Is~~a~~~~l~~~~~~~~~~R~~p~~~~~~~a~~~~~~~~~w~~va~ii~~ 152 (405)
T cd06385 73 HNPWAFIGPGCDYTASPVARFTTHWDVPLVTAGAPALGFGVKDEYATITRTGPTHKKLGEFVLHIHQHFGWRSHAMLIYS 152 (405)
T ss_pred cCCcEEECCCccchHHHHHHHHhccCCcEEccccChhhcCCcccCcceEEecCchHHHHHHHHHHHHhCCCeEEEEEEEe
Confidence 58999999999999999999999999999999999999987 6799999999999999999999999999999984 565
Q ss_pred cCC-cccc---hHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 81 DDD-YGRN---GISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 81 d~~-~g~~---~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
|+. +|+. ..+.+.+.+++.|++|+..+..+. +..+++.+|.+|++.. |+||++++...+..++++|.++||++
T Consensus 153 ~~~~~~~~~~~~~~~l~~~~~~~gi~v~~~~~~~~--~~~d~~~~l~~ik~~~-~iii~~~~~~~~~~i~~~a~~~g~~~ 229 (405)
T cd06385 153 DNKVDDRPCYFAMEGLYMELKKNNITVVDLVFEED--DLINYTTLLQDIKQKG-RVIYVCCSPDIFRRLMLQFWREGLPS 229 (405)
T ss_pred cCcccccchHHHHHHHHHHHHhCCeEEEEeeccCC--chhhHHHHHHHHhhcc-eEEEEeCCHHHHHHHHHHHHHcCCCC
Confidence 543 3333 468899999999999998764432 3578999999998754 99999999999999999999999999
Q ss_pred CCeEEEEeCCCcccCCC---------CCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhh----hcCCCCCCCccc
Q 003275 157 GSYVWIATDWLPSVLDS---------TEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNL----KYKENSPSGFNS 223 (834)
Q Consensus 157 ~~~vwi~~~~~~~~~~~---------~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~----~~~~~~~~~~~~ 223 (834)
++|+||.++++...++. ....+....+++++++.+..+.+.++..++|.++|+++ +........++.
T Consensus 230 ~~y~~i~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~ 309 (405)
T cd06385 230 EDYVFFYIDLFGASLQGPDPKRPWYRGDADDAAAREAFQSVKILTYKEPQNPEYKEFLSDLKTDAKEMFNFTVEDSLMNI 309 (405)
T ss_pred CcEEEEEeecchhhccCCCCCCCCCCCCcccHHHHHhhheeEEEeCCCCCChhHHHHHHHHHHHhhccCCCccchhhHHH
Confidence 99999998765432221 01112344577899988887878888899999999885 311111112678
Q ss_pred hhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCC
Q 003275 224 YALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNL 303 (834)
Q Consensus 224 ~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~ 303 (834)
+++++|||||++|+|++++++..+. +.+|++|.++|++++|+|++|++.||++|++
T Consensus 310 ~aa~~YDav~l~a~Al~~~~~~~~~------------------------~~~g~~i~~~l~~~~f~G~tG~v~fd~~G~r 365 (405)
T cd06385 310 IAGGFYDGVMLYAHALNETMAKGGT------------------------RPPGTAITQRMWNRTFYGVTGFVKIDDNGDR 365 (405)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCC------------------------CCCHHHHHHHhhCceEeeceeEEEEcCCCCE
Confidence 9999999999999999998665332 3369999999999999999999999999998
Q ss_pred CCCcEEEEEe---eccceEEEEEecCCC
Q 003275 304 VNPAYDVLNI---GGTGSRRIGYWSNYS 328 (834)
Q Consensus 304 ~~~~~~I~~~---~~~~~~~vG~w~~~~ 328 (834)
. +.|.++++ ++++++.||+|+..+
T Consensus 366 ~-~~~~~~~~~~~~~g~~~~v~~~~~~~ 392 (405)
T cd06385 366 E-TDFALWDMTDTESGDFQVVSVYNGTQ 392 (405)
T ss_pred e-ceeEEEEccCCCCCcEEEEEEEcccC
Confidence 5 78888855 677899999998654
No 25
>cd06371 PBP1_sensory_GC_DEF_like Ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. This group includes the ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. They share a similar topology with an N-terminal extracellular ligand-binding domain, a single transmembrane domain, and a C-terminal cytosolic region that contains kinase-like and catalytic domains. GC-D is specifically expressed in a subpopulation of olfactory sensory neurons. GC-E and GC-F are colocalized within the same photoreceptor cells of the retina and have important roles in phototransduction. Unlike the other family members, GC-E and GC-F have no known extracellular ligands. Instead, they are activated under low calcium conditions by guanylyl cyclase activating proteins called GCAPs. GC-D expressing neurons have been implicated in pheromone detection and GC-D is phyloge
Probab=100.00 E-value=6.1e-35 Score=319.54 Aligned_cols=292 Identities=21% Similarity=0.329 Sum_probs=238.0
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
+++|.|||||.||..+.++++++++++||+||+++++|.+++ .+||+|+|+.|++ ..++++++++|+|++|++|++
T Consensus 64 ~~~V~aviGp~~S~~~~a~a~va~~~~iP~Is~~a~~~~lt~~~~y~~f~r~~~~~---~~~~~~~~~~~~w~~vaii~~ 140 (382)
T cd06371 64 EGYASAFVGPVNPGYCEAAALLAKEWDKALFSWGCVNYELDDVRSYPTFARTLPSP---SRVLFTVLRYFRWAHVAIVSS 140 (382)
T ss_pred cCCceEEECCCCchHHHHHHHHHHhcCceEEecccCchhhcCcccCCCceecCCCc---HHHHHHHHHHCCCeEEEEEEe
Confidence 468999999999999999999999999999999999999997 7799999999886 467889999999999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCC-ceEEEEEeCh-----hhHHHHHHHHHhCCC
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLME-SRVFVVHVNP-----DTGLTIFSVAKSLGM 154 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~-~~vivl~~~~-----~~~~~i~~~a~~~g~ 154 (834)
+++||....+.+.+.+++.|++|+....++. +..|++.+|++|+.++ +||||++++. .++..++++|+++||
T Consensus 141 ~~~~~~~~~~~l~~~l~~~gi~v~~~~~~~~--~~~d~~~~L~~lk~~~~~~viv~~~~~~~~~~~~~~~i~~qa~~~Gm 218 (382)
T cd06371 141 PQDIWVETAQKLASALRAHGLPVGLVTSMGP--DEKGAREALKKVRSADRVRVVIMCMHSVLIGGEEQRLLLETALEMGM 218 (382)
T ss_pred cccchHHHHHHHHHHHHHCCCcEEEEEEecC--CHHHHHHHHHHHhcCCCcEEEEEEeeccccCcHHHHHHHHHHHHcCC
Confidence 9999999999999999999999998877764 4479999999999987 6999998775 677899999999999
Q ss_pred CCCCeEEEEeCCCcccCCC----CC--CCChhhHhhcccceEEEecCCCChhHHHHHHHHHhh-hcCCCCCCCccchhHH
Q 003275 155 TAGSYVWIATDWLPSVLDS----TE--PVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNL-KYKENSPSGFNSYALY 227 (834)
Q Consensus 155 ~~~~~vwi~~~~~~~~~~~----~~--~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~-~~~~~~~~~~~~~~~~ 227 (834)
+..+|+||.+++.....+. .. ..+++..++++|++++..+.+..+..+.|.+.|+.. ++...+...++.++++
T Consensus 219 ~~~~y~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~ 298 (382)
T cd06371 219 TDGRYVFIPYDTLLYSLPYRNVSYPALRNNSKLRRAYDAVLTITMDSGEQSFYEAFRAAQERGEIPSDLEPEQVSPLFGT 298 (382)
T ss_pred cCCcEEEEEeccccccCCCCCccccCCCCCHHHHHHhHhhEEEEecCCCCcHHHHHHHHHhcCCCCCCCCccccchhHHH
Confidence 9999999999864311110 01 013455578899988877765555555566554321 1101112234566678
Q ss_pred HhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCc
Q 003275 228 AYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPA 307 (834)
Q Consensus 228 ~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~ 307 (834)
+|||++++|+|++++++.+++ .+|.+++++|++++|+|++|+++||++|++ .+.
T Consensus 299 ~YDav~~~a~Al~~a~~~g~~-------------------------~d~~~l~~~l~~~~f~GvtG~v~fd~~g~~-~~~ 352 (382)
T cd06371 299 IYNSIYLLAHAVENARAAGGG-------------------------VSGANLAQHTRNLEFQGFNQRLRTDSGGGG-QAP 352 (382)
T ss_pred HHHHHHHHHHHHHHHHHhCCC-------------------------ccHHHHHHHHhCccccccceEEEecCCCCc-ccc
Confidence 999999999999998765332 158999999999999999999999999986 699
Q ss_pred EEEEEeeccceEEEEEe
Q 003275 308 YDVLNIGGTGSRRIGYW 324 (834)
Q Consensus 308 ~~I~~~~~~~~~~vG~w 324 (834)
|.|+++.+.++|-+-.+
T Consensus 353 ~~v~~~~~~~~~~~~~~ 369 (382)
T cd06371 353 YVVLDTDGKGDQLYPTY 369 (382)
T ss_pred eEEEecCCCCCeeeeeE
Confidence 99999999888866555
No 26
>cd06373 PBP1_NPR_like Ligand binding domain of natriuretic peptide receptor (NPR) family. Ligand binding domain of natriuretic peptide receptor (NPR) family which consists of three different subtypes: type A natriuretic peptide receptor (NPR-A, or GC-A), type B natriuretic peptide receptors (NPR-B, or GC-B), and type C natriuretic peptide receptor (NPR-C). There are three types of natriuretic peptide (NP) ligands specific to the receptors: atrial NP (ANP), brain or B-type NP (BNP), and C-type NP (CNP). The NP family is thought to have arisen through gene duplication during evolution and plays an essential role in cardiovascular and body fluid homeostasis. ANP and BNP bind mainly to NPR-A, while CNP binds specifically to NPR-B. Both NPR-A and NPR-B have guanylyl cyclase catalytic activity and produces intracellular secondary messenger cGMP in response to peptide-ligand binding. Consequently, the NPR-A activation results in vasodilation and inhibition of vascular smooth muscle cell proli
Probab=100.00 E-value=3.4e-35 Score=324.93 Aligned_cols=300 Identities=22% Similarity=0.308 Sum_probs=247.1
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
+++|.|||||.||..+.+++++++.++||+|++++++|.+++ ..|||+||+.|++..++.++++++++++|++|++||.
T Consensus 71 ~~~v~aiiGp~~S~~~~av~~~~~~~~ip~Is~~as~~~lt~~~~~~~~fr~~p~~~~~~~a~~~~~~~~~w~~vaii~~ 150 (396)
T cd06373 71 QHKPDAFLGPGCEYAAAPVARFAAHWNVPVLTAGAPAAGFSDKSEYSTLTRTGPSYTKLGEFVLALHEHFNWSRAALLYH 150 (396)
T ss_pred ccCCeEEECCCccchhHHHHHHHhcCCCceECccCCccccccchhcCceeeccccHHHHHHHHHHHHHHcCCeEEEEEEE
Confidence 468999999999999999999999999999999999999987 6799999999999999999999999999999999999
Q ss_pred cCCcc----cchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 81 DDDYG----RNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 81 d~~~g----~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
+++++ ....+.+.+++++.|++|+... +.......|+..+|+++++.. |+||++++..++..++++|+++||+.
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~-~~~~~~~~d~~~~l~~ik~~~-~vii~~~~~~~~~~~~~qa~~~g~~~ 228 (396)
T cd06373 151 DDKNDDRPCYFTLEGVYTVLKEENITVSDFP-FDEDKELDDYKELLRDISKKG-RVVIMCASPDTVREIMLAAHRLGLTS 228 (396)
T ss_pred CCCCCcchHHHHHHHHHHHHhhcCceeeEEe-ecCCccccCHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCC
Confidence 88774 4567889999999999988543 432211378999999999875 99999999999999999999999999
Q ss_pred CCeEEEEeCCCcccCCC--------CCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhh----hcCCCCCCCccch
Q 003275 157 GSYVWIATDWLPSVLDS--------TEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNL----KYKENSPSGFNSY 224 (834)
Q Consensus 157 ~~~vwi~~~~~~~~~~~--------~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~----~~~~~~~~~~~~~ 224 (834)
.+|+||..+.....+.. .........+..+|++++..+.++++..++|.++|+++ +....+...++.+
T Consensus 229 ~~yv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~ 308 (396)
T cd06373 229 GEYVFFNIDLFGSSLYGGGPWWWERGDEDDEKAKEAYQALMTITLREPDNPEYKEFSLEVKERAKKKFNTTSDDSLVNFF 308 (396)
T ss_pred CcEEEEEEccchhhhccCCCCcCCCCCcccHHHHHHHHHheEEecCCCCChHHHHHHHHHHHHhhhcCCCCcchhHHHHH
Confidence 99999997755321100 11112344466789999988888888899999999875 3111112246789
Q ss_pred hHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCC
Q 003275 225 ALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLV 304 (834)
Q Consensus 225 ~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~ 304 (834)
++++||||+++|+|++++..+++. +.+|++|.++|++++|+|++|++.||++|++.
T Consensus 309 a~~~YDav~~~a~Al~~~~~~~~~------------------------~~~~~~i~~~l~~~~f~G~tG~v~fd~~G~~~ 364 (396)
T cd06373 309 AGAFYDAVLLYALALNETLAEGGD------------------------PRDGTNITRRMWNRTFEGITGNVSIDENGDRE 364 (396)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCC------------------------CCChHHHHHHhcCCceecccCceEeecCCccc
Confidence 999999999999999998654322 12689999999999999999999999999974
Q ss_pred CCcEEEEEe---eccceEEEEEecCCC
Q 003275 305 NPAYDVLNI---GGTGSRRIGYWSNYS 328 (834)
Q Consensus 305 ~~~~~I~~~---~~~~~~~vG~w~~~~ 328 (834)
..|.|+++ +++.++.||++++.+
T Consensus 365 -~~~~v~~~~~~~~g~~~~~~~~~~~~ 390 (396)
T cd06373 365 -SDFSLWDMTDTETGTFEVVANYNGSN 390 (396)
T ss_pred -ceeeeeeccCCCCceEEEEeeccccc
Confidence 77888765 567899999998765
No 27
>cd06384 PBP1_NPR_B Ligand-binding domain of type B natriuretic peptide receptor. Ligand-binding domain of type B natriuretic peptide receptor (NPR-B). NPR-B is one of three known single membrane-spanning natriuretic peptide receptors that have been identified. Natriuretic peptides are family of structurally related but genetically distinct hormones/paracrine factors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. In mammals there are three natriuretic peptides: ANP, BNP, and CNP. Like NPR-A (or GC-A), NPR-B (or GC-B) is a transmembrane guanylyl cyclase, an enzyme that catalyzes the synthesis of cGMP. NPR-B is the predominant natriuretic peptide receptor in the brain. The rank of order activation of NPR-B by natriuretic peptides is CNPANPBNP. Homozygous inactivating mutations in human NPR-B cause a form of short-limbed dwarfism known as acromesomelic dysplasia type Maroteaux.
Probab=100.00 E-value=8.4e-35 Score=321.49 Aligned_cols=298 Identities=19% Similarity=0.207 Sum_probs=243.6
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC--CCCCceEEccCChHHHHHHHHHHHHHcCCe-EEEEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS--LQYPYFLRTTQSDYYQMHAVADLVEYYGWR-EVIAIF 79 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~--~~~p~~~r~~ps~~~q~~aia~ll~~~~W~-~v~iI~ 79 (834)
++|.|||||.||..+.+++++++.++||+|++++++|.+++ .+|||+||+.|++..++.++..++++|+|+ ++++||
T Consensus 72 ~~v~aviGp~~S~~~~av~~i~~~~~iP~Is~~at~~~ls~~~~~y~~~fR~~p~~~~~~~~~~~i~~~~~w~~~vaiiy 151 (399)
T cd06384 72 SDPDVFFGPGCVYPTASVARFATHWRLPLITAGAPAFGFSNKTDEYRTTVRTGPSTTKLGEFVNHLHEHFNWTSRAALLY 151 (399)
T ss_pred cCCCEEECCCCchHHHHHHHHHhhcCCcEEeeccchhhhccccccCCceEEecCcHHHHHHHHHHHHHhCCCcEEEEEEE
Confidence 56889999999999999999999999999999999999986 478999999999999999988889999999 688998
Q ss_pred EcCCccc----chHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 80 VDDDYGR----NGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 80 ~d~~~g~----~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
.++..+. ...+.+.+.+++.|++|+....+.. +..|++.+|.+++. ++|+|+++++..++..++++|+++||+
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~gi~v~~~~~~~~--~~~d~~~~l~~ik~-~~~vIi~~~~~~~~~~i~~qa~~~g~~ 228 (399)
T cd06384 152 LDLKTDDRPHYFISEGVFLALQEENANVSAHPYHIE--KNSDIIEIIQFIKQ-NGRIVYICGPLETFLEIMLQAQREGLT 228 (399)
T ss_pred ecCCccCCcceEehHHHHHHHHhcCceEEEEEEecc--chhhHHHHHHHHhh-cccEEEEeCCchHHHHHHHHHHHcCCC
Confidence 7543221 1356788888999999998665542 34799999999997 899999999999999999999999999
Q ss_pred CCCeEEEEeCCCcccCCC----------CCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcC-CCCCCC---c
Q 003275 156 AGSYVWIATDWLPSVLDS----------TEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYK-ENSPSG---F 221 (834)
Q Consensus 156 ~~~~vwi~~~~~~~~~~~----------~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~-~~~~~~---~ 221 (834)
+++|+||..++....+.. .....+...+++++++++..+.|.++..++|.++|++++.. -+.+.. .
T Consensus 229 ~~~y~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~p~~~ 308 (399)
T cd06384 229 PGDYVFFYLDVFGESLRVKSPRESYKQMNHSSWTVLKEAFKSVFVITYREPENPEYKEFQRELHARAKEDFGVELEPSLM 308 (399)
T ss_pred CCcEEEEEehhcccccccCCCCccccCCCCcccHHHHHHHhheEEeecCCCCCchHHHHHHHHHHHHhhhcCCCcCcchH
Confidence 999999998865432210 00012455568999999998888888899999999875321 011112 3
Q ss_pred cchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCC
Q 003275 222 NSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADK 301 (834)
Q Consensus 222 ~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g 301 (834)
+++++++||||+++|.|+++++++++ .|.+|.+|.++|++++|+|++|++.||++|
T Consensus 309 ~~~aa~~YDav~l~a~Al~~~~~~~~------------------------~~~~g~~i~~~l~~~~f~GvtG~v~fd~~G 364 (399)
T cd06384 309 NFIAGCFYDGVMLYAMALNETLAEGG------------------------SQKDGLNITRKMQDRRFWGVTGLVSIDKNN 364 (399)
T ss_pred hhhhhhhHHHHHHHHHHHHHHHhcCC------------------------CCCCcHhHHHHHhCceeecceeEEEECCCC
Confidence 67899999999999999999865432 244689999999999999999999999999
Q ss_pred CCCCCcEEE---EEeeccceEEEEEecCCC
Q 003275 302 NLVNPAYDV---LNIGGTGSRRIGYWSNYS 328 (834)
Q Consensus 302 ~~~~~~~~I---~~~~~~~~~~vG~w~~~~ 328 (834)
++. ..|.+ .+++++++..||+|+..+
T Consensus 365 ~r~-~~~~~~~~~~~~~g~~~~v~~~~~~~ 393 (399)
T cd06384 365 DRD-IDFDLWAMTDHETGKYEVVAHYNGIT 393 (399)
T ss_pred Ccc-cceEEEEeecCCCCeEEEEEEEcCCC
Confidence 974 66777 466788999999998754
No 28
>KOG1056 consensus Glutamate-gated metabotropic ion channel receptor subunit GRM2 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=4e-35 Score=327.20 Aligned_cols=326 Identities=25% Similarity=0.452 Sum_probs=271.3
Q ss_pred CcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 4 EVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 4 ~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
.|+|+|||..|+.+.+++.+..-.+||||||++|+|.|++ .+|+||.|+.|+|.+|++||++++++|+|++|..+++++
T Consensus 125 ~v~~VIG~s~Ssvsi~vanlLrlf~ipQisyaSts~~LSdk~ry~~F~RtVP~D~~Qa~Am~~il~~f~W~yVstv~s~~ 204 (878)
T KOG1056|consen 125 PVVAVIGPSYSSVSIAVANLLRLFLIPQISYASTSPDLSDKTRYDYFLRTVPSDVFQAQAMVDILKKFNWNYVSTVASEG 204 (878)
T ss_pred ceeEEeCCCCchHHHHHHHHHHhhcCceeccccCCcccccchhhhceeeecCChHHHHHHHHHHHHHhCeeEeeehhcCc
Confidence 5899999999999999999999999999999999999999 899999999999999999999999999999999999999
Q ss_pred CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc-CCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 83 DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANL-MESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~-~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
+||+.++++|.+..+++|+||...+.++....+..+..+++++.. .+++++|+++..++++.++++|.++++.+ .++|
T Consensus 205 dYGE~Gieaf~~~a~~~~iCIa~s~ki~~~~~~~~~~~~l~kl~~~~~a~vvV~F~~~~~~r~~~~aa~~~n~~g-~~~w 283 (878)
T KOG1056|consen 205 DYGESGIEAFKEEAAERGICIAFSEKIYQLSIEQEFDCVLRKLLETPNARVVVVFCRGEDARRLLKAARRANLTG-EFLW 283 (878)
T ss_pred cchhhhHHHHHHhHHhcCceEEehhhcccccchhHHHHHHHHHhhcCCCeEEEEecCcchHHHHHHHHHHhCCCc-ceEE
Confidence 999999999999999999999999888776677889999999988 78999999999999999999999999865 6999
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHH---------------HHHHhhhcCC-----------
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFI---------------SRWKNLKYKE----------- 215 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~---------------~~~~~~~~~~----------- 215 (834)
|.+|+|...-+... ......+|++++....+..+.+++|. +.|+..|.+.
T Consensus 284 iaSd~W~~~~~~~~----~~e~~a~g~i~i~l~~~~v~~F~~y~~s~~p~nn~~n~w~~e~w~~~f~C~l~~~~~~~~~~ 359 (878)
T KOG1056|consen 284 IASDGWASQNSPTE----APEREAEGAITIKLASPQVPGFDRYFQSLHPENNRRNPWFAEFWEDKFNCSLPNSAFKNENL 359 (878)
T ss_pred EecchhhccCChhh----hhhhhhceeEEEEecCCcchhHHHHHHhcCccccccCcccchhhhhcccCCCCcccccchhh
Confidence 99999876443321 11236889999988777666655544 4466555411
Q ss_pred ------CC-CCCc-----cchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHH
Q 003275 216 ------NS-PSGF-----NSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTL 283 (834)
Q Consensus 216 ------~~-~~~~-----~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l 283 (834)
.+ .... ..-...++|||+++|+|||++.++... +....|..+... +|.+|++.+
T Consensus 360 ~~~Ct~~e~~~~~~~~~q~~k~~~Vi~aVya~A~aLh~m~~~lc~-------------~~~~~C~~m~~~-dg~~L~~~l 425 (878)
T KOG1056|consen 360 IRLCTAVERITLDSAYEQDSKVQFVIDAVYAMAHALHNMHQDLCP-------------GTSGLCSAMKAI-DGSLLLKYL 425 (878)
T ss_pred hhhcccchhhccccchhhhcccccHHHHHHHHHHHHHHHHHhhcC-------------CccccCcCcccc-CHHHHHhhh
Confidence 00 0011 113457999999999999999765221 123356666665 699999999
Q ss_pred HhcccccceeeEEEccCCCCCCCcEEEEEeecc----ceEEEEEecCCCCcccccccccccCCCCCCCCCccceeeecCC
Q 003275 284 LRMNFTGLSGEIRFDADKNLVNPAYDVLNIGGT----GSRRIGYWSNYSGLSVVAPEILYTKPPNSSSNRHLYSVIWPGE 359 (834)
Q Consensus 284 ~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~~----~~~~vG~w~~~~gl~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~ 359 (834)
++++|.+..|.+.||++||. ...|+|++++.. ....||+|++..-|. .+.+.|.++
T Consensus 426 ~~vnF~~~~~~v~Fd~~gD~-~~~y~I~~~~~~~~~~~y~~vg~w~~~~~l~-------------------i~~~~w~~~ 485 (878)
T KOG1056|consen 426 LNVNFTGPAGSVRFDENGDG-PGRYDILNYQLTNGSYTYKEVGYWSEGLSLN-------------------IEDLDWTTK 485 (878)
T ss_pred heeEEecCCCceeecCCCCC-ccceeEEEeeccCCCccceeeeeeccccccc-------------------ceeeeeccC
Confidence 99999999999999999995 699999999843 478999998765322 357889999
Q ss_pred ccccCcccc
Q 003275 360 ITATPRGWV 368 (834)
Q Consensus 360 ~~~~pr~~~ 368 (834)
..++|++.|
T Consensus 486 ~~~v~~S~C 494 (878)
T KOG1056|consen 486 PSGVPKSVC 494 (878)
T ss_pred CCCCccccc
Confidence 888999988
No 29
>cd06363 PBP1_Taste_receptor Ligand-binding domain of the T1R taste receptor. Ligand-binding domain of the T1R taste receptor. The T1R is a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptors, GABAb receptors, the calcium-sensing receptor (CaSR), the V2R pheromone receptors, and a small group of uncharacterized orphan receptors.
Probab=100.00 E-value=2.2e-34 Score=319.05 Aligned_cols=285 Identities=27% Similarity=0.421 Sum_probs=239.1
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|+|||||.+|..+.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.++++++.+++|++|++|+.|
T Consensus 106 ~~V~aIiGp~~S~~~~av~~i~~~~~vp~is~~~~~~~lt~~~~~~~~fr~~~~~~~~~~al~~~l~~~~~k~vaii~~~ 185 (410)
T cd06363 106 PRVVAVIGPDSSTLALTVAPLFSFFLIPQISYGASSEVLSNKELYPSFLRTVPSDKDQIEAMVQLLQEFGWNWVAFLGSD 185 (410)
T ss_pred CCeEEEECCCccHHHHHHHHHhcccccccccccccCccccccccCCCeeEecCCcHHHHHHHHHHHHHCCCcEEEEEEeC
Confidence 68999999999999999999999999999999999999987 67899999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCC-CChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPG-ASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~-~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
++||....+.+.+.+++.|++|+..+.++.. .+..|+..++.+|+++++|+|++++.++++..++++|+++||.. .+
T Consensus 186 ~~~g~~~~~~~~~~l~~~gi~i~~~~~~~~~~~~~~d~~~~l~~i~~~~~dvIil~~~~~~~~~il~qa~~~g~~~--~~ 263 (410)
T cd06363 186 DEYGRDGLQLFSELIANTGICIAYQGLIPLDTDPETDYQQILKQINQTKVNVIVVFASRQPAEAFFNSVIQQNLTG--KV 263 (410)
T ss_pred ChhHHHHHHHHHHHHHHCCeEEEEEEEecCCCchHHHHHHHHHHHhcCCCeEEEEEcChHHHHHHHHHHHhcCCCC--CE
Confidence 9999999999999999999999998888753 24579999999999999999999999999999999999999854 48
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHALD 240 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al~ 240 (834)
|+.++++........ ....+...+++++....+..+..++|.++ +++.+||||+++|+|++
T Consensus 264 ~i~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~f~~~----------------~~~~~YDaV~~~a~Al~ 324 (410)
T cd06363 264 WIASEAWSLNDELPS---LPGIRNIGTVLGVAQQTVTIPGFSDFIYS----------------FAFSVYAAVYAVAHALH 324 (410)
T ss_pred EEEeCcccccccccC---CccceeeccEEEEEeCCCCCccHHHHHHH----------------HHHHHHHHHHHHHHHHH
Confidence 999876542211111 11123455778887777778888888766 45679999999999999
Q ss_pred HHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeecc----
Q 003275 241 ALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGGT---- 316 (834)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~~---- 316 (834)
+++.++.. .|... ...+++.|.++|++++|+|++|++.||++|++ ...+.|++++..
T Consensus 325 ~a~~~~~~-----------------~~~~~-~~~~~~~l~~~L~~~~~~g~~g~i~fd~~G~~-~~~~~i~~~~~~~~~~ 385 (410)
T cd06363 325 NVLQCGSG-----------------GCPKR-VPVYPWQLLEELKKVNFTLLGQTVRFDENGDP-NFGYDIVVWWWDNSSG 385 (410)
T ss_pred HHhCCCCC-----------------CCCCC-CCCCHHHHHHHHhccEEecCCcEEEeCCCCCC-ccceEEEEEEEcCCce
Confidence 98765321 11110 12358899999999999999999999999995 467999999533
Q ss_pred ceEEEEEecCC
Q 003275 317 GSRRIGYWSNY 327 (834)
Q Consensus 317 ~~~~vG~w~~~ 327 (834)
+.++||+|++.
T Consensus 386 ~~~~vG~~~~~ 396 (410)
T cd06363 386 TFEEVGSYSFY 396 (410)
T ss_pred eEEEEEEEECC
Confidence 58899999874
No 30
>cd06372 PBP1_GC_G_like Ligand-binding domain of membrane guanylyl cyclase G. This group includes the ligand-binding domain of membrane guanylyl cyclase G (GC-G) which is a sperm surface receptor and might function, similar to its sea urchin counterpart, in the early signaling event that regulates the Ca2+ influx/efflux and subsequent motility response in sperm. GC-G appears to be a pseudogene in human. Furthermore, in contrast to the other orphan receptor GCs, GC-G has a broad tissue distribution in rat, including lung, intestine, kidney, and skeletal muscle.
Probab=100.00 E-value=6.9e-34 Score=313.96 Aligned_cols=298 Identities=15% Similarity=0.248 Sum_probs=233.9
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|.|||||.||..+.+++++++.++||+|++++++|.+++ ..||+++|+.|++..++.++++++++|||++|++||.+
T Consensus 67 ~~v~aiiGp~~S~~~~av~~va~~~~iP~is~~s~s~~ls~~~~~~~~~r~~p~~~~~~~a~~~l~~~~~w~~vaii~~~ 146 (391)
T cd06372 67 EHISALFGPACPEAAEVTGLLASQWNIPMFGFVGQTAKLDNRFLYDTYVKLVPPKQKIGEVLQKSLQHFGWKHIGLFGGS 146 (391)
T ss_pred cCceEEECCCCCcHHHHHHHHHhccCccEEEeecCCccccccccCCceEEecCchhhHHHHHHHHHHHCCCeEEEEEEec
Confidence 58999999999999999999999999999999999999997 67899999999999999999999999999999999854
Q ss_pred C---Cccc--chHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 82 D---DYGR--NGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 82 ~---~~g~--~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
+ .||+ ...+.+.+.++ .+++|+..+.++.+ ..++...+.+.+++++|+||++++..++..++++|+++||+.
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~-~~~~i~~~~~~~~~--~~d~~~~~l~~~~~~~~vii~~~~~~~~~~i~~~a~~~g~~~ 223 (391)
T cd06372 147 SRDSSWDEVDELWKAVENQLK-FHFNITATVRYSSS--NPDLLQEKLRYISSVARVIILICSSEDAKAILQAAEKLGLMK 223 (391)
T ss_pred cccchhhhHHHHHHHHHHHHh-hCEEEEEEEecCCC--ChHHHHHHHHhhhccceEEEEEcChHHHHHHHHHHHHcCCCC
Confidence 3 3432 23444555554 57889888777644 367666666666788999999999999999999999999998
Q ss_pred CCeEEEEeCCCcccC-CCC-C-CCChhhHhhcccceEEEecCCC-ChhHHHHHHHHHhhhcCCC------CCCCccchhH
Q 003275 157 GSYVWIATDWLPSVL-DST-E-PVDIDTMNLLQGVVALRHHTPD-TDLKKNFISRWKNLKYKEN------SPSGFNSYAL 226 (834)
Q Consensus 157 ~~~vwi~~~~~~~~~-~~~-~-~~~~~~~~~~~Gv~~~~~~~~~-~~~~~~F~~~~~~~~~~~~------~~~~~~~~~~ 226 (834)
++|+||.+.+....+ ... . ..+....+.++|++++.+..+. .+..++|.++|++++.... .....+.+++
T Consensus 224 ~~y~~i~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~f~~~~~~~~~~~p~~~~~~~~~~~~~~a~ 303 (391)
T cd06372 224 GKFVFFLLQQFEDNFWKEVLTDDQVQHLPKVYESVFLIAPSSYGGYSGGYEFRKQVYQKLKRPPFQSSLSSEEQVSPYSA 303 (391)
T ss_pred CCEEEEEehhhcCccccccCCCcchHHHHHHHhhEEEEecCCCCCCcchhHHHHHHHHHHhcCCccccccccccchHHHH
Confidence 889999964322211 110 0 0112344567899888776542 3556788888887763110 1113467899
Q ss_pred HHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHH---hcccccceeeEEEccCCCC
Q 003275 227 YAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLL---RMNFTGLSGEIRFDADKNL 303 (834)
Q Consensus 227 ~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~---~~~f~g~tG~i~Fd~~g~~ 303 (834)
++|||||++|+|++++++++.. |.+|.+|.++|+ +++|+|++|+|.||++|++
T Consensus 304 ~~yDav~~~A~Al~~~~~~g~~------------------------~~~g~~l~~~l~~~~~~~f~G~tG~v~fd~~G~r 359 (391)
T cd06372 304 YLHDAVLLYALAVKEMLKAGKD------------------------FRNGRQLVSTLRGANQVELQGITGLVLLDEQGKR 359 (391)
T ss_pred HHHHHHHHHHHHHHHHHhcCCC------------------------CCCHHHHHHHHhhccCceEeccceeEEECCCCCc
Confidence 9999999999999998764221 346899999999 6899999999999999997
Q ss_pred CCCcEEEEEeec----cceEEEEEecCCC
Q 003275 304 VNPAYDVLNIGG----TGSRRIGYWSNYS 328 (834)
Q Consensus 304 ~~~~~~I~~~~~----~~~~~vG~w~~~~ 328 (834)
.+.|.|+++++ .....||.|+..+
T Consensus 360 -~~~y~i~~~~~~~~~~~~~~vg~~~~~~ 387 (391)
T cd06372 360 -QMDYSVYALQKSGNSSLFLPFLHYDSHQ 387 (391)
T ss_pred -ceeEEEEeccccCCccceeeEEEecchh
Confidence 58999999975 2378999998654
No 31
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=100.00 E-value=6.3e-34 Score=309.98 Aligned_cols=280 Identities=46% Similarity=0.794 Sum_probs=245.2
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|++||||.+|..+.+++++++.++||+|+++++++.+++ ..+||+||+.|++..++.++++++++++|++|++|+.|
T Consensus 65 ~~v~~viG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~~~r~~p~~~~~~~a~~~~~~~~~~~~v~ii~~~ 144 (350)
T cd06366 65 KPVVAIIGPQCSSVAEFVAEVANEWNVPVLSFAATSPSLSSRLQYPYFFRTTPSDSSQNPAIAALLKKFGWRRVATIYED 144 (350)
T ss_pred CCceEEECCCcHHHHHHHHHHhhcCCeeEEeccCCCccccccccCCceEEcccchHhHHHHHHHHHHHCCCcEEEEEEEc
Confidence 58999999999999999999999999999999999999965 56899999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
++||....+.+.+.+++.|++|+....++.+.+..|+..++.+|+++++|+|++++...++..++++|+++||..++|+|
T Consensus 145 ~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~dvvi~~~~~~~~~~~~~~a~~~g~~~~~~~~ 224 (350)
T cd06366 145 DDYGSGGLPDLVDALQEAGIEISYRAAFPPSANDDDITDALKKLKEKDSRVIVVHFSPDLARRVFCEAYKLGMMGKGYVW 224 (350)
T ss_pred CcccchhHHHHHHHHHHcCCEEEEEeccCCCCChhHHHHHHHHHhcCCCeEEEEECChHHHHHHHHHHHHcCCcCCCEEE
Confidence 99999999999999999999999998888653358999999999999999999999999999999999999998889999
Q ss_pred EEeCCCcccCCC-CCCCChhhHhhcccceEEEecCCC-ChhHHHHHHHHHhhhcCC-CCCCCccchhHHHhhHHHHHHHH
Q 003275 162 IATDWLPSVLDS-TEPVDIDTMNLLQGVVALRHHTPD-TDLKKNFISRWKNLKYKE-NSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 162 i~~~~~~~~~~~-~~~~~~~~~~~~~Gv~~~~~~~~~-~~~~~~F~~~~~~~~~~~-~~~~~~~~~~~~~YDav~~la~A 238 (834)
+.++++...++. .....+...+..+|++++.++.++ ++..++|.++|++++... .....++.+++.+|||+++
T Consensus 225 i~~~~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~p~~~a~~~YDav~~---- 300 (350)
T cd06366 225 ILTDWLSSNWWSSSDCTDEEMLEAMQGVIGVRSYVPNSSMTLQEFTSRWRKRFGNENPELTEPSIYALYAYDAVWA---- 300 (350)
T ss_pred EECcchhhhhccCCCCChHHHHHhhceEEEEeecccccCccHHHHHHHHHHHhcccCcCcCCCCcccchhhhheee----
Confidence 999876544321 011223455778999999999887 888999999999988310 0012578899999999988
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeeccce
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGGTGS 318 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~~~~ 318 (834)
+.+|.|++|+++||++|++.+..|+++++.++++
T Consensus 301 ----------------------------------------------~~~~~G~~G~v~fd~~~~~~~~~~~~~~~~~~~~ 334 (350)
T cd06366 301 ----------------------------------------------STNFNGLSGPVQFDGGRRLASPAFEIINIIGKGY 334 (350)
T ss_pred ----------------------------------------------eceEEeeeeeEEEcCCCccCCcceEEEEecCCce
Confidence 1358899999999999998889999999999999
Q ss_pred EEEEEecCCCCccc
Q 003275 319 RRIGYWSNYSGLSV 332 (834)
Q Consensus 319 ~~vG~w~~~~gl~~ 332 (834)
+.||+|++..|++.
T Consensus 335 ~~vg~~~~~~~~~~ 348 (350)
T cd06366 335 RKIGFWSSESGLSV 348 (350)
T ss_pred EEEEEEeCCCCccc
Confidence 99999999888764
No 32
>cd06370 PBP1_Speract_GC_like Ligand-binding domain of membrane bound guanylyl cyclases. Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model.
Probab=100.00 E-value=2.2e-33 Score=310.55 Aligned_cols=293 Identities=18% Similarity=0.295 Sum_probs=238.1
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
+++|.|||||.+|.. +++.+++.++||+|+++++++.+++ ..||+|||+.|++..|+.++++++++++|++|++|+.
T Consensus 67 ~~~v~aiiGp~~S~~--~~a~i~~~~~iP~Is~~a~~~~l~~~~~~~~f~r~~~~~~~~~~a~~~~~~~~~w~~vaii~~ 144 (404)
T cd06370 67 KRGVVAFIGPECTCT--TEARLAAAWNLPMISYKCDEEPVSDKSKYPTFARTVPPSIQVVKSVIALLKHFNWNKFSVVYE 144 (404)
T ss_pred hcCceEEECCCchhH--HHHHHHhhcCCcEEecccCCccccccccCCCeEEcCCCHHHHHHHHHHHHHHCCCcEEEEEEe
Confidence 358999999999854 4567999999999999999999987 5799999999999999999999999999999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCC-----ChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGA-----SRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~-----~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
+++||+...+.+.+.+++.|++|+..+.++... ...++...+.+++.. ++++|+++...++..++++|+++||+
T Consensus 145 ~~~~g~~~~~~~~~~~~~~g~~iv~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~v~~~~~~~~~~~l~qa~~~g~~ 223 (404)
T cd06370 145 NDSKYSSVFETLKEEAELRNITISHVEYYADFYPPDPIMDNPFEDIIQRTKET-TRIYVFIGEANELRQFLMSMLDEGLL 223 (404)
T ss_pred cCcccHHHHHHHHHHHHHcCCEEEEEEEECCCCCchhhhHHHHHHHHHhccCC-CEEEEEEcCHHHHHHHHHHHHHcCCC
Confidence 999999999999999999999999988887541 246888999988765 68888888888999999999999999
Q ss_pred -CCCeEEEEeCCCccc---------------CCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCC----
Q 003275 156 -AGSYVWIATDWLPSV---------------LDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKE---- 215 (834)
Q Consensus 156 -~~~~vwi~~~~~~~~---------------~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~---- 215 (834)
..+|+||..+..... ............++++|++++.+..+ ++..++|.++|+++....
T Consensus 224 ~~~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~ 302 (404)
T cd06370 224 ESGDYMVLGVDIEYYDRDSQDYYSLHRGFQSREYNRSDDEKALEAMKSVLIIVPTPV-SPDYDSFSIFVRKYNLEPPFNG 302 (404)
T ss_pred CCCcEEEEEEchhhccccchhhhhhhhhhccccccccccHHHHHHhHheEEEecCCC-CchHHHHHHHHHHhccCCCCcc
Confidence 688999986531100 01011112345568899998876655 777899999998875310
Q ss_pred -----CCCCCccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhccccc
Q 003275 216 -----NSPSGFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTG 290 (834)
Q Consensus 216 -----~~~~~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g 290 (834)
.....++.+++++||||+++|+|+++++++++. ..+|.+|.++|++++|+|
T Consensus 303 ~~~~~~~~~~~~~~aa~~yDAv~~~a~Al~~~~~~~~~------------------------~~~g~~i~~~l~~~~f~G 358 (404)
T cd06370 303 DLGESELVLEIDIEAAYLYDAVMLYAKALDETLLEGGD------------------------IYNGTAIVSHILNRTYRS 358 (404)
T ss_pred cccccccccccceeeehhHHHHHHHHHHHHHHHHhcCC------------------------CCCHHHHHHHHhCccccc
Confidence 022356788999999999999999998765322 026899999999999999
Q ss_pred cee-eEEEccCCCCCCCcEEEEEeeccceEEEEE
Q 003275 291 LSG-EIRFDADKNLVNPAYDVLNIGGTGSRRIGY 323 (834)
Q Consensus 291 ~tG-~i~Fd~~g~~~~~~~~I~~~~~~~~~~vG~ 323 (834)
++| ++.||++|++ ...|.+++++++.|..-|.
T Consensus 359 vtG~~v~fd~~G~~-~~~y~v~~~~~~~~~~~~~ 391 (404)
T cd06370 359 ITGFDMYIDENGDA-EGNYSVLALQPIPPGDNGS 391 (404)
T ss_pred ccCceEEEcCCCCc-ccceEEEEeccccccCCCC
Confidence 999 8999999997 4899999998875544443
No 33
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=100.00 E-value=5.9e-33 Score=307.04 Aligned_cols=302 Identities=23% Similarity=0.396 Sum_probs=257.7
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
+++|.|||||.+|..+.+++++++.++||+|+++++++.+++ ..+||+||+.|++..++.++++++++++|+++++++.
T Consensus 66 ~~~v~aiiG~~~s~~~~a~~~~~~~~~ip~Is~~~~~~~~~~~~~~~~~fr~~~~~~~~~~a~~~~l~~~~~~~v~ii~~ 145 (389)
T cd06352 66 EHNVDAFIGPGCPYACAPVARLAAHWNIPMISWGCVALSLSDKSEYPTLTRTLPPARKLGEAVLALLRWFNWHVAVVVYS 145 (389)
T ss_pred hcCCcEEECCCChhHHHHHHHHHhcCCCCEecccccccccCccccCCceeecCCcHHHHHHHHHHHHHHcCceEEEEEEe
Confidence 368999999999999999999999999999999999999987 5789999999999999999999999999999999998
Q ss_pred cCC-cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 81 DDD-YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 81 d~~-~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
++. ||....+.+.+++++.|++|+....++...+..++..++.++++.. |+||+.+.+.++..++++++++||...++
T Consensus 146 ~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~d~~~~l~~i~~~~-~vii~~~~~~~~~~~l~q~~~~g~~~~~~ 224 (389)
T cd06352 146 DDSENCFFTLEALEAALREFNLTVSHVVFMEDNSGAEDLLEILQDIKRRS-RIIIMCGSSEDVRELLLAAHDLGLTSGDY 224 (389)
T ss_pred cCCccHHHHHHHHHHHHHhcCCeEEEEEEecCCccchhHHHHHHHhhhcc-eEEEEECCHHHHHHHHHHHHHcCCCCCcE
Confidence 888 9999999999999999999999888875422478999999999887 99999999999999999999999988899
Q ss_pred EEEEeCCCcccCCC--------CCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCC-----CCCCccchhH
Q 003275 160 VWIATDWLPSVLDS--------TEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKEN-----SPSGFNSYAL 226 (834)
Q Consensus 160 vwi~~~~~~~~~~~--------~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~-----~~~~~~~~~~ 226 (834)
+||.++.+...... .....+...+.++|++++.++.+.++..++|.++|++++.... ....++.++.
T Consensus 225 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~a~ 304 (389)
T cd06352 225 VFILIDLFNYSLPYQNSYPWERGDGDDEKAKEAYDAVLTITLRPPDNPEYEEFSEEVKEAAKRPPFNTDAEPEQVSPYAG 304 (389)
T ss_pred EEEEEehhccccccCCCCCcccCCcccHHHHHHHHhheEEEecCCCCchHHHHHHHHHHHHhcccCccCCCccccchhhh
Confidence 99998766544211 1111234557789999998888888899999999998873111 1234678999
Q ss_pred HHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCC
Q 003275 227 YAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNP 306 (834)
Q Consensus 227 ~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~ 306 (834)
.+||||+++|+|++++..+++. +.++..+.+.|+++.|.|++|++.||++|++. .
T Consensus 305 ~~YDav~~~a~Al~~~~~~~~~------------------------~~~~~~v~~~l~~~~f~g~~G~v~fd~~G~~~-~ 359 (389)
T cd06352 305 YLYDAVLLYAHALNETLAEGGD------------------------YNGGLIITRRMWNRTFSGITGPVTIDENGDRE-G 359 (389)
T ss_pred hHHHHHHHHHHHHHHHHHhCCC------------------------CCchHHHHHHhcCcEEEeeeeeEEEcCCCCee-e
Confidence 9999999999999998765321 23688999999999999999999999999975 7
Q ss_pred cEEEEEeec--cceEEEEEecCCCC
Q 003275 307 AYDVLNIGG--TGSRRIGYWSNYSG 329 (834)
Q Consensus 307 ~~~I~~~~~--~~~~~vG~w~~~~g 329 (834)
.|.|+++++ +....++.+++.+|
T Consensus 360 ~~~v~~~~~~~~~~~~~~~~~~~~~ 384 (389)
T cd06352 360 DYSLLDLDSTGGQLEVVYLYDTSSG 384 (389)
T ss_pred eEEEEEecCCCceEEEEEeccccce
Confidence 899999986 46788998877664
No 34
>PF01094 ANF_receptor: Receptor family ligand binding region The Prosite family is a sub-family of the Pfam family; InterPro: IPR001828 This describes a ligand binding domain and includes extracellular ligand binding domains of a wide range of receptors, as well as the bacterial amino acid binding proteins of known structure [].; PDB: 3SAJ_D 3Q41_B 3QEM_C 3QEK_A 3QEL_C 3MQ4_A 3QLV_G 3OM1_A 3QLU_A 3OM0_A ....
Probab=100.00 E-value=1.6e-33 Score=307.38 Aligned_cols=290 Identities=33% Similarity=0.579 Sum_probs=241.9
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC--CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS--LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~--~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
++|.|||||.|+..+.+++.+++.++||+|+++++++.+++ .+||+++|+.|++..++.++++++++|+|++|++||+
T Consensus 50 ~~v~aviGp~~~~~~~~~~~~~~~~~ip~is~~~~~~~ls~~~~~~~~~~r~~p~~~~~~~a~~~~l~~~~w~~v~vv~~ 129 (348)
T PF01094_consen 50 QGVVAVIGPSCSSSAEAVASLASEWNIPQISPGSTSPSLSDRKTRYPTFFRTVPSDSSQARALVDLLKHFGWTRVSVVYS 129 (348)
T ss_dssp HTECEEEETSSHHHHHHHHHHHHHTT-EEEESSGGSGGGGSTTTTTTTEEESSB-HHHHHHHHHHHHHHTTSSEEEEEEE
T ss_pred CCcEEEECCCcccccchhheeecccccceeeccccccccccchhhccccccccccHHHHHHHHHHhhhcCCCceeeeecc
Confidence 57999999999999999999999999999999999999988 4799999999999999999999999999999999999
Q ss_pred cCCcccchHHHHHHHHhcCC-cEEEeeecCCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHhCCCCCC
Q 003275 81 DDDYGRNGISVLGDALSKKR-AKISYKAPFSPGASRSAINSLLVGANL--MESRVFVVHVNPDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g-~~I~~~~~~~~~~~~~~~~~~l~~l~~--~~~~vivl~~~~~~~~~i~~~a~~~g~~~~ 157 (834)
++++|.+..+.+.+.+++.+ .++......+.. ..+....+.+++. .++|+||++++...+..++++|.++||...
T Consensus 130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~rvvil~~~~~~~~~~l~~a~~~~~~~~ 207 (348)
T PF01094_consen 130 DDDYGNSLADSFQDLLRERGGICVAFISVVISS--DSDAEELLKKLKEIKSGARVVILCSSPEDARQFLEAAYELGMTSG 207 (348)
T ss_dssp SSHHHHHHHHHHHHHHHHHTTCEEEEEEEEETT--TSHHHHHHHHHHHHTTTTSEEEEESBHHHHHHHHHHHHHTTTSST
T ss_pred ccccccccchhhhhhhcccccceeccccccccc--ccchhhhhhhhhhccccceeeeeecccccccccccchhhhhcccc
Confidence 99999999999999999964 555541223222 2344444555544 999999999999999999999999999999
Q ss_pred CeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhc---CCCCCCCccchhHHHhhHHHH
Q 003275 158 SYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKY---KENSPSGFNSYALYAYDSVWL 234 (834)
Q Consensus 158 ~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~---~~~~~~~~~~~~~~~YDav~~ 234 (834)
+|+||.++.+...... .++.......|+++++...+..+.+++|.++|+.... .......+..+++++||||++
T Consensus 208 ~~~~i~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~yDAv~~ 284 (348)
T PF01094_consen 208 DYVWILTDLDNSSFWQ---NNEDFREAFQGVLGFTPPPPSSPEFEDFMKKWKESNNQSSTSGSDQEPSPYAAYAYDAVYL 284 (348)
T ss_dssp TSEEEEETTTTTTHTS---THCHHHCCHTTEEEEEESTTTSHHHHHHHHHHHTTTHTTTTTTTTSSGCHHHHHHHHHHHH
T ss_pred ceeEEeeccccccccc---ccccccccccceeeeeeecccccchhhhhcccChhhccCcccccccccceeeeeehhhhHH
Confidence 9999999987654321 1246678899999999999999999999999997532 122345678899999999999
Q ss_pred HHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEcc-CCCCCCCcEEEEEe
Q 003275 235 VAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDA-DKNLVNPAYDVLNI 313 (834)
Q Consensus 235 la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~-~g~~~~~~~~I~~~ 313 (834)
+|+|+++++++++.... ....|.+|..|.++|++++|+|++|++.||+ +|++.+..|+|+|+
T Consensus 285 ~a~al~~~~~~~~~~~~-----------------~~~~~~~g~~l~~~l~~~~f~G~tG~v~f~~~~G~~~~~~~~i~~~ 347 (348)
T PF01094_consen 285 LAHALNRALQDGGPVTN-----------------GRNPWQNGSQLLKYLRNVSFEGLTGRVSFDSNDGDRTNYDYDILNM 347 (348)
T ss_dssp HHHHHHHHHHHHSTTTS-----------------SSGTSTTHHHHHHHHHTEEEEETTEEEEEETTTSBEESEEEEEEEE
T ss_pred HHHHHHHHHHhccCCCC-----------------CccccccHHHHHHHHhheeeeCCCCCEEEeCCCCCcCCCEEEEEEC
Confidence 99999999876443210 0045778999999999999999999999999 99998999999998
Q ss_pred e
Q 003275 314 G 314 (834)
Q Consensus 314 ~ 314 (834)
+
T Consensus 348 ~ 348 (348)
T PF01094_consen 348 Q 348 (348)
T ss_dssp -
T ss_pred C
Confidence 5
No 35
>cd06394 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels act
Probab=100.00 E-value=1.4e-33 Score=298.20 Aligned_cols=263 Identities=22% Similarity=0.327 Sum_probs=206.6
Q ss_pred CCCcEEEECCCChhh-HHHHHHhhccCCccEEecccCC-CCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEE
Q 003275 2 ENEVVAAIGPQSSGI-AHVISHVVNELNVPLLSFGATD-PTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIF 79 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~-~~~~~~~~~~~~vP~Is~~at~-~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~ 79 (834)
+++|+|||||.+|.. +.+++++|++.+||+|+++.+. |.+...++++ +++.|++..|+.|+++++++|+|++|++||
T Consensus 63 ~~gV~AIiGp~ss~~~~~~v~~i~~~~~VP~Is~~~~~~~~~~~~~~~~-i~l~P~~~~~~~Ai~dli~~~~W~~v~~iY 141 (333)
T cd06394 63 PKGVVSVLGPSSSPASSSIVSHICGEKEIPHFKVGPEETPKLQYLRFAS-VNLHPSNEDISVAVAGILNSFNYPTASLIC 141 (333)
T ss_pred hcCeEEEECCCCchHHHHHHHHHhhccCCceEEeccccCcccccccceE-EEecCCHHHHHHHHHHHHHhcCCCEEEEEE
Confidence 569999999999975 6799999999999999986443 3333344444 899999999999999999999999999999
Q ss_pred EcCCcccchHHHHHHHHhcCCcEEEeeecCCCC--CChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCC
Q 003275 80 VDDDYGRNGISVLGDALSKKRAKISYKAPFSPG--ASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 80 ~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~--~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~ 157 (834)
+|+++ +..|.+.++..+. +...++.. .++.|++++|.+|+++++|+||++|+++.+..++++|+++||+.+
T Consensus 142 e~d~~----l~~L~~~l~~~~~---~~~~i~~~~~~~~~d~~~~L~~ik~~~~~~iVv~~~~~~a~~il~qa~~lGm~~~ 214 (333)
T cd06394 142 AKAEC----LLRLEELLRQFLI---SKETLSVRMLDDSRDPTPLLKEIRDDKTATIIIDANASMSHTILLKASELGMTSA 214 (333)
T ss_pred eCcHH----HHHHHHHHHhhcc---cCCceeeEEccCcccHHHHHHHHHhcCCCEEEEECChHHHHHHHHHHHHcCCCCC
Confidence 99986 5666676665432 22333322 135789999999999999999999999999999999999999999
Q ss_pred CeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCC---CCccchhHHHhhHHHH
Q 003275 158 SYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSP---SGFNSYALYAYDSVWL 234 (834)
Q Consensus 158 ~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~---~~~~~~~~~~YDav~~ 234 (834)
+|+|++|+.....++.. +.....-.+.+++...++.+..++|.++|++++...... ......++.+||||++
T Consensus 215 ~y~~i~T~l~~~~~~L~-----~~~~~~~niTgF~l~d~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~~al~~D~v~~ 289 (333)
T cd06394 215 FYKYILTTMDFPLLRLD-----SIVDDRSNILGFSMFNQSHAFYQEFIRSLNQSWRENCDHSPYTGPALSSALLFDAVYA 289 (333)
T ss_pred ceEEEEecCCcccccHH-----HhhcCCcceEEEEeecCCcHHHHHHHHHHHHhhhhhcccccCCCcccceeeecceEEE
Confidence 99999988655433331 122223457888898999999999999988765210001 0111245555666533
Q ss_pred HHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEee
Q 003275 235 VAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIG 314 (834)
Q Consensus 235 la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~ 314 (834)
+ |+||+|+||++|.|.+...+|+++.
T Consensus 290 ~------------------------------------------------------glTg~i~f~~~g~R~~~~l~v~~l~ 315 (333)
T cd06394 290 V------------------------------------------------------GLTGRIEFNSKGQRSNYTLKILQKT 315 (333)
T ss_pred E------------------------------------------------------eeecceecCCCCcCcccEEEEEEec
Confidence 2 8999999999999999999999999
Q ss_pred ccceEEEEEecCCCCcc
Q 003275 315 GTGSRRIGYWSNYSGLS 331 (834)
Q Consensus 315 ~~~~~~vG~w~~~~gl~ 331 (834)
.+|.++||+|++..||+
T Consensus 316 ~~g~~kig~W~~~~gl~ 332 (333)
T cd06394 316 RSGFRQIGQWHSNETLS 332 (333)
T ss_pred CCcceEEEEEeCCCCcC
Confidence 99999999999999876
No 36
>cd06382 PBP1_iGluR_Kainate N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeri
Probab=100.00 E-value=5e-32 Score=292.00 Aligned_cols=260 Identities=21% Similarity=0.320 Sum_probs=216.5
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
+++|.|||||.+|..+.+++++++.++||+|+++++++.++ .++++||+.|++..|+.++++++++++|++|++||++
T Consensus 61 ~~~V~aiiG~~~S~~~~av~~~~~~~~vP~Is~~~~~~~~~--~~~~~fr~~p~~~~~~~a~~~~~~~~~w~~vavl~~~ 138 (327)
T cd06382 61 QQGVAAIFGPSSSEASSIVQSICDAKEIPHIQTRWDPEPKS--NRQFTINLYPSNADLSRAYADIVKSFNWKSFTIIYES 138 (327)
T ss_pred hcCcEEEECCCChhHHHHHHHHHhccCCCceeccCCcCccc--cccceEEeCCCHHHHHHHHHHHHHhcCCcEEEEEecC
Confidence 35899999999999999999999999999999988888776 5589999999999999999999999999999999998
Q ss_pred CCcccchHHHHHHHHhcCCc---EEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 82 DDYGRNGISVLGDALSKKRA---KISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~---~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
++++. .+.+.+++.|. .|.. ..++.. . |++.+|.+|+++++|+|++++...++..++++|+++||+.+.
T Consensus 139 ~~~~~----~l~~~~~~~~~~g~~v~~-~~~~~~--~-d~~~~l~~i~~~~~d~vv~~~~~~~~~~~~~qa~~~g~~~~~ 210 (327)
T cd06382 139 AEGLL----RLQELLQAFGISGITITV-RQLDDD--L-DYRPLLKEIKNSGDNRIIIDCSADILIELLKQAQQVGMMSEY 210 (327)
T ss_pred hHHHH----HHHHHHHhhccCCCeEEE-EEccCC--c-cHHHHHHHHHhcCceEEEEECCHHHHHHHHHHHHHhCccccc
Confidence 87554 34455555544 4544 345533 3 999999999999999999999999999999999999999999
Q ss_pred eEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCC---CCCCCccchhHHHhhHHHHH
Q 003275 159 YVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKE---NSPSGFNSYALYAYDSVWLV 235 (834)
Q Consensus 159 ~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~---~~~~~~~~~~~~~YDav~~l 235 (834)
|+|+.+++.....+.. .......++++++.+.++++..++|.++|++++... .....|+.+++.+|||++++
T Consensus 211 ~~~i~~~~~~~~~~l~-----~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~~a~~yDav~~~ 285 (327)
T cd06382 211 YHYIITNLDLHTLDLE-----DYRYSGVNITGFRLVDPDSPEVKEVIRSLELSWDEGCRILPSTGVTTESALMYDAVYLF 285 (327)
T ss_pred eEEEEecCCccccchh-----hhccCceeEEEEEEecCCchhHHHHHHHHHhhcccccccCCCCCcchhhhhhhceEEEe
Confidence 9999987654433321 112233467888888888899999999999998421 12224778899999998655
Q ss_pred HHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeec
Q 003275 236 AHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGG 315 (834)
Q Consensus 236 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~ 315 (834)
|+||+++||++|+|.+..++|+|+++
T Consensus 286 ------------------------------------------------------g~tG~v~f~~~g~r~~~~~~~~~~~~ 311 (327)
T cd06382 286 ------------------------------------------------------GLTGRIEFDSSGQRSNFTLDVIELTE 311 (327)
T ss_pred ------------------------------------------------------ecccceeeCCCCCEeeeEEEEEeccc
Confidence 89999999999999999999999999
Q ss_pred cceEEEEEecCCCCc
Q 003275 316 TGSRRIGYWSNYSGL 330 (834)
Q Consensus 316 ~~~~~vG~w~~~~gl 330 (834)
+++++||+|++..||
T Consensus 312 ~~~~~vg~w~~~~~~ 326 (327)
T cd06382 312 SGLRKVGTWNSSEGL 326 (327)
T ss_pred cCceEEEEECCCCCc
Confidence 999999999988775
No 37
>cd06381 PBP1_iGluR_delta_like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. This CD represents the N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. G
Probab=99.98 E-value=1.7e-30 Score=280.00 Aligned_cols=278 Identities=17% Similarity=0.237 Sum_probs=209.4
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCC---CC-----CCC-CCCCceEEccCChHHHHHHHHHHHHHcCC
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATD---PT-----LTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGW 72 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~---~~-----ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W 72 (834)
+++|+|||||.+|..+.+++++++..+||+|++.+.. |. +.+ ...+|.|++.|++ .+..++++++++|||
T Consensus 60 ~~gV~AI~G~~~s~~~~av~~i~~~~~IP~Is~~~~~~~~~~~~~~~~~~~~~~~~~f~~rp~~-~~~~ai~~lv~~~~w 138 (363)
T cd06381 60 NQGILALVTSTGCASAIALQSLTDAMHIPHLFIQRGYGGSPRTACGLNPSPRGQQYTLALRPPV-RLNDVMLRLVTEWRW 138 (363)
T ss_pred hcCcEEEEecCChhHHHHHHHHhhCCCCCEEEeecCcCCCcccccccCCCcccceeEEEEeccH-HHHHHHHHHHHhCCC
Confidence 4599999999999999999999999999999965421 11 111 1224555555664 688999999999999
Q ss_pred eEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhh-------cCCceEEEEEeChhhHHHH
Q 003275 73 REVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGAN-------LMESRVFVVHVNPDTGLTI 145 (834)
Q Consensus 73 ~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~-------~~~~~vivl~~~~~~~~~i 145 (834)
++|+++|++++ |...++.+.+++++.|+.+.... ...+ ....+...++.++ ..+.++||++|+++.+..+
T Consensus 139 kkvavly~~d~-g~~~l~~~~~~~~~~g~~v~~~~-~~~~-~~~~~~~l~~~~~~~~l~~~~~~~~~vIl~~~~~~~~~~ 215 (363)
T cd06381 139 QKFVYFYDNDY-DIRGLQEFLDQLSRQGIDVLLQK-VDLN-ISKMATALFTTMRCEELNRYRDTLRRALLLLSPNGAYTF 215 (363)
T ss_pred eEEEEEEECCc-hHHHHHHHHHHHHhcCceEEEEe-cccc-cchhhhhhhhHHHHHHHHhhcccceEEEEEcCcHHHHHH
Confidence 99999998776 55667888899999998766432 2211 1123334333332 3455688999999999999
Q ss_pred HHHHHhCCCCCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHH----HHHHHHHhhhcCC-CCCCC
Q 003275 146 FSVAKSLGMTAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKK----NFISRWKNLKYKE-NSPSG 220 (834)
Q Consensus 146 ~~~a~~~g~~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~----~F~~~~~~~~~~~-~~~~~ 220 (834)
+++|.++||+..+|+|+.++.+...... -........|++|++...|..+..+ +|.+.|++...+. .....
T Consensus 216 l~~a~~~gm~~~~~~wi~~~~l~~~~~~----l~~~~~~~~nitgfrl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 (363)
T cd06381 216 IDASVETNLAIKDSHWFLINEEISDTEI----DELVRYAHGRMTVIRQTFSKEKTNQRCLRNNHRISSLLCDPKDGYLQM 291 (363)
T ss_pred HHHHHHcCCCcCceEEEEeccccccchh----hHHHhhcCccEEEEEEecCCcCchHHHHHHHHHHHHhhcCCCCCCCCC
Confidence 9999999999999999988766542111 1345677899999999988777766 4555665433221 11224
Q ss_pred ccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccC
Q 003275 221 FNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDAD 300 (834)
Q Consensus 221 ~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~ 300 (834)
+...++++|||||++ +++|++++|+|+||+|+||++
T Consensus 292 ~~~~~al~yDaV~~~--------------------------------------------~~~~~~~~~~GLTG~i~F~~~ 327 (363)
T cd06381 292 LEISNLYIYDSVLLL--------------------------------------------LETIKKGPITGLTGKLEFNEG 327 (363)
T ss_pred hhHHHHHHHHHHHHH--------------------------------------------HHHHHhcCccCcceeEEeCCC
Confidence 577899999999998 356677889999999999999
Q ss_pred CCCCCCcEEEEEeeccc-----eEEEEEecCCCCcc
Q 003275 301 KNLVNPAYDVLNIGGTG-----SRRIGYWSNYSGLS 331 (834)
Q Consensus 301 g~~~~~~~~I~~~~~~~-----~~~vG~w~~~~gl~ 331 (834)
|.|.+..++|+++.-.+ .+.||+|++..||+
T Consensus 328 g~r~~~~l~i~~~~~~~~~~~~~~~~~~w~~~~~~~ 363 (363)
T cd06381 328 GDNSNVQFEILGTGYSETLGKDGRWLATWNPSKGLN 363 (363)
T ss_pred CCccccEEEEEEeccCCccccceEEeeeccCCCCCC
Confidence 99999999999998544 78999999988764
No 38
>cd06383 PBP1_iGluR_AMPA_Like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excitatory synaptic current.
Probab=99.97 E-value=4.8e-31 Score=284.76 Aligned_cols=282 Identities=13% Similarity=0.139 Sum_probs=203.5
Q ss_pred CCCc--EEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEE
Q 003275 2 ENEV--VAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIF 79 (834)
Q Consensus 2 ~~~V--~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~ 79 (834)
+++| +|||||.+|..+..++.+++.++||+|+++.. ..++.++|||+|+.|++..|+.|+++++++|+|++|++||
T Consensus 63 ~~gv~~~AIiGp~ss~~a~~V~si~~~~~IP~Is~s~~--~~~~~~~p~~ir~~Ps~~~~~~Ai~dlI~~f~W~~v~iIY 140 (368)
T cd06383 63 DSAIVPHLVLDTTTCGDASEIKSVTGALGIPTFSASYG--QEGDLEQPYLIQLMPPADDIVEAIRDIVSYYNITNAAILY 140 (368)
T ss_pred HccCCcEEEECCCcchhHHHHHHHHhccCCCEEEccCC--CcCcccCceEEEEeCChHHHHHHHHHHHHHCCCcEEEEEE
Confidence 4677 89999999999999999999999999997543 3344689999999999999999999999999999999999
Q ss_pred EcCCcccchHHHHHH-HHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhhHHHHHHHHHhCCCCCC
Q 003275 80 VDDDYGRNGISVLGD-ALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-PDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 80 ~d~~~g~~~~~~l~~-~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-~~~~~~i~~~a~~~g~~~~ 157 (834)
+|++++......+.. .....+.++. +. ...++..+|++|++++.+.||+.+. ++.+..|+++|.++||++.
T Consensus 141 ddd~gl~~~l~~~l~~~~~~~~~~v~-----~~--~~~~~~~~Lk~lk~~~~~rIIi~~s~~~~~~~il~qA~~lgm~~~ 213 (368)
T cd06383 141 DDDFVMDHKYKSLLQNWPTRHVITII-----NS--IIDEVREQIKRLRNLDIKNIFILGSTEEIIRYVLDQALAEGFMGR 213 (368)
T ss_pred EcCchhhHHHHHHHHhHHhcCCEEEE-----ec--cchhHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHHHHHcCCcCC
Confidence 776643323333333 3334455543 11 2257889999999998855555555 5999999999999999999
Q ss_pred CeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHH
Q 003275 158 SYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAH 237 (834)
Q Consensus 158 ~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~ 237 (834)
+|+||++++....++. ......-.++.+++...+.....+.+.++|......+.........++.+||||+++|+
T Consensus 214 ~y~wilt~ld~~~~dl-----~~~~~~~~Nitgfrl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~Dav~~~~~ 288 (368)
T cd06383 214 KYAWFLGNPDLGIYDD-----LSCQLRNASIFVTRPMMDYQSSVRGALLRTDEPTLRPVFYFEWAFRLFLAYDAVLAVGE 288 (368)
T ss_pred ceEEEEcCCCchhhhh-----hhhccccCcEEEeeccccchhhhccceeeccCCccCchhHHHHHHHHHHHHHHHHHhcc
Confidence 9999999876554333 12223345789999876655555888877733210111111345678999999999999
Q ss_pred HHHHHHhcCCCccccCCCCCCCCCCCCccCCCc---ccc-CchHHHHHHHHhcccccceeeEEEccCCCCCC
Q 003275 238 ALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSL---RVF-DGGQQFLQTLLRMNFTGLSGEIRFDADKNLVN 305 (834)
Q Consensus 238 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~ 305 (834)
|++.+..+.... .. .......|.+. .+| .+|..+.++|+.++|+|+||+|+||++|.|.+
T Consensus 289 a~~~l~~~~~~~-----~~---~~~~~~~~~g~~~~~~w~~~g~~~~~~~k~~~~~gltG~i~f~~~g~R~~ 352 (368)
T cd06383 289 WPRRMRKKRVED-----GS---TGTSVLPGFGISPESPLMTLQSSPFNGSSEIKFEMLAGRVAIDEGSSVST 352 (368)
T ss_pred ccchhheeeccC-----CC---cCccccCCCCCCcccchhhcccccccCccceeEeeecCeEEEecCceeee
Confidence 999763211111 00 00011122222 256 67779999999999999999999999998753
No 39
>cd06368 PBP1_iGluR_non_NMDA_like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors, characterized by their response to glutamate agonists: N-methyl-d -aspartate (NMDA) and non-NMDA receptors. NMDA receptors
Probab=99.97 E-value=4.9e-30 Score=276.45 Aligned_cols=261 Identities=24% Similarity=0.381 Sum_probs=216.1
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
+++|.|||||.+|..+.+++++++.++||+|+++++++.++ .+++ ++..|++..|+.++++++++++|++|++||+|
T Consensus 60 ~~~V~aiiG~~~S~~~~av~~i~~~~~ip~is~~~~~~~~~-~~~~--~~~~~~~~~~~~a~~~~~~~~~w~~vaii~~~ 136 (324)
T cd06368 60 SQGVAAIFGPSSSSSANTVQSICDALEIPHITTSWSPNPKP-RQFT--INLYPSMRDLSDALLDLIKYFGWRKFVYIYDS 136 (324)
T ss_pred hcCcEEEECCCCHHHHHHHHHHHhccCCCcEEecCCcCCCC-Ccce--EEecCCHHHHHHHHHHHHHhcCCCEEEEEECC
Confidence 36899999999999999999999999999999999998886 2344 44457777999999999999999999999977
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
++ |...++.+.+.+++.|++|+.....+ . + .+++.+|.+|+++++|+||++++..++..++++|+++||+.++|+|
T Consensus 137 ~~-~~~~l~~~~~~~~~~g~~v~~~~~~~-~-~-~d~~~~l~~i~~~~~d~Vi~~~~~~~~~~i~~qa~~~g~~~~~~~~ 212 (324)
T cd06368 137 DE-GLLRLQELLDALSPKGIQVTVRRLDD-D-T-DMYRPLLKEIKREKERRIILDCSPERLKEFLEQAVEVGMMSEYYHY 212 (324)
T ss_pred cH-hHHHHHHHHHhhccCCceEEEEEecC-C-c-hHHHHHHHHHhhccCceEEEECCHHHHHHHHHHHHHhccccCCcEE
Confidence 66 44566778788888899998765444 2 2 3899999999999999999999999999999999999999899999
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCC---CCCCCccchhHHHhhHHHHHHHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKE---NSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~---~~~~~~~~~~~~~YDav~~la~A 238 (834)
|+++......+. ........++.++....++++..++|.++|++++... .....|+.+++.+||||+++
T Consensus 213 i~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~aa~~yDav~~~--- 284 (324)
T cd06368 213 ILTNLDFHTLDL-----ELFRYGGVNITGFRLVDPDNPEVQKFIQRWERSDHRICPGSGLKPIKTESALTYDAVLLF--- 284 (324)
T ss_pred EEccCCccccch-----hhhhcCCceEEEEEEecCCChHHHHHHHHHHhccccccCCCCCCCcchhhHhhhcEEEEe---
Confidence 998754432221 1222334467777777888999999999999988421 11226788999999998655
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeeccce
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGGTGS 318 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~~~~ 318 (834)
||+++||++|++.+..++|+++.++++
T Consensus 285 -----------------------------------------------------tg~~~f~~~g~~~~~~~~i~~~~~~~~ 311 (324)
T cd06368 285 -----------------------------------------------------TGRIQFDENGQRSNFTLDILELKEGGL 311 (324)
T ss_pred -----------------------------------------------------eeeeEeCCCCcCcceEEEEEEEcCCCc
Confidence 888999999999999999999999999
Q ss_pred EEEEEecCCCCc
Q 003275 319 RRIGYWSNYSGL 330 (834)
Q Consensus 319 ~~vG~w~~~~gl 330 (834)
+.||+|++..|+
T Consensus 312 ~~~g~W~~~~~~ 323 (324)
T cd06368 312 RKVGTWNPEDGL 323 (324)
T ss_pred eEEEEECCCCCC
Confidence 999999988765
No 40
>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.
Probab=99.96 E-value=2.7e-28 Score=264.25 Aligned_cols=267 Identities=22% Similarity=0.277 Sum_probs=230.1
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHH-HHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLV-EYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll-~~~~W~~v~iI~~d 81 (834)
++|.+|+||.+|..+.+++++++..+||+|+++++++.+.+..+|++||+.|++..++.++++++ ++++|++|++++.|
T Consensus 65 ~~v~aiiG~~~s~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~ 144 (334)
T cd06342 65 DGVVGVVGHLNSGVTIPASPIYADAGIVMISPAATNPKLTERGYKNVFRVVARDDQQGPAAAKYAVETLKAKKVAIIDDK 144 (334)
T ss_pred CCceEEECCCccHhHHHhHHHHHhCCCeEEecCCCCchhhcCCCceEEeccCCcHHHHHHHHHHHHHhcCCCEEEEEeCC
Confidence 48999999999999999999999999999999888777776678999999999999999999986 67899999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
++||+...+.+.+.+++.|++|+....++.+ ..+++..+.++++.++++|++.+...++..+++++++.|+.. .|
T Consensus 145 ~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~--~~d~~~~l~~i~~~~~~~vi~~~~~~~~~~~~~~~~~~g~~~---~~ 219 (334)
T cd06342 145 TAYGQGLADEFKKALKAAGGKVVAREGTTDG--ATDFSAILTKIKAANPDAVFFGGYYPEAGPLVRQMRQLGLKA---PF 219 (334)
T ss_pred cchhhHHHHHHHHHHHHcCCEEEEEecCCCC--CccHHHHHHHHHhcCCCEEEEcCcchhHHHHHHHHHHcCCCC---cE
Confidence 9999999999999999999999998888754 378999999999999999999999999999999999999843 56
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHAL 239 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al 239 (834)
+.++++... .. .....+..+|++...++.+ .++..++|.++|++++ +..++.++..+||+++++++|+
T Consensus 220 ~~~~~~~~~-~~----~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~-----~~~~~~~~~~~yda~~~~~~al 289 (334)
T cd06342 220 MGGDGLCDP-EF----IKIAGDAAEGTYATFPGGPLEKMPAGKAFVARYKAKF-----GDPPGAYAPYAYDAANVLAEAI 289 (334)
T ss_pred EecCccCCH-HH----HHHhhHhhCCcEEEecCCCCCCChHHHHHHHHHHHHh-----CCCCchhHHHHHHHHHHHHHHH
Confidence 766543210 00 0122356789988877766 4678899999999888 4446788999999999999999
Q ss_pred HHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEe
Q 003275 240 DALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNI 313 (834)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~ 313 (834)
+++.. .++..++++|++.+|+|++|+++|+++|++.+..|+|+||
T Consensus 290 ~~~~~-----------------------------~~~~~v~~~l~~~~~~g~~g~i~f~~~g~~~~~~~~~~~~ 334 (334)
T cd06342 290 KKAGS-----------------------------TDPAKVADALRKVDFDGVTGKISFDAKGDLKGAAVTVYQV 334 (334)
T ss_pred HHhCC-----------------------------CCHHHHHHHHHhCCCCCcceeeEECCCCCcccCcEEEEeC
Confidence 98511 1588999999999999999999999999999999999886
No 41
>cd06350 PBP1_GPCR_family_C_like Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). The metabotropic glutamate receptors (mGluR) are key receptors in the modulation of excitatory synaptic transmission in the central nervous system. The mGluRs are coupled to G proteins and are thus distinct from the iGluRs which internally contain ligand-gated ion channels. The mGluR structure is divided into three regions: the extracellular region, the seven-spanning transmembrane region and the cytoplasmic region. The extr
Probab=99.96 E-value=3.4e-28 Score=265.04 Aligned_cols=246 Identities=34% Similarity=0.610 Sum_probs=211.1
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|.|||||.+|..+.+++++++.++||+|+++++++.+++ ..+||+||+.|++..++.+++++++++||++|++|+.|
T Consensus 90 ~~v~aiiG~~~S~~~~a~~~~~~~~~vp~is~~~~~~~ls~~~~~~~~fr~~p~~~~~~~a~~~~~~~~~~~~v~~l~~~ 169 (348)
T cd06350 90 PKVVAVIGPGSSSVSMAVAELLGLFKIPQISYGATSPLLSDKLQFPSFFRTVPSDTSQALAIVALLKHFGWTWVGLVYSD 169 (348)
T ss_pred CceEEEECCCccHHHHHHHHHHhcCcCceecccCCChhhccccccCCeeEecCCcHHHHHHHHHHHHHCCCeEEEEEEec
Confidence 58999999999999999999999999999999999999976 67899999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
++||....+.+.+.+++.|+||+..+.++...+..++..++++|+++++|+||++++..++..++++|+++|+ ...++|
T Consensus 170 ~~~g~~~~~~~~~~~~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vvv~~~~~~~~~~~~~~a~~~g~-~~~~~i 248 (348)
T cd06350 170 DDYGRSGLSDLEEELEKNGICIAFVEAIPPSSTEEDIKRILKKLKSSTARVIVVFGDEDDALRLFCEAYKLGM-TGKYWI 248 (348)
T ss_pred chhHHHHHHHHHHHHHHCCCcEEEEEEccCCCcHHHHHHHHHHHHhCCCcEEEEEeCcHHHHHHHHHHHHhCC-CCeEEE
Confidence 9999999999999999999999999888865335899999999999999999999999999999999999999 444445
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHHHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHALDA 241 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al~~ 241 (834)
+...+... .... ....+.++|++++..+.|.....+.|.+.|++ +++++|||||+
T Consensus 249 ~~~~~~~~-~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~-------------~~~~~YDav~~------- 303 (348)
T cd06350 249 ISTDWDTS-TCLL----LFTLDAFQGVLGFSGHAPRSGEIPGFKDFLRK-------------YAYNVYDAVYA------- 303 (348)
T ss_pred EEccccCc-cccc----cCCcceeeeEEEEEEEeecCCcCCChHHHHHH-------------HHHHHHhheeE-------
Confidence 44444332 1110 12236789999999988876666777777764 67889999876
Q ss_pred HHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeec----cc
Q 003275 242 LLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGG----TG 317 (834)
Q Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~----~~ 317 (834)
.+.||++|++. ..|.|++++. .+
T Consensus 304 ----------------------------------------------------~v~f~~~gd~~-~~~~i~~~~~~~~~~~ 330 (348)
T cd06350 304 ----------------------------------------------------EVKFDENGDRL-ASYDIINWQIFPGGGG 330 (348)
T ss_pred ----------------------------------------------------EEEecCCCCcc-cceeEEEEEEcCCcEE
Confidence 58999999975 7799999976 67
Q ss_pred eEEEEEecCC
Q 003275 318 SRRIGYWSNY 327 (834)
Q Consensus 318 ~~~vG~w~~~ 327 (834)
++.||.|++.
T Consensus 331 ~~~vg~~~~~ 340 (348)
T cd06350 331 FVKVGFWDPQ 340 (348)
T ss_pred EEEEEEEcCC
Confidence 9999999873
No 42
>cd06338 PBP1_ABC_ligand_binding_like_5 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT); however their ligand specificity has not been determined experimentally.
Probab=99.96 E-value=8.3e-28 Score=261.52 Aligned_cols=267 Identities=16% Similarity=0.206 Sum_probs=223.3
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcC--CeEEEEEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYG--WREVIAIFV 80 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~--W~~v~iI~~ 80 (834)
++|.+||||.+|..+.++++++++.+||+|+++++++.++...+||+||+.|++..+..++++++.+++ |+++++|+.
T Consensus 70 ~~v~aviG~~~s~~~~a~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~ 149 (345)
T cd06338 70 DKVDFLLGPYSSGLTLAAAPVAEKYGVPMVAGSGASDSIFAQGFKYVFGTLPPASQYAKSLLEMLVALDPRPKKVAILYA 149 (345)
T ss_pred cCccEEecCCcchhHHHHHHHHHHhCCcEEecCCCCchHhhcCCceEEEecCchHHHHHHHHHHHHhcCCCCceEEEEec
Confidence 489999999999999999999999999999999988888766789999999999999999999999888 999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|++||+...+.+.+.+++.|++|+....++.. ..|++.++++|++.++|+|++.+...++..+++++++.|+..+ .+
T Consensus 150 ~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~--~~d~~~~v~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~~-~~ 226 (345)
T cd06338 150 DDPFSQDVAEGAREKAEAAGLEVVYDETYPPG--TADLSPLISKAKAAGPDAVVVAGHFPDAVLLVRQMKELGYNPK-AL 226 (345)
T ss_pred CCcccHHHHHHHHHHHHHcCCEEEEEeccCCC--ccchHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCCC-EE
Confidence 99999999999999999999999988888754 3789999999999999999999999999999999999999653 22
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCC-------ChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPD-------TDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVW 233 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~-------~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~ 233 (834)
+. +.+.... .. -....+..+|+++...+.|. .+..++|.++|++++ +..|+.++..+||+++
T Consensus 227 ~~-~~~~~~~-~~----~~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~-----~~~p~~~~~~~y~a~~ 295 (345)
T cd06338 227 YM-TVGPAFP-AF----VKALGADAEGVFGPTQWTPALDYKDDLFPSAAEFAAAYKEKY-----GKAPDYHAAGAYAAGQ 295 (345)
T ss_pred EE-ecCCCcH-HH----HHHHhhhhCceeecceeccCcccccccCccHHHHHHHHHHHh-----CCCCCcccHHHHHHHH
Confidence 22 2222110 00 01223456888887776664 367899999999998 3446778899999999
Q ss_pred HHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEe
Q 003275 234 LVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNI 313 (834)
Q Consensus 234 ~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~ 313 (834)
++++|++++... +++.+.++|++++|.|++|++.|+++|++.. .+.+++|
T Consensus 296 ~~~~a~~~ag~~-----------------------------~~~~v~~al~~~~~~~~~G~~~f~~~~~~~~-~~~~~~~ 345 (345)
T cd06338 296 VLQEAVERAGSL-----------------------------DPAAVRDALASNDFDTFYGPIKFDETGQNNH-PMTVVQW 345 (345)
T ss_pred HHHHHHHHhCCC-----------------------------CHHHHHHHHHhCCCcccccCeeECCCCCcCC-CceeeeC
Confidence 999999985211 4789999999999999999999999998754 5555543
No 43
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=99.96 E-value=2.1e-27 Score=258.81 Aligned_cols=273 Identities=15% Similarity=0.195 Sum_probs=231.0
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHH-HHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLV-EYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll-~~~~W~~v~iI~~ 80 (834)
+++|.+||||.+|..+.++++++++.+||+|++.+++|.+++..++|+||+.+.+..++.++++++ ++++|+++++|+.
T Consensus 90 ~~~V~~iiG~~~s~~~~a~~~~~~~~~ip~i~~~s~~~~l~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~k~va~i~~ 169 (369)
T PRK15404 90 NDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATAPELTARGYQLIFRTIGLDSDQGPTAAKYILEKVKPKRIAVLHD 169 (369)
T ss_pred hCCceEEEcCCCchhHHHhHHHHHHCCCeEEecCCCCHHHhcCCCceEEeCCCCcHHHHHHHHHHHHHhcCCCEEEEEeC
Confidence 468999999999999999999999999999999999999988778999999999999999999976 5679999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|++||+...+.+.+.+++.|++|+....++.+. .|+..++.++++.++|+|++.+...++..+++++++.|+.. .
T Consensus 170 d~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~g~--~D~~~~v~~l~~~~~d~v~~~~~~~~~~~~~k~~~~~G~~~---~ 244 (369)
T PRK15404 170 KQQYGEGLARSVKDGLKKAGANVVFFEGITAGD--KDFSALIAKLKKENVDFVYYGGYHPEMGQILRQAREAGLKT---Q 244 (369)
T ss_pred CCchhHHHHHHHHHHHHHcCCEEEEEEeeCCCC--CchHHHHHHHHhcCCCEEEECCCchHHHHHHHHHHHCCCCC---e
Confidence 999999999999999999999999888888653 78999999999999999988887888899999999999854 4
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecC-CCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHT-PDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHAL 239 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~-~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al 239 (834)
|+.+++.... .. .....+..+|+++..++. ..++..++|.++|++++ ..+++.++..+||++++++.|+
T Consensus 245 ~i~~~~~~~~-~~----~~~~~~~~~Gv~~~~~~~~~~~~~~~~f~~~~~~~~-----~~~~~~~~~~~Y~~~~~l~~Al 314 (369)
T PRK15404 245 FMGPEGVGNK-SL----SNIAGPASEGMLVTLPKRYDQDPANKAIVDAFKAKK-----QDPSGPFVWTTYAAVQSLAAGI 314 (369)
T ss_pred EEecCcCCCH-HH----HHhhhhhhcCcEEEccCCCccChhHHHHHHHHHHhc-----CCCCccchHHHHHHHHHHHHHH
Confidence 6666543221 00 011235678988765533 34678899999999876 3345677889999999999999
Q ss_pred HHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeeccce
Q 003275 240 DALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGGTGS 318 (834)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~~~~ 318 (834)
+++... +++.|.++|++.+|+|++|++.|+++|++....|.|++|++++.
T Consensus 315 ~~aG~~-----------------------------~~~~l~~al~~~~~~~~~G~~~~~~~g~~~~~~~~i~~~~~~~~ 364 (369)
T PRK15404 315 NRAGSD-----------------------------DPAKVAKYLKANTFDTVIGPLSWDEKGDLKGFEFGVFEWHADGT 364 (369)
T ss_pred HhhCCC-----------------------------CHHHHHHHHHhCCCCcceEeeEECCCCCcccCCEEEEEEEcCCe
Confidence 985211 47899999999999999999999999998889999999987653
No 44
>cd06345 PBP1_ABC_ligand_binding_like_10 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.95 E-value=6.8e-27 Score=253.92 Aligned_cols=259 Identities=19% Similarity=0.269 Sum_probs=216.4
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC----CCCCceEEccCChHHHHHHHHHHHHH-----cCCe
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS----LQYPYFLRTTQSDYYQMHAVADLVEY-----YGWR 73 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~----~~~p~~~r~~ps~~~q~~aia~ll~~-----~~W~ 73 (834)
++|.+||||.+|..+.++++++++.+||+|+++++++.++. ..+|++||+.|++..+..++++++.+ ++|+
T Consensus 66 ~~v~aiiG~~~s~~~~a~~~~~~~~~vp~i~~~~~~~~~t~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (344)
T cd06345 66 DKVDAVVGGYSSEVVLALQDVAAENKVPFIVTGAASPEITTADDYETYKYVFRAGPTNSSYAQSVADALKETLVDKHGFK 145 (344)
T ss_pred CCceEEECCcchHHHHHHHHHHHHcCCcEEeccCCCCcccccccccCCceEEecCCCcHHHHHHHHHHHHHhhcccCCCc
Confidence 48999999999999999999999999999999988888873 46899999999999999999999876 8999
Q ss_pred EEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCC
Q 003275 74 EVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLG 153 (834)
Q Consensus 74 ~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g 153 (834)
+|++|+.|++||....+.+.+.+++.|++|+....++.+ ..+++.++.+|++.++|+|++.+...++..+++++.+.|
T Consensus 146 ~va~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g 223 (344)
T cd06345 146 TAAIVAEDAAWGKGIDAGIKALLPEAGLEVVSVERFSPD--TTDFTPILQQIKAADPDVIIAGFSGNVGVLFTQQWAEQK 223 (344)
T ss_pred eEEEEecCchhhhHHHHHHHHHHHHcCCeEEEEEecCCC--CCchHHHHHHHHhcCCCEEEEeecCchHHHHHHHHHHcC
Confidence 999999999999999999999999999999998888754 478999999999999999999999999999999999999
Q ss_pred CCCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCC----CChhHHHHHHHHHhhhcCCCCCCCccchhHHHh
Q 003275 154 MTAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP----DTDLKKNFISRWKNLKYKENSPSGFNSYALYAY 229 (834)
Q Consensus 154 ~~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~----~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~Y 229 (834)
+..+ ++..+........ -....+..+|+++...+.| .++..++|.++|++++ +..++.+++.+|
T Consensus 224 ~~~~---~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~-----g~~p~~~~~~~y 291 (344)
T cd06345 224 VPIP---TIGISVEGNSPAF----WKATNGAGNYVITAESGAPGVEAITDKTVPFTEAYEAKF-----GGPPNYMGASTY 291 (344)
T ss_pred CCCc---eEEecCCcCCHHH----HHhhchhcceEEeecccccCccCCCHHHHHHHHHHHHHh-----CCCCcccchHHH
Confidence 8432 2222211100000 0112245667766655544 5677899999999988 456888999999
Q ss_pred hHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCC
Q 003275 230 DSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLV 304 (834)
Q Consensus 230 Dav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~ 304 (834)
|+++++++|++++.. .+++.+.++|++.+|+|++|+++||++|++.
T Consensus 292 da~~~l~~A~~~ag~-----------------------------~~~~~i~~al~~~~~~g~~G~i~f~~~g~~~ 337 (344)
T cd06345 292 DSIYILAEAIERAGS-----------------------------TDGDALVEALEKTDFVGTAGRIQFYGDDSAF 337 (344)
T ss_pred HHHHHHHHHHHHhcC-----------------------------CCHHHHHHHHHhCCCcCCceeEEECCCCCcC
Confidence 999999999998522 1478999999999999999999999999975
No 45
>cd06377 PBP1_iGluR_NMDA_NR3 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=99.95 E-value=5.7e-26 Score=239.79 Aligned_cols=280 Identities=15% Similarity=0.210 Sum_probs=194.4
Q ss_pred CCCcEEEEC-CCChhhHHHHHHhhccCCccEEecccCCCCC-CCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEE
Q 003275 2 ENEVVAAIG-PQSSGIAHVISHVVNELNVPLLSFGATDPTL-TSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIF 79 (834)
Q Consensus 2 ~~~V~aiiG-p~~S~~~~~~~~~~~~~~vP~Is~~at~~~l-s~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~ 79 (834)
.+||.||+| |.++..+..+..+|+.++||+|+++..++.. +...+.+.+++.|+...+..|+++++++|+|++|++||
T Consensus 79 ~~GV~AIfg~p~s~~~~~~v~sic~~l~IP~I~~~~~~~~~~~~~~~~l~L~l~P~~~~l~~a~~~ll~~~~W~~f~~iy 158 (382)
T cd06377 79 VQGVSALLAFPQTRPELVQLDFVSAALEIPVVSIVRREFPRGSQNPFHLQMSWASPLSTLLDVLLSVLQRNGWEDVSLVL 158 (382)
T ss_pred hCCeEEEEecCCCHHHHHHHHHHhcCCCCCEEEecCCcccccCCCceeEEEEecCCHHHHHHHHHHHHHHCCCcEEEEEE
Confidence 689999999 4888888999999999999999986655333 22333344577999999999999999999999999999
Q ss_pred EcCCcccchHHHHHHHHhcCC--cEEEeeecCCC-CCChHHH-HHHHHHhhcCC-ceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 80 VDDDYGRNGISVLGDALSKKR--AKISYKAPFSP-GASRSAI-NSLLVGANLME-SRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 80 ~d~~~g~~~~~~l~~~l~~~g--~~I~~~~~~~~-~~~~~~~-~~~l~~l~~~~-~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
+.++ |....+.+.+.....+ ..|..+ ..+. ..+..++ +..|++|++.+ +++|+++|+.+.+..+++++.+
T Consensus 159 ~~~~-gl~~lq~l~~~~~~~~~~~~i~v~-~~~~~~~d~~~~~~~~L~~i~~~~~~~~ill~cs~e~~~~il~~~~~--- 233 (382)
T cd06377 159 CRER-DPTGLLLLWTNHARFHLGSVLNLS-RNDPSTADLLDFLRAQLELLKDPPGPAVVLFGCDVARARRVLELTPP--- 233 (382)
T ss_pred ecCc-CHHHHHHHHHHhcccccCceEEEE-eccCccCChhHHHHHHHHHhhcccCceEEEEECCHHHHHHHHHhhcc---
Confidence 8776 3333333333332222 223222 2221 1123455 99999999999 9999999999999999977654
Q ss_pred CCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHH
Q 003275 155 TAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWL 234 (834)
Q Consensus 155 ~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~ 234 (834)
+|+||+++.. .++... ....--|+++ |.+.. ....++++||||++
T Consensus 234 ---~y~wIv~~~~--~le~~~-----~~g~nigLl~-----------------~~~~~--------~~~l~ali~DAV~l 278 (382)
T cd06377 234 ---GPHWILGDPL--PPEALR-----TEGLPPGLLA-----------------HGETT--------QPPLEAYVQDALEL 278 (382)
T ss_pred ---ceEEEEcCCc--Chhhcc-----CCCCCceEEE-----------------Eeecc--------cccHHHHHHHHHHH
Confidence 4999998721 111110 0011123331 21110 11238899999999
Q ss_pred HHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCc--c-ccCchHHHHHHHHhcccccceeeEEEccCCCC--CCCcEE
Q 003275 235 VAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSL--R-VFDGGQQFLQTLLRMNFTGLSGEIRFDADKNL--VNPAYD 309 (834)
Q Consensus 235 la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~-~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~--~~~~~~ 309 (834)
+|+|++.+........+ .....+|... + +|++|..|.++|++++|+|+||+|.| ++|.+ .+..++
T Consensus 279 vA~a~~~l~~~~~~~~l---------~~~~~~C~~~~~~~~W~~G~~l~~~Lknv~~eGlTG~I~F-~~g~R~~~~~~l~ 348 (382)
T cd06377 279 VARAVGSATLVQPELAL---------IPATVNCMDLPTKGNESSGQYLARFLANTSFDGRTGPVWV-TGSSQVHSSRHFK 348 (382)
T ss_pred HHHHHHHhhhccccccc---------CCCCCCcccCCCCCCCCchHHHHHHHHhCcccccceeEEE-ccCeeecccceEE
Confidence 99999986321111111 1112345433 5 89999999999999999999999999 45777 789999
Q ss_pred EEEee--ccc---eEEEEEecCCCCcc
Q 003275 310 VLNIG--GTG---SRRIGYWSNYSGLS 331 (834)
Q Consensus 310 I~~~~--~~~---~~~vG~w~~~~gl~ 331 (834)
|++++ ..| |++||+|++...+.
T Consensus 349 I~~L~~~~~G~~~W~kVG~W~~~~~~~ 375 (382)
T cd06377 349 VWSLRRDPVGQPTWTTVGSWQGGRKIV 375 (382)
T ss_pred EEEeccccCCCccceEEEEecCCCcee
Confidence 99998 444 59999999864333
No 46
>cd06351 PBP1_iGluR_N_LIVBP_like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors characterized by their response to glutamate agonists: N-methyl-aspartate (NMDA) and non-NMDA receptors
Probab=99.95 E-value=1.6e-26 Score=249.79 Aligned_cols=259 Identities=24% Similarity=0.339 Sum_probs=207.2
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
+++|.|||||.+|..+.+++++++.++||+|+++++.+.+++ ..+||++|+.|++..++.++++++.+++|++|++||+
T Consensus 61 ~~~v~ai~G~~~s~~~~~v~~~~~~~~iP~is~~~~~~~~~~~~~~~~~~~~~p~~~~~~~a~~~~l~~~~w~~v~iiy~ 140 (328)
T cd06351 61 SQGVAAIFGPTSSESASAVQSICDALEIPHISISGGSEGLSDKEESSTTLQLYPSLEDLADALLDLLEYYNWTKFAIIYD 140 (328)
T ss_pred ccCcEEEECCCCHHHHHHHHHHhccCCCCeEEeecCcccccccccccceEEecCCHHHHHHHHHHHHHHcCCcEEEEEEe
Confidence 568999999999999999999999999999999998888876 5789999999999999999999999999999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCc-eEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMES-RVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~-~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
+++++. .++.+.+.....+..+... .+.... .+++..+.++++.++ ++|++++....+..++++|.++||++++|
T Consensus 141 ~~~~~~-~l~~~~~~~~~~~~~v~~~-~~~~~~--~~~~~~l~~l~~~~~~~vil~~~~~~~~~~~l~~a~~~gm~~~~~ 216 (328)
T cd06351 141 SDEGLS-RLQELLDESGIKGIQVTVR-RLDLDD--DNYRQLLKELKRSESRRIILDCSSEEEAKEILEQAVELGMMGYGY 216 (328)
T ss_pred CchHHH-HHHHHHHhhcccCceEEEE-EecCCc--hhHHHHHHHHhhcccceEEEECCcHHHHHHHHHHHHHhccccCCc
Confidence 888543 3344444444444455543 344332 379999999999998 55555555599999999999999999999
Q ss_pred EEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHH
Q 003275 160 VWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHAL 239 (834)
Q Consensus 160 vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al 239 (834)
+||.++......+. ........|+++++...+..+..++|..+|.... .......+...++.+||+++++
T Consensus 217 ~~i~~~~~~~~~d~-----~~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~d~~~~~---- 286 (328)
T cd06351 217 HWILTNLDLSDIDL-----EPFQYGPANITGFRLVDPDSPDVSQFLQRWLEES-PGVNLRAPIYDAALLYDAVLLL---- 286 (328)
T ss_pred EEEEecCCccccch-----hhhccCCcceEEEEEeCCCchHHHHHHHhhhhcc-CCCCcCccchhhHhhhcEEEEE----
Confidence 99999876654432 2344667899999999999999999999994433 1122233444566666664222
Q ss_pred HHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEee-ccce
Q 003275 240 DALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIG-GTGS 318 (834)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~-~~~~ 318 (834)
||+++||++|++.+..++|+++. +.++
T Consensus 287 ----------------------------------------------------tg~i~f~~~g~r~~~~l~i~~l~~~~~~ 314 (328)
T cd06351 287 ----------------------------------------------------TGTVSFDEDGVRSNFTLDIIELNRSRGW 314 (328)
T ss_pred ----------------------------------------------------EeeEEECCCCcccceEEEEEEecCCCCc
Confidence 89999999999999999999999 8999
Q ss_pred EEEEEecC
Q 003275 319 RRIGYWSN 326 (834)
Q Consensus 319 ~~vG~w~~ 326 (834)
++||.|++
T Consensus 315 ~~vg~W~~ 322 (328)
T cd06351 315 RKVGTWNG 322 (328)
T ss_pred eEEEEecC
Confidence 99999984
No 47
>cd06346 PBP1_ABC_ligand_binding_like_11 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.95 E-value=1.7e-26 Score=246.84 Aligned_cols=243 Identities=25% Similarity=0.332 Sum_probs=206.9
Q ss_pred CCcEEEECCCChhhHHHH-HHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 3 NEVVAAIGPQSSGIAHVI-SHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~-~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
++|.+||||.+|..+.++ ++++++.++|+|+++++++.++. ..++|+||+.|++..++.++++++.+++|+++++|+.
T Consensus 66 ~~v~~viG~~~s~~~~a~~~~~~~~~~vp~i~~~~~~~~l~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~~vail~~ 145 (312)
T cd06346 66 DGVPGIVGAACSGVTIAALTSVAVPNGVVMISPSSTSPTLTTLDDNGLFFRTAPSDALQGQALAQLAAERGYKSVATTYI 145 (312)
T ss_pred cCCCEEEccccchhhHhhhhhhhccCCcEEEecCCCCccceecCCCceEEEecCCcHHHHHHHHHHHHHcCCCeEEEEEc
Confidence 589999999999999999 99999999999999999999987 4579999999999999999999999999999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|++||+...+.+++.+++.|++|+....++.+ ..|++.++.+|+++++|+|++.+.+.++..++++++++|+.. .
T Consensus 146 ~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~---~ 220 (312)
T cd06346 146 NNDYGVGLADAFTKAFEALGGTVTNVVAHEEG--KSSYSSEVAAAAAGGPDALVVIGYPETGSGILRSAYEQGLFD---K 220 (312)
T ss_pred cCchhhHHHHHHHHHHHHcCCEEEEEEeeCCC--CCCHHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCCCC---c
Confidence 99999999999999999999999998888865 489999999999999999999999999999999999999843 3
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHALD 240 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al~ 240 (834)
|+.+++.... ... .....+.++|+++..+..+. +..++|.++|+++| +..|+.+++.+||+++++++|
T Consensus 221 ~~~~~~~~~~-~~~---~~~~~~~~~g~~~~~~~~~~-~~~~~f~~~~~~~~-----g~~p~~~~~~~Yd~~~~l~~A-- 288 (312)
T cd06346 221 FLLTDGMKSD-SFL---PADGGYILAGSYGTSPGAGG-PGLEAFTSAYKAAY-----GESPSAFADQSYDAAALLALA-- 288 (312)
T ss_pred eEeeccccCh-HHH---HhhhHHHhCCcEEccCCCCc-hhHHHHHHHHHHHh-----CCCCCccchhhHHHHHHHHHH--
Confidence 6666543221 100 01112467898887665544 78899999999998 445888999999999999877
Q ss_pred HHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEE
Q 003275 241 ALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDV 310 (834)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I 310 (834)
|.|++|++.||++|++.. .|+-
T Consensus 289 -----------------------------------------------~~g~~g~~~f~~~g~~~~-~~~~ 310 (312)
T cd06346 289 -----------------------------------------------YQGASGVVDFDENGDVAG-SYDE 310 (312)
T ss_pred -----------------------------------------------hCCCccceeeCCCCCccc-ceee
Confidence 558899999999998653 5543
No 48
>cd06348 PBP1_ABC_ligand_binding_like_13 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.95 E-value=9.7e-26 Score=244.96 Aligned_cols=273 Identities=19% Similarity=0.298 Sum_probs=218.1
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHH-HHHHHHHHHc-CCeEEEEEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQM-HAVADLVEYY-GWREVIAIFV 80 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~-~aia~ll~~~-~W~~v~iI~~ 80 (834)
++|++||||.+|..+.++.+++++.+||+|+++++++.+.. .++|+||+.+++..+. .++..+++++ ||+++++||.
T Consensus 66 ~~v~~iiG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~~~~~-~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~ 144 (344)
T cd06348 66 DRVLAIIGPTLSQQAFAADPIAERAGVPVVGPSNTAKGIPE-IGPYVFRVSAPEAVVAPAAIAAALKLNPGIKRVAVFYA 144 (344)
T ss_pred cCceEEECCCCcHHHHhhhHHHHhCCCCEEeccCCCCCcCC-CCCeEEEccCcHHHHHHHHHHHHHHHhcCCeEEEEEEe
Confidence 48999999999999999999999999999999887776643 4689999987766554 4455667788 9999999997
Q ss_pred cCC-cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 81 DDD-YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 81 d~~-~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
+++ ||+...+.+++.+++.|++|+....++.+ ..|+..++.+|+++++|+|++.+.+.++..+++++++.|+..
T Consensus 145 ~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~--~~d~~~~v~~i~~~~~d~vi~~~~~~~~~~~~~~~~~~g~~~--- 219 (344)
T cd06348 145 QDDAFSVSETEIFQKALRDQGLNLVTVQTFQTG--DTDFQAQITAVLNSKPDLIVISALAADGGNLVRQLRELGYNG--- 219 (344)
T ss_pred CCchHHHHHHHHHHHHHHHcCCEEEEEEeeCCC--CCCHHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCC---
Confidence 655 99999999999999999999998888854 479999999999999999999999999999999999999864
Q ss_pred EEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHH
Q 003275 160 VWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAH 237 (834)
Q Consensus 160 vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~ 237 (834)
.|+.++++... .. -+...+..+|++...++.+ +.+..++|.++|++++ +..++.++..+||+++++++
T Consensus 220 ~~~~~~~~~~~-~~----~~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~-----g~~p~~~~~~~yda~~~~~~ 289 (344)
T cd06348 220 LIVGGNGFNTP-NV----FPVCQAACDGVLVAQAYSPENDTPVNRDFVEAYKKKY-----GKAPPQFSAQAFDAVQVVAE 289 (344)
T ss_pred ceeccccccCH-HH----HHhhhHhhcCeEEEeeccCCCCCHHHHHHHHHHHHHH-----CCCccHHHHHHHHHHHHHHH
Confidence 24554433211 11 0123356789888877665 4467899999999888 34577889999999999999
Q ss_pred HHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEE
Q 003275 238 ALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDV 310 (834)
Q Consensus 238 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I 310 (834)
|++++...++.. .+. ....+..|.++|++.+|.|++|++.||++|++....|.+
T Consensus 290 A~~~a~~~~~~~----------------~~~---~~~~~~~l~~~l~~~~~~g~~G~v~f~~~g~~~~~~~~~ 343 (344)
T cd06348 290 ALKRLNQKQKLA----------------ELP---LPELRTALNAALLSGQYDTPLGEISFTPDGEVLQKAFYV 343 (344)
T ss_pred HHHHhcCCCccc----------------cch---hhhHHHHHHHHHhccCCccceeeeEECCCCCcccCceec
Confidence 999976432110 000 011367899999999999999999999999987776644
No 49
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.94 E-value=6.4e-26 Score=246.19 Aligned_cols=262 Identities=16% Similarity=0.199 Sum_probs=218.3
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc------CCeEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY------GWREVI 76 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~------~W~~v~ 76 (834)
++|.+|+||.+|..+.++++++++.+||+|+++++++.++...+||+||+.|++..++.++++++.++ +|++++
T Consensus 69 ~~v~aiiG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~fr~~p~~~~~~~~~~~~l~~~~~~~~~~~~~v~ 148 (347)
T cd06340 69 EGVVALVGAYQSAVTLAASQVAERYGVPFVVDGAVSDSITERGFKYTFRITPHDGMFTRDMFDFLKDLNEKTGKPLKTVA 148 (347)
T ss_pred CCceEEecccchHhHHHHHHHHHHhCCCEEeccccchHHhhcCCceEEecCCChHHHHHHHHHHHHHhhHhcCCCCceEE
Confidence 48999999999999999999999999999999988888887678999999999999999999999876 469999
Q ss_pred EEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 77 AIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 77 iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
+|+.|++||....+.+.+.+++.|++|+....++.. ..|++.++.+|+++++|+|++.++..++..+++++++.|+..
T Consensus 149 ~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~G~~~ 226 (347)
T cd06340 149 LVHEDTEFGTSVAEAIKKFAKERGFEIVEDISYPAN--ARDLTSEVLKLKAANPDAILPASYTNDAILLVRTMKEQRVEP 226 (347)
T ss_pred EEecCchHhHHHHHHHHHHHHHcCCEEEEeeccCCC--CcchHHHHHHHHhcCCCEEEEcccchhHHHHHHHHHHcCCCC
Confidence 999999999999999999999999999998888855 479999999999999999999999999999999999999864
Q ss_pred CCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCC-ChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHH
Q 003275 157 GSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPD-TDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLV 235 (834)
Q Consensus 157 ~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~-~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~l 235 (834)
+ .++...++.... ... ....+..+|++...++.++ .+..++|.++|++++ +..++.++..+||+++++
T Consensus 227 ~-~~~~~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~f~~~y~~~~-----~~~~~~~~~~~Y~a~~~l 295 (347)
T cd06340 227 K-AVYSVGGGAEDP-SFV----KALGKDAEGILTRNEWSDPKDPMAKDLNKRFKARF-----GVDLSGNSARAYTAVLVI 295 (347)
T ss_pred c-EEEecCCCcCcH-HHH----HHhhHhhheEEeccccCCCCChHHHHHHHHHHHHh-----CCCCChHHHHHHHHHHHH
Confidence 3 333322222111 000 1223567899888777664 678899999999998 345888999999999999
Q ss_pred HHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHH--HHHHhcccc---cceeeEEEccCCCCCCC
Q 003275 236 AHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFL--QTLLRMNFT---GLSGEIRFDADKNLVNP 306 (834)
Q Consensus 236 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~--~~l~~~~f~---g~tG~i~Fd~~g~~~~~ 306 (834)
++|++++.+. +++.+. .+|++..+. ++.|++.||++|+..++
T Consensus 296 ~~A~~~ag~~-----------------------------~~~~v~~~~~~~~~~~~~~~~~~g~~~f~~~g~~~~~ 342 (347)
T cd06340 296 ADALERAGSA-----------------------------DPEKIRDLAALASTSGEDLIMPYGPIKFDAKGQNTNA 342 (347)
T ss_pred HHHHHHhcCC-----------------------------CHHHHHHHHHhccCCccccccCCCCeeECCCCCcccc
Confidence 9999995321 467777 478777765 56899999999997654
No 50
>cd06344 PBP1_ABC_ligand_binding_like_9 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine/isoleucine/valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.94 E-value=2.5e-25 Score=240.30 Aligned_cols=260 Identities=20% Similarity=0.199 Sum_probs=212.7
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcC-CeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYG-WREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~-W~~v~iI~~d 81 (834)
++|++|+|+.+|..+.++++++++.++|+|+++++++.++ ..+||+||+.+++..++.++++++.+.+ |++|++|+.|
T Consensus 65 ~~v~aiiG~~~s~~~~a~~~~~~~~~ip~i~~~a~~~~lt-~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~ 143 (332)
T cd06344 65 PEILGVVGHYSSDATLAALDIYQKAKLVLISPTSTSVKLS-NPGPYFFRTVPSNAVAARALAKYLKKKNKIKKVAIFYNS 143 (332)
T ss_pred cCceEEEcCCCcHHHHHHHHHHhhcCceEEccCcCchhhc-CCCCcEEEeCCCcHHHHHHHHHHHHhhcCCCeEEEEeCC
Confidence 5899999999999999999999999999999988888887 4679999999999999999999998876 9999999988
Q ss_pred CC-cccchHHHHHHHHhc-CCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 82 DD-YGRNGISVLGDALSK-KRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 82 ~~-~g~~~~~~l~~~l~~-~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
++ ||+...+.+.+.+++ .|++|.....++ .++.++..++.++++.++++|++.++......+++++.+.+. ..
T Consensus 144 ~~~~g~~~~~~~~~~~~~~~g~~v~~~~~~~--~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~~---~~ 218 (332)
T cd06344 144 TSPYSQSLKQEFTSALLERGGGIVVTPCDLS--SPDFNANTAVSQAINNGATVLVLFPDTDTLDKALEVAKANKG---RL 218 (332)
T ss_pred CchHhHHHHHHHHHHHHHhcCCeeeeeccCC--CCCCCHHHHHHHHHhcCCCEEEEeCChhHHHHHHHHHHhcCC---Cc
Confidence 76 999999999999999 599987655444 334678899999999999999999988888889999888664 22
Q ss_pred EEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHH
Q 003275 160 VWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHAL 239 (834)
Q Consensus 160 vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al 239 (834)
.++.++.+... +.. .......+|+++..++.++.+..++|.++|++++ +.+++.++..+||+++++++|+
T Consensus 219 ~i~~~~~~~~~-~~~----~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~-----~~~~~~~a~~~Yda~~~l~~A~ 288 (332)
T cd06344 219 TLLGGDSLYTP-DTL----LDGGKDLEGLVLAVPWHPLASPNSPFAKLAQQLW-----GGDVSWRTATAYDATKALIAAL 288 (332)
T ss_pred eEEecccccCH-HHH----HhchhhhcCeEEEEecccccccchHHHHHHHHHh-----cCCchHHHHhHHHHHHHHHHHH
Confidence 34444443221 110 0122567899999888888788899999999998 4467889999999999999999
Q ss_pred HHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHH-HHHHhcccccceeeEEEccCCCCCCCc
Q 003275 240 DALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFL-QTLLRMNFTGLSGEIRFDADKNLVNPA 307 (834)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~-~~l~~~~f~g~tG~i~Fd~~g~~~~~~ 307 (834)
+++.+. ++..+. .++++..|.|+.|+++||++|++..+.
T Consensus 289 ~~ag~~-----------------------------~~~~~~~~~~~~~~~~g~~g~i~f~~~g~~~~~~ 328 (332)
T cd06344 289 SQGPTR-----------------------------EGVQQVELSLRNFSVQGATGKIKFLPSGDRNGQA 328 (332)
T ss_pred HhCCCh-----------------------------hhhhhhhhhcccccccCCCceeEeCCCCcccCcC
Confidence 985211 234444 677788899999999999999976543
No 51
>cd06360 PBP1_alkylbenzenes_like Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene. This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.
Probab=99.94 E-value=9.1e-25 Score=236.82 Aligned_cols=266 Identities=20% Similarity=0.276 Sum_probs=224.3
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCC-CCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSL-QYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~-~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|.+||||.+|..+.++++++++.++|+|+++++++.++.. .+||+||+.+++..++..+++++...+|+++++|+.|
T Consensus 64 ~~v~~iig~~~s~~~~~~~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~~~~~v~~l~~~ 143 (336)
T cd06360 64 DKVDVVVGPVHSGEALAMVKVLREPGTPLINPNAGADDLTGRLCAPNFFRTSFSNAQWAAPMGKYAADDGYKKVVTVAWD 143 (336)
T ss_pred hCCcEEEccCccHhHHHHHHHHHhcCceEEecCCCCccccccCCCCcEEEEeCchHHHHHHHHHHHHHcCCCeEEEEecc
Confidence 589999999999999999999999999999998888888873 4799999999999999999999998999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
+.||+...+.+.+.+++.|++++....++.. ..|++.++.++++.++|+|++.+...++..+++++.+.|+.+ ...|
T Consensus 144 ~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~v~~~~~~~pd~v~~~~~~~~~~~~~~~~~~~g~~~-~~~~ 220 (336)
T cd06360 144 YAFGYEVVEGFKEAFTEAGGKIVKELWVPFG--TSDFASYLAQIPDDVPDAVFVFFAGGDAIKFVKQYDAAGLKA-KIPL 220 (336)
T ss_pred chhhHHHHHHHHHHHHHcCCEEEEEEecCCC--CcchHHHHHHHHhcCCCEEEEecccccHHHHHHHHHHcCCcc-CCeE
Confidence 9999999999999999999999988777754 479999999999999999999989999999999999999853 2345
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHAL 239 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al 239 (834)
+.++++.... . .....+..+|++...++.+ +++..+.|.++|++++ +..++.++..+||+++++++|+
T Consensus 221 ~~~~~~~~~~-~----~~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~-----~~~~~~~~~~~yda~~~~~~A~ 290 (336)
T cd06360 221 IGSGFLTDGT-T----LGAAGEAAEGVITALHYADTLDNPANQAFVKAYRAAY-----PDTPSVYAVQGYDAGQALILAL 290 (336)
T ss_pred EecccccCHH-H----HHhhHhhhcCceeccccCCCCCCHHHHHHHHHHHHHh-----CCCccHHHHHHHHHHHHHHHHH
Confidence 5554432210 0 1223366789888777655 4678899999999998 3467889999999999999999
Q ss_pred HHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcE
Q 003275 240 DALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAY 308 (834)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~ 308 (834)
+++... -.+++.+.++|+++.|.|+.|+++|+++|++..+.|
T Consensus 291 ~~a~~~---------------------------~~~~~~v~~al~~~~~~~~~g~~~f~~~~~~~~~~~ 332 (336)
T cd06360 291 EAVGGD---------------------------LSDGQALIAAMAAAKIDSPRGPFTLDKAHNPIQDNY 332 (336)
T ss_pred HHhCCC---------------------------CCCHHHHHHHHhcCCccCCCcceEECCCCCcccceE
Confidence 996321 014778999999999999999999999998765543
No 52
>cd06327 PBP1_SBP_like_1 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Solute binding proteins are the primary specific receptors that initiate uptake of a broad range of solutes, including amino acids, peptides and inorganic ions. The members are predicted to have a similar function to an active transport system for short chain amides and urea by sequence comparison and phylogenetic analysis. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus may also be involved in transport of amino acids.
Probab=99.93 E-value=6.7e-25 Score=237.27 Aligned_cols=261 Identities=16% Similarity=0.165 Sum_probs=217.3
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCC-CCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSL-QYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~-~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|.+||||.+|..+.++++++++.+||+|+++++++.++.. .+||+||+.+++..|+.++++++...+++++++++.|
T Consensus 65 ~~V~aviG~~~s~~~~a~~~~~~~~~vp~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~ 144 (334)
T cd06327 65 DGVDMIVGGPNSAVALAVQEVAREKKKIYIVTGAGSDDLTGKDCSPYTFHWAYDTYMLANGTAPALVKAGGKKWFFLTAD 144 (334)
T ss_pred cCceEEECCccHHHHHHHHHHHHHhCceEEecCCCccccccCCCCCceEEccCChHHHHHHHHHHHHHhcCCeEEEEecc
Confidence 589999999999999999999999999999999999888874 4799999999999999999998877779999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
++||+.....+.+++++.|++|+....++.. ..|+..++.++++.++|+|++.+.+.++..+++++++.|+... ..+
T Consensus 145 ~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~-~~~ 221 (334)
T cd06327 145 YAFGHSLERDARKVVKANGGKVVGSVRHPLG--TSDFSSYLLQAQASGADVLVLANAGADTVNAIKQAAEFGLTKG-QKL 221 (334)
T ss_pred hHHhHHHHHHHHHHHHhcCCEEcCcccCCCC--CccHHHHHHHHHhCCCCEEEEeccchhHHHHHHHHHHhCCccC-CcE
Confidence 9999999999999999999999998888854 4789999999999999999999999999999999999998632 223
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHAL 239 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al 239 (834)
+........+. ....+..+|++...++.+ +.+..++|.++|++++ +..++.++..+||+++++++|+
T Consensus 222 ~~~~~~~~~~~------~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~-----g~~p~~~~~~~Y~~~~~~~~A~ 290 (334)
T cd06327 222 AGLLLFLTDVH------SLGLDAAQGLYLTTAWYWDLPNDETRAFVKRFQAKY-----GKMPSMVQAGAYSAVLHYLKAV 290 (334)
T ss_pred EEecccHHHHH------hhchhhhcCeEEeeeccccCCCHHHHHHHHHHHHHH-----CcCCCcHHHHHHHHHHHHHHHH
Confidence 33221111100 111245789888877654 3678899999999998 3457888999999999999999
Q ss_pred HHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcc-cccceeeEEEcc-CCCCCCC
Q 003275 240 DALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMN-FTGLSGEIRFDA-DKNLVNP 306 (834)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~-f~g~tG~i~Fd~-~g~~~~~ 306 (834)
+++... ++.++.++|+++. ++++.|+++|+. +|+...+
T Consensus 291 ~~ag~~-----------------------------~~~~v~~al~~~~~~~~~~g~~~~~~~~~~~~~~ 330 (334)
T cd06327 291 EAAGTD-----------------------------DADKVVAKMKETPIYDLFAGNGYIRACDHQMVHD 330 (334)
T ss_pred HHHCCC-----------------------------ChHHHHHhccccceeccCCCCceeeccccchhcc
Confidence 996332 4677999999975 588899999987 7765543
No 53
>cd06329 PBP1_SBP_like_3 Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=99.93 E-value=7.6e-25 Score=237.43 Aligned_cols=258 Identities=15% Similarity=0.147 Sum_probs=215.5
Q ss_pred CCCcEEEECCCChhhHHHH-------HHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcC-C
Q 003275 2 ENEVVAAIGPQSSGIAHVI-------SHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYG-W 72 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~-------~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~-W 72 (834)
+++|++||||.+|..+.++ +++++..++|+|+++++++.++. ..+||+||+.|++..++.++++++...+ |
T Consensus 64 ~~~v~aiiG~~~s~~~~~~~~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~ 143 (342)
T cd06329 64 DDGVRLVVQGNSSSVALALTEAVRKHNQRNPGKEVLYLNYASVAPALTGEKCSFWHFRTDANTDMKMEALASYIKKQPDG 143 (342)
T ss_pred HhCCeEEEcccchHHHHHhhhhhhhhhhhhccCCeEEEecCCCCchhhhccCcceEEEecCChHHHHHHHHHHHHhcccC
Confidence 3589999999999999999 78888999999999888888887 5679999999999999999999998775 9
Q ss_pred eEEEEEEEcCCcccchHHHHHHHHhc--CCcEEEeeecCCCCCCh-HHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003275 73 REVIAIFVDDDYGRNGISVLGDALSK--KRAKISYKAPFSPGASR-SAINSLLVGANLMESRVFVVHVNPDTGLTIFSVA 149 (834)
Q Consensus 73 ~~v~iI~~d~~~g~~~~~~l~~~l~~--~g~~I~~~~~~~~~~~~-~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a 149 (834)
|++++|+.|+.||+...+.+.+.+++ .|++|+....++. +. .|+..++.++++.++|+|++...+.++..+++++
T Consensus 144 k~v~i~~~~~~~g~~~~~~~~~~~~~~~~G~~vv~~~~~~~--~~~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~ 221 (342)
T cd06329 144 KKVYLINQDYSWGQDVAAAFKAMLAAKRPDIQIVGEDLHPL--GKVKDFSPYVAKIKASGADTVITGNWGNDLLLLVKQA 221 (342)
T ss_pred ceEEEEeCChHHHHHHHHHHHHHHHhhcCCcEEeceeccCC--CCCCchHHHHHHHHHcCCCEEEEcccCchHHHHHHHH
Confidence 99999999999999999999999999 9999998877774 34 7899999999999999999988888999999999
Q ss_pred HhCCCCCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHH
Q 003275 150 KSLGMTAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALY 227 (834)
Q Consensus 150 ~~~g~~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~ 227 (834)
++.|+..+ |+...+.... . .....+..+|++...++.+ +++..++|.++|++++ +..++.++..
T Consensus 222 ~~~g~~~~---~~~~~~~~~~--~----~~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~-----~~~~~~~~~~ 287 (342)
T cd06329 222 ADAGLKLP---FYTPYLDQPG--N----PAALGEAGLGLVVAVAYWHPNDTPANRAFVEAFKAKY-----GRVPDYYEGQ 287 (342)
T ss_pred HHcCCCce---EEeccccchh--H----HHhhcccccceEEeeeccCCCCCHHHHHHHHHHHHHh-----CCCCCchHHH
Confidence 99998542 4444332221 1 0122345688887777654 4678899999999988 3467788999
Q ss_pred HhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEcc-CCCCC
Q 003275 228 AYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDA-DKNLV 304 (834)
Q Consensus 228 ~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~-~g~~~ 304 (834)
+||+++++++|++++... +++.+.++|++++|+|+.|+++|+. +++..
T Consensus 288 ~y~~~~~~~~a~~~ag~~-----------------------------~~~~v~~al~~~~~~~~~g~~~~~~~~~~~~ 336 (342)
T cd06329 288 AYNGIQMLADAIEKAGST-----------------------------DPEAVAKALEGMEVDTPVGPVTMRASDHQAQ 336 (342)
T ss_pred HHHHHHHHHHHHHHhCCC-----------------------------CHHHHHHHHhCCccccCCCCeEEcccCcchh
Confidence 999999999999984211 4789999999999999999999985 44443
No 54
>cd06347 PBP1_ABC_ligand_binding_like_12 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.93 E-value=3.2e-24 Score=232.42 Aligned_cols=259 Identities=22% Similarity=0.323 Sum_probs=215.6
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHH-HHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLV-EYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll-~~~~W~~v~iI~~d 81 (834)
++|++||||.+|..+.+++++++..+||+|+++++.+.+++.. +|+||+.+++..++.++++++ ++++|++|++|+.+
T Consensus 66 ~~v~aiiG~~~s~~~~~v~~~~~~~~ip~i~~~~~~~~~~~~~-~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~ 144 (334)
T cd06347 66 DKVVAIIGPVTSGATLAAGPIAEDAKVPMITPSATNPKVTQGK-DYVFRVCFIDPFQGTVMAKFATENLKAKKAAVLYDN 144 (334)
T ss_pred cCeEEEEcCCccHhHHHhHHHHHHCCCeEEcCCCCCCCcccCC-CeEEEeeCCcHHHHHHHHHHHHHhcCCcEEEEEEeC
Confidence 4899999999999999999999999999999998887776532 589999999999999999987 67899999999988
Q ss_pred C-CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 82 D-DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 82 ~-~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
+ +|+....+.+.+++++.|++|+....++.+ ..++...+.++++.++++|++.+...+...+++++++.|+. ..
T Consensus 145 ~~~~~~~~~~~~~~~~~~~g~~v~~~~~~~~~--~~d~~~~~~~~~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~---~~ 219 (334)
T cd06347 145 SSDYSKGLAKAFKEAFKKLGGEIVAEETFNAG--DTDFSAQLTKIKAKNPDVIFLPGYYTEVGLIAKQARELGIK---VP 219 (334)
T ss_pred CCchhHHHHHHHHHHHHHcCCEEEEEEEecCC--CCcHHHHHHHHHhcCCCEEEEcCchhhHHHHHHHHHHcCCC---Cc
Confidence 6 899999999999999999999988888754 36899999999999999999999999999999999999974 35
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCC--ChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPD--TDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~--~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~A 238 (834)
|+.++.+..... .....+..+|++...++.+. .+..++|.++|++++ +..++.++..+||+++++++|
T Consensus 220 i~~~~~~~~~~~-----~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~-----~~~~~~~~~~~yda~~~~~~A 289 (334)
T cd06347 220 ILGGDGWDSPKL-----EEAGGAAAEGVYFTTHFSADDPTPKAKKFVKAYKAKY-----GKEPDAFAALGYDAYYLLADA 289 (334)
T ss_pred EEecccccCHHH-----HHHHHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHH-----CCCcchhHHHHHHHHHHHHHH
Confidence 666655432100 01223568898888776663 577899999999888 356788899999999999999
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhc-ccccceeeEEEccCCCCCCC
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRM-NFTGLSGEIRFDADKNLVNP 306 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~-~f~g~tG~i~Fd~~g~~~~~ 306 (834)
++++... ++..+.++|.+. +|+|++|+++|+.+|+..+.
T Consensus 290 l~~ag~~-----------------------------~~~~v~~~l~~~~~~~g~~G~v~f~~~g~~~~~ 329 (334)
T cd06347 290 IERAGST-----------------------------DPEAIRDALAKTKDFDGVTGKITIDENGNPVKS 329 (334)
T ss_pred HHHhCCC-----------------------------CHHHHHHHHHhCCCcccceeeeEECCCCCcCCC
Confidence 9984210 478899998765 69999999999999986544
No 55
>cd06359 PBP1_Nba_like Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway. This group includes the type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; their substrate specificities are not well characterized.
Probab=99.93 E-value=3.3e-24 Score=231.65 Aligned_cols=259 Identities=15% Similarity=0.195 Sum_probs=212.2
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|.+||||.+|..+.++++++++.+||+|+++++.+.+.+ ..+||+||+.+++..+..++++++...||++|++++.|
T Consensus 64 ~~v~~viG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~g~~~vail~~~ 143 (333)
T cd06359 64 DKVDFVTGVVFSNVLLAVVPPVLESGTFYISTNAGPSQLAGKQCSPYFFSTSWQNDQVHEAMGKYAQDKGYKRVFLIAPN 143 (333)
T ss_pred cCCcEEEccCCcHHHHHHHHHHHHcCCeEEecCCCccccccccCCCcEEEeeCChHhhHHHHHHHHHHhCCCeEEEEecC
Confidence 48999999999999999999999999999998777666665 34799999999999999999999988999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
++||+...+.+.+.++ .+++....++. +..|+..++.+++++++|+|++......+..+++++++.|+.. ...+
T Consensus 144 ~~~g~~~~~~~~~~~~---~~v~~~~~~~~--~~~d~~~~i~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~-~~~~ 217 (333)
T cd06359 144 YQAGKDALAGFKRTFK---GEVVGEVYTKL--GQLDFSAELAQIRAAKPDAVFVFLPGGMGVNFVKQYRQAGLKK-DIPL 217 (333)
T ss_pred chhhHHHHHHHHHHhC---ceeeeeecCCC--CCcchHHHHHHHHhCCCCEEEEEccCccHHHHHHHHHHcCccc-CCee
Confidence 9999999998988774 45665555553 3479999999999999999999888888999999999999854 2335
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHAL 239 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al 239 (834)
+.+.+.... +. .....+..+|+++..++.+ +++..++|.++|++++ +..++.++..+||+++++++|+
T Consensus 218 ~~~~~~~~~-~~----~~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~-----~~~~~~~~~~~yda~~~~~~A~ 287 (333)
T cd06359 218 YSPGFSDEE-DT----LPAVGDAALGLYNTAQWAPDLDNPANKKFVADFEKKY-----GRLPTLYAAQAYDAAQLLDSAV 287 (333)
T ss_pred eccCcccCH-HH----HHhcchhhcCeeeccccCCCCCCHHHHHHHHHHHHHh-----CCCCcHHHHHHHHHHHHHHHHH
Confidence 544433211 00 0122356789888887766 5688899999999998 3468889999999999999999
Q ss_pred HHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCC
Q 003275 240 DALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLV 304 (834)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~ 304 (834)
+++..+ ..+++.+.++|+++.|+|++|+++|+++|+..
T Consensus 288 ~~ag~~---------------------------~~~~~~v~~al~~~~~~~~~G~~~~~~~~~~~ 325 (333)
T cd06359 288 RKVGGN---------------------------LSDKDALRAALRAADFKSVRGAFRFGTNHFPI 325 (333)
T ss_pred HHhcCC---------------------------CCCHHHHHHHHhcCccccCccceEECCCCCcc
Confidence 986321 01478999999999999999999999998754
No 56
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=99.93 E-value=4.6e-24 Score=231.45 Aligned_cols=270 Identities=19% Similarity=0.143 Sum_probs=214.6
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHH-HcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVE-YYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~-~~~W~~v~iI~~ 80 (834)
+++|.+|+|+.+|..+.++.+++++.++|+|++.++.. ....||+||+.+.+..++..+++++. ..++++|++|+.
T Consensus 65 ~~~V~~iiG~~~S~~~~a~~~~~~~~~~~~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~k~vaii~~ 141 (348)
T cd06355 65 QDKVAAVFGCWTSASRKAVLPVFERHNGLLFYPVQYEG---LEQSPNVFYTGAAPNQQIIPAVDWLMSNKGGKRFYLVGS 141 (348)
T ss_pred hCCCcEEEeccchhhHHHHHHHHhccCCceecCCCccC---CCCCCCEEEeCCChHHhHHHHHHHHHhccCCCeEEEECC
Confidence 35899999999999999999999999999998654321 23569999999999999999999875 457999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|++||....+.+.+.+++.|++|+....++.+ ..|++.++.+|++.++|+|++...+.++..+++++++.|+..+...
T Consensus 142 d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~D~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~~~ 219 (348)
T cd06355 142 DYVYPRTANKILKAQLESLGGEVVGEEYLPLG--HTDFQSIINKIKAAKPDVVVSTVNGDSNVAFFKQLKAAGITASKVP 219 (348)
T ss_pred cchHHHHHHHHHHHHHHHcCCeEEeeEEecCC--hhhHHHHHHHHHHhCCCEEEEeccCCchHHHHHHHHHcCCCccCCe
Confidence 99999999999999999999999998888854 4899999999999999999999999999999999999998754444
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~A 238 (834)
++........+.. ...+..+|++....+.+ +++..++|.++|++++. ....++.++..+||+++++++|
T Consensus 220 ~~~~~~~~~~~~~------~g~~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~g---~~~~~~~~a~~~Y~a~~~~~~A 290 (348)
T cd06355 220 VLSFSVAEEELRG------IGPENLAGHYAAWNYFQSVDTPENKKFVAAFKARYG---QDRVTNDPMEAAYIGVYLWKQA 290 (348)
T ss_pred eEEccccHHHHhh------cChHhhcCCEEeccchhhcCCHHHHHHHHHHHHHcC---CCCCCCcHHHHHHHHHHHHHHH
Confidence 5543321111111 11135678776654433 56788999999999882 1123456788899999999999
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEee
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIG 314 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~ 314 (834)
++++... ++++|.++|++.+|+++.|+++|+++++.....+.|.+++
T Consensus 291 l~~ag~~-----------------------------~~~~i~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~i~~~~ 337 (348)
T cd06355 291 VEKAGSF-----------------------------DVDKVRAALPGQSFDAPEGPVTVDPANHHLWKPVRIGRIQ 337 (348)
T ss_pred HHHhCCC-----------------------------CHHHHHHHhccCcccCCCcceEeecCCCeeeeeeEEEEEc
Confidence 9995221 5889999999999999999999998443334556666775
No 57
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=99.93 E-value=4e-24 Score=232.55 Aligned_cols=275 Identities=24% Similarity=0.270 Sum_probs=221.4
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCC-CceEEccCChHHHHHHHHHHHH-HcCCeEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQY-PYFLRTTQSDYYQMHAVADLVE-YYGWREVIAIF 79 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~-p~~~r~~ps~~~q~~aia~ll~-~~~W~~v~iI~ 79 (834)
+++|.+|||+.+|..+.++.+++++.++|+|++++++|.++...+ +++||+.|++..|+.++++++. ..+.++|++|+
T Consensus 76 ~~~V~~vvG~~~S~~~~a~~~v~~~~~i~~i~p~st~~~~~~~~~~~~vfr~~~~~~~q~~~~~~~l~~~~~~k~v~ii~ 155 (366)
T COG0683 76 QDGVDAVVGPTTSGVALAASPVAEEAGVPLISPSATAPQLTGRGLKPNVFRTGPTDNQQAAAAADYLVKKGGKKRVAIIG 155 (366)
T ss_pred hcCceEEEEeccCcccccchhhHhhcCceEEeecCCCCcccccccccceEEecCChHHHHHHHHHHHHHhcCCcEEEEEe
Confidence 478999999999999999999999999999999999999877555 4599999999999999999985 56666999999
Q ss_pred EcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 80 VDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 80 ~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
.|+.||++..+.+++.+++.|++++..+.+.+.. .++..++.++++.++|+|++.+...++..+++++++.|+... .
T Consensus 156 ~~~~yg~~~~~~~~~~l~~~G~~~~~~~~~~~~~--~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~~~~~G~~~~-~ 232 (366)
T COG0683 156 DDYAYGEGLADAFKAALKALGGEVVVEEVYAPGD--TDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQAREQGLKAK-L 232 (366)
T ss_pred CCCCcchhHHHHHHHHHHhCCCeEEEEEeeCCCC--CChHHHHHHHHhcCCCEEEECCCCccchHHHHHHHHcCCCCc-c
Confidence 9999999999999999999999866656666543 459999999999999999999999999999999999998653 2
Q ss_pred EEEEeCCCcccCCCCCCCChhhHhhccc-ceEE-EecCC-CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHH
Q 003275 160 VWIATDWLPSVLDSTEPVDIDTMNLLQG-VVAL-RHHTP-DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVA 236 (834)
Q Consensus 160 vwi~~~~~~~~~~~~~~~~~~~~~~~~G-v~~~-~~~~~-~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la 236 (834)
.++........... .....++ +... ..+.+ ++|..+.|.++|++++. .+..++.++..+||++++++
T Consensus 233 ~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~~g---~~~~~~~~~~~~y~a~~~~~ 302 (366)
T COG0683 233 IGGDGAGTAEFEEI-------AGAGGAGAGLLATAYSTPDDSPANKKFVEAYKAKYG---DPAAPSYFAAAAYDAVKLLA 302 (366)
T ss_pred ccccccCchhhhhh-------cccCccccEEEEecccccccCcchHHHHHHHHHHhC---CCCCcccchHHHHHHHHHHH
Confidence 33332221111101 0112233 3232 23333 56678889999999982 34567779999999999999
Q ss_pred HHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcc-cccceeeEEEccCCCCCCCcEEEEEeec
Q 003275 237 HALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMN-FTGLSGEIRFDADKNLVNPAYDVLNIGG 315 (834)
Q Consensus 237 ~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~-f~g~tG~i~Fd~~g~~~~~~~~I~~~~~ 315 (834)
+|++++.. + .+++++.++|+... +.+.+|.+.||++|++....+.|.++..
T Consensus 303 ~ai~~a~~---~-------------------------~d~~~v~~al~~~~~~~~~~G~v~~~~~~~~~~~~~~i~~~~~ 354 (366)
T COG0683 303 KAIEKAGK---S-------------------------SDREAVAEALKGGKFFDTAGGPVTFDEKGDRGSKPVYVGQVQK 354 (366)
T ss_pred HHHHHHhc---C-------------------------CCHHHHHHHHhhCCCCccCCcceeECCCCCcCCCceEEEEEEe
Confidence 99999753 0 03788999999987 7899999999999999999999999985
Q ss_pred cc
Q 003275 316 TG 317 (834)
Q Consensus 316 ~~ 317 (834)
.+
T Consensus 355 ~~ 356 (366)
T COG0683 355 GG 356 (366)
T ss_pred cC
Confidence 43
No 58
>cd06336 PBP1_ABC_ligand_binding_like_3 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.93 E-value=1.4e-24 Score=235.75 Aligned_cols=262 Identities=18% Similarity=0.245 Sum_probs=214.9
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
++|.+||||.+|..+.+ ++++++.++|+|+++++++.++...+||+||+.|++..++.++++++...+|++|++|+.|+
T Consensus 70 ~~v~~iiG~~~s~~~~~-~~~~~~~~ip~i~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~ 148 (347)
T cd06336 70 DGVKFILGPIGGGITAA-QQITERNKVLLLTAYSSDLSIDTAGNPLTFRVPPIYNVYGVPFLAYAKKPGGKKVALLGPND 148 (347)
T ss_pred cCceEEEeCCCCchhhh-hhhhhhcCceEEeccCCcccccccCCceEEEecCCchhHHHHHHHHHhhcCCceEEEEccCC
Confidence 48999999999999998 99999999999999999998875567999999999999999999999889999999999999
Q ss_pred CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHHHhCCCCCCCeEE
Q 003275 83 DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPD-TGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~-~~~~i~~~a~~~g~~~~~~vw 161 (834)
+||+...+.+.+.+++.|++|+....++.+ ..|++.++.+|+++++|+|++.+... ++..+++++++.|+..+ ..+
T Consensus 149 ~~g~~~~~~~~~~l~~~G~~vv~~~~~~~~--~~D~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~g~~~~-~~~ 225 (347)
T cd06336 149 AYGQPWVAAYKAAWEAAGGKVVSEEPYDPG--TTDFSPIVTKLLAEKPDVIFLGGPSPAPAALVIKQARELGFKGG-FLS 225 (347)
T ss_pred chhHHHHHHHHHHHHHcCCEEeeecccCCC--CcchHHHHHHHHhcCCCEEEEcCCCchHHHHHHHHHHHcCCCcc-EEe
Confidence 999999999999999999999988888854 48999999999999999999999988 99999999999998653 222
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCC----CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP----DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAH 237 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~----~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~ 237 (834)
+........+. ....+.++|++...++.+ .++..++|.++|++++ +..++.++..+||+++++++
T Consensus 226 ~~~~~~~~~~~------~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~-----~~~p~~~~~~~y~~~~~~~~ 294 (347)
T cd06336 226 CTGDKYDELLV------ATGADFMEGVYFQFPDVDDPALAFPRAKAFVEEYKKRY-----GEPPNSEAAVSYDAVYILKA 294 (347)
T ss_pred ccCCCchHHHH------HhcHHhhCceEEEeecccccccCCHHHHHHHHHHHHHH-----CCCCcHHHHHHHHHHHHHHH
Confidence 22221111010 112256789988887655 4777899999999998 34478889999999999999
Q ss_pred HHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHH-H-------hcccccceeeEEEccCCCCCCCcE
Q 003275 238 ALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTL-L-------RMNFTGLSGEIRFDADKNLVNPAY 308 (834)
Q Consensus 238 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l-~-------~~~f~g~tG~i~Fd~~g~~~~~~~ 308 (834)
|++++... ++..+.+++ + ...|+++.|.+.||++|++..+.+
T Consensus 295 Al~~ag~~-----------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 344 (347)
T cd06336 295 AMEAAGSV-----------------------------DDTAAVAALAAMLGVGKPAFGYARWWGKELFGVNGALVGPWP 344 (347)
T ss_pred HHHhcCCC-----------------------------CcHHHHHHHhhccCCCcCccccccccccccccCCCccccCcc
Confidence 99985321 133344443 3 256889999999999999876544
No 59
>cd06349 PBP1_ABC_ligand_binding_like_14 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.92 E-value=1.2e-23 Score=228.11 Aligned_cols=270 Identities=18% Similarity=0.261 Sum_probs=216.8
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHH-HHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLV-EYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll-~~~~W~~v~iI~~ 80 (834)
+++|.+|+||.+|..+.++++++++.+||+|+++++++.+++ ..+|+||+.+++..+..++++++ ++++|++|++|+.
T Consensus 65 ~~~V~~i~G~~~s~~~~a~~~~~~~~~vp~i~~~~~~~~~~~-~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~ 143 (340)
T cd06349 65 DPRIVAVLGDFSSGVSMAASPIYQRAGLVQLSPTNSHPDFTK-GGDFIFRNSTSQAIEAPLLADYAVKDLGFKKVAILSV 143 (340)
T ss_pred cCCeEEEECCCccHhHHHhHHHHHhCCCeEEecCCCCCcccc-CCCeEEEccCCcHHHHHHHHHHHHHHcCCcEEEEEec
Confidence 357999999999999999999999999999999888887765 45899999999999999999986 6789999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|++||....+.+++++++.|++|+....+++. ..|++..+.+++++++|+|++.+...++..+++++++.|+..+
T Consensus 144 ~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~--~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~--- 218 (340)
T cd06349 144 NTDWGRTSADIFVKAAEKLGGQVVAHEEYVPG--EKDFRPTITRLRDANPDAIILISYYNDGAPIARQARAVGLDIP--- 218 (340)
T ss_pred CChHhHHHHHHHHHHHHHcCCEEEEEEEeCCC--CCcHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCCCCc---
Confidence 99999999999999999999999988877754 4789999999999999999999999999999999999998643
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCC--ChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPD--TDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~--~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~A 238 (834)
++.+...... .. -....+..+|++...++.|+ .+..++|.++|++++ +..++.++..+||++.++++|
T Consensus 219 ~~~~~~~~~~-~~----~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~-----~~~p~~~~~~~y~~~~~~~~a 288 (340)
T cd06349 219 VVASSSVYSP-KF----IELGGDAVEGVYTPTAFFPGDPRPEVQSFVSAYEAKY-----GAQPDAFAAQAYDAVGILAAA 288 (340)
T ss_pred EEccCCcCCH-HH----HHHhHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHH-----CCCcchhhhhHHHHHHHHHHH
Confidence 3333222110 00 01122467898888777664 567899999999888 345788999999999999999
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHH-HHhcccccceeeEEEccC-CCCCCCcEEEEEeecc
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQT-LLRMNFTGLSGEIRFDAD-KNLVNPAYDVLNIGGT 316 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~-l~~~~f~g~tG~i~Fd~~-g~~~~~~~~I~~~~~~ 316 (834)
++++... +...+... +.+..+.|++|+++|+++ |+.. ..|.++.++++
T Consensus 289 ~~~ag~~-----------------------------~~~~~~~~~~~~~~~~~~~g~i~~~~~~~~~~-~~~~~~~~~~g 338 (340)
T cd06349 289 VRRAGTD-----------------------------RRAARDGFAKAEDVYSGVTGSTKFDPNTRRVI-KRFVPLVVRNG 338 (340)
T ss_pred HHHhCCC-----------------------------CHHHHHHHHHhccCcccceEeEEECCCCCCcc-CceEEEEEeCC
Confidence 9985211 12222232 245568899999999987 6544 57888877665
Q ss_pred c
Q 003275 317 G 317 (834)
Q Consensus 317 ~ 317 (834)
+
T Consensus 339 ~ 339 (340)
T cd06349 339 K 339 (340)
T ss_pred c
Confidence 4
No 60
>cd06330 PBP1_Arsenic_SBP_like Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds. Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa.
Probab=99.92 E-value=3.7e-24 Score=232.89 Aligned_cols=259 Identities=20% Similarity=0.158 Sum_probs=211.9
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIF 79 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~ 79 (834)
++|.|||||.+|..+.++++++++.+||+|++.++++.+++ ..++++||+.+++..+..++++++.++ +|++|++|+
T Consensus 66 ~~v~aiig~~~s~~~~~~~~~~~~~~ip~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~ 145 (346)
T cd06330 66 EGVDMLIGLISSGVALAVAPVAEELKVFFIATDPGTPRLTEEPDNPYVFRTRNSTIMDAVAGALYAAKLDKKAKTWATIN 145 (346)
T ss_pred cCCcEEEcccchHHHHHHHHHHHHcCCeEEEcCCCCcccccCCCCCceEEecCChHHHHHHHHHHHHHhCcCccEEEEEC
Confidence 48999999999999999999999999999999888888876 578999999999999999999999877 499999999
Q ss_pred EcCCcccchHHHHHHHHhcCC--cEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCC
Q 003275 80 VDDDYGRNGISVLGDALSKKR--AKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 80 ~d~~~g~~~~~~l~~~l~~~g--~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~ 157 (834)
.|++||....+.+.+.+++.| ++++....++. ...|+..++.+|++.++|+|++.+.+.+...+++++++.|+..
T Consensus 146 ~~~~~g~~~~~~~~~~~~~~g~~~~~v~~~~~~~--~~~d~~~~v~~i~~~~~d~ii~~~~~~~~~~~~~~~~~~g~~~- 222 (346)
T cd06330 146 PDYAYGQDAWADFKAALKRLRPDVEVVSEQWPKL--GAPDYGSEITALLAAKPDAIFSSLWGGDLVTFVRQANARGLFD- 222 (346)
T ss_pred CchHHHHHHHHHHHHHHHHhCCCCeecccccCCC--CCcccHHHHHHHHhcCCCEEEEecccccHHHHHHHHHhcCccc-
Confidence 999999999999999999984 55655444443 3479999999999999999999999999999999999999865
Q ss_pred CeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecC--C--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHH
Q 003275 158 SYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHT--P--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVW 233 (834)
Q Consensus 158 ~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~--~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~ 233 (834)
+..|+.+.+....+. ....+..+|++....+. . +++..++|.++|++++ +..++.++..+||+++
T Consensus 223 ~~~~~~~~~~~~~~~------~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~-----g~~p~~~~~~~y~a~~ 291 (346)
T cd06330 223 GTTVVLTLTGAPELA------PLGDEMPEGVIIGGRGPYFIPPDTPENKAFVDAYQEKY-----GDYPTYGAYGAYQAVM 291 (346)
T ss_pred CceEEeeccchhhhh------hhhcccCCceEEeccccCCCCCCChHHHHHHHHHHHHH-----CCCCChHHHHHHHHHH
Confidence 567777665432211 11224567876554321 1 4778999999999988 4557788999999999
Q ss_pred HHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccC
Q 003275 234 LVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDAD 300 (834)
Q Consensus 234 ~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~ 300 (834)
++++|++++...... . ..+.+.++|+++.+.|+.|++.|+++
T Consensus 292 ~l~~a~~~a~~~~~~------------------------~-~~~~v~~al~~~~~~~~~G~~~f~~~ 333 (346)
T cd06330 292 ALAAAVEKAGATDGG------------------------A-PPEQIAAALEGLSFETPGGPITMRAA 333 (346)
T ss_pred HHHHHHHHhcCCCCC------------------------C-cHHHHHHHHcCCCccCCCCceeeecC
Confidence 999999996432110 1 12679999999999999999999874
No 61
>cd06343 PBP1_ABC_ligand_binding_like_8 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.92 E-value=1.4e-23 Score=229.67 Aligned_cols=277 Identities=17% Similarity=0.201 Sum_probs=224.1
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHH-HHcCCeEEEEEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLV-EYYGWREVIAIFV 80 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll-~~~~W~~v~iI~~ 80 (834)
++|.+||||.+|..+.++++++++.+||+|+++++++.+++ ..+||+||+.|++..++.++++++ +++||++|++|+.
T Consensus 73 ~~v~avvG~~~s~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~ii~~ 152 (362)
T cd06343 73 DEVFAMVGGLGTPTNLAVQKYLNEKKVPQLFPASGASKWNDPKPFPWTFGWQPSYQDEARIYAKYLVEEKPNAKIAVLYQ 152 (362)
T ss_pred cCeEEEEecCCcHHHHHhHHHHHhcCCceEecccccHhhhCCCCCCceEecCCChHHHHHHHHHHHHHhCCCceEEEEEe
Confidence 68999999999999999999999999999998888888887 478999999999999999999975 6789999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|++||+...+.+.+.+++.|++|+....++.. ..|++.++.++++.++|+|++.+...++..+++++++.|+...
T Consensus 153 ~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~--- 227 (362)
T cd06343 153 NDDFGKDYLKGLKDGLGDAGLEIVAETSYEVT--EPDFDSQVAKLKAAGADVVVLATTPKFAAQAIRKAAELGWKPT--- 227 (362)
T ss_pred ccHHHHHHHHHHHHHHHHcCCeEEEEeeecCC--CccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHHcCCCce---
Confidence 99999999999999999999999998888854 4799999999999999999999999999999999999998642
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecC-------CCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHT-------PDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVW 233 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~-------~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~ 233 (834)
++.+++........ .....+..+|+++...+. ...+..++|.++|+++++ ...+++.++..+||++.
T Consensus 228 ~~~~~~~~~~~~~~---~~~~~~~~~g~~~~~~~~~~~~p~~~~~~~~~~f~~~~~~~~~---~~~~~~~~~~~~y~a~~ 301 (362)
T cd06343 228 FLLSSVSASVASVL---KPAGLEAAEGVIAAAYLKDPTDPAWADDPGVKEFIAFYKKYFP---EGDPPDTYAVYGYAAAE 301 (362)
T ss_pred EEEEecccccHHHH---HHhhhHhhCceEEEEEecCCCccccccCHHHHHHHHHHHHhcC---CCCCCchhhhHHHHHHH
Confidence 55555432211000 011224578887776543 246778999999998882 11247889999999999
Q ss_pred HHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhccc---cc-ceeeEEEccCCCCCCCcEE
Q 003275 234 LVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNF---TG-LSGEIRFDADKNLVNPAYD 309 (834)
Q Consensus 234 ~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f---~g-~tG~i~Fd~~g~~~~~~~~ 309 (834)
++++|++++.. . .+++.+.++|+++++ .+ ..|++.|+++++.....+.
T Consensus 302 ~~~~a~~~ag~---~-------------------------~~~~~v~~aL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (362)
T cd06343 302 TLVKVLKQAGD---D-------------------------LTRENIMKQAESLKDVLPDLLPGIRINTSPDDHLPIEQMQ 353 (362)
T ss_pred HHHHHHHHhCC---C-------------------------CCHHHHHHHHHhCCCCCccccCccceecCccccccceeEE
Confidence 99999998521 1 147899999999987 33 3458999876555566788
Q ss_pred EEEeeccce
Q 003275 310 VLNIGGTGS 318 (834)
Q Consensus 310 I~~~~~~~~ 318 (834)
|.++++++|
T Consensus 354 i~~~~~g~~ 362 (362)
T cd06343 354 LMRFEGGRW 362 (362)
T ss_pred EEEEecCcC
Confidence 888876653
No 62
>cd06331 PBP1_AmiC_like Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two t
Probab=99.92 E-value=9.9e-24 Score=228.01 Aligned_cols=259 Identities=17% Similarity=0.134 Sum_probs=210.7
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
++|++|+||.+|..+.++++++++.++|+|++++.... ...|++||+.+++..+..++++++...+|++|++|+.|+
T Consensus 66 ~~V~aiiG~~~s~~~~a~~~~~~~~~vp~i~~~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~ 142 (333)
T cd06331 66 DKVDAVFGCYTSASRKAVLPVVERGRGLLFYPTQYEGG---ECSPNVFYTGATPNQQLLPLIPYLMEKYGKRFYLIGSDY 142 (333)
T ss_pred cCCcEEEecccHHHHHHHHHHHHhcCceEEeCCCCCCC---cCCCCeEEccCChHHhHHHHHHHHHHhcCCeEEEECCCc
Confidence 48999999999999999999999999999997543321 235899999999999999999988666699999999999
Q ss_pred CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEE
Q 003275 83 DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWI 162 (834)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi 162 (834)
.||....+.+.+.+++.|.+|+....++.+ ..|+++++.++++.++|+|++.+...++..+++++.+.|+......++
T Consensus 143 ~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~~ 220 (333)
T cd06331 143 VWPRESNRIARALLEELGGEVVGEEYLPLG--TSDFGSVIEKIKAAGPDVVLSTLVGDSNVAFYRQFAAAGLDADRIPIL 220 (333)
T ss_pred hhHHHHHHHHHHHHHHcCCEEEEEEEecCC--cccHHHHHHHHHHcCCCEEEEecCCCChHHHHHHHHHcCCCcCCCeeE
Confidence 999999999999999999999988888854 489999999999999999999999999999999999999974333333
Q ss_pred EeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHHH
Q 003275 163 ATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHALD 240 (834)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al~ 240 (834)
........+.. ......+|+++..++.+ +.+..+.|.++|+++++ ....++.+++.+||+++++++|++
T Consensus 221 ~~~~~~~~~~~------~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~---~~~~~~~~~~~~yda~~~~~~A~~ 291 (333)
T cd06331 221 SLTLDENELAA------IGAEAAEGHYSAASYFQSLDTPENKAFVARYRARYG---DDAVINSPAEAAYEAVYLWAAAVE 291 (333)
T ss_pred Ecccchhhhhc------cChhhhCCcEeechhhhhcCChhHHHHHHHHHHHcC---CCcCCCchhHHHHHHHHHHHHHHH
Confidence 22211111111 11245689888877655 46778999999998872 112478889999999999999999
Q ss_pred HHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCC
Q 003275 241 ALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLV 304 (834)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~ 304 (834)
++.+ .+++.|.++|++++|+|++|++.|++++++.
T Consensus 292 ~ag~-----------------------------~~~~~l~~al~~~~~~~~~G~i~f~~~~~~~ 326 (333)
T cd06331 292 KAGS-----------------------------TDPEAVRAALEGVSFDAPQGPVRIDPDNHHT 326 (333)
T ss_pred HcCC-----------------------------CCHHHHHHHhhcCcccCCCCceEecCCCCcc
Confidence 8421 1488999999999999999999999876543
No 63
>cd06328 PBP1_SBP_like_2 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=99.92 E-value=2.4e-23 Score=224.46 Aligned_cols=261 Identities=17% Similarity=0.169 Sum_probs=208.9
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCC-CCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQ-YPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~-~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|.+|+||.+|..+.++++++++.++|+|+++++++.++... .+|+||+.+++..+..++++++... +++|++|+.|
T Consensus 67 ~~V~avvG~~~S~~~~a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~-~~~v~~i~~~ 145 (333)
T cd06328 67 DGVDILVGSTSSGVALAVLPVAEENKKILIVEPAAADSITGKNWNRYTFRTGRNSSQDAIAAAAALGKP-GKKIATLAQD 145 (333)
T ss_pred cCCeEEEccCCcHHHHHHHHHHHHhCCcEEecCCCCchhhccCCCCcEEEecCChHHHHHHHHHHHHhc-CCeEEEEecC
Confidence 5899999999999999999999999999999988999888643 5999999998888888888887665 8999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHHHhCCCCCCCeE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPD-TGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~-~~~~i~~~a~~~g~~~~~~v 160 (834)
++||++..+.+++.+++.|++|+....++.+ ..|+..++.+|+++++|+|++...+. ....+++++.+.|+...
T Consensus 146 ~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~~g~~~~--- 220 (333)
T cd06328 146 YAFGRDGVAAFKAALEKLGAAIVTEEYAPTD--TTDFTPYAQRLLDALKKVLFVIWAGAGGPWPKLQQMGVLGYGIE--- 220 (333)
T ss_pred ccccHHHHHHHHHHHHhCCCEEeeeeeCCCC--CcchHHHHHHHHhcCCCEEEEEecCchhHHHHHHHhhhhcCCCe---
Confidence 9999999999999999999999998888864 47899999999999999998876554 67777888887776532
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecC-CCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHT-PDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHAL 239 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~-~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al 239 (834)
............. ....+..+|++....+. +.++..+.|.++|++++ +..|+.+++.+||++.++++|+
T Consensus 221 ~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~-----g~~p~~~~~~~y~a~~~l~~Ai 290 (333)
T cd06328 221 ITLAGDILANLTM-----YKAGPGMSGASYYYHYFLPKNPVNDWLVEEHKARF-----GSPPDLFTAGGMSAAIAVVEAL 290 (333)
T ss_pred EEecccccCcccc-----ccccccccceeeeecCCCCCCHHHHHHHHHHHHHh-----CCCcchhhHHHHHHHHHHHHHH
Confidence 1112211111110 11223456766655554 67788899999999998 4557889999999999999999
Q ss_pred HHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEcc-CCCCCCCcE
Q 003275 240 DALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDA-DKNLVNPAY 308 (834)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~-~g~~~~~~~ 308 (834)
+++.. .+++.+.++|++..|+++.|+++|+. +|+...+.|
T Consensus 291 ~~ag~-----------------------------~~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~ 331 (333)
T cd06328 291 EETGD-----------------------------TDTEALIAAMEGMSFETPKGTMTFRKEDHQALQPMY 331 (333)
T ss_pred HHhCC-----------------------------CCHHHHHHHHhCCeeecCCCceEECcccchhhhccc
Confidence 98531 15889999999999999999999985 555444433
No 64
>TIGR03669 urea_ABC_arch urea ABC transporter, substrate-binding protein, archaeal type. Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization.
Probab=99.92 E-value=4.5e-23 Score=224.08 Aligned_cols=278 Identities=12% Similarity=0.098 Sum_probs=213.9
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHH-cCCeEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEY-YGWREVIAIF 79 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~-~~W~~v~iI~ 79 (834)
+++|.+||||.+|..+.++++++++.++|+|.... ++. ...||+||+.+++..++.++++++.. .+ +++++|+
T Consensus 66 ~d~v~~viG~~~S~~~~A~~~~~~~~~~~~i~~~~----~~~~~~~~~~Fr~~~~~~~~~~~~~~~~~~~~g-~~va~l~ 140 (374)
T TIGR03669 66 RDKVDALWAGYSSATREAIRPIIDRNEQLYFYTNQ----YEGGVCDEYTFAVGATARQQLGTVVPYMVEEYG-KKIYTIA 140 (374)
T ss_pred hCCCCEEEcCCchHHHHHHHHHHHhcCceEEcCcc----cccccCCCCEEEcCCChHHHHHHHHHHHHHcCC-CeEEEEc
Confidence 36899999999999999999999999999996422 122 23589999999999999999999854 56 6799999
Q ss_pred EcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 80 VDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 80 ~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
.|++||+...+.+.+.+++.|++|+....++.+ ..|+..++.+|++++||+|++.....+...++++++++|+..+
T Consensus 141 ~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~g--~~Df~~~l~~i~~~~pD~V~~~~~g~~~~~~~kq~~~~G~~~~-- 216 (374)
T TIGR03669 141 ADYNFGQLSADWVRVIAKENGAEVVGEEFIPLS--VSQFSSTIQNIQKADPDFVMSMLVGANHASFYEQAASANLNLP-- 216 (374)
T ss_pred CCcHHHHHHHHHHHHHHHHcCCeEEeEEecCCC--cchHHHHHHHHHHcCCCEEEEcCcCCcHHHHHHHHHHcCCCCc--
Confidence 999999999999999999999999998888854 4899999999999999999999888899999999999998643
Q ss_pred EEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHH
Q 003275 160 VWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAH 237 (834)
Q Consensus 160 vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~ 237 (834)
++............. ...+..+|+++...+.+ +++..++|.++|+++++ ....++.++..+||+++++++
T Consensus 217 -~~~~~~~~~~~~~~~----~~~~~~~g~~~~~~~~~~~~~~~~~~F~~~y~~~~g---~~p~~~~~a~~~Yda~~~l~~ 288 (374)
T TIGR03669 217 -MGTSTAMAQGYEHKR----FEPPALKDVYAGVNYMEEIDTPENEAFVERFYAKFP---DAPYINQEAENNYFSVYMYKQ 288 (374)
T ss_pred -ccchhhhhhhhhhhh----cCchhhCCcEEeeeccccCCCHHHHHHHHHHHHHcC---CCCCCChHHHHHHHHHHHHHH
Confidence 111111111000000 01134678777666655 46788999999999982 111246678899999999999
Q ss_pred HHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHh-cccccceeeEEEccCCCCCCCcEEEEEeecc
Q 003275 238 ALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLR-MNFTGLSGEIRFDADKNLVNPAYDVLNIGGT 316 (834)
Q Consensus 238 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~-~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~~ 316 (834)
|++++.+. +++++.++|++ ..+.|+.|+++||++++.....+.|.++..+
T Consensus 289 Ai~~AGs~-----------------------------d~~av~~aL~~~~~~~~~~G~i~fd~~~~~~~~~~~v~~~~~~ 339 (374)
T TIGR03669 289 AVEEAGTT-----------------------------DQDAVRDVLESGVEMDAPEGKVCIDGATHHMSHTMRLARADAD 339 (374)
T ss_pred HHHHhCCC-----------------------------CHHHHHHHHHcCCeEECCCccEEEcCCCCeeeeeeEEEEEcCC
Confidence 99996321 58899999997 6799999999999766544455556666533
Q ss_pred -ceEEEEEec
Q 003275 317 -GSRRIGYWS 325 (834)
Q Consensus 317 -~~~~vG~w~ 325 (834)
+.+.+..|+
T Consensus 340 ~~~~~~~~~~ 349 (374)
T TIGR03669 340 HNITFVKEQE 349 (374)
T ss_pred CCEEEEEecC
Confidence 344444454
No 65
>cd06332 PBP1_aromatic_compounds_like Type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes. This group includes the type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; their substrate specificities are not well characterized, however. Members also exhibit close similarity to active transport systems for short chain amides and/or urea found in bacteria and archaea.
Probab=99.91 E-value=4.3e-23 Score=223.52 Aligned_cols=261 Identities=18% Similarity=0.256 Sum_probs=213.9
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCC-CCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQ-YPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~-~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|.+||||.+|..+.++.+.+++.++|+|+++++.+.+++.. +|++||+.+++..++..+++++...||+++++|+.+
T Consensus 64 ~~v~~iig~~~s~~~~~~~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~g~~~v~il~~~ 143 (333)
T cd06332 64 DKVDVVVGPVFSNVALAVVPSLTESGTFLISPNAGPSDLAGKLCSPNFFRTSWQNDQVHEAMGKYAADKGYKKVVIIAPD 143 (333)
T ss_pred cCCcEEEcCCccHHHHHHHHHHhhcCCeEEecCCCCccccccCCCCcEEEeeCChHHhHHHHHHHHHHhCCceEEEEecC
Confidence 4899999999999999999999999999999988888787643 799999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
+.||+...+.+.+.++ ..+.....++.. ..|+..++.++++.++|+|++...+..+..+++++++.|+.+ ...+
T Consensus 144 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~--~~d~~~~i~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~-~~~~ 217 (333)
T cd06332 144 YAAGKDAVAGFKRTFK---GEVVEEVYTPLG--QLDFSAELAQIRAAKPDAVFVFLPGGMAVNFVKQYDQAGLKK-KIPL 217 (333)
T ss_pred cchhHHHHHHHHHhhc---EEEeeEEecCCC--CcchHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCccc-CCce
Confidence 9999999999999987 456656666543 367889999999999999999888889999999999999853 3345
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHAL 239 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~Al 239 (834)
+.++.+... .. .....+.++|++...++.+ +++..++|.++|++++ +..++.++..+||+++++++|+
T Consensus 218 ~~~~~~~~~-~~----~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~-----~~~~~~~~~~~yda~~~~~~a~ 287 (333)
T cd06332 218 YGPGFLTDQ-DT----LPAQGDAAVGVLTALHWAPDLDNPANKRFVAAYKAAY-----GRVPSVYAAQGYDAAQLLDAAL 287 (333)
T ss_pred eccCCCCCH-HH----HHhhchhhcCeeeeeccCCCCCCHHHHHHHHHHHHHh-----CCCCcHHHHHHHHHHHHHHHHH
Confidence 555433221 00 0123356789988887766 3578899999999998 3457889999999999999999
Q ss_pred HHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCC
Q 003275 240 DALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNP 306 (834)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~ 306 (834)
+++... ..++..+.++|++++|+|++|++.|+++|+...+
T Consensus 288 ~~ag~~---------------------------~~~~~~v~~al~~~~~~~~~g~i~f~~~~~~~~~ 327 (333)
T cd06332 288 RAVGGD---------------------------LSDKDALRAALRAADFDSPRGPFKFNPNHNPIQD 327 (333)
T ss_pred HHhcCC---------------------------CCCHHHHHHHHhcCceecCccceeECCCCCcccc
Confidence 995321 1146789999999999999999999999986544
No 66
>KOG1055 consensus GABA-B ion channel receptor subunit GABABR1 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=99.91 E-value=1.5e-24 Score=234.36 Aligned_cols=304 Identities=18% Similarity=0.320 Sum_probs=240.6
Q ss_pred cEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC
Q 003275 5 VVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD 83 (834)
Q Consensus 5 V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~ 83 (834)
-+.++|+ ||+.+..++.-+..++.-++||++++|.|++ ..||+|||+.||+..+...+..++++|+|++|+.++.+..
T Consensus 114 k~mll~G-Cs~v~~~iaea~~~w~l~~lsy~~ssp~ls~r~rfp~~frt~PS~~~~np~rl~l~~~~~w~rvgt~~q~e~ 192 (865)
T KOG1055|consen 114 KLMLLGG-CSSVTTLIAEAAKMWNLIVLSYGASSPALSNRKRFPTFFRTHPSANAHNPTRIKLLKKFGWKRVATLQQTEE 192 (865)
T ss_pred hheeccC-CCCcchHHHhhccccceeeecccCCCccccchhhcchhhhcCCccccCCcceeeechhcCcceeeeeeeehh
Confidence 4577888 9999999999999999999999999999998 7899999999999999999999999999999999999988
Q ss_pred cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 84 YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 84 ~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
-.....+.+...+.+.+++|+.+..+. .|....+.++++..+|+|+-..+...|+++++++++.+|.+..|+|+.
T Consensus 193 ~f~~~~~dl~~~~~~~~ieiv~~qsf~-----~dp~~~vk~l~~~D~RiI~g~f~~~~Arkv~C~~Y~~~myg~ky~w~~ 267 (865)
T KOG1055|consen 193 VFSSTLNDLEARLKEAGIEIVFRQSFS-----SDPADSVKNLKRQDARIIVGLFYETEARKVFCEAYKERLYGRKYVWFL 267 (865)
T ss_pred hhcchHHHHHHhhhccccEEEEeeccc-----cCHHHHHhhccccchhheeccchHhhhhHHHHhhchhhcccceeEEEE
Confidence 888889999999999999999888776 455678899999999999999999999999999999999999999988
Q ss_pred eCCCcccCC-----CCCCCChhhHhhcccceEEEecC--CC------ChhHHHHHHHHHhhhcCCCCCCCccchhHHHhh
Q 003275 164 TDWLPSVLD-----STEPVDIDTMNLLQGVVALRHHT--PD------TDLKKNFISRWKNLKYKENSPSGFNSYALYAYD 230 (834)
Q Consensus 164 ~~~~~~~~~-----~~~~~~~~~~~~~~Gv~~~~~~~--~~------~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YD 230 (834)
..|....+- ...+.-.++..+++|.+++.... +. .-..++|...+.+................++||
T Consensus 268 ~g~y~d~w~ev~~~~~~ctveem~~A~eg~~s~e~~pl~~~~~~tisg~T~~~~l~~~~~~r~~~~~~~~~~~~~~~ayd 347 (865)
T KOG1055|consen 268 IGWYADNWWEITHPSENCTVEEMTEAAEGHITTEFVMLSPANITTISGMTAQEFLEELTKYRKRHPEETGGFQEAPLAYD 347 (865)
T ss_pred EEeeccchhhccCchhhhhHHHHHHHHhhheeeeeeccccccceeeccchhHHHHHHHHhhhccccccccCcccCchHHH
Confidence 765544332 11122246678899988886532 21 112356766665544211112345667889999
Q ss_pred HHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEE
Q 003275 231 SVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDV 310 (834)
Q Consensus 231 av~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I 310 (834)
++|++|+|+.+++...+.-.. ... +.+ ...-.-.++|+++|.+++|.|++|.+.|.. |+|. ..-.|
T Consensus 348 ~Iwa~ala~n~t~e~l~~~~~---------~l~--~f~-y~~k~i~d~i~eamn~tsF~GvsG~V~F~~-geR~-a~t~i 413 (865)
T KOG1055|consen 348 AIWALALALNKTMEGLGRSHV---------RLE--DFN-YNNKTIADQIYEAMNSTSFEGVSGHVVFSN-GERM-ALTLI 413 (865)
T ss_pred HHHHHHHHHHHHHhcCCccce---------ecc--ccc-hhhhHHHHHHHHHhhcccccccccceEecc-hhhH-HHHHH
Confidence 999999999998765331100 000 000 001113788999999999999999999966 9875 77889
Q ss_pred EEeeccceEEEEEecCCC
Q 003275 311 LNIGGTGSRRIGYWSNYS 328 (834)
Q Consensus 311 ~~~~~~~~~~vG~w~~~~ 328 (834)
-|+++++.+++|+|+...
T Consensus 414 eQ~qdg~y~k~g~Yds~~ 431 (865)
T KOG1055|consen 414 EQFQDGKYKKIGYYDSTK 431 (865)
T ss_pred HHHhCCceEeeccccccc
Confidence 999999999999998765
No 67
>cd06357 PBP1_AmiC Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. This group includes the periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. AmiC controls expression of the amidase operon by the ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon are induced.
Probab=99.91 E-value=2.3e-22 Score=219.14 Aligned_cols=279 Identities=15% Similarity=0.135 Sum_probs=216.4
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
+++|.+|||+.+|..+.++++++++.++|++++++... . ...|++|++.+++..+..++++++...+-+++++|+.|
T Consensus 65 ~~~V~aiiG~~~s~~~~a~~~~~~~~~~~~~~~~~~~~-~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~d 141 (360)
T cd06357 65 EDGVRVIFGCYTSSSRKAVLPVVERHDALLWYPTLYEG-F--EYSPNVIYTGAAPNQNSVPLADYLLRHYGKRVFLVGSN 141 (360)
T ss_pred hCCCcEEEeCccHHHHHHHHHHHHhcCceEEeCCCccC-C--cccCCEEEeCCCcHHHHHHHHHHHHhcCCcEEEEECCC
Confidence 36899999999999999999999999999998754321 1 22377888888877778889998765555899999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
++||+...+.+.+.+++.|++|+....++.+.+..|+..++.+++++++|+|++.+...++..++++++++|+.+.. +.
T Consensus 142 ~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~~~d~s~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~~~-~~ 220 (360)
T cd06357 142 YIYPYESNRIMRDLLEQRGGEVLGERYLPLGASDEDFARIVEEIREAQPDFIFSTLVGQSSYAFYRAYAAAGFDPAR-MP 220 (360)
T ss_pred CcchHHHHHHHHHHHHHcCCEEEEEEEecCCCchhhHHHHHHHHHHcCCCEEEEeCCCCChHHHHHHHHHcCCCccC-ce
Confidence 99999999999999999999998876666554468999999999999999999999999999999999999987542 33
Q ss_pred EEeCCCcc-cCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHH
Q 003275 162 IATDWLPS-VLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 162 i~~~~~~~-~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~A 238 (834)
+.+.+... .+. ....+..+|+++..++.+ +++..++|.++|+++++ ....++.+++.+||+++++++|
T Consensus 221 ~~~~~~~~~~~~------~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~g---~~~~~~~~~~~~yda~~~l~~A 291 (360)
T cd06357 221 IASLTTSEAEVA------AMGAEAAAGHITAAPYFSSIDTPANRAFVARYRARFG---EDAPVSACAEAAYFQVHLFARA 291 (360)
T ss_pred eEEeeccHHHHh------hcchHhhCCcEEecccccccCChhHHHHHHHHHHHcC---CCCCCCcHHHHHHHHHHHHHHH
Confidence 33322111 110 112356789988876644 56788999999999882 1123577899999999999999
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEe-eccc
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNI-GGTG 317 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~-~~~~ 317 (834)
++++... +++.+.++|++++|+|+.|.+.||..++.......+.++ ++++
T Consensus 292 l~~ag~~-----------------------------~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~~~~~~~~G~ 342 (360)
T cd06357 292 LQRAGSD-----------------------------DPEDVLAALLGFSFDAPQGPVRIDPDNNHTYLWPRIARVNADGQ 342 (360)
T ss_pred HHHcCCC-----------------------------CHHHHHHHhccCcccCCCcceEEeCCCCeeeeeeEEEEEcCCCC
Confidence 9985211 478899999999999999999998765444444555566 4444
Q ss_pred eEEEE
Q 003275 318 SRRIG 322 (834)
Q Consensus 318 ~~~vG 322 (834)
+..+.
T Consensus 343 ~~~~~ 347 (360)
T cd06357 343 FDIVR 347 (360)
T ss_pred EEEEE
Confidence 44443
No 68
>TIGR03407 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane.
Probab=99.91 E-value=1.9e-22 Score=219.60 Aligned_cols=268 Identities=16% Similarity=0.148 Sum_probs=207.6
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHH-cCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEY-YGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~-~~W~~v~iI~~ 80 (834)
+++|.+|+||.+|..+.++.+++++.++|+|++.... .....|++||+.+++..++.++++++.. .|.+++++|+.
T Consensus 66 ~~~V~~iiG~~~S~~~~a~~~~~~~~~~~~i~~~~~~---~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~g~k~v~~l~~ 142 (359)
T TIGR03407 66 QDKVAAVFGCWTSASRKAVLPVFEENNGLLFYPVQYE---GEECSPNIFYTGAAPNQQIIPAVDYLLSKKGAKRFFLLGS 142 (359)
T ss_pred hCCCcEEEcCCcHHHHHHHHHHHhccCCceEeCCccc---CcccCCCEEEcCCChHHHHHHHHHHHHhccCCceEEEecC
Confidence 3689999999999999999999999999999764321 1235689999999999999999998765 59999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|++||+...+.+.+.+++.|++|+....++.+ ..|++.++.+|+++++|+|++......+..+++++++.|+......
T Consensus 143 d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~D~s~~v~~l~~~~pDav~~~~~~~~~~~~~~~~~~~G~~~~~~~ 220 (359)
T TIGR03407 143 DYVFPRTANKIIKAYLKSLGGTVVGEDYTPLG--HTDFQTIINKIKAFKPDVVFNTLNGDSNVAFFKQLKNAGITAKDVP 220 (359)
T ss_pred ccHHHHHHHHHHHHHHHHcCCEEEeeEEecCC--hHhHHHHHHHHHHhCCCEEEEeccCCCHHHHHHHHHHcCCCccCCc
Confidence 99999999999999999999999988888754 4899999999999999999988888788899999999998654333
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEec--CCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHH--TPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~--~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~A 238 (834)
++.+......+.. ...+.++|+++...+ ..+.+..++|.++|+++++ ....++.+++.+||+++++++|
T Consensus 221 ~~~~~~~~~~~~~------~g~~~~~G~~~~~~~~~~~~~~~~~~f~~~~~~~~~---~~~~~~~~~~~~y~a~~~~~~A 291 (359)
T TIGR03407 221 VVSFSVAEEEIRG------IGPENLVGHLAAWNYFQSVDTPANKKFVKAFKAKYG---DDRVTNDPMEAAYLGVYLWKAA 291 (359)
T ss_pred EEEeecCHHHHhh------cChHhhCCeEEeccchhcCCCHHHHHHHHHHHHHcC---CCCCCCcHHHHHHHHHHHHHHH
Confidence 3433211111111 112456887655433 2356788999999999872 1122345567899999999999
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEcc-CCCCCCCcEEEEEe
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDA-DKNLVNPAYDVLNI 313 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~-~g~~~~~~~~I~~~ 313 (834)
++++.+. ++..+.++|++++|+++.|+++|++ +++ ....+.+.++
T Consensus 292 ~~~ag~~-----------------------------~~~~i~~al~~~~~~~~~G~i~f~~~~~~-~~~~~~~~~~ 337 (359)
T TIGR03407 292 VEKAGSF-----------------------------DVDAVRDAAIGIEFDAPEGKVKVDGKNHH-LTKTVRIGEI 337 (359)
T ss_pred HHHhCCC-----------------------------CHHHHHHHhcCCcccCCCccEEEeCCCCe-eeeeeEEEEE
Confidence 9995221 4889999999999999999999987 444 3233444444
No 69
>PF13458 Peripla_BP_6: Periplasmic binding protein; PDB: 4EVS_A 4EY3_A 4EYG_B 4EYK_A 3H5L_B 3TD9_A 3EAF_A 1Z18_A 1Z17_A 2LIV_A ....
Probab=99.90 E-value=1.1e-22 Score=221.14 Aligned_cols=270 Identities=24% Similarity=0.351 Sum_probs=221.0
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHH-HHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLV-EYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll-~~~~W~~v~iI~~ 80 (834)
+++|.+||||.+|..+.+++++++..++|+|++++.++ ....+|+||+.|++..++.++++++ +++|.+++++|+.
T Consensus 67 ~~~v~~vvg~~~s~~~~~~~~~~~~~~ip~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~iv~~ 143 (343)
T PF13458_consen 67 DDGVDAVVGPLSSAQAEAVAPIAEEAGIPYISPSASSP---SPDSPNVFRLSPSDSQQAAALAEYLAKKLGAKKVAIVYP 143 (343)
T ss_dssp TSTESEEEESSSHHHHHHHHHHHHHHT-EEEESSGGGG---TTTHTTEEESS--HHHHHHHHHHHHHHTTTTSEEEEEEE
T ss_pred hcCcEEEEecCCcHHHHHHHHHHHhcCcEEEEeeccCC---CCCCCcEEEEeccccHHHHHHHHHHHHHcCCcEEEEEec
Confidence 36899999999999999999999999999999654442 3567999999999999999999986 5689999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|++||+...+.+.+.+++.|++|+....++.+. .|+..+++++++.++++|++.+.+.++..+++++.+.|+..+.+.
T Consensus 144 ~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~d~~~~~~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (343)
T PF13458_consen 144 DDPYGRSLAEAFRKALEAAGGKVVGEIRYPPGD--TDFSALVQQLKSAGPDVVVLAGDPADAAAFLRQLRQLGLKPPRIP 221 (343)
T ss_dssp SSHHHHHHHHHHHHHHHHTTCEEEEEEEE-TTS--SHHHHHHHHHHHTTTSEEEEESTHHHHHHHHHHHHHTTGCSCTEE
T ss_pred CchhhhHHHHHHHHHHhhcCceeccceeccccc--ccchHHHHHHhhcCCCEEEEeccchhHHHHHHHHHhhccccccce
Confidence 999999999999999999999998888888554 899999999999999999999999999999999999998654444
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~A 238 (834)
...+......+. ....+.++|++...++.| +.+..++|.++|++.++ ....++.++..+||++.++++|
T Consensus 222 ~~~~~~~~~~l~------~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~---~~~~~~~~~~~~yda~~~~~~a 292 (343)
T PF13458_consen 222 LFGTSLDDASLQ------QLGGDALEGVYIVSPWFPDPDSPAVKQFQERYRAAYG---EEPPPSLYAAQGYDAARLLAQA 292 (343)
T ss_dssp EEEGGGSSHHHH------HHHGGGGTTEEEEESGGGTGGSHHHHHHHHHHHHHHS---STGGTCHHHHHHHHHHHHHHHH
T ss_pred eeccccCcHHHH------HhhhhhccCceeecccCCCCCCHHHHHHHHHHHHHcC---CCCCCchhHHHHHHHHHHHHHH
Confidence 443332222111 112246889999888776 46788999999999982 1124788999999999999999
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEee
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIG 314 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~ 314 (834)
++++.. .+++.+.++|+++.|+|+.|++.|+..+......+.|++++
T Consensus 293 l~~~g~-----------------------------~~~~~v~~al~~~~~~g~~g~~~~~~~~~~~~~~~~i~~v~ 339 (343)
T PF13458_consen 293 LERAGS-----------------------------LDREAVREALESLKYDGLFGPISFDPPDHQANKPVYIVQVK 339 (343)
T ss_dssp HHHHTS-----------------------------HHHHHHHHHHHTSEEEETTEEEEEETTTSBEEEEEEEEEEE
T ss_pred HHHhCC-----------------------------CCHHHHHHHHHhCCCcccccceEEeCCCCccccCeEEEEEe
Confidence 999621 15899999999999999999999976555567888898887
No 70
>cd06358 PBP1_NHase Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides. This group includes the type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and characterized. In Rhodococcus sp., the nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit, and NHase activator. The operon produces a constitutive hydratase that has a broad substrate spectrum: aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles, and a constitutive amidase of equally low substrate specificity. NHases are metalloenzymes containing either cobalt or iron, and therefore can be classified int
Probab=99.90 E-value=4.1e-22 Score=215.32 Aligned_cols=254 Identities=14% Similarity=0.148 Sum_probs=205.1
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHH-HHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLV-EYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll-~~~~W~~v~iI~~d 81 (834)
++|.+||||.+|..+.++.++++ .+||+|++++.+. ....||+||+.+++..++.++++++ +..+|++|++++.|
T Consensus 66 ~~v~aviG~~~s~~a~a~~~~~~-~~vp~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~i~~~~ 141 (333)
T cd06358 66 GGVDAIIGWHTSAVRNAVAPVVA-GRVPYVYTSLYEG---GECNPGVFLTGETPEQQLAPAIPWLAEEKGARRWYLIGND 141 (333)
T ss_pred CCCcEEEecCcHHHHHHHHHHHh-cCceEEeCCCcCC---CCCCCCEEEcCCCcHHHHHHHHHHHHHhcCCCeEEEEecc
Confidence 58999999999999999999999 9999999754332 1345899999999999988788776 66799999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
+.||+...+.+.+.+++.|++|+....++.+ ..|+++.+.++++.++|+|++.+...+...+++++++.|+..+ |
T Consensus 142 ~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~---~ 216 (333)
T cd06358 142 YVWPRGSLAAAKRYIAELGGEVVGEEYVPLG--TTDFTSVLERIAASGADAVLSTLVGQDAVAFNRQFAAAGLRDR---I 216 (333)
T ss_pred chhhHHHHHHHHHHHHHcCCEEeeeeeecCC--hHHHHHHHHHHHHcCCCEEEEeCCCCchHHHHHHHHHcCCCcc---C
Confidence 9999999999999999999999988888854 5899999999999999999998888888999999999999764 2
Q ss_pred EEe-CCCcc-cCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHH
Q 003275 162 IAT-DWLPS-VLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAH 237 (834)
Q Consensus 162 i~~-~~~~~-~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~ 237 (834)
+.. ..+.. .+.. ......+|++....+.+ ..+..++|.++|+++++ .....++.++..+||+++++++
T Consensus 217 ~~~~~~~~~~~~~~------~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g--~~~~~~~~~~~~~yda~~~~~~ 288 (333)
T cd06358 217 LRLSPLMDENMLLA------SGAEAAEGLYSSSGYFASLQTPANAAFLARYRARFG--DDAPPLNSLSESCYEAVHALAA 288 (333)
T ss_pred ceeecccCHHHHHh------cChHhhCCcEEeccchhhcCCHHHHHHHHHHHHHcC--CCCCCCChHHHHHHHHHHHHHH
Confidence 221 11111 1110 11145688877765544 56889999999999883 1123467789999999999999
Q ss_pred HHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCC
Q 003275 238 ALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKN 302 (834)
Q Consensus 238 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~ 302 (834)
|+++... .++..|.++|++.+|+|++|++.|++++.
T Consensus 289 A~~~ag~-----------------------------~~~~~v~~al~~~~~~~~~G~~~~~~~~~ 324 (333)
T cd06358 289 AAERAGS-----------------------------LDPEALIAALEDVSYDGPRGTVTMRGRHA 324 (333)
T ss_pred HHHHhCC-----------------------------CCHHHHHHHhccCeeeCCCcceEEccccc
Confidence 9997421 14789999999999999999999988864
No 71
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.90 E-value=6.4e-22 Score=214.89 Aligned_cols=258 Identities=19% Similarity=0.231 Sum_probs=203.2
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC--CCCCceEEccCChHHHHHHHHHHH-HHcCCeEEEEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS--LQYPYFLRTTQSDYYQMHAVADLV-EYYGWREVIAIF 79 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~--~~~p~~~r~~ps~~~q~~aia~ll-~~~~W~~v~iI~ 79 (834)
++|.+|+||.+|..+.++.+++++.+||+|++.++.+.++. ..++|+||+.+++..++.++++++ ++.+|++|+++|
T Consensus 66 ~~V~aiiG~~~s~~~~a~~~~~~~~~vp~i~~~~~~~~l~~~~~~~~~~Fr~~~~~~~~~~~~a~~~~~~~~~~~v~ii~ 145 (347)
T cd06335 66 EKVVAVLGGLHTPVALANLEFIQQNKIPLIGPWAAGTPITRNGAPPNYIFRVSADDSIQAPFLVDEAVKRGGFKKVALLL 145 (347)
T ss_pred CCeEEEEcCCCCHHHHhhhHHHHhcCCcEEecCCCCcccccCCCCCCCEEEeccChHHHHHHHHHHHHHhcCCCeEEEEe
Confidence 48999999999999999999999999999998888777765 346899999999999999999987 556799999999
Q ss_pred EcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 80 VDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 80 ~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
.|++||+...+.+.+.+++.|++|+....++.. ..|++..+.+|++.++++|++.+...++..+++++++.|+..+
T Consensus 146 ~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~-- 221 (347)
T cd06335 146 DNTGWGRSNRKDLTAALAARGLKPVAVEWFNWG--DKDMTAQLLRAKAAGADAIIIVGNGPEGAQIANGMAKLGWKVP-- 221 (347)
T ss_pred ccCchhhhHHHHHHHHHHHcCCeeEEEeeecCC--CccHHHHHHHHHhCCCCEEEEEecChHHHHHHHHHHHcCCCCc--
Confidence 999999999999999999999999988888755 3799999999999999999999999999999999999998532
Q ss_pred EEEEeCCCcccCCCCCCCChhhHhhcccceEEEecC---CCChhHHHHHHHHHhhhcCCC-CCCCccchhHHHhhHHHHH
Q 003275 160 VWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHT---PDTDLKKNFISRWKNLKYKEN-SPSGFNSYALYAYDSVWLV 235 (834)
Q Consensus 160 vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~---~~~~~~~~F~~~~~~~~~~~~-~~~~~~~~~~~~YDav~~l 235 (834)
+...+.....+.. ....+..+|++....+. +.++..++|.++|+++++... ....++.++..+||+++++
T Consensus 222 --~~~~~~~~~~~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYd~~~~l 295 (347)
T cd06335 222 --IISHWGLSGGNFI----EGAGPAANDALMIQTFIFEPPSNPKAKAFLAAYHKKYPEKKPADIPAPVGAAHAYDAVHLL 295 (347)
T ss_pred --EecccCCcCchhh----hccchhhcCcEEEEeeccccCCCHHHHHHHHHHHHHhCCCcccccCcchhHHHHHHHHHHH
Confidence 2222111111110 11224567887765543 256788999999999983110 0113566778899999999
Q ss_pred HHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhc--ccccceee--EEEcc
Q 003275 236 AHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRM--NFTGLSGE--IRFDA 299 (834)
Q Consensus 236 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~--~f~g~tG~--i~Fd~ 299 (834)
++|++++... .++.+.++|+++ .+.|+.|. +.|++
T Consensus 296 ~~A~~~ag~~-----------------------------~~~~v~~al~~~~~~~~G~~~~~~~~~~~ 334 (347)
T cd06335 296 AAAIKQAGST-----------------------------DGRAIKRALENLKKPVEGLVKTYDKPFSK 334 (347)
T ss_pred HHHHHHhcCC-----------------------------CHHHHHHHHHhccCCceeeecccCCCCCh
Confidence 9999985321 246889999876 46788775 45654
No 72
>cd06356 PBP1_Amide_Urea_BP_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the type I periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis.
Probab=99.89 E-value=7.2e-22 Score=213.13 Aligned_cols=255 Identities=12% Similarity=0.111 Sum_probs=202.1
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
+++|++|||+.+|..+.++.+++++.++|+|+.++... ....||+||+.+++..++.++++++...+-+++++|+.|
T Consensus 65 ~~~V~aiiG~~~s~~~~a~~~~~~~~~vp~i~~~~~~~---~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~vail~~d 141 (334)
T cd06356 65 QDKVDVVWGGISSASREAIRPIMDRTKQLYFYTTQYEG---GVCDRNTFCTGATPAQQFSTLVPYMMEKYGKKVYTIAAD 141 (334)
T ss_pred hCCCCEEEeCcchHHHHHHHHHHHhcCceEEeCCCccC---CcccCCEEEeCCCcHHHHHHHHHHHHHccCCeEEEECCC
Confidence 36899999999999999999999999999998543322 123489999999999999999999866544889999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCC-CCCCeE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGM-TAGSYV 160 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~-~~~~~v 160 (834)
++||......+.+.+++.|++++....++.+ ..|++.++.+|++.++|+|++.....+...+++++++.|+ ..+
T Consensus 142 ~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~--- 216 (334)
T cd06356 142 YNFGQISAEWVRKIVEENGGEVVGEEFIPLD--VSDFGSTIQKIQAAKPDFVMSILVGANHLSFYRQWAAAGLGNIP--- 216 (334)
T ss_pred chhhHHHHHHHHHHHHHcCCEEEeeeecCCC--chhHHHHHHHHHhcCCCEEEEeccCCcHHHHHHHHHHcCCccCc---
Confidence 9999999999999999999999998888864 4899999999999999999999888889999999999998 221
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCC-CccchhHHHhhHHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPS-GFNSYALYAYDSVWLVAH 237 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~-~~~~~~~~~YDav~~la~ 237 (834)
.+...+....... . .......+|+++...+.+ +.+..++|.++|+++++ .. .++.+++.+||+++++++
T Consensus 217 ~~~~~~~~~~~~~-~---~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~----~~p~~~~~~~~~y~a~~~~~~ 288 (334)
T cd06356 217 MASSTLGAQGYEH-K---RLKPPALKDMYATANYIEELDTPANKAFVERFRAKFP----DAPYINEEAENNYEAIYLYKE 288 (334)
T ss_pred eeeeecccchhHH-h---ccCchhcCCeEEecchhhhcCCHHHHHHHHHHHHHcC----CCCCCCchhHHHHHHHHHHHH
Confidence 2221111111000 0 001245688887766544 36778999999999982 22 236789999999999999
Q ss_pred HHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHh-cccccceeeEEEccCC
Q 003275 238 ALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLR-MNFTGLSGEIRFDADK 301 (834)
Q Consensus 238 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~-~~f~g~tG~i~Fd~~g 301 (834)
|++++.+. +++.|.++|++ ..++|+.|++.|++.+
T Consensus 289 A~~~ag~~-----------------------------~~~~v~~aL~~~~~~~~~~g~~~~~~~~ 324 (334)
T cd06356 289 AVEKAGTT-----------------------------DRDAVIEALESGLVCDGPEGKVCIDGKT 324 (334)
T ss_pred HHHHHCCC-----------------------------CHHHHHHHHHhCCceeCCCceEEEecCC
Confidence 99985321 47899999997 5789999999999743
No 73
>cd06337 PBP1_ABC_ligand_binding_like_4 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.89 E-value=3.4e-22 Score=217.63 Aligned_cols=267 Identities=12% Similarity=0.093 Sum_probs=205.5
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCC------C-CCCCCceEEccCChHHHHHHHHHHHHHcC-CeE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTL------T-SLQYPYFLRTTQSDYYQMHAVADLVEYYG-WRE 74 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~l------s-~~~~p~~~r~~ps~~~q~~aia~ll~~~~-W~~ 74 (834)
++|.+|||+.+|..+.++++++++.+||+|++.+..+.+ . ...++|+||..+++..+..+++++++..+ +++
T Consensus 68 d~v~~iiG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~k~ 147 (357)
T cd06337 68 DKVDLLLAGGTPDTTNPVSDQCEANGVPCISTMAPWQAWFFGRGGNPATGFKWTYHFFWGAEDVVATYVGMWKQLETNKK 147 (357)
T ss_pred cCccEEEecCCcchhhHHHHHHHHhCCCeEEeccchhhhhccCCCCcccCCceeEEecCCHHHHHHHHHHHHHhCCCCce
Confidence 589999999999999999999999999999875432221 1 13478999999999888899998888777 999
Q ss_pred EEEEEEcCCcccchHHHHH---HHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHh
Q 003275 75 VIAIFVDDDYGRNGISVLG---DALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~d~~~g~~~~~~l~---~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~ 151 (834)
|++++.|++||+...+.+. +++++.|++|+..+.++++. .|++.++.+|+++++|+|++.+.+.++..+++++++
T Consensus 148 v~ii~~~~~~g~~~~~~~~~~~~~~~~~G~~vv~~~~~~~~~--~D~~~~v~~ik~a~pD~v~~~~~~~~~~~~~~~~~~ 225 (357)
T cd06337 148 VGILYPNDPDGNAFADPVIGLPAALADAGYKLVDPGRFEPGT--DDFSSQINAFKREGVDIVTGFAIPPDFATFWRQAAQ 225 (357)
T ss_pred EEEEeecCchhHHHHHhhhcccHHHHhCCcEEecccccCCCC--CcHHHHHHHHHhcCCCEEEeCCCccHHHHHHHHHHH
Confidence 9999999999997766554 67778999999988888654 799999999999999999999999999999999999
Q ss_pred CCCCCCCeEEEE-eCCC--cccCCCCCCCChhhHhhcccceEEEecCCC--------ChhHHHHHHHHHhhhcCCCCCCC
Q 003275 152 LGMTAGSYVWIA-TDWL--PSVLDSTEPVDIDTMNLLQGVVALRHHTPD--------TDLKKNFISRWKNLKYKENSPSG 220 (834)
Q Consensus 152 ~g~~~~~~vwi~-~~~~--~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~--------~~~~~~F~~~~~~~~~~~~~~~~ 220 (834)
+|+..+ ++. ..+. ..... ...+..+|++....+.|. ++..++|.++|++++ +..
T Consensus 226 ~G~~~~---~~~~~~~~~~~~~~~-------~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~-----g~~ 290 (357)
T cd06337 226 AGFKPK---IVTIAKALLFPEDVE-------ALGDRGDGMSTEVWWSPSHPFRSSLTGQSAAELADAYEAAT-----GRQ 290 (357)
T ss_pred CCCCCC---eEEEeccccCHHHHH-------HhhhhhcCccccceeccCCCcccccCCccHHHHHHHHHHHh-----CCC
Confidence 998654 222 2221 11111 112345777765444443 234789999999988 334
Q ss_pred ccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccC
Q 003275 221 FNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDAD 300 (834)
Q Consensus 221 ~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~ 300 (834)
+.....++||++.++++|++++... .+++.|.++|++++++++.|++.|+++
T Consensus 291 ~~~~~~~~~~~~~~l~~Ai~~Ags~----------------------------~d~~~v~~aL~~~~~~~~~G~~~f~~~ 342 (357)
T cd06337 291 WTQPLGYAHALFEVGVKALVRADDP----------------------------DDPAAVADAIATLKLDTVVGPVDFGNS 342 (357)
T ss_pred ccCcchHHHHHHHHHHHHHHHcCCC----------------------------CCHHHHHHHHHcCCcccceeeeecCCC
Confidence 5566778999999999999985321 147899999999999999999999865
Q ss_pred CCCCCCcEEEEEeeccc
Q 003275 301 KNLVNPAYDVLNIGGTG 317 (834)
Q Consensus 301 g~~~~~~~~I~~~~~~~ 317 (834)
. .....|+.+.|+.
T Consensus 343 --~-~~~~~~~~~~~~~ 356 (357)
T cd06337 343 --P-IKNVAKTPLVGGQ 356 (357)
T ss_pred --C-CccccccccccCC
Confidence 2 2345565665543
No 74
>cd06269 PBP1_glutamate_receptors_like Family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domain of the ionotropic glutamate receptors. This CD represents the ligand-binding domain of the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domain of the ionotropic glutamate receptors, all of which are structurally similar and related to the periplasmic-binding fold type I family. The family C GPCRs consist of metabotropic glutamate receptor (mGluR) receptors, a calcium-sensing receptor (CaSR), gamma-aminobutyric receptors (GABAb), the promiscuous L-alpha-amino acid receptor GPR6A, families of taste and pheromone receptors, and orphan receptors. Truncated splicing va
Probab=99.89 E-value=2.4e-22 Score=213.88 Aligned_cols=164 Identities=35% Similarity=0.599 Sum_probs=153.9
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
+++.|||||.+|..+.+++++++.++||+|+++++++.+++ .++|+++|+.|++..++.+++++++++||++|+++|+|
T Consensus 70 ~~v~aiiG~~~s~~~~~v~~~~~~~~iP~is~~~~~~~~~~~~~~~~~~~~~p~~~~~~~a~~~~l~~~~w~~v~~v~~~ 149 (298)
T cd06269 70 RGVVAVIGPSSSSSAEAVASLLGALHIPQISYSATSPLLSDKEQFPSFLRTVPSDSSQAQAIVDLLKHFGWTWVGLVYSD 149 (298)
T ss_pred CceEEEECCCCchHHHHHHHHhccCCCcEEecccCchhhcChhhCCCeEecCCCcHHHHHHHHHHHHHCCCeEEEEEEec
Confidence 68999999999999999999999999999999999999887 67899999999999999999999999999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
+++|....+.+.+.+++.|+|+.....++... .++...++++++.+++|||+++.+.++..++++|.+.||+ .+++|
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~--~~~~~~l~~l~~~~~~viv~~~~~~~~~~~l~~a~~~g~~-~~~~~ 226 (298)
T cd06269 150 DDYGRRLLELLEEELEKNGICVAFVESIPDGS--EDIRRLLKELKSSTARVIVVFSSEEDALRLLEEAVELGMM-TGYHW 226 (298)
T ss_pred chhhHHHHHHHHHHHHHCCeeEEEEEEcCCCH--HHHHHHHHHHHhcCCcEEEEEechHHHHHHHHHHHHcCCC-CCeEE
Confidence 99999999999999999999999988887443 7899999999999999999999999999999999999999 89999
Q ss_pred EEeCCCcc
Q 003275 162 IATDWLPS 169 (834)
Q Consensus 162 i~~~~~~~ 169 (834)
|.++.+..
T Consensus 227 i~~~~~~~ 234 (298)
T cd06269 227 IITDLWLT 234 (298)
T ss_pred EEEChhhc
Confidence 99986653
No 75
>cd06334 PBP1_ABC_ligand_binding_like_1 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.88 E-value=4.4e-21 Score=207.64 Aligned_cols=271 Identities=13% Similarity=0.136 Sum_probs=209.0
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcC-----CeEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYG-----WREVI 76 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~-----W~~v~ 76 (834)
++|.+|+ +.+|..+.++++++++.+||+|+++++++.+++ ..+||+||+.|++..++.++++++...+ .++|+
T Consensus 66 ~~V~~i~-~~~S~~~~a~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~~Fr~~~~~~~~~~~l~~~~~~~~~~~~~~~kva 144 (351)
T cd06334 66 DGAVAFQ-GWSTGITEALIPKIAADKIPLMSGSYGATLADDGAVFPYNFPVGPTYSDQARALVQYIAEQEGGKLKGKKIA 144 (351)
T ss_pred CCcEEEe-cCcHHHHHHhhHHHhhcCCcEEecccchhhccCCCCCCeeeeCCCCHHHHHHHHHHHHHHhcccCCCCCeEE
Confidence 4687765 578999999999999999999999877777764 6689999999999999999999986654 79999
Q ss_pred EEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 77 AIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 77 iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
+|+.|++||+...+.+.+.+++.|++|+....++.+ ..|++.++.+|++.++|+|++.+...++..+++++++.|+..
T Consensus 145 iv~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~D~~~~v~~i~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~ 222 (351)
T cd06334 145 LVYHDSPFGKEPIEALKALAEKLGFEVVLEPVPPPG--PNDQKAQWLQIRRSGPDYVILWGWGVMNPVAIKEAKRVGLDD 222 (351)
T ss_pred EEeCCCccchhhHHHHHHHHHHcCCeeeeeccCCCC--cccHHHHHHHHHHcCCCEEEEecccchHHHHHHHHHHcCCCc
Confidence 999999999999999999999999999998888855 479999999999999999999999999999999999999843
Q ss_pred CCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCC-CCCCccchhHHHhhHHH
Q 003275 157 GSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKEN-SPSGFNSYALYAYDSVW 233 (834)
Q Consensus 157 ~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~-~~~~~~~~~~~~YDav~ 233 (834)
.|+.+++... ... -....+..+|+++..++.+ ++|..++|.++|++++.... ....++.++..+||+++
T Consensus 223 ---~~~~~~~~~~-~~~----~~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~~~~~~~~~~~~~~~~~gy~a~~ 294 (351)
T cd06334 223 ---KFIGNWWSGD-EED----VKPAGDAAKGYKGVTPFAGGADDPVGKEIVKEVYDKGKGSGNDKEIGSVYYNRGVVNAM 294 (351)
T ss_pred ---eEEEeeccCc-HHH----HHHhhhhhcCcEEeecccCCCCchHHHHHHHHHHHccCCCCCcccccccHHHHHHHHHH
Confidence 2444433221 001 0122356789888777655 67889999999999882100 01234678999999999
Q ss_pred HHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccC
Q 003275 234 LVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDAD 300 (834)
Q Consensus 234 ~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~ 300 (834)
++++|++++.+....-.... +.. .+ +-...++.+.+....|+.|+++|...
T Consensus 295 ~l~~Al~~ag~~~~~~~~~~--------~~~-------~~-~~~~~~~~~~~~~~~g~~~~~~~~~~ 345 (351)
T cd06334 295 IMVEAIRRAQEKGGETTIAG--------EEQ-------LE-NLKLDAARLEELGAEGLGPPVSVSCD 345 (351)
T ss_pred HHHHHHHHHHHhcCCCCCcH--------HHH-------HH-hhhhhhhhhhhcCcccccCCceeccc
Confidence 99999999976543210000 000 00 01233566777788899999999763
No 76
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.88 E-value=4.3e-21 Score=202.19 Aligned_cols=224 Identities=19% Similarity=0.233 Sum_probs=186.4
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHH----hCCC-CcCEEEEecCCCCCCCChHHHHHHHHhCccc
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVN----LLPY-PVPHNYIMYGNGKRNPIYNDIVQQVALNKFD 447 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~----~l~~-~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D 447 (834)
.+.|+||+ ...|+||.+.+. ++.+.||++|+++.|++ ++|. .+++++++ .+|..++..|..|++|
T Consensus 39 ~g~L~Vg~--~~~~pP~~f~~~-~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~-------~~~~~~i~~L~~G~~D 108 (302)
T PRK10797 39 NGVIVVGH--RESSVPFSYYDN-QQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIP-------ITSQNRIPLLQNGTFD 108 (302)
T ss_pred CCeEEEEE--cCCCCCcceECC-CCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEE-------cChHhHHHHHHCCCcc
Confidence 46799999 456889988764 67899999998777765 6653 35688887 3588899999999999
Q ss_pred EEeeeeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCC
Q 003275 448 AAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGP 527 (834)
Q Consensus 448 ~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~ 527 (834)
|+++++++|++|.+.++||.||+.++..+++++..
T Consensus 109 i~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~--------------------------------------------- 143 (302)
T PRK10797 109 FECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG--------------------------------------------- 143 (302)
T ss_pred EEecCCccCcchhhcceecccEeeccEEEEEECCC---------------------------------------------
Confidence 99999999999999999999999999999998654
Q ss_pred CCcchhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEe
Q 003275 528 PSQQLVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQ 607 (834)
Q Consensus 528 ~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~ 607 (834)
.|++++||. |++||+.
T Consensus 144 --------------------------------------------------------------~i~sl~dL~--Gk~V~v~ 159 (302)
T PRK10797 144 --------------------------------------------------------------DIKDFADLK--GKAVVVT 159 (302)
T ss_pred --------------------------------------------------------------CCCChHHcC--CCEEEEe
Confidence 478899996 8899999
Q ss_pred eCchhhHHHHhhhc--ccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcC-Cc-cEEEeCCcccccceE
Q 003275 608 DGSFAWNYLVDELK--IAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKT-NC-EFRTVGQEFTKSGWG 683 (834)
Q Consensus 608 ~~s~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~-~~-~l~~v~~~~~~~~~~ 683 (834)
.|+....++..... ....+++.+.+.++.+++|.. |++|+++.+...+.+.+.+. .. .+.++++.+...+++
T Consensus 160 ~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~----GrvDa~i~d~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~ 235 (302)
T PRK10797 160 SGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLES----GRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYG 235 (302)
T ss_pred CCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHc----CCceEEEccHHHHHHHHHcCCCCcceEECCccCCcCcee
Confidence 99988887754221 123577889999999999999 99999999987766544331 22 578888777778899
Q ss_pred EEEcCCCc-chHHHHHHHHhhhccccHHHHHHhhcCC
Q 003275 684 FAFQRDSP-LAIDLSTAILQLSENGDLQKIHNKWLTY 719 (834)
Q Consensus 684 ~~~~k~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~~~ 719 (834)
++++++++ +++.+|.+|.++.++|.+++|.+||+..
T Consensus 236 ~a~~k~~~~L~~~in~~L~~l~~~G~l~~i~~kw~~~ 272 (302)
T PRK10797 236 CMLRKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFKN 272 (302)
T ss_pred EEEeCCCHHHHHHHHHHHHHHHhCchHHHHHHHHcCC
Confidence 99999888 9999999999999999999999999984
No 77
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.87 E-value=3.8e-21 Score=198.12 Aligned_cols=219 Identities=25% Similarity=0.433 Sum_probs=187.1
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
.++|+||+ ..+|+||.+.+ ++.+.|+++|+++++++++|.+ +++++ .+|.+++.++.+|++|+++++
T Consensus 24 ~~~l~v~~--~~~~~P~~~~~--~g~~~G~~vdl~~~ia~~lg~~--~~~~~-------~~~~~~~~~l~~G~vDi~~~~ 90 (247)
T PRK09495 24 DKKLVVAT--DTAFVPFEFKQ--GDKYVGFDIDLWAAIAKELKLD--YTLKP-------MDFSGIIPALQTKNVDLALAG 90 (247)
T ss_pred CCeEEEEe--CCCCCCeeecC--CCceEEEeHHHHHHHHHHhCCc--eEEEe-------CCHHHHHHHHhCCCcCEEEec
Confidence 46899998 44688998764 4779999999999999999987 44444 349999999999999999888
Q ss_pred eeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcch
Q 003275 453 ITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQL 532 (834)
Q Consensus 453 ~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 532 (834)
++.+++|.+.++||.||+.++..+++++..
T Consensus 91 ~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~-------------------------------------------------- 120 (247)
T PRK09495 91 ITITDERKKAIDFSDGYYKSGLLVMVKANN-------------------------------------------------- 120 (247)
T ss_pred CccCHHHHhhccccchheecceEEEEECCC--------------------------------------------------
Confidence 999999999999999999999999987654
Q ss_pred hhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCchh
Q 003275 533 VTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSFA 612 (834)
Q Consensus 533 ~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~~ 612 (834)
..+++++||. +++||+..|+..
T Consensus 121 --------------------------------------------------------~~~~~~~dL~--g~~I~v~~g~~~ 142 (247)
T PRK09495 121 --------------------------------------------------------NDIKSVKDLD--GKVVAVKSGTGS 142 (247)
T ss_pred --------------------------------------------------------CCCCChHHhC--CCEEEEecCchH
Confidence 3578999996 889999999988
Q ss_pred hHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCc-cEEEeCCcccccceEEEEcCCCc
Q 003275 613 WNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNC-EFRTVGQEFTKSGWGFAFQRDSP 691 (834)
Q Consensus 613 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~-~l~~v~~~~~~~~~~~~~~k~sp 691 (834)
..++... .+..+++.+++..+++++|.+ |++|+++.+.....+++++... ++..++.......+++++++++.
T Consensus 143 ~~~l~~~--~~~~~i~~~~~~~~~~~~L~~----grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ 216 (247)
T PRK09495 143 VDYAKAN--IKTKDLRQFPNIDNAYLELGT----GRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSE 216 (247)
T ss_pred HHHHHhc--CCCCceEEcCCHHHHHHHHHc----CceeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEEEcCcHH
Confidence 8888543 344577788999999999999 9999999998888887766333 57777766666789999999999
Q ss_pred chHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 692 LAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 692 l~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+++.+|++|.++.++|.+++|.+||+.
T Consensus 217 l~~~~n~al~~~~~~g~~~~i~~k~~~ 243 (247)
T PRK09495 217 LREKVNGALKTLKENGTYAEIYKKWFG 243 (247)
T ss_pred HHHHHHHHHHHHHHCCcHHHHHHHHcC
Confidence 999999999999999999999999997
No 78
>cd06369 PBP1_GC_C_enterotoxin_receptor Ligand-binding domain of the membrane guanylyl cyclase C. Ligand-binding domain of the membrane guanylyl cyclase C (GC-C or StaR). StaR is a key receptor for the STa (Escherichia coli Heat Stable enterotoxin), a potent stimulant of intestinal chloride and bicarbonate secretion that cause acute secretory diarrhea. The catalytic domain of the STa/guanylin receptor type membrane GC is highly similar to those of the natriuretic peptide receptor (NPR) type and sensory organ-specific type membrane GCs (GC-D, GC-E and GC-F). The GC-C receptor is mainly expressed in the intestine of most vertebrates, but is also found in the kidney and other organs. Moreover, GC-C is activated by guanylin and uroguanylin, endogenous peptide ligands synthesized in the intestine and kidney. Consequently, the receptor activation results in increased cGMP levels and phosphorylation of the CFTR chloride channel and secretion.
Probab=99.87 E-value=1.5e-20 Score=192.93 Aligned_cols=274 Identities=15% Similarity=0.203 Sum_probs=209.4
Q ss_pred CcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHH------HHcCCeEEEE
Q 003275 4 EVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLV------EYYGWREVIA 77 (834)
Q Consensus 4 ~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll------~~~~W~~v~i 77 (834)
.-.+++||.|...+..|+++...+++|+||.++- .++-...+++-|+.|+....+..+.++. .+++|+.+.
T Consensus 81 ~gcv~lGP~CtYat~~~~~~~~~~~~P~ISaGsf--glscd~k~~LTR~~pparK~~~~~~~f~~~~~~~~~~~W~~ay- 157 (380)
T cd06369 81 LGCVLLGPSCTYATFQMVDDEFNLSLPIISAGSF--GLSCDYKENLTRLLPPARKISDFFVDFWKEKNFPKKPKWETAY- 157 (380)
T ss_pred cCcEEEcCccceehhhhhhhhhcCCCceEecccc--ccCCCchhhhhhcCchHHHHHHHHHHHHhcccccCCCCCceeE-
Confidence 3468999999999999999999999999996653 3333344689999999999999999998 489998765
Q ss_pred EEEcCCccc---chHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 78 IFVDDDYGR---NGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 78 I~~d~~~g~---~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
||.+++-.+ -.+.++....+..+..+.+.+... +.+++...++.++ ..+||||+++++++.+.|+.+ ++
T Consensus 158 vyk~~~~~edCf~~i~al~a~~~~f~~~~~~~~~l~---~~~~~~~il~~~~-~~sRIiImCG~p~~ir~lm~~----~~ 229 (380)
T cd06369 158 VYKKQENTEDCFWYINALEAGVAYFSSALKFKELLR---TEEELQKLLTDKN-RKSNVIIMCGTPEDIVNLKGD----RA 229 (380)
T ss_pred EEcCCCCccceeeEhHhhhhhhhhhhhcccceeeec---CchhHHHHHHHhc-cCccEEEEeCCHHHHHHHHhc----Cc
Confidence 997764211 235555555555555555444443 3478888888876 558999999999999998876 44
Q ss_pred CCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCcc-chhHHHhhHHH
Q 003275 155 TAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFN-SYALYAYDSVW 233 (834)
Q Consensus 155 ~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~-~~~~~~YDav~ 233 (834)
...+|++|..|-.....- .+....++++.|+.+++..|+.+.++++ ..+ ..... .+++..||||.
T Consensus 230 ~~gDYVf~~IDlF~~sy~----~d~~a~~amqsVLvIT~~~p~~~~~~~~-----~~f-----n~~l~~~~aa~fyDaVL 295 (380)
T cd06369 230 VAEDIVIILIDLFNDVYY----ENTTSPPYMRNVLVLTLPPRNSTNNSSF-----TTD-----NSLLKDDYVAAYHDGVL 295 (380)
T ss_pred cCCCEEEEEEecccchhc----cCcchHHHHhceEEEecCCCCCcccccC-----CCC-----CcchHHHHHHHHHHHHH
Confidence 457999999986643321 1235567899999999888866554331 111 22232 88999999999
Q ss_pred HHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEe
Q 003275 234 LVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNI 313 (834)
Q Consensus 234 ~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~ 313 (834)
++|+||++++..+++. .+.++.+.|+|.+|.|++|.+.+|+|||+ ...|.++.+
T Consensus 296 LYa~AL~EtL~~G~~~-------------------------~~~~I~~~m~NrTF~GitG~V~IDeNGDR-d~dfsLl~m 349 (380)
T cd06369 296 LFGHVLKKFLESQEGV-------------------------QTFSFINEFRNISFEGAGGPYTLDEYGDR-DVNFTLLYT 349 (380)
T ss_pred HHHHHHHHHHHhCCCC-------------------------CcHHHHHHHhCcceecCCCceEeCCCCCc-cCceEEEEe
Confidence 9999999999876542 23789999999999999999999999997 599999988
Q ss_pred e--ccceEEEEEecCCC
Q 003275 314 G--GTGSRRIGYWSNYS 328 (834)
Q Consensus 314 ~--~~~~~~vG~w~~~~ 328 (834)
. .++++.||.|+...
T Consensus 350 s~~tg~y~vV~~y~t~~ 366 (380)
T cd06369 350 STDTSKYKVLFEFDTST 366 (380)
T ss_pred eCCCCCeEEEEEEECCC
Confidence 5 36799999998644
No 79
>TIGR03863 PQQ_ABC_bind ABC transporter, substrate binding protein, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are putative substrate-binding proteins of an ABC transporter family that associates, in gene neighborhood and phylogenomic profile, with pyrroloquinoline-quinone (PQQ)-dependent degradation of certain alcohols, such as 2-phenylethanol in Pseudomonas putida U.
Probab=99.86 E-value=5.3e-21 Score=204.78 Aligned_cols=245 Identities=18% Similarity=0.172 Sum_probs=185.8
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
+++|.+|+|+.+|+++.++.+++++.++|+|+++++++.++. ..+||+||+.+++..++.++++++...+.++|++|+.
T Consensus 57 ~~~V~~vvG~~~S~~~~Av~~~a~~~~vp~i~~~a~~~~lt~~~c~~~~Fr~~~~~~~~~~ala~~~~~~g~kkvaii~~ 136 (347)
T TIGR03863 57 AQGVRFFVLDLPAAALLALADAAKAKGALLFNAGAPDDALRGADCRANLLHTLPSRAMLADALAQYLAAKRWRRILLIQG 136 (347)
T ss_pred HCCCCEEEecCChHHHHHHHHHHHhCCcEEEeCCCCChHHhCCCCCCCEEEecCChHhHHHHHHHHHHHcCCCEEEEEeC
Confidence 467999999999999999999999999999999999999987 4579999999999999999999987779999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCC--hHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGAS--RSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~--~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
|++||....+.+.+.+++.|++|+..+.++...+ ..++.......+.+++|+|++.....+....+. +.
T Consensus 137 ~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~~~~~d~s~~~~~~~~s~pDvv~~~~~~~~~~~~~~------~~--- 207 (347)
T TIGR03863 137 PLPADALYADAFRRSAKRFGAKIVAERPFTFSGDPRRTDQSEVPLFTQGADYDVVVVADEAGEFARYLP------YA--- 207 (347)
T ss_pred CCcccHHHHHHHHHHHHHCCCEEEEeEEeccCCchhhhhcccCceeecCCCCCEEEEecchhhHhhhcc------cc---
Confidence 9999999999999999999999999888875432 134442222233488999998755433211110 00
Q ss_pred eEEEEeCCCcccCCCCCCCChhhHhhcccceEEEec-CCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHH
Q 003275 159 YVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHH-TPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAH 237 (834)
Q Consensus 159 ~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~-~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~ 237 (834)
.++ ... .....|+.....+ ..+.+..++|.++|++++ +..|+.+++.+||++++++.
T Consensus 208 -~~~-~~~---------------~~g~~G~~~~~~~~~~~~~~~~~f~~~f~~~~-----g~~p~~~~a~aY~av~~~a~ 265 (347)
T TIGR03863 208 -TWL-PRP---------------VAGSAGLVPTAWHRAWERWGATQLQSRFEKLA-----GRPMTELDYAAWLAVRAVGE 265 (347)
T ss_pred -ccc-ccc---------------cccccCccccccCCcccchhHHHHHHHHHHHh-----CCCCChHHHHHHHHHHHHHH
Confidence 000 000 0111233222111 223466789999999998 45577888999999999999
Q ss_pred HHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhccc--cccee-eEEEcc-CCCCCCC
Q 003275 238 ALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNF--TGLSG-EIRFDA-DKNLVNP 306 (834)
Q Consensus 238 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f--~g~tG-~i~Fd~-~g~~~~~ 306 (834)
|++++.+. +++++.++|+++.+ .+..| +++|++ ||+...+
T Consensus 266 Ai~~AGs~-----------------------------d~~aV~~aL~~~~~~~~~~~g~~~~~R~~Dhq~~~~ 309 (347)
T TIGR03863 266 AVTRTRSA-----------------------------DPATLRDYLLSDEFELAGFKGRPLSFRPWDGQLRQP 309 (347)
T ss_pred HHHHhcCC-----------------------------CHHHHHHHHcCCCceecccCCCcceeeCCCcccccc
Confidence 99997432 68999999999877 47777 699985 8876544
No 80
>cd06339 PBP1_YraM_LppC_lipoprotein_like Periplasmic binding component of lipoprotein LppC, an immunodominant antigen. This subgroup includes periplasmic binding component of lipoprotein LppC, an immunodominant antigen, whose molecular function is not characterized. Members of this subgroup are predicted to be involved in transport of lipid compounds, and they are sequence similar to the family of ABC-type hydrophobic amino acid transporters (HAAT).
Probab=99.86 E-value=6.1e-21 Score=205.67 Aligned_cols=248 Identities=17% Similarity=0.148 Sum_probs=191.8
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
++|.+||||.+|..+.++++++.+.+||+|+++++.+ +.. .|++||+.+++..++.++++++...|+++|++|+.++
T Consensus 58 ~~V~~iiG~~~s~~~~a~~~~~~~~~ip~i~~~~~~~-~~~--~~~~f~~~~~~~~~~~~~~~~~~~~g~k~vaii~~~~ 134 (336)
T cd06339 58 EGADIIVGPLLKENVAALAAAAAELGVPVLALNNDES-VAA--GPNLFYFGLSPEDEARRAAEYARSQGKRRPLVLAPDG 134 (336)
T ss_pred cCCCEEEccCCHHHHHHHHhhhccCCCCEEEccCCcc-ccC--CCCEEEecCChHHHHHHHHHHHHhcCccceEEEecCC
Confidence 5899999999999999999999999999999765443 322 5899999999999999999999888999999999999
Q ss_pred CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC---------------------CceEEEEEeChh-
Q 003275 83 DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM---------------------ESRVFVVHVNPD- 140 (834)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~---------------------~~~vivl~~~~~- 140 (834)
+||+...+.+.+++++.|++|+....++. +..|++.++.+|++. ++|+|++.+.+.
T Consensus 135 ~~g~~~~~~f~~~~~~~G~~vv~~~~~~~--~~~d~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~~~~~~~~ 212 (336)
T cd06339 135 AYGQRVADAFRQAWQQLGGTVVAIESYDP--SPTDLSDAIRRLLGVDDSEQRIAQLKSLESEPRRRQDIDAIDAVALPDG 212 (336)
T ss_pred hHHHHHHHHHHHHHHHcCCceeeeEecCC--CHHHHHHHHHHHhccccchhhhhhhhhcccCccccCCCCcEEEEecChh
Confidence 99999999999999999999999888875 458999999999998 999999988886
Q ss_pred hHHHHHHHHHhCCCCCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCC
Q 003275 141 TGLTIFSVAKSLGMTAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSG 220 (834)
Q Consensus 141 ~~~~i~~~a~~~g~~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~ 220 (834)
.+..+.+++...+.....-.++.++++.... .. ....+..+|++...+.. ....+|.++|++++ +..
T Consensus 213 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~----~~~g~~~~g~~~~~~~~---~~~~~f~~~y~~~~-----~~~ 279 (336)
T cd06339 213 EARLIKPQLLFYYGVPGDVPLYGTSRWYSGT-PA----PLRDPDLNGAWFADPPW---LLDANFELRYRAAY-----GWP 279 (336)
T ss_pred hhhhhcchhhhhccCcCCCCEEEeccccCCC-CC----cccCcccCCcEEeCCCc---ccCcchhhhHHHHh-----cCC
Confidence 6777777766655311123466666554321 11 11124567876554421 12237999999988 445
Q ss_pred c-cchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHH-HhcccccceeeEEEc
Q 003275 221 F-NSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTL-LRMNFTGLSGEIRFD 298 (834)
Q Consensus 221 ~-~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l-~~~~f~g~tG~i~Fd 298 (834)
| +.+++.+|||+.+++.++++... +. +| +...|+|++|+++||
T Consensus 280 p~~~~~a~~YDa~~l~~~~~~~~~~------------------------------~~-----al~~~~~~~g~~G~~~f~ 324 (336)
T cd06339 280 PLSRLAALGYDAYALAAALAQLGQG------------------------------DA-----ALTPGAGFSGVTGVLRLD 324 (336)
T ss_pred CCchHHHHHHhHHHHHHHHHHcccc------------------------------cc-----ccCCCCccccCcceEEEC
Confidence 6 88999999999999887766210 01 22 234689999999999
Q ss_pred cCCCC
Q 003275 299 ADKNL 303 (834)
Q Consensus 299 ~~g~~ 303 (834)
++|+.
T Consensus 325 ~~g~~ 329 (336)
T cd06339 325 PDGVI 329 (336)
T ss_pred CCCeE
Confidence 99874
No 81
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=99.86 E-value=6.7e-21 Score=193.65 Aligned_cols=222 Identities=25% Similarity=0.373 Sum_probs=183.4
Q ss_pred eEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeee
Q 003275 376 LRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITI 455 (834)
Q Consensus 376 lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i 455 (834)
||||+ ...++||.+.+. ++...|+++|+++++++++|++++++.. +|.+++.+|.+|++|+++++++.
T Consensus 1 l~V~~--~~~~~P~~~~~~-~~~~~G~~~dl~~~i~~~~g~~~~~~~~---------~~~~~~~~l~~g~~D~~~~~~~~ 68 (225)
T PF00497_consen 1 LRVGV--DEDYPPFSYIDE-DGEPSGIDVDLLRAIAKRLGIKIEFVPM---------PWSRLLEMLENGKADIIIGGLSI 68 (225)
T ss_dssp EEEEE--ESEBTTTBEEET-TSEEESHHHHHHHHHHHHHTCEEEEEEE---------EGGGHHHHHHTTSSSEEESSEB-
T ss_pred CEEEE--cCCCCCeEEECC-CCCEEEEhHHHHHHHHhhcccccceeec---------ccccccccccccccccccccccc
Confidence 68999 346889999885 7899999999999999999998555543 49999999999999999999999
Q ss_pred ecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcchhhH
Q 003275 456 VTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQLVTI 535 (834)
Q Consensus 456 ~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~ 535 (834)
+++|.+.++||.||+....++++++.....
T Consensus 69 ~~~r~~~~~~s~p~~~~~~~~~~~~~~~~~-------------------------------------------------- 98 (225)
T PF00497_consen 69 TPERAKKFDFSDPYYSSPYVLVVRKGDAPP-------------------------------------------------- 98 (225)
T ss_dssp BHHHHTTEEEESESEEEEEEEEEETTSTCS--------------------------------------------------
T ss_pred cccccccccccccccchhheeeeccccccc--------------------------------------------------
Confidence 999999999999999999999999753110
Q ss_pred HHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCchhhHH
Q 003275 536 FWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSFAWNY 615 (834)
Q Consensus 536 ~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~~~~~ 615 (834)
...+++++||. +.+||+..|+...++
T Consensus 99 ----------------------------------------------------~~~~~~~~dl~--~~~i~~~~g~~~~~~ 124 (225)
T PF00497_consen 99 ----------------------------------------------------IKTIKSLDDLK--GKRIGVVRGSSYADY 124 (225)
T ss_dssp ----------------------------------------------------TSSHSSGGGGT--TSEEEEETTSHHHHH
T ss_pred ----------------------------------------------------cccccchhhhc--CcccccccchhHHHH
Confidence 13677888994 789999999988888
Q ss_pred HHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCcc-EEEeCCcccccceEEEEcCCCc-ch
Q 003275 616 LVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCE-FRTVGQEFTKSGWGFAFQRDSP-LA 693 (834)
Q Consensus 616 l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~-l~~v~~~~~~~~~~~~~~k~sp-l~ 693 (834)
+.+... ...+++.+.+.++++++|.+ |++|+++.+...+.+++++.... ...........++++++.++.+ ++
T Consensus 125 l~~~~~-~~~~~~~~~~~~~~~~~l~~----g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 199 (225)
T PF00497_consen 125 LKQQYP-SNINIVEVDSPEEALEALLS----GRIDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRKKNPELL 199 (225)
T ss_dssp HHHHTH-HTSEEEEESSHHHHHHHHHT----TSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEETTTHHHH
T ss_pred hhhhcc-chhhhcccccHHHHHHHHhc----CCeeeeeccchhhhhhhhhcccccccccccccccceeEEeecccccHHH
Confidence 865331 14667789999999999999 99999999999999998874443 3332455556677777776555 99
Q ss_pred HHHHHHHHhhhccccHHHHHHhhcC
Q 003275 694 IDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 694 ~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+.||++|.++.++|.+++|.+||++
T Consensus 200 ~~~n~~i~~l~~~G~~~~i~~ky~g 224 (225)
T PF00497_consen 200 EIFNKAIRELKQSGEIQKILKKYLG 224 (225)
T ss_dssp HHHHHHHHHHHHTTHHHHHHHHHHS
T ss_pred HHHHHHHHHHHhCcHHHHHHHHHcC
Confidence 9999999999999999999999986
No 82
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.85 E-value=4.8e-20 Score=191.35 Aligned_cols=223 Identities=19% Similarity=0.315 Sum_probs=178.4
Q ss_pred CCCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEee
Q 003275 372 NGMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVG 451 (834)
Q Consensus 372 ~g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~ 451 (834)
..++|+||+ .+.|+||.+.++ ++.+.|+++||++++++.+|.++ ++++ .+|+.++.++..|++|++++
T Consensus 24 ~~~~l~v~~--~~~~pPf~~~~~-~g~~~G~~vdl~~~ia~~lg~~~--~~~~-------~~~~~~~~~l~~g~~Di~~~ 91 (260)
T PRK15010 24 LPETVRIGT--DTTYAPFSSKDA-KGDFVGFDIDLGNEMCKRMQVKC--TWVA-------SDFDALIPSLKAKKIDAIIS 91 (260)
T ss_pred cCCeEEEEe--cCCcCCceeECC-CCCEEeeeHHHHHHHHHHhCCce--EEEe-------CCHHHHHHHHHCCCCCEEEe
Confidence 357899999 446899998764 68999999999999999999884 4444 35999999999999999999
Q ss_pred eeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcc
Q 003275 452 DITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQ 531 (834)
Q Consensus 452 ~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 531 (834)
++..+++|.+.++||.||+.+..++++++...
T Consensus 92 ~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~------------------------------------------------ 123 (260)
T PRK15010 92 SLSITDKRQQEIAFSDKLYAADSRLIAAKGSP------------------------------------------------ 123 (260)
T ss_pred cCcCCHHHHhhcccccceEeccEEEEEECCCC------------------------------------------------
Confidence 99999999999999999999999999887651
Q ss_pred hhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCch
Q 003275 532 LVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSF 611 (834)
Q Consensus 532 ~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~ 611 (834)
...+++||. |++||+..|+.
T Consensus 124 ----------------------------------------------------------~~~~~~dl~--g~~Igv~~gs~ 143 (260)
T PRK15010 124 ----------------------------------------------------------IQPTLDSLK--GKHVGVLQGST 143 (260)
T ss_pred ----------------------------------------------------------CCCChhHcC--CCEEEEecCch
Confidence 123678885 88999999998
Q ss_pred hhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHH-HhhcCCc-cEEEeCCcc-----cccceEE
Q 003275 612 AWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIEL-FMSKTNC-EFRTVGQEF-----TKSGWGF 684 (834)
Q Consensus 612 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~-~~~~~~~-~l~~v~~~~-----~~~~~~~ 684 (834)
...++.........+++.+.+.++++++|.+ |++|+++.+.....+ +..+... ++......+ ...++++
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~----griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 219 (260)
T PRK15010 144 QEAYANETWRSKGVDVVAYANQDLVYSDLAA----GRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGV 219 (260)
T ss_pred HHHHHHHhcccCCceEEecCCHHHHHHHHHc----CCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEE
Confidence 7777754332223456778899999999999 999999998776654 3333222 455554322 2234678
Q ss_pred EEcCCCc-chHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 685 AFQRDSP-LAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 685 ~~~k~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+++++.+ |+..+|++|.++.++|.+++|.+||++
T Consensus 220 a~~~~~~~L~~~ln~~l~~l~~~G~~~~i~~ky~~ 254 (260)
T PRK15010 220 GLRKDDAELTAAFNKALGELRQDGTYDKMAKKYFD 254 (260)
T ss_pred EEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 9998876 999999999999999999999999987
No 83
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.85 E-value=6.3e-20 Score=189.44 Aligned_cols=219 Identities=15% Similarity=0.247 Sum_probs=179.9
Q ss_pred CCCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhC-CCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEe
Q 003275 372 NGMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLL-PYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAV 450 (834)
Q Consensus 372 ~g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l-~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~ 450 (834)
+.++|+||+. .+++||.+.+..++.+.||++|+++++++++ |..+++++.+ -+|.....+|.+|++|+++
T Consensus 36 ~~g~l~vg~~--~~~pP~~~~~~~~g~~~G~~vdl~~~ia~~llg~~~~~~~~~-------~~~~~~~~~l~~g~~D~~~ 106 (259)
T PRK11917 36 SKGQLIVGVK--NDVPHYALLDQATGEIKGFEIDVAKLLAKSILGDDKKIKLVA-------VNAKTRGPLLDNGSVDAVI 106 (259)
T ss_pred hCCEEEEEEC--CCCCCceeeeCCCCceeEeeHHHHHHHHHHhcCCCccEEEEE-------cChhhHHHHHHCCCccEEE
Confidence 4578999994 5688998865336899999999999999994 8666677665 3477778999999999999
Q ss_pred eeeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCc
Q 003275 451 GDITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQ 530 (834)
Q Consensus 451 ~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~ 530 (834)
+++++|++|.+.++||.||+.++..+++++..
T Consensus 107 ~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~------------------------------------------------ 138 (259)
T PRK11917 107 ATFTITPERKRIYNFSEPYYQDAIGLLVLKEK------------------------------------------------ 138 (259)
T ss_pred ecccCChhhhheeeeccCceeeceEEEEECCC------------------------------------------------
Confidence 99999999999999999999999999998765
Q ss_pred chhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCc
Q 003275 531 QLVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGS 610 (834)
Q Consensus 531 ~~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s 610 (834)
.+++++||. |++||+..|+
T Consensus 139 -----------------------------------------------------------~~~s~~dL~--g~~V~v~~gs 157 (259)
T PRK11917 139 -----------------------------------------------------------NYKSLADMK--GANIGVAQAA 157 (259)
T ss_pred -----------------------------------------------------------CCCCHHHhC--CCeEEEecCC
Confidence 477899996 8999999999
Q ss_pred hhhHHHHhhhc--ccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCcccccceEEEEcC
Q 003275 611 FAWNYLVDELK--IAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQEFTKSGWGFAFQR 688 (834)
Q Consensus 611 ~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~k 688 (834)
...+.+.+... ....+++.+++..+.+++|.. |++|+++.+...+..+..+ +..++++.+...+++++++|
T Consensus 158 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~----GrvDa~~~d~~~~~~~~~~---~~~~~~~~~~~~~~~~a~~k 230 (259)
T PRK11917 158 TTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDA----KRVDAFSVDKSILLGYVDD---KSEILPDSFEPQSYGIVTKK 230 (259)
T ss_pred cHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHc----CCCcEEEecHHHHHHhhhc---CCeecCCcCCCCceEEEEeC
Confidence 87766643221 112356678899999999999 9999999998776665554 23566667777889999999
Q ss_pred CCc-chHHHHHHHHhhhccccHHHHHHhhc
Q 003275 689 DSP-LAIDLSTAILQLSENGDLQKIHNKWL 717 (834)
Q Consensus 689 ~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~ 717 (834)
+++ ++..+|+.|.++.. .+++|.+||-
T Consensus 231 ~~~~l~~~ln~~l~~~~~--~~~~i~~kw~ 258 (259)
T PRK11917 231 DDPAFAKYVDDFVKEHKN--EIDALAKKWG 258 (259)
T ss_pred CCHHHHHHHHHHHHHHHH--HHHHHHHHhC
Confidence 988 99999999999864 7999999993
No 84
>PRK11260 cystine transporter subunit; Provisional
Probab=99.85 E-value=5e-20 Score=191.90 Aligned_cols=222 Identities=19% Similarity=0.325 Sum_probs=187.7
Q ss_pred CCCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEee
Q 003275 372 NGMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVG 451 (834)
Q Consensus 372 ~g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~ 451 (834)
..++|+||+. ..++||.+.+. ++.+.|+.+|+++.+++++|.+ +++++ ..|.+++.+|.+|++|++++
T Consensus 39 ~~~~l~v~~~--~~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~--~e~~~-------~~~~~~~~~l~~G~~D~~~~ 106 (266)
T PRK11260 39 ERGTLLVGLE--GTYPPFSFQGE-DGKLTGFEVEFAEALAKHLGVK--ASLKP-------TKWDGMLASLDSKRIDVVIN 106 (266)
T ss_pred cCCeEEEEeC--CCcCCceEECC-CCCEEEehHHHHHHHHHHHCCe--EEEEe-------CCHHHHHHHHhcCCCCEEEe
Confidence 4578999983 46889987664 6889999999999999999988 55554 34999999999999999998
Q ss_pred eeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcc
Q 003275 452 DITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQ 531 (834)
Q Consensus 452 ~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 531 (834)
+++.+++|.+.+.||.||+..+..+++++..
T Consensus 107 ~~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~------------------------------------------------- 137 (266)
T PRK11260 107 QVTISDERKKKYDFSTPYTVSGIQALVKKGN------------------------------------------------- 137 (266)
T ss_pred ccccCHHHHhccccCCceeecceEEEEEcCC-------------------------------------------------
Confidence 8899999999999999999999999887654
Q ss_pred hhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCch
Q 003275 532 LVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSF 611 (834)
Q Consensus 532 ~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~ 611 (834)
...+++++||. ++++|+..|+.
T Consensus 138 --------------------------------------------------------~~~~~~~~dL~--g~~Igv~~G~~ 159 (266)
T PRK11260 138 --------------------------------------------------------EGTIKTAADLK--GKKVGVGLGTN 159 (266)
T ss_pred --------------------------------------------------------cCCCCCHHHcC--CCEEEEecCCc
Confidence 12578889985 88999999998
Q ss_pred hhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCcccccceEEEEcCCCc
Q 003275 612 AWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQEFTKSGWGFAFQRDSP 691 (834)
Q Consensus 612 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~k~sp 691 (834)
...++.+ +.+..++..+++..+++++|.+ |++|+++.+.....+++++..-.+.+....+...+++++++++++
T Consensus 160 ~~~~l~~--~~~~~~i~~~~~~~~~l~~L~~----GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~ 233 (266)
T PRK11260 160 YEQWLRQ--NVQGVDVRTYDDDPTKYQDLRV----GRIDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGVALRKGNP 233 (266)
T ss_pred HHHHHHH--hCCCCceEecCCHHHHHHHHHc----CCCCEEEechHHHHHHHHhCCCcceecCCccccCceEEEEeCCCH
Confidence 8888754 3444677889999999999999 999999999888787777622235555666667789999999988
Q ss_pred -chHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 692 -LAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 692 -l~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+++.+|++|.++.++|.+++|.+||+.
T Consensus 234 ~l~~~ln~~l~~~~~~g~~~~i~~k~~~ 261 (266)
T PRK11260 234 DLLKAVNQAIAEMQKDGTLKALSEKWFG 261 (266)
T ss_pred HHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 999999999999999999999999987
No 85
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=99.84 E-value=1.3e-19 Score=187.06 Aligned_cols=269 Identities=17% Similarity=0.171 Sum_probs=190.2
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC--CCCCceEEccCChHHHHHHHHHHH-HHcCCeEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS--LQYPYFLRTTQSDYYQMHAVADLV-EYYGWREVIAI 78 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~--~~~p~~~r~~ps~~~q~~aia~ll-~~~~W~~v~iI 78 (834)
+++|.+|||.++|.+..++.++.++++-.++.+. ..+ ...|++|-+.....+|...+++++ .++|-+++.+|
T Consensus 66 ~d~V~~ifGc~TSasRKaVlPvvE~~~~LL~Yp~-----~YEG~E~S~nviYtGa~PNQ~~~pl~~~~~~~~G~~r~~lv 140 (363)
T PF13433_consen 66 EDGVRAIFGCYTSASRKAVLPVVERHNALLFYPT-----QYEGFECSPNVIYTGAAPNQQLLPLIDYLLENFGAKRFYLV 140 (363)
T ss_dssp HS---EEEE--SHHHHHHHHHHHHHCT-EEEE-S-------------TTEEE-S--GGGTHHHHHHHHHHHS--SEEEEE
T ss_pred hCCccEEEecchhhhHHHHHHHHHhcCceEEecc-----ccccccCCCceEEcCCCchhhHHHHHHHHHhccCCceEEEe
Confidence 4799999999999999999999999999999632 222 345899999999999999999885 78898999999
Q ss_pred EEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 79 FVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 79 ~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
.+|+.|++.....+++.+++.|++|+.+..+|.+ .+|+..++.+|++.+||+|+-...++....|+++.+++|+...
T Consensus 141 GSdYv~pre~Nri~r~~l~~~GgevvgE~Y~plg--~td~~~ii~~I~~~~Pd~V~stlvG~s~~aF~r~~~~aG~~~~- 217 (363)
T PF13433_consen 141 GSDYVYPRESNRIIRDLLEARGGEVVGERYLPLG--ATDFDPIIAEIKAAKPDFVFSTLVGDSNVAFYRAYAAAGLDPE- 217 (363)
T ss_dssp EESSHHHHHHHHHHHHHHHHTT-EEEEEEEE-S---HHHHHHHHHHHHHHT-SEEEEE--TTCHHHHHHHHHHHH-SSS-
T ss_pred cCCccchHHHHHHHHHHHHHcCCEEEEEEEecCC--chhHHHHHHHHHhhCCCEEEEeCcCCcHHHHHHHHHHcCCCcc-
Confidence 9999999999999999999999999999999965 4999999999999999999999999999999999999998754
Q ss_pred eEEEEeCCCcc-cCCCCCCCChhhHhhcccceEEEecCC--CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHH
Q 003275 159 YVWIATDWLPS-VLDSTEPVDIDTMNLLQGVVALRHHTP--DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLV 235 (834)
Q Consensus 159 ~vwi~~~~~~~-~~~~~~~~~~~~~~~~~Gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~l 235 (834)
..-|.+-.... .+... ..+...|.++..+|.. ++|++++|+++|+++++ ++..++..+..+|.+|+++
T Consensus 218 ~~Pi~S~~~~E~E~~~~------g~~~~~Gh~~~~~YFqsidtp~N~~Fv~~~~~~~g---~~~v~s~~~eaaY~~v~l~ 288 (363)
T PF13433_consen 218 RIPIASLSTSEAELAAM------GAEAAAGHYTSAPYFQSIDTPENQAFVARFRARYG---DDRVTSDPMEAAYFQVHLW 288 (363)
T ss_dssp ---EEESS--HHHHTTS-------HHHHTT-EEEES--TT-SSHHHHHHHHHHHTTS----TT----HHHHHHHHHHHHH
T ss_pred cCeEEEEecCHHHHhhc------ChhhcCCcEEeehhhhhCCcHHHHHHHHHHHHHhC---CCCCCCcHHHHHHHHHHHH
Confidence 34444432221 11111 1257889999998876 68999999999999983 2335677788899999999
Q ss_pred HHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEEeec
Q 003275 236 AHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLNIGG 315 (834)
Q Consensus 236 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~~~~ 315 (834)
|+|++++.+. +.++++++|...+|+++.|.+++|+..+...
T Consensus 289 a~Av~~ags~-----------------------------d~~~vr~al~g~~~~aP~G~v~id~~n~H~~---------- 329 (363)
T PF13433_consen 289 AQAVEKAGSD-----------------------------DPEAVREALAGQSFDAPQGRVRIDPDNHHTW---------- 329 (363)
T ss_dssp HHHHHHHTS-------------------------------HHHHHHHHTT--EEETTEEEEE-TTTSBEE----------
T ss_pred HHHHHHhCCC-----------------------------CHHHHHHHhcCCeecCCCcceEEcCCCCeec----------
Confidence 9999997332 5899999999999999999999998332221
Q ss_pred cceEEEEEecCC
Q 003275 316 TGSRRIGYWSNY 327 (834)
Q Consensus 316 ~~~~~vG~w~~~ 327 (834)
.+..||.++..
T Consensus 330 -l~~rIg~~~~d 340 (363)
T PF13433_consen 330 -LPPRIGRVNAD 340 (363)
T ss_dssp -B--EEEEE-TT
T ss_pred -ccceEEEEcCC
Confidence 34567777653
No 86
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.83 E-value=2e-19 Score=185.08 Aligned_cols=217 Identities=21% Similarity=0.429 Sum_probs=178.1
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
..+|+||+ ...++||.+.+. ++.+.|+++|+++++++.+|++++| +. .+|+.++..+..|++|+++++
T Consensus 20 ~~~l~v~~--~~~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~~~~--~~-------~~~~~~~~~l~~g~~D~~~~~ 87 (243)
T PRK15007 20 AETIRFAT--EASYPPFESIDA-NNQIVGFDVDLAQALCKEIDATCTF--SN-------QAFDSLIPSLKFRRVEAVMAG 87 (243)
T ss_pred CCcEEEEe--CCCCCCceeeCC-CCCEEeeeHHHHHHHHHHhCCcEEE--Ee-------CCHHHHhHHHhCCCcCEEEEc
Confidence 46899999 346889988764 6899999999999999999988544 43 359999999999999999888
Q ss_pred eeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcch
Q 003275 453 ITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQL 532 (834)
Q Consensus 453 ~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 532 (834)
++.+++|.+.++||.||+..+.+++.+..
T Consensus 88 ~~~~~~r~~~~~fs~p~~~~~~~~v~~~~--------------------------------------------------- 116 (243)
T PRK15007 88 MDITPEREKQVLFTTPYYDNSALFVGQQG--------------------------------------------------- 116 (243)
T ss_pred CccCHHHhcccceecCccccceEEEEeCC---------------------------------------------------
Confidence 88999999999999999998877665422
Q ss_pred hhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCchh
Q 003275 533 VTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSFA 612 (834)
Q Consensus 533 ~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~~ 612 (834)
.+++++||. +.+||+..|+..
T Consensus 117 ---------------------------------------------------------~~~~~~dL~--g~~Igv~~g~~~ 137 (243)
T PRK15007 117 ---------------------------------------------------------KYTSVDQLK--GKKVGVQNGTTH 137 (243)
T ss_pred ---------------------------------------------------------CCCCHHHhC--CCeEEEecCcHH
Confidence 356788885 889999999988
Q ss_pred hHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCc-----ccccceEEEEc
Q 003275 613 WNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQE-----FTKSGWGFAFQ 687 (834)
Q Consensus 613 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~-----~~~~~~~~~~~ 687 (834)
.+++.+. .+..+++.+++.++.+++|.+ |++|+++.+...+.+++++ ..++..++.. +...+++++++
T Consensus 138 ~~~l~~~--~~~~~~~~~~~~~~~~~~L~~----grvDa~i~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 (243)
T PRK15007 138 QKFIMDK--HPEITTVPYDSYQNAKLDLQN----GRIDAVFGDTAVVTEWLKD-NPKLAAVGDKVTDKDYFGTGLGIAVR 210 (243)
T ss_pred HHHHHHh--CCCCeEEEcCCHHHHHHHHHc----CCCCEEEeCHHHHHHHHhc-CCCceeecCcccccccCCcceEEEEe
Confidence 8887642 344567778899999999999 9999999998888887766 4445444322 22335789999
Q ss_pred CCCc-chHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 688 RDSP-LAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 688 k~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
++.+ ++..||++|..+.++|.+++|.+||+.
T Consensus 211 ~~~~~l~~~ln~~l~~l~~~g~~~~i~~~w~~ 242 (243)
T PRK15007 211 QGNTELQQKLNTALEKVKKDGTYETIYNKWFQ 242 (243)
T ss_pred CCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 8776 999999999999999999999999985
No 87
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.83 E-value=3.2e-19 Score=184.50 Aligned_cols=219 Identities=22% Similarity=0.429 Sum_probs=182.4
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
++|+|++ ...++||.+.++ ++++.|+++|+++.+++.+|.+ +++++ .+|.+++.++.+|++|++++++
T Consensus 24 ~~l~v~~--~~~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~--~~~~~-------~~~~~~~~~l~~G~~D~~~~~~ 91 (250)
T TIGR01096 24 GSVRIGT--ETGYPPFESKDA-NGKLVGFDVDLAKALCKRMKAK--CKFVE-------QNFDGLIPSLKAKKVDAIMATM 91 (250)
T ss_pred CeEEEEE--CCCCCCceEECC-CCCEEeehHHHHHHHHHHhCCe--EEEEe-------CCHHHHHHHHhCCCcCEEEecC
Confidence 6899999 456889988764 6899999999999999999977 55554 4599999999999999998888
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcchh
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQLV 533 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~ 533 (834)
+.+.+|.+.+.||.|++..+..++++...
T Consensus 92 ~~~~~r~~~~~~s~p~~~~~~~~~~~~~~--------------------------------------------------- 120 (250)
T TIGR01096 92 SITPKRQKQIDFSDPYYATGQGFVVKKGS--------------------------------------------------- 120 (250)
T ss_pred ccCHHHhhccccccchhcCCeEEEEECCC---------------------------------------------------
Confidence 88999999999999999999999988765
Q ss_pred hHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCchhh
Q 003275 534 TIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSFAW 613 (834)
Q Consensus 534 ~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~~~ 613 (834)
+.+.+++||. +.++|+..|+...
T Consensus 121 -------------------------------------------------------~~~~~~~dl~--g~~i~~~~g~~~~ 143 (250)
T TIGR01096 121 -------------------------------------------------------DLAKTLEDLD--GKTVGVQSGTTHE 143 (250)
T ss_pred -------------------------------------------------------CcCCChHHcC--CCEEEEecCchHH
Confidence 2345778885 8899999999888
Q ss_pred HHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCC--ccEEEeCCcccc-----cceEEEE
Q 003275 614 NYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTN--CEFRTVGQEFTK-----SGWGFAF 686 (834)
Q Consensus 614 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~--~~l~~v~~~~~~-----~~~~~~~ 686 (834)
.++.+.... ..+++.+.+.++++++|.+ |++|+++.+...+.+++++.. .++.++...+.. ..+++++
T Consensus 144 ~~l~~~~~~-~~~~~~~~s~~~~~~~L~~----g~vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 218 (250)
T TIGR01096 144 QYLKDYFKP-GVDIVEYDSYDNANMDLKA----GRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGL 218 (250)
T ss_pred HHHHHhccC-CcEEEEcCCHHHHHHHHHc----CCCCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccCCceEEEE
Confidence 888654321 3567788999999999999 999999999998888876622 237666644332 2478999
Q ss_pred cCCCc-chHHHHHHHHhhhccccHHHHHHhhc
Q 003275 687 QRDSP-LAIDLSTAILQLSENGDLQKIHNKWL 717 (834)
Q Consensus 687 ~k~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~ 717 (834)
+++++ |+..+|++|.++.++|.+++|.+||+
T Consensus 219 ~~~~~~l~~~ln~~l~~l~~~g~~~~i~~kw~ 250 (250)
T TIGR01096 219 RKGDTELKAAFNKALAAIRADGTYQKISKKWF 250 (250)
T ss_pred eCCCHHHHHHHHHHHHHHHHCCcHHHHHHhhC
Confidence 99887 99999999999999999999999996
No 88
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.83 E-value=3.4e-19 Score=184.83 Aligned_cols=223 Identities=16% Similarity=0.272 Sum_probs=176.8
Q ss_pred CCCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEee
Q 003275 372 NGMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVG 451 (834)
Q Consensus 372 ~g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~ 451 (834)
...+|+|++ .+.++||.+.++ ++++.|+++||+++++++++.+++++.. .|++++.++.+|++|++++
T Consensus 24 ~~~~l~v~~--~~~~~P~~~~~~-~g~~~G~~vdi~~~ia~~lg~~i~~~~~---------pw~~~~~~l~~g~~D~~~~ 91 (259)
T PRK15437 24 IPQNIRIGT--DPTYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVEN---------PLDALIPSLKAKKIDAIMS 91 (259)
T ss_pred cCCeEEEEe--CCCCCCcceeCC-CCCEEeeeHHHHHHHHHHcCCceEEEeC---------CHHHHHHHHHCCCCCEEEe
Confidence 357899998 445889988764 6889999999999999999988555543 4999999999999999999
Q ss_pred eeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcc
Q 003275 452 DITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQ 531 (834)
Q Consensus 452 ~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 531 (834)
+++.+++|.+.++||.||...+..+++++..
T Consensus 92 ~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~------------------------------------------------- 122 (259)
T PRK15437 92 SLSITEKRQQEIAFTDKLYAADSRLVVAKNS------------------------------------------------- 122 (259)
T ss_pred cCCCCHHHhhhccccchhhcCceEEEEECCC-------------------------------------------------
Confidence 9999999999999999999999999988765
Q ss_pred hhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCch
Q 003275 532 LVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSF 611 (834)
Q Consensus 532 ~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~ 611 (834)
+...+++||. +.+||+..|+.
T Consensus 123 ---------------------------------------------------------~~~~~~~dl~--g~~Igv~~g~~ 143 (259)
T PRK15437 123 ---------------------------------------------------------DIQPTVESLK--GKRVGVLQGTT 143 (259)
T ss_pred ---------------------------------------------------------CCCCChHHhC--CCEEEEecCcH
Confidence 1223678885 88999999998
Q ss_pred hhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHH-HhhcC-CccEEEeC-----CcccccceEE
Q 003275 612 AWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIEL-FMSKT-NCEFRTVG-----QEFTKSGWGF 684 (834)
Q Consensus 612 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~-~~~~~-~~~l~~v~-----~~~~~~~~~~ 684 (834)
...++.........+++.+.+.++.+++|.+ |++|+++.+.....+ ++++. ..++.+.+ +.+...++++
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~----grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i 219 (259)
T PRK15437 144 QETFGNEHWAPKGIEIVSYQGQDNIYSDLTA----GRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGM 219 (259)
T ss_pred HHHHHHhhccccCceEEecCCHHHHHHHHHc----CCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEE
Confidence 8777754322223567788899999999999 999999988766543 33331 12343332 2222345678
Q ss_pred EEcCCCc-chHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 685 AFQRDSP-LAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 685 ~~~k~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+++++.+ +++.+|.+|.++..+|.+++|.+||++
T Consensus 220 a~~~~~~~l~~~~n~~l~~~~~~G~~~~i~~k~~~ 254 (259)
T PRK15437 220 GLRKEDNELREALNKAFAEMRADGTYEKLAKKYFD 254 (259)
T ss_pred EEeCCCHHHHHHHHHHHHHHHHCCcHHHHHHHhcC
Confidence 8887766 999999999999999999999999987
No 89
>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=99.82 E-value=1.1e-18 Score=189.09 Aligned_cols=255 Identities=13% Similarity=0.142 Sum_probs=200.4
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
++|.+|||+.+|..+.++.+++.+.++|+|+++++++.++....|++||+.+++..++..+++++.+.||+++++|+.|+
T Consensus 67 ~~v~avig~~~s~~~~~~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~v~~l~~~~ 146 (336)
T cd06326 67 DKVFALFGYVGTPTTAAALPLLEEAGVPLVGPFTGASSLRDPPDRNVFNVRASYADEIAAIVRHLVTLGLKRIAVFYQDD 146 (336)
T ss_pred cCcEEEEeCCCchhHHHHHHHHHHcCCeEEEecCCcHHhcCCCCCceEEeCCChHHHHHHHHHHHHHhCCceEEEEEecC
Confidence 48999999998888888889999999999998776666654456899999999999999999999999999999999999
Q ss_pred CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEE
Q 003275 83 DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWI 162 (834)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi 162 (834)
.||....+.+.+.+++.|+++.....++.. ..++..++.++++.++++|++..+...+..+++++++.|+..+ .++.
T Consensus 147 ~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~--~~d~~~~~~~l~~~~~dav~~~~~~~~a~~~i~~~~~~G~~~~-~~~~ 223 (336)
T cd06326 147 AFGKDGLAGVEKALAARGLKPVATASYERN--TADVAAAVAQLAAARPQAVIMVGAYKAAAAFIRALRKAGGGAQ-FYNL 223 (336)
T ss_pred cchHHHHHHHHHHHHHcCCCeEEEEeecCC--cccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHhcCCCCc-EEEE
Confidence 999999999999999999998877777744 3689999999999999999999888889999999999998542 2222
Q ss_pred EeCCCcccCCCCCCCChhhHhhcccceEEEec----CCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHH
Q 003275 163 ATDWLPSVLDSTEPVDIDTMNLLQGVVALRHH----TPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~----~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~A 238 (834)
......... .......+|++....+ ....+..+.|.+.|+++++ ..+++.++..+||+++++++|
T Consensus 224 ~~~~~~~~~-------~~~g~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~----~~~~~~~~~~~y~~~~~~~~a 292 (336)
T cd06326 224 SFVGADALA-------RLLGEYARGVIVTQVVPNPWSRTLPIVREYQAAMKAYGP----GAPPSYVSLEGYIAAKVLVEA 292 (336)
T ss_pred eccCHHHHH-------HHhhhhhcceEEEEEecCccccCCHHHHHHHHHHHhhCC----CCCCCeeeehhHHHHHHHHHH
Confidence 211111110 1223456787654321 1236778999999998872 236778888999999999999
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccce-eeEEEcc
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLS-GEIRFDA 299 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~t-G~i~Fd~ 299 (834)
++++... .+++.+.++|+++...... |.+.|++
T Consensus 293 ~~~~g~~----------------------------~~~~~v~~al~~~~~~~~~g~~~~~~~ 326 (336)
T cd06326 293 LRRAGPD----------------------------PTRESLLAALEAMGKFDLGGFRLDFSP 326 (336)
T ss_pred HHHcCCC----------------------------CCHHHHHHHHHhcCCCCCCCeEEecCc
Confidence 9985211 1588999999998765444 5899965
No 90
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein. Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes.
Probab=99.82 E-value=4.7e-19 Score=185.38 Aligned_cols=223 Identities=17% Similarity=0.192 Sum_probs=179.7
Q ss_pred CCCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCC-cCEEEEecCCCCCCCChHHHHHHHHhCcccEEe
Q 003275 372 NGMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYP-VPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAV 450 (834)
Q Consensus 372 ~g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~-~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~ 450 (834)
..+.|+|++. +++||.+.+. ++.+.|+++||++++++.+|.+ +.++. .+|++++..+..|++|+++
T Consensus 31 ~~~~l~v~~~---~~pP~~~~~~-~g~~~G~~~dl~~~i~~~lg~~~~~~~~---------~~w~~~~~~l~~G~~Di~~ 97 (275)
T TIGR02995 31 EQGFARIAIA---NEPPFTYVGA-DGKVSGAAPDVARAIFKRLGIADVNASI---------TEYGALIPGLQAGRFDAIA 97 (275)
T ss_pred hCCcEEEEcc---CCCCceeECC-CCceecchHHHHHHHHHHhCCCceeecc---------CCHHHHHHHHHCCCcCEEe
Confidence 3478999994 4788887654 6788999999999999999975 33333 4599999999999999998
Q ss_pred eeeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCc
Q 003275 451 GDITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQ 530 (834)
Q Consensus 451 ~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~ 530 (834)
++++++++|...++||.||+.+...+++++...
T Consensus 98 ~~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~----------------------------------------------- 130 (275)
T TIGR02995 98 AGLFIKPERCKQVAFTQPILCDAEALLVKKGNP----------------------------------------------- 130 (275)
T ss_pred ecccCCHHHHhccccccceeecceeEEEECCCC-----------------------------------------------
Confidence 889999999999999999999999999887651
Q ss_pred chhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhc-CCCCeeEeeC
Q 003275 531 QLVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLIS-STEPIGVQDG 609 (834)
Q Consensus 531 ~~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~-~~~~v~~~~~ 609 (834)
..+++++||.. .+.+||+..|
T Consensus 131 ----------------------------------------------------------~~i~~~~dl~~~~g~~Igv~~g 152 (275)
T TIGR02995 131 ----------------------------------------------------------KGLKSYKDIAKNPDAKIAAPGG 152 (275)
T ss_pred ----------------------------------------------------------CCCCCHHHhccCCCceEEEeCC
Confidence 24678888853 2678999999
Q ss_pred chhhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCc-cEEEeCCcc-c--ccceEEE
Q 003275 610 SFAWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNC-EFRTVGQEF-T--KSGWGFA 685 (834)
Q Consensus 610 s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~-~l~~v~~~~-~--~~~~~~~ 685 (834)
+...+++.+ .+.+..+++.+++.++.+++|.+ |++|+++.+...+.+++++... ++..+.... . ...++++
T Consensus 153 ~~~~~~l~~-~~~~~~~i~~~~~~~~~i~~L~~----grvDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 (275)
T TIGR02995 153 GTEEKLARE-AGVKREQIIVVPDGQSGLKMVQD----GRADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPVRYYGGAA 227 (275)
T ss_pred cHHHHHHHH-cCCChhhEEEeCCHHHHHHHHHc----CCCCEEecChHHHHHHHHhCCCCCceeecCccCCccccceeEE
Confidence 998888854 34444577788999999999999 9999999999888888765222 444433211 1 1233788
Q ss_pred EcCCCc-chHHHHHHHHhhhccccHHHHHHhhc
Q 003275 686 FQRDSP-LAIDLSTAILQLSENGDLQKIHNKWL 717 (834)
Q Consensus 686 ~~k~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~ 717 (834)
++++++ |.+.||++|.++.++|.+++|.+||-
T Consensus 228 ~~~~~~~l~~~~n~~l~~~~~sG~~~~i~~ky~ 260 (275)
T TIGR02995 228 FRPEDKELRDAFNVELAKLKESGEFAKIIAPYG 260 (275)
T ss_pred ECCCCHHHHHHHHHHHHHHHhChHHHHHHHHhC
Confidence 888776 99999999999999999999999994
No 91
>cd04509 PBP1_ABC_transporter_GCPR_C_like Family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. This CD includes members of the family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. The family C GPCR includes glutamate/glycine-gated ion channels such as the NMDA receptor, G-protein-coupled receptors, metabotropic glutamate, GABA-B, calcium sensing, phermone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. The glutamate receptors that form cation-selective ion channels, iGluR, can be classified into three different subgroups according to their binding-affinity for the agonists NMDA (N-methyl-D-asparate), AMPA (alpha-amino-3-dihydro-5-methyl-3-oxo-4-isoxazolepropionic acid), and kainate. L-glutamate is a major neurotransmitter in the brain of vertebrates and acts th
Probab=99.80 E-value=2e-18 Score=183.63 Aligned_cols=218 Identities=31% Similarity=0.424 Sum_probs=180.6
Q ss_pred CcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 4 EVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 4 ~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
+|.+||||.++..+.+++++++..+||+|++.++++.+.+ ..+|++||+.|++..++.++++++.+++|+++++++.++
T Consensus 67 ~v~~iig~~~~~~~~~~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~v~iv~~~~ 146 (299)
T cd04509 67 GVDALVGPVSSGVALAVAPVAEALKIPLISPGATAPGLTDKKGYPYLFRTGPSDEQQAEALADYIKEYNWKKVAILYDDD 146 (299)
T ss_pred CceEEEcCCCcHHHHHHHHHHhhCCceEEeccCCCcccccccCCCCEEEecCCcHHHHHHHHHHHHHcCCcEEEEEecCc
Confidence 8999999999999999999999999999999888777665 568999999999999999999999999999999999999
Q ss_pred CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEE
Q 003275 83 DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWI 162 (834)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi 162 (834)
.++....+.+.+.+++.|+++.....++... .++...++++++.++++|++++.+..+..+++++++.|+. .++.|+
T Consensus 147 ~~~~~~~~~~~~~~~~~g~~i~~~~~~~~~~--~~~~~~~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~g~~-~~~~~i 223 (299)
T cd04509 147 SYGRGLLEAFKAAFKKKGGTVVGEEYYPLGT--TDFTSLLQKLKAAKPDVIVLCGSGEDAATILKQAAEAGLT-GGYPIL 223 (299)
T ss_pred hHHHHHHHHHHHHHHHcCCEEEEEecCCCCC--ccHHHHHHHHHhcCCCEEEEcccchHHHHHHHHHHHcCCC-CCCcEE
Confidence 9999999999999999999998776666432 6788899999888899999998889999999999999998 788999
Q ss_pred EeCCCcccCCCCCCCChhhHhhcccceEEEecCCCCh--hHHHHH---HHHHhhhcCCCCCCCccchhHHHhhHHHH
Q 003275 163 ATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTD--LKKNFI---SRWKNLKYKENSPSGFNSYALYAYDSVWL 234 (834)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~--~~~~F~---~~~~~~~~~~~~~~~~~~~~~~~YDav~~ 234 (834)
..+.+...... ....+.++|+++..++.+..+ ..+.|. ..+++.+ ...++.+++++||++++
T Consensus 224 ~~~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~yda~~~ 290 (299)
T cd04509 224 GITLGLSDVLL-----EAGGEAAEGVLTGTPYFPGDPPPESFFFVRAAAREKKKY-----EDQPDYFAALAYDAVLL 290 (299)
T ss_pred ecccccCHHHH-----HHhHHhhcCcEEeeccCCCCCChHHHHHHhHHHHHHHHh-----CCCCChhhhhhcceeee
Confidence 98765432111 123467889999888766433 333443 3344443 45688899999999988
No 92
>cd06341 PBP1_ABC_ligand_binding_like_7 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.77 E-value=2e-17 Score=179.65 Aligned_cols=248 Identities=14% Similarity=0.133 Sum_probs=193.6
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
++|.+|||+.+|....++ +++.+.++|+|+++++++.++. .|++|++.+++..++.++++++...+.+++++|+.++
T Consensus 66 ~~V~~iig~~~s~~~~~~-~~~~~~~ip~v~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~i~~~~ 142 (341)
T cd06341 66 DKVVAVVGGSSGAGGSAL-PYLAGAGIPVIGGAGTSAWELT--SPNSFPFSGGTPASLTTWGDFAKDQGGTRAVALVTAL 142 (341)
T ss_pred cCceEEEecccccchhHH-HHHhhcCCceecCCCCCchhhc--CCCeEEecCCCcchhHHHHHHHHHcCCcEEEEEEeCC
Confidence 389999999999888776 8899999999998777766553 5788999999999999999999888899999998776
Q ss_pred C-cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 83 D-YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 83 ~-~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
. ||+...+.+++++++.|++++....++.. ..|+...+.++++.++|+|++......+..+++++++.|+..+. ..
T Consensus 143 ~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~~~~i~~~~pdaV~~~~~~~~a~~~~~~~~~~G~~~~~-~~ 219 (341)
T cd06341 143 SAAVSAAAALLARSLAAAGVSVAGIVVITAT--APDPTPQAQQAAAAGADAIITVLDAAVCASVLKAVRAAGLTPKV-VL 219 (341)
T ss_pred cHHHHHHHHHHHHHHHHcCCccccccccCCC--CCCHHHHHHHHHhcCCCEEEEecChHHHHHHHHHHHHcCCCCCE-EE
Confidence 5 99999999999999999998877666643 37899999999999999999998888999999999999987642 22
Q ss_pred EEeCCCcccCCCCCCCChhhHhhcccceEEEecCC---CChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHHHH
Q 003275 162 IATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTP---DTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVAHA 238 (834)
Q Consensus 162 i~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~---~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la~A 238 (834)
.........+ ....+..+|++...++.| +.|..+.|.+.+++... ..+..++.++..+||+++++++|
T Consensus 220 ~~~~~~~~~~-------~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~~~~--~~~~~~~~~~~~~yda~~~~~~a 290 (341)
T cd06341 220 SGTCYDPALL-------AAPGPALAGVYIAVFYRPFESGTPAVALYLAAMARYAP--QLDPPEQGFALIGYIAADLFLRG 290 (341)
T ss_pred ecCCCCHHHH-------HhcCcccCceEEEeeeccccCCCHHHHHHHHHHHHhCC--CCCCCcchHHHHHHHHHHHHHHH
Confidence 2111111111 122356789888877765 46778888876664331 11246888999999999999999
Q ss_pred HHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHH-HHHHHHhccccccee
Q 003275 239 LDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQ-FLQTLLRMNFTGLSG 293 (834)
Q Consensus 239 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~-l~~~l~~~~f~g~tG 293 (834)
++++... .+++. ++++|+++......|
T Consensus 291 ~~~ag~~----------------------------~~~~~~v~~al~~~~~~~~~g 318 (341)
T cd06341 291 LSGAGGC----------------------------PTRASQFLRALRAVTDYDAGG 318 (341)
T ss_pred HHhcCCC----------------------------CChHHHHHHHhhcCCCCCCCC
Confidence 9995221 13566 999999997665544
No 93
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.77 E-value=7.5e-18 Score=189.11 Aligned_cols=221 Identities=18% Similarity=0.174 Sum_probs=175.2
Q ss_pred CCCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEee
Q 003275 372 NGMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVG 451 (834)
Q Consensus 372 ~g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~ 451 (834)
+.++||||+.. .|+.+.+. .+...||++||++++++.+|.+++++ .. .+|++++.+|.+|++|++++
T Consensus 41 ~~g~LrVg~~~----~P~~~~~~-~~~~~G~~~DLl~~ia~~LGv~~e~v--~~------~~~~~ll~aL~~G~iDi~~~ 107 (482)
T PRK10859 41 ERGELRVGTIN----SPLTYYIG-NDGPTGFEYELAKRFADYLGVKLEIK--VR------DNISQLFDALDKGKADLAAA 107 (482)
T ss_pred hCCEEEEEEec----CCCeeEec-CCCcccHHHHHHHHHHHHhCCcEEEE--ec------CCHHHHHHHHhCCCCCEEec
Confidence 45789999953 23333332 23349999999999999999885444 32 56999999999999999988
Q ss_pred eeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcc
Q 003275 452 DITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQ 531 (834)
Q Consensus 452 ~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 531 (834)
++++|++|.+.++||.||+....++++++..
T Consensus 108 ~lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~------------------------------------------------- 138 (482)
T PRK10859 108 GLTYTPERLKQFRFGPPYYSVSQQLVYRKGQ------------------------------------------------- 138 (482)
T ss_pred cCcCChhhhccCcccCCceeeeEEEEEeCCC-------------------------------------------------
Confidence 9999999999999999999999999988665
Q ss_pred hhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCch
Q 003275 532 LVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSF 611 (834)
Q Consensus 532 ~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~ 611 (834)
+.+++++||. |++|++..|+.
T Consensus 139 ---------------------------------------------------------~~i~~l~dL~--Gk~I~V~~gS~ 159 (482)
T PRK10859 139 ---------------------------------------------------------PRPRSLGDLK--GGTLTVAAGSS 159 (482)
T ss_pred ---------------------------------------------------------CCCCCHHHhC--CCeEEEECCCc
Confidence 3578899996 89999999998
Q ss_pred hhHHHHhhhc-ccccce--EecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCcccccceEEEEcC
Q 003275 612 AWNYLVDELK-IAESRL--VKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQEFTKSGWGFAFQR 688 (834)
Q Consensus 612 ~~~~l~~~~~-~~~~~~--~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~k 688 (834)
....+.+... .+...+ ..+.+.++++++|.+ |++|+++.+...+.+.... ..++.+........+++++++|
T Consensus 160 ~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~----G~iDa~v~d~~~~~~~~~~-~p~l~v~~~l~~~~~~~~av~k 234 (482)
T PRK10859 160 HVETLQELKKKYPELSWEESDDKDSEELLEQVAE----GKIDYTIADSVEISLNQRY-HPELAVAFDLTDEQPVAWALPP 234 (482)
T ss_pred HHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHC----CCCCEEEECcHHHHHHHHh-CCCceeeeecCCCceeEEEEeC
Confidence 8877753211 122222 345789999999999 9999999998766654333 4566665544455678999999
Q ss_pred -CCc-chHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 689 -DSP-LAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 689 -~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+.+ |+..+|++|.++.++|.+++|.+||+.
T Consensus 235 ~~~~~L~~~ln~~L~~i~~~G~l~~L~~kyfg 266 (482)
T PRK10859 235 SGDDSLYAALLDFFNQIKEDGTLARLEEKYFG 266 (482)
T ss_pred CCCHHHHHHHHHHHHHhhcCCHHHHHHHHHhh
Confidence 455 999999999999999999999999998
No 94
>cd06333 PBP1_ABC-type_HAAT_like Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. This subgroup includes the type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. Members of this subgroup are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=99.75 E-value=6.6e-17 Score=173.14 Aligned_cols=218 Identities=17% Similarity=0.249 Sum_probs=173.8
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
++|.+|||+.+|..+.++.+++.+.++|+|+++++++.+. ...+++||+.+++..++..+++++...||++|++++.++
T Consensus 65 ~~v~~vig~~~s~~~~~~~~~~~~~~vP~v~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~vail~~~~ 143 (312)
T cd06333 65 DKVDAIIGPSTTPATMAVAPVAEEAKTPMISLAPAAAIVE-PKRKWVFKTPQNDRLMAEAILADMKKRGVKTVAFIGFSD 143 (312)
T ss_pred CCeEEEECCCCCHHHHHHHHHHHhcCCCEEEccCCccccC-CCCCcEEEcCCCcHHHHHHHHHHHHHcCCCEEEEEecCc
Confidence 4899999999888888888999999999999877655443 356899999999999999999999999999999999999
Q ss_pred CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEE
Q 003275 83 DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWI 162 (834)
Q Consensus 83 ~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi 162 (834)
.+|+...+.+.+.+++.|+++.....++... .++...+.+++..++|+|++......+..+++++++.|+..+ ++
T Consensus 144 ~~~~~~~~~~~~~~~~~G~~v~~~~~~~~~~--~d~~~~~~~l~~~~pdaIi~~~~~~~~~~~~~~l~~~g~~~p--~~- 218 (312)
T cd06333 144 AYGESGLKELKALAPKYGIEVVADERYGRTD--TSVTAQLLKIRAARPDAVLIWGSGTPAALPAKNLRERGYKGP--IY- 218 (312)
T ss_pred HHHHHHHHHHHHHHHHcCCEEEEEEeeCCCC--cCHHHHHHHHHhCCCCEEEEecCCcHHHHHHHHHHHcCCCCC--EE-
Confidence 9999999999999999999998777776433 578889999988889999998888788889999999998653 33
Q ss_pred EeCCCcccCCCCCCCChhhHhhcccceEEEec------CC----CChhHHHHHHHHHhhhcCCCCCCC-ccchhHHHhhH
Q 003275 163 ATDWLPSVLDSTEPVDIDTMNLLQGVVALRHH------TP----DTDLKKNFISRWKNLKYKENSPSG-FNSYALYAYDS 231 (834)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~------~~----~~~~~~~F~~~~~~~~~~~~~~~~-~~~~~~~~YDa 231 (834)
.+++... .+. -+...+..+|++....+ .| .++..++|.++|++++ +.. +..+++.+||+
T Consensus 219 ~~~~~~~-~~~----~~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~f~~~~~~~~-----g~~~~~~~~~~~Yda 288 (312)
T cd06333 219 QTHGVAS-PDF----LRLAGKAAEGAILPAGPVLVADQLPDSDPQKKVALDFVKAYEAKY-----GAGSVSTFGGHAYDA 288 (312)
T ss_pred eecCcCc-HHH----HHHhhHhhcCcEeecccceeeeeCCCCCcchHHHHHHHHHHHHHh-----CCCCCCchhHHHHHH
Confidence 3332221 000 01223567888765422 22 2457899999999988 344 78899999999
Q ss_pred HHHHH
Q 003275 232 VWLVA 236 (834)
Q Consensus 232 v~~la 236 (834)
+++++
T Consensus 289 ~~~~~ 293 (312)
T cd06333 289 LLLLA 293 (312)
T ss_pred HHHHH
Confidence 99999
No 95
>cd06268 PBP1_ABC_transporter_LIVBP_like Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity. Members of this group include ABC
Probab=99.74 E-value=1.1e-16 Score=170.11 Aligned_cols=220 Identities=28% Similarity=0.365 Sum_probs=180.9
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcC-CeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYG-WREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~-W~~v~iI~~ 80 (834)
+++|.+||||.++..+.++.+.+.+.+||+|++.++++.+.+..+|++|++.+++..++.++++++...+ |+++++|+.
T Consensus 64 ~~~v~~iig~~~~~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~ 143 (298)
T cd06268 64 DDGVDAVIGPLSSGVALAAAPVAEEAGVPLISPGATSPALTGKGNPYVFRTAPSDAQQAAALADYLAEKGKVKKVAIIYD 143 (298)
T ss_pred hCCceEEEcCCcchhHHhhHHHHHhCCCcEEccCCCCcccccCCCceEEEcccCcHHHHHHHHHHHHHhcCCCEEEEEEc
Confidence 4579999999999988899999999999999998887766544579999999999999999999998887 999999999
Q ss_pred cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 81 DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 81 d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
+++++....+.+.+++++.|+++.....++.. ..++...+.++++.++++|++.+.+..+..+++++++.|+ ...
T Consensus 144 ~~~~~~~~~~~~~~~~~~~g~~i~~~~~~~~~--~~~~~~~~~~l~~~~~~~vi~~~~~~~~~~~~~~~~~~g~---~~~ 218 (298)
T cd06268 144 DYAYGRGLAAAFREALKKLGGEVVAEETYPPG--ATDFSPLIAKLKAAGPDAVFLAGYGGDAALFLKQAREAGL---KVP 218 (298)
T ss_pred CCchhHHHHHHHHHHHHHcCCEEEEEeccCCC--CccHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCC---CCc
Confidence 99999999999999999999999887777643 2678899999999899999999888899999999999997 345
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCC--ChhHHHHH-HHHHhhhcCCCCCCCccchhHHHhhHHHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPD--TDLKKNFI-SRWKNLKYKENSPSGFNSYALYAYDSVWLVA 236 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~--~~~~~~F~-~~~~~~~~~~~~~~~~~~~~~~~YDav~~la 236 (834)
|+..+........ +...+..+|++...++.+. .+....|. ++|++.+ +..++.++..+||++++++
T Consensus 219 ~~~~~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~y~~~~~~~ 287 (298)
T cd06268 219 IVGGDGAAAPALL-----ELAGDAAEGVLGTTPYAPDDDDPAAAAFFQKAFKAKY-----GRPPDSYAAAAYDAVRLLA 287 (298)
T ss_pred EEecCccCCHHHH-----HhhhHhhCCcEEeccCCCCCCChhhhHHHHHHHHHHh-----CCCcccchHHHHHHHHHHc
Confidence 7776654332111 1223567899988887664 33445565 7777776 5678899999999999998
No 96
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.72 E-value=2e-16 Score=200.17 Aligned_cols=217 Identities=15% Similarity=0.168 Sum_probs=178.3
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
.++|+||+ .+.|+||.+.+. ++++.||++|++++|++++|++ +++++. .+|..+...|.+|++|++.+
T Consensus 301 ~~~l~v~~--~~~~pP~~~~d~-~g~~~G~~~Dll~~i~~~~g~~--~~~v~~------~~~~~~~~~l~~g~~D~i~~- 368 (1197)
T PRK09959 301 HPDLKVLE--NPYSPPYSMTDE-NGSVRGVMGDILNIITLQTGLN--FSPITV------SHNIHAGTQLNPGGWDIIPG- 368 (1197)
T ss_pred CCceEEEc--CCCCCCeeEECC-CCcEeeehHHHHHHHHHHHCCe--EEEEec------CCHHHHHHHHHCCCceEeec-
Confidence 46899998 667999999875 6899999999999999999977 666653 45888999999999998765
Q ss_pred eeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcch
Q 003275 453 ITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQL 532 (834)
Q Consensus 453 ~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 532 (834)
+..+++|.+.++||.||+....++++++...
T Consensus 369 ~~~t~~r~~~~~fs~py~~~~~~~v~~~~~~------------------------------------------------- 399 (1197)
T PRK09959 369 AIYSEDRENNVLFAEAFITTPYVFVMQKAPD------------------------------------------------- 399 (1197)
T ss_pred ccCCccccccceeccccccCCEEEEEecCCC-------------------------------------------------
Confidence 5579999999999999999999999875431
Q ss_pred hhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCchh
Q 003275 533 VTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSFA 612 (834)
Q Consensus 533 ~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~~ 612 (834)
.+. ++. .|++||+..|+..
T Consensus 400 ---------------------------------------------------------~~~---~~~-~g~~vav~~g~~~ 418 (1197)
T PRK09959 400 ---------------------------------------------------------SEQ---TLK-KGMKVAIPYYYEL 418 (1197)
T ss_pred ---------------------------------------------------------Ccc---ccc-cCCEEEEeCCcch
Confidence 111 122 4889999999988
Q ss_pred hHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCc-c-EEEeCCcccccceEEEEcCCC
Q 003275 613 WNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNC-E-FRTVGQEFTKSGWGFAFQRDS 690 (834)
Q Consensus 613 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~-~-l~~v~~~~~~~~~~~~~~k~s 690 (834)
.+++.+. .+..+++.+++.++++++|.+ |++||++.+.....|++++.+. + +......+....++|+++|+.
T Consensus 419 ~~~~~~~--~p~~~~~~~~~~~~~l~av~~----G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~av~k~~ 492 (1197)
T PRK09959 419 HSQLKEM--YPEVEWIKVDNASAAFHKVKE----GELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGE 492 (1197)
T ss_pred HHHHHHH--CCCcEEEEcCCHHHHHHHHHc----CCCCEEehhhHHHHHHHHhcccccceeeecCCCCchheEEeeCCCC
Confidence 8887543 345788999999999999999 9999999999999998876322 2 233334445567899999998
Q ss_pred c-chHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 691 P-LAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 691 p-l~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
| |...+|++|..+.++ .+++|.+||+.
T Consensus 493 ~~L~~~lnk~l~~i~~~-~~~~i~~kW~~ 520 (1197)
T PRK09959 493 PELKDIINKALNAIPPS-EVLRLTEKWIK 520 (1197)
T ss_pred HHHHHHHHHHHHhCCHH-HHHHHHhhccc
Confidence 8 999999999999998 78899999987
No 97
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=99.72 E-value=1.2e-16 Score=163.87 Aligned_cols=209 Identities=17% Similarity=0.190 Sum_probs=156.6
Q ss_pred ceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHH---HHHHhCcccEEee
Q 003275 375 PLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIV---QQVALNKFDAAVG 451 (834)
Q Consensus 375 ~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~---~~l~~g~~D~~~~ 451 (834)
+||||+ .+.|+||.+.+ + .||++||+++|++++|++ +++++ .+|++++ ..|.+|++|+++
T Consensus 1 ~l~vg~--~~~~pPf~~~~---~--~Gfdvdl~~~ia~~lg~~--~~~~~-------~~~~~~~~~~~~L~~g~~Dii~- 63 (246)
T TIGR03870 1 TLRVCA--ATKEAPYSTKD---G--SGFENKIAAALAAAMGRK--VVFVW-------LAKPAIYLVRDGLDKKLCDVVL- 63 (246)
T ss_pred CeEEEe--CCCCCCCccCC---C--CcchHHHHHHHHHHhCCC--eEEEE-------eccchhhHHHHHHhcCCccEEE-
Confidence 489999 56799999864 2 699999999999999988 55544 3477766 699999999998
Q ss_pred eeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcc
Q 003275 452 DITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQ 531 (834)
Q Consensus 452 ~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 531 (834)
+++++++| ++||.||+.++.++++++.+.
T Consensus 64 ~~~~t~~r---~~fS~PY~~~~~~~v~~k~~~------------------------------------------------ 92 (246)
T TIGR03870 64 GLDTGDPR---VLTTKPYYRSSYVFLTRKDRN------------------------------------------------ 92 (246)
T ss_pred eCCCChHH---HhcccCcEEeeeEEEEeCCCC------------------------------------------------
Confidence 48888777 679999999999999997761
Q ss_pred hhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhh--hhcCCC-CeeEee
Q 003275 532 LVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDS--LISSTE-PIGVQD 608 (834)
Q Consensus 532 ~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~d--L~~~~~-~v~~~~ 608 (834)
..+++++| |. |+ +||+..
T Consensus 93 ---------------------------------------------------------~~~~~~~d~~L~--g~~~vgv~~ 113 (246)
T TIGR03870 93 ---------------------------------------------------------LDIKSWNDPRLK--KVSKIGVIF 113 (246)
T ss_pred ---------------------------------------------------------CCCCCccchhhc--cCceEEEec
Confidence 24677654 54 87 999999
Q ss_pred CchhhHHHHhhhccc-----ccceEecC---------CHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccE--EE
Q 003275 609 GSFAWNYLVDELKIA-----ESRLVKLK---------NMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEF--RT 672 (834)
Q Consensus 609 ~s~~~~~l~~~~~~~-----~~~~~~~~---------~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l--~~ 672 (834)
|+..+.++.+..... ...++.+. +.++++++|.. |++||++.+.+.+.+++.+...++ ..
T Consensus 114 gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~----GrvDa~i~~~~~~~~~~~~~~~~~~~~~ 189 (246)
T TIGR03870 114 GSPAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVAT----GKADLAVAFAPEVARYVKASPEPLRMTV 189 (246)
T ss_pred CChHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHc----CCCCEEEeeHHhHHHHHHhCCCCceEEe
Confidence 999998886421110 01122222 35789999999 999999998777777776522223 33
Q ss_pred eCCcc-------c--ccceEEEEcCCCc-chHHHHHHHHhhhccccHHHHHHhh
Q 003275 673 VGQEF-------T--KSGWGFAFQRDSP-LAIDLSTAILQLSENGDLQKIHNKW 716 (834)
Q Consensus 673 v~~~~-------~--~~~~~~~~~k~sp-l~~~~~~~i~~l~e~G~~~~i~~kw 716 (834)
+++.. . ..+++++++|+.+ |++.||++|.+|. |.+++|.++|
T Consensus 190 ~~~~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~~l~--~~~~~i~~~y 241 (246)
T TIGR03870 190 IPDDATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALAKAK--PRIDAILKEE 241 (246)
T ss_pred ccccccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHHHhH--HHHHHHHHHc
Confidence 33221 1 1136899999998 9999999999999 4899999998
No 98
>TIGR02285 conserved hypothetical protein. Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown.
Probab=99.71 E-value=2e-16 Score=164.93 Aligned_cols=230 Identities=13% Similarity=0.159 Sum_probs=165.2
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhC-CCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLL-PYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVG 451 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l-~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~ 451 (834)
.++|++++ ..|+||.+.+. ++...|+..++++++++++ +++++++.. .|++++.++ .|+.|+++.
T Consensus 17 ~~~l~~~~---~~~pPf~~~~~-~~~~~G~~~~i~~~i~~~~~~~~~~~~~~---------pw~r~l~~l-~~~~d~~~~ 82 (268)
T TIGR02285 17 KEAITWIV---NDFPPFFIFSG-PSKGRGVFDVILQEIRRALPQYEHRFVRV---------SFARSLKEL-QGKGGVCTV 82 (268)
T ss_pred cceeEEEe---cccCCeeEeCC-CCCCCChHHHHHHHHHHHcCCCceeEEEC---------CHHHHHHHH-hcCCCeEEe
Confidence 57899988 46888888753 5788999999999999998 877555544 499999999 788888887
Q ss_pred eeeeecCceeeEEecceeee-ceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCc
Q 003275 452 DITIVTNRTKLVDFTQPYME-SGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQ 530 (834)
Q Consensus 452 ~~~i~~~r~~~vdfs~p~~~-~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~ 530 (834)
++++|++|.+.++||.||+. ...++++++......
T Consensus 83 ~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~~-------------------------------------------- 118 (268)
T TIGR02285 83 NLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAGV-------------------------------------------- 118 (268)
T ss_pred eccCCcchhhceeecCCccccCCceEEEccchhhhc--------------------------------------------
Confidence 89999999999999999975 568888876541100
Q ss_pred chhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhc-CCCCeeEeeC
Q 003275 531 QLVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLIS-STEPIGVQDG 609 (834)
Q Consensus 531 ~~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~-~~~~v~~~~~ 609 (834)
..+.....++.+|.+ +++++|+..|
T Consensus 119 ------------------------------------------------------~~~~d~~~~~~~l~~l~g~~vgv~~g 144 (268)
T TIGR02285 119 ------------------------------------------------------RDEQDGDVDLKKLLASKKKRLGVIAS 144 (268)
T ss_pred ------------------------------------------------------cccCCCCccHHHHhcCCCeEEEEecc
Confidence 000010112333321 3678999988
Q ss_pred chhhHHHHh---hhcc-cccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCC---ccEEEeCCcc--ccc
Q 003275 610 SFAWNYLVD---ELKI-AESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTN---CEFRTVGQEF--TKS 680 (834)
Q Consensus 610 s~~~~~l~~---~~~~-~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~---~~l~~v~~~~--~~~ 680 (834)
+.....+.+ ..+. ...++..+.+.++++++|.+ |++|+++.+...+.+++.+.. ..+..+.... ...
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~----GrvD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (268)
T TIGR02285 145 RSYGQQIDDILSDSGYQHNTRIIGNAAMGNLFKMLEK----GRVNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMPAHI 220 (268)
T ss_pred eeccHHHHHHHHhCCcccceeeeccchHHHHHHHHHc----CCccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCccce
Confidence 755333222 1211 11245556778889999999 999999999988888876422 1344443211 223
Q ss_pred ceEEEEcCCC---cchHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 681 GWGFAFQRDS---PLAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 681 ~~~~~~~k~s---pl~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+++++++|+. .+++.||++|.+|.++|.+++|.+||+.
T Consensus 221 ~~~i~~~k~~~~~~l~~~in~~L~~l~~dG~~~~i~~k~~~ 261 (268)
T TIGR02285 221 SVWVACPKTEWGRKVIADIDQALSELNVDPKYYKYFDRWLS 261 (268)
T ss_pred EEEEEeCCCHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhCC
Confidence 5789999974 3999999999999999999999999997
No 99
>PF00060 Lig_chan: Ligand-gated ion channel; InterPro: IPR001320 The ability of synapses to modify their synaptic strength in response to activity is a fundamental property of the nervous system and may be an essential component of learning and memory. There are three classes of ionotropic glutamate receptor, namely NMDA (N-methyl-D-aspartate), AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole-4-propionic acid) and kainate receptors. They are believed to play critical roles in synaptic plasticity. At many synapses in the brain, transient activation of NMDA receptors leads to a persistent modification in the strength of synaptic transmission mediated by AMPA receptors and kainate receptors can act as the induction trigger for long-term changes in synaptic transmission [].; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 3FAT_A 3KFM_A 3KEI_A 3EN3_A 3EPE_B 3FAS_A 2F34_A 3C34_B 3S2V_A 3GBB_B ....
Probab=99.70 E-value=7.9e-19 Score=165.36 Aligned_cols=107 Identities=32% Similarity=0.538 Sum_probs=82.1
Q ss_pred chhhHHHHHHHHHHHHhhhheeecccCCCCCC-------CCCcchhhHHHHHHHHhhccC-CCcccccchhhhHHHHHHH
Q 003275 495 TIPMWLVTGGFFLFVGAVVWILEHRFNNEFRG-------PPSQQLVTIFWFSFSTMFFSH-RENTVSSLGRVVLIVWLFV 566 (834)
Q Consensus 495 ~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~~~~-~~~~~s~~~R~~~~~w~~~ 566 (834)
++++|++++++++++++++|++++..+.+++. ....++.+++|++++++++++ ...|++.++|++.++|+++
T Consensus 1 s~~vW~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~s~s~Ril~~~w~l~ 80 (148)
T PF00060_consen 1 SWSVWLLILLSILLVSLVLWLFERFSPYEWRKNQSSPPRRWRFSLSNSFWYTFGTLLQQGSSIRPRSWSGRILLAFWWLF 80 (148)
T ss_dssp -HHHHHHHHHHHHHHHTTGGGT------------------HHHHHHHHHHHCCCCCHHHHH------HHHHHHHHHHHHH
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccccccCcccHHHHHHHHHHhhccccccccccchHHHHHHHHHHHH
Confidence 57899999999999999999999987766655 223568899999999999664 5689999999999999999
Q ss_pred HHHhhhccccceeeEEEEeecccCCCChhhhhcCC
Q 003275 567 VLIINSSYTASLTSILTVQQLTSQIEGIDSLISST 601 (834)
Q Consensus 567 ~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~ 601 (834)
++++.++|+|+|+|+||.+++.++|+|++||.+++
T Consensus 81 ~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~ 115 (148)
T PF00060_consen 81 SLILIASYTANLTSFLTVPKYEPPIDSLEDLANSG 115 (148)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHTSS-SSHHHHHTHS
T ss_pred HHHHHHHHHHHHHHHhcccCcCCCCCCHHHHHHCC
Confidence 99999999999999999999999999999999765
No 100
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.69 E-value=1.2e-15 Score=160.26 Aligned_cols=226 Identities=22% Similarity=0.296 Sum_probs=180.8
Q ss_pred CCCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEee
Q 003275 372 NGMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVG 451 (834)
Q Consensus 372 ~g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~ 451 (834)
....++|++... ..+||.+.+.+.+.+.||++|+++.+++.++.....++++ ..|++++..|..|++|++++
T Consensus 32 ~~~~~~v~~~~~-~~~p~~~~~~~~~~~~G~dvdl~~~ia~~l~~~~~~~~~~-------~~~~~~~~~l~~g~~D~~~~ 103 (275)
T COG0834 32 ARGKLRVGTEAT-YAPPFEFLDAKGGKLVGFDVDLAKAIAKRLGGDKKVEFVP-------VAWDGLIPALKAGKVDIIIA 103 (275)
T ss_pred hcCeEEEEecCC-CCCCcccccCCCCeEEeeeHHHHHHHHHHhCCcceeEEec-------cchhhhhHHHhcCCcCEEEe
Confidence 357788998532 3458888775235999999999999999998764344443 46999999999999999999
Q ss_pred eeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcc
Q 003275 452 DITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQ 531 (834)
Q Consensus 452 ~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 531 (834)
++++|++|.+.++||.||+..+..+++++...
T Consensus 104 ~~~~t~er~~~~~fs~py~~~~~~~~~~~~~~------------------------------------------------ 135 (275)
T COG0834 104 GMTITPERKKKVDFSDPYYYSGQVLLVKKDSD------------------------------------------------ 135 (275)
T ss_pred ccccCHHHhccccccccccccCeEEEEECCCC------------------------------------------------
Confidence 99999999999999999999999999988771
Q ss_pred hhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCch
Q 003275 532 LVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSF 611 (834)
Q Consensus 532 ~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~ 611 (834)
..+.+++||. ++++|++.|+.
T Consensus 136 ---------------------------------------------------------~~~~~~~DL~--gk~v~v~~gt~ 156 (275)
T COG0834 136 ---------------------------------------------------------IGIKSLEDLK--GKKVGVQLGTT 156 (275)
T ss_pred ---------------------------------------------------------cCcCCHHHhC--CCEEEEEcCcc
Confidence 1378899997 89999999998
Q ss_pred --hhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHH--hhcCCccEEEeCCcccc-cceEEEE
Q 003275 612 --AWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELF--MSKTNCEFRTVGQEFTK-SGWGFAF 686 (834)
Q Consensus 612 --~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~--~~~~~~~l~~v~~~~~~-~~~~~~~ 686 (834)
...... .......++.+++..+.+++|.+ |++|+++.+.+.+.++ ..+.............. .++++++
T Consensus 157 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~al~~----Gr~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (275)
T COG0834 157 DEAEEKAK--KPGPNAKIVAYDSNAEALLALKN----GRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIAL 230 (275)
T ss_pred hhHHHHHh--hccCCceEEeeCCHHHHHHHHHc----CCccEEEcchHhhhhhhhhhcCCCCceeeeccCCCcceeEEEe
Confidence 344332 22234678889999999999999 9999999999988883 33311122333333333 6899999
Q ss_pred cCC--CcchHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 687 QRD--SPLAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 687 ~k~--spl~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+++ ..+++.+|..|.++.++|.+++|.++|+.
T Consensus 231 ~~~~~~~l~~~in~~l~~l~~~G~~~~i~~kw~~ 264 (275)
T COG0834 231 RKGDDPELLEAVNKALKELKADGTLQKISDKWFG 264 (275)
T ss_pred ccCCcHHHHHHHHHHHHHHHhCccHHHHHHHhcC
Confidence 999 46999999999999999999999999997
No 101
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=99.68 E-value=2.5e-15 Score=151.11 Aligned_cols=215 Identities=26% Similarity=0.448 Sum_probs=176.7
Q ss_pred eEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeee
Q 003275 376 LRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITI 455 (834)
Q Consensus 376 lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i 455 (834)
|+|++. +.++||.+.+. ++.+.|++.|+++.+.+++|.+ +++.+ ..|.+++.+|.+|++|++++....
T Consensus 1 l~i~~~--~~~~p~~~~~~-~g~~~G~~~~~~~~~~~~~g~~--~~~~~-------~~~~~~~~~l~~g~~D~~~~~~~~ 68 (218)
T cd00134 1 LTVGTA--GTYPPFSFRDA-NGELTGFDVDLAKAIAKELGVK--VKFVE-------VDWDGLITALKSGKVDLIAAGMTI 68 (218)
T ss_pred CEEecC--CCCCCeeEECC-CCCEEeeeHHHHHHHHHHhCCe--EEEEe-------CCHHHHHHHHhcCCcCEEeecCcC
Confidence 578884 55788888764 7999999999999999999976 55554 239999999999999999987777
Q ss_pred ecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcchhhH
Q 003275 456 VTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQLVTI 535 (834)
Q Consensus 456 ~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~ 535 (834)
+.+|...+.|+.|+.....++++++..
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------------------------- 95 (218)
T cd00134 69 TPERAKQVDFSDPYYKSGQVILVKKGS----------------------------------------------------- 95 (218)
T ss_pred CHHHHhhccCcccceeccEEEEEECCC-----------------------------------------------------
Confidence 888888899999999999999998776
Q ss_pred HHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCchhhHH
Q 003275 536 FWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSFAWNY 615 (834)
Q Consensus 536 ~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~~~~~ 615 (834)
++.+++||. |+++++..|+....+
T Consensus 96 ------------------------------------------------------~~~~~~dl~--g~~i~~~~~~~~~~~ 119 (218)
T cd00134 96 ------------------------------------------------------PIKSVKDLK--GKKVAVQKGSTAEKY 119 (218)
T ss_pred ------------------------------------------------------CCCChHHhC--CCEEEEEcCchHHHH
Confidence 345888885 888999988877777
Q ss_pred HHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCc--ccccceEEEEcCCCc-c
Q 003275 616 LVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQE--FTKSGWGFAFQRDSP-L 692 (834)
Q Consensus 616 l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~--~~~~~~~~~~~k~sp-l 692 (834)
+.+... ...+..+.+.++.+++|.+ |++|+++.+.....++..+..+++.++... .....++++..++++ +
T Consensus 120 ~~~~~~--~~~~~~~~~~~~~~~~l~~----g~~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l 193 (218)
T cd00134 120 LKKALP--EAKVVSYDDNAEALAALEN----GRADAVIVDEIALAALLKKHPPELKIVGPSIDLEPLGFGVAVGKDNKEL 193 (218)
T ss_pred HHHhCC--cccEEEeCCHHHHHHHHHc----CCccEEEeccHHHHHHHHhcCCCcEEeccccCCCccceEEEEcCCCHHH
Confidence 754332 3567778899999999999 999999999888888776633677777653 334456777777774 9
Q ss_pred hHHHHHHHHhhhccccHHHHHHhhc
Q 003275 693 AIDLSTAILQLSENGDLQKIHNKWL 717 (834)
Q Consensus 693 ~~~~~~~i~~l~e~G~~~~i~~kw~ 717 (834)
...++++|..+.++|.++.|.+||+
T Consensus 194 ~~~~~~~l~~~~~~g~~~~i~~~~~ 218 (218)
T cd00134 194 LDAVNKALKELRADGELKKISKKWF 218 (218)
T ss_pred HHHHHHHHHHHHhCccHHHHHHhhC
Confidence 9999999999999999999999996
No 102
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.67 E-value=3.4e-15 Score=150.07 Aligned_cols=216 Identities=25% Similarity=0.458 Sum_probs=180.0
Q ss_pred ceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeee
Q 003275 375 PLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDIT 454 (834)
Q Consensus 375 ~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~ 454 (834)
+|+||+. ..++||...+. ++...|+++|+++.+.+.+|++ +++.+ .+|..++.++.+|++|++++...
T Consensus 1 ~l~v~~~--~~~~p~~~~~~-~g~~~G~~~~~~~~~~~~~g~~--~~~~~-------~~~~~~~~~l~~g~~D~~~~~~~ 68 (219)
T smart00062 1 TLRVGTN--GDYPPFSFADE-DGELTGFDVDLAKAIAKELGLK--VEFVE-------VSFDNLLTALKSGKIDVVAAGMT 68 (219)
T ss_pred CEEEEec--CCCCCcEEECC-CCCcccchHHHHHHHHHHhCCe--EEEEe-------ccHHHHHHHHHCCcccEEecccc
Confidence 4889994 56888888764 6789999999999999999976 55555 35999999999999999998777
Q ss_pred eecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcchhh
Q 003275 455 IVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQLVT 534 (834)
Q Consensus 455 i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~ 534 (834)
.+.+|...+.++.|+.....++++++..
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------------------------------- 96 (219)
T smart00062 69 ITPERAKQVDFSDPYYKSGQVILVRKDS---------------------------------------------------- 96 (219)
T ss_pred CCHHHHhheeeccceeeceeEEEEecCC----------------------------------------------------
Confidence 7788888899999999999999887665
Q ss_pred HHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCchhhH
Q 003275 535 IFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSFAWN 614 (834)
Q Consensus 535 ~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~~~~ 614 (834)
++++++||. |+++++..|+....
T Consensus 97 -------------------------------------------------------~~~~~~dL~--g~~i~~~~g~~~~~ 119 (219)
T smart00062 97 -------------------------------------------------------PIKSLEDLK--GKKVAVVAGTTGEE 119 (219)
T ss_pred -------------------------------------------------------CCCChHHhC--CCEEEEecCccHHH
Confidence 578899995 88999999888777
Q ss_pred HHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCC-ccEEEeCCcccc-cceEEEEcCCCc-
Q 003275 615 YLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTN-CEFRTVGQEFTK-SGWGFAFQRDSP- 691 (834)
Q Consensus 615 ~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~-~~l~~v~~~~~~-~~~~~~~~k~sp- 691 (834)
++... ....++..+.+..+.+.+|.+ |++|+++...+...+...+.. .++.++...... ..++++++++++
T Consensus 120 ~~~~~--~~~~~~~~~~~~~~~~~~l~~----g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 (219)
T smart00062 120 LLKKL--YPEAKIVSYDSQAEALAALKA----GRADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFAVRKGDPE 193 (219)
T ss_pred HHHHh--CCCceEEEcCCHHHHHHHhhc----CcccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEEEECCCHH
Confidence 77543 233567778889999999998 999999999888887776622 567777665555 778999999987
Q ss_pred chHHHHHHHHhhhccccHHHHHHhhc
Q 003275 692 LAIDLSTAILQLSENGDLQKIHNKWL 717 (834)
Q Consensus 692 l~~~~~~~i~~l~e~G~~~~i~~kw~ 717 (834)
+.+.+++.|..+.++|.+++|.++|+
T Consensus 194 ~~~~~~~~l~~~~~~~~~~~i~~~~~ 219 (219)
T smart00062 194 LLDKINKALKELKADGTLKKIYEKWF 219 (219)
T ss_pred HHHHHHHHHHHHHhCchHHHHHhccC
Confidence 99999999999999999999999985
No 103
>TIGR03871 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein. This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme.
Probab=99.67 E-value=3e-15 Score=152.86 Aligned_cols=212 Identities=15% Similarity=0.176 Sum_probs=158.6
Q ss_pred ceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeee
Q 003275 375 PLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDIT 454 (834)
Q Consensus 375 ~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~ 454 (834)
.||||+ .+.|+||.+. ...||++||++++++++|.+++++..+ ..+..++..+.+|++|++++
T Consensus 1 ~l~v~~--~~~~~P~~~~-----~~~G~~~el~~~i~~~~g~~i~~~~~~-------~~~~~~~~~l~~g~~Di~~~--- 63 (232)
T TIGR03871 1 ALRVCA--DPNNLPFSNE-----KGEGFENKIAQLLADDLGLPLEYTWFP-------QRRGFVRNTLNAGRCDVVIG--- 63 (232)
T ss_pred CeEEEe--CCCCCCccCC-----CCCchHHHHHHHHHHHcCCceEEEecC-------cchhhHHHHHhcCCccEEEe---
Confidence 378998 5668898763 236999999999999999986666554 12444577899999999876
Q ss_pred eecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcchhh
Q 003275 455 IVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQLVT 534 (834)
Q Consensus 455 i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~ 534 (834)
+++|.+.++||.||...+.++++++...
T Consensus 64 -~~~r~~~~~fs~py~~~~~~lv~~~~~~--------------------------------------------------- 91 (232)
T TIGR03871 64 -VPAGYEMVLTTRPYYRSTYVFVTRKDSL--------------------------------------------------- 91 (232)
T ss_pred -ccCccccccccCCcEeeeEEEEEeCCCc---------------------------------------------------
Confidence 4678888999999999999999987751
Q ss_pred HHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCchhhH
Q 003275 535 IFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSFAWN 614 (834)
Q Consensus 535 ~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~~~~ 614 (834)
..+++++|+...+.+||+..|+...+
T Consensus 92 ------------------------------------------------------~~~~~~~d~~l~g~~V~v~~g~~~~~ 117 (232)
T TIGR03871 92 ------------------------------------------------------LDVKSLDDPRLKKLRIGVFAGTPPAH 117 (232)
T ss_pred ------------------------------------------------------ccccchhhhhhcCCeEEEEcCChHHH
Confidence 25678887322478999999998888
Q ss_pred HHHhhhcccccceE---------ecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCcc------cc
Q 003275 615 YLVDELKIAESRLV---------KLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQEF------TK 679 (834)
Q Consensus 615 ~l~~~~~~~~~~~~---------~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~------~~ 679 (834)
++.+. +.. .++. ...+..+.+.+|.. |++|+++.+.....+++++.+.++.+..... ..
T Consensus 118 ~l~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~----G~~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (232)
T TIGR03871 118 WLARH-GLV-ENVVGYSLFGDYRPESPPGRMVEDLAA----GEIDVAIVWGPIAGYFAKQAGPPLVVVPLLPEDGGIPFD 191 (232)
T ss_pred HHHhc-Ccc-cccccccccccccccCCHHHHHHHHHc----CCcCEEEeccHHHHHHHHhCCCCceeeccccCCCCCCcc
Confidence 88542 221 1211 13477899999999 9999999998888777765333444433211 22
Q ss_pred cceEEEEcCCCc-chHHHHHHHHhhhccccHHHHHHhhc
Q 003275 680 SGWGFAFQRDSP-LAIDLSTAILQLSENGDLQKIHNKWL 717 (834)
Q Consensus 680 ~~~~~~~~k~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~ 717 (834)
.+++++++++.+ ++..||.+|.++. |.+++|.+||.
T Consensus 192 ~~~~~~~~~~~~~l~~~~n~~l~~~~--~~~~~i~~kyg 228 (232)
T TIGR03871 192 YRIAMGVRKGDKAWKDELNAVLDRRQ--AEIDAILREYG 228 (232)
T ss_pred ceEEEEEecCCHHHHHHHHHHHHHHH--HHHHHHHHHcC
Confidence 357888998877 9999999999985 47999999994
No 104
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.67 E-value=1.4e-15 Score=192.35 Aligned_cols=222 Identities=13% Similarity=0.107 Sum_probs=182.0
Q ss_pred CCCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEee
Q 003275 372 NGMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVG 451 (834)
Q Consensus 372 ~g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~ 451 (834)
+.++|+||+ .++++|+.+..+.++++.||.+|+++.+++.+|.+ ++++++ .+|++++.+|.+|++|++.+
T Consensus 54 ~~~~l~vgv--~~~~~p~~~~~~~~g~~~G~~~D~l~~ia~~lG~~--~e~v~~------~~~~~~l~~l~~g~iDl~~~ 123 (1197)
T PRK09959 54 SKKNLVIAV--HKSQTATLLHTDSQQRVRGINADYLNLLKRALNIK--LTLREY------ADHQKAMDALEEGEVDIVLS 123 (1197)
T ss_pred hCCeEEEEe--cCCCCCCceeecCCCccceecHHHHHHHHHhcCCc--eEEEeC------CCHHHHHHHHHcCCCcEecC
Confidence 457899999 44565544432237899999999999999999977 777663 47999999999999999999
Q ss_pred eeeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcc
Q 003275 452 DITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQ 531 (834)
Q Consensus 452 ~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~ 531 (834)
.++.+++|.+.++||.||+....++++++..
T Consensus 124 ~~~~~~~r~~~~~fs~py~~~~~~~v~~~~~------------------------------------------------- 154 (1197)
T PRK09959 124 HLVASPPLNDDIAATKPLIITFPALVTTLHD------------------------------------------------- 154 (1197)
T ss_pred ccccccccccchhcCCCccCCCceEEEeCCC-------------------------------------------------
Confidence 8999999999999999999999999998755
Q ss_pred hhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCch
Q 003275 532 LVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSF 611 (834)
Q Consensus 532 ~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~ 611 (834)
.+++++++. +.++++..|+.
T Consensus 155 ----------------------------------------------------------~~~~~~~l~--~~~i~~~~g~~ 174 (1197)
T PRK09959 155 ----------------------------------------------------------SMRPLTSSK--PVNIARVANYP 174 (1197)
T ss_pred ----------------------------------------------------------CCCCccccc--CeEEEEeCCCC
Confidence 345556664 77899999998
Q ss_pred hhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCc-cEEEeCCc-ccccceEEEEcCC
Q 003275 612 AWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNC-EFRTVGQE-FTKSGWGFAFQRD 689 (834)
Q Consensus 612 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~-~l~~v~~~-~~~~~~~~~~~k~ 689 (834)
..+++++. .+..+++.|++..+++++|.. |++||++++...+.+++++... ++.+++.. .......++++|+
T Consensus 175 ~~~~~~~~--~p~~~i~~~~s~~~al~av~~----G~~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 248 (1197)
T PRK09959 175 PDEVIHQS--FPKATIISFTNLYQALASVSA----GQNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKE 248 (1197)
T ss_pred CHHHHHHh--CCCCEEEeCCCHHHHHHHHHc----CCCCEEEccHHHHHHHHhcccccceEEEeeccCCCCceeEEEcCC
Confidence 88888653 466889999999999999999 9999999999999998876322 45555422 2233466888999
Q ss_pred Cc-chHHHHHHHHhhhccccHHHHHHhhcCC
Q 003275 690 SP-LAIDLSTAILQLSENGDLQKIHNKWLTY 719 (834)
Q Consensus 690 sp-l~~~~~~~i~~l~e~G~~~~i~~kw~~~ 719 (834)
.| |...+|++|..+.++|.. +|.+||+..
T Consensus 249 ~~~L~~~lnkal~~i~~~~~~-~i~~kW~~~ 278 (1197)
T PRK09959 249 SVILNEVLNRFVDALTNEVRY-EVSQNWLDT 278 (1197)
T ss_pred cHHHHHHHHHHHHhCCHHHHH-HHHHhccCC
Confidence 88 899999999999999987 999999974
No 105
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.38 E-value=2.4e-12 Score=118.84 Aligned_cols=123 Identities=34% Similarity=0.524 Sum_probs=106.7
Q ss_pred CCCChhhhhcC-CCCeeEeeCchhhHHHHhhhccc------c---cceEecCCHHHHHHHHhcCCCCCceEEEEechhhH
Q 003275 590 QIEGIDSLISS-TEPIGVQDGSFAWNYLVDELKIA------E---SRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYI 659 (834)
Q Consensus 590 ~i~s~~dL~~~-~~~v~~~~~s~~~~~l~~~~~~~------~---~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~ 659 (834)
+|++++||..+ +.+||++.|++.+.++.+..... . .+++.|++..+++.+|.. |+ ||++.+.+.+
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~----g~-da~v~d~~~~ 75 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRV----SN-YAFLMESTYL 75 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHc----CC-CEEEeehHhH
Confidence 47899999843 36899999999999986532210 0 256778999999999999 89 9999999999
Q ss_pred HHHhhcCCccEEEeCCcccccceEEEEcCCCcchHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 660 ELFMSKTNCEFRTVGQEFTKSGWGFAFQRDSPLAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 660 ~~~~~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
.++..+ .|++.+++..+...+++++++|+++|++.+|.+|.++.++|.+++|.++|+.
T Consensus 76 ~~~~~~-~~~~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~G~~~~l~~kw~~ 133 (134)
T smart00079 76 DYELSQ-NCDLMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELQKLENKWWK 133 (134)
T ss_pred HHHHhC-CCCeEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhcCcHHHHHHhhcc
Confidence 998887 7999999988888899999999999999999999999999999999999985
No 106
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=99.33 E-value=1.7e-11 Score=123.03 Aligned_cols=220 Identities=17% Similarity=0.136 Sum_probs=175.3
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
.+.|||++.+. |..+... ++...|+++++.+++++.||.+ .+..+. .+-+.++.+|.+|++|++..+
T Consensus 22 rGvLrV~tins----p~sy~~~-~~~p~G~eYelak~Fa~yLgV~--Lki~~~------~n~dqLf~aL~ng~~DL~Aag 88 (473)
T COG4623 22 RGVLRVSTINS----PLSYFED-KGGPTGLEYELAKAFADYLGVK--LKIIPA------DNIDQLFDALDNGNADLAAAG 88 (473)
T ss_pred cCeEEEEeecC----ccceecc-CCCccchhHHHHHHHHHHhCCe--EEEEec------CCHHHHHHHHhCCCcceeccc
Confidence 46899999755 3333332 5667799999999999999966 666663 457999999999999999999
Q ss_pred eeeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcch
Q 003275 453 ITIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQL 532 (834)
Q Consensus 453 ~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 532 (834)
+...++|.+.+.....|+...+.+|.++..
T Consensus 89 l~~~~~~l~~~~~gP~y~svs~qlVyRkG~-------------------------------------------------- 118 (473)
T COG4623 89 LLYNSERLKNFQPGPTYYSVSQQLVYRKGQ-------------------------------------------------- 118 (473)
T ss_pred ccCChhHhcccCCCCceecccHHHHhhcCC--------------------------------------------------
Confidence 999999999999999999999999888877
Q ss_pred hhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCchh
Q 003275 533 VTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSFA 612 (834)
Q Consensus 533 ~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~~ 612 (834)
...+++++|. +..+.+..|+..
T Consensus 119 --------------------------------------------------------~Rp~~l~~L~--g~~i~v~~gs~~ 140 (473)
T COG4623 119 --------------------------------------------------------YRPRSLGQLK--GRQITVAKGSAH 140 (473)
T ss_pred --------------------------------------------------------CCCCCHHHcc--CceeeccCCcHH
Confidence 3456778886 777888888876
Q ss_pred hHHHHhhhc-ccccceEec---CCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCcccccceEEEEcC
Q 003275 613 WNYLVDELK-IAESRLVKL---KNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQEFTKSGWGFAFQR 688 (834)
Q Consensus 613 ~~~l~~~~~-~~~~~~~~~---~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~k 688 (834)
.+.+..... .-+..+... ...+|.++.+.. |.++..+.+.+.+..+.+- ++++.+.-..-...+.++++|.
T Consensus 141 ~~~l~~lk~~kyP~l~~k~d~~~~~~dLle~v~~----Gkldytiads~~is~~q~i-~P~laVafd~tde~~v~Wy~~~ 215 (473)
T COG4623 141 VEDLKLLKETKYPELIWKVDDKLGVEDLLEMVAE----GKLDYTIADSVEISLFQRV-HPELAVAFDLTDEQPVAWYLPR 215 (473)
T ss_pred HHHHHHHHHhhcchhhhhhcccccHHHHHHHHhc----CCcceeeeccHHHHHHHHh-CccceeeeecccccCceeeccC
Confidence 655532111 111222222 367899999999 9999999999888877555 7788877766667899999999
Q ss_pred CCc--chHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 689 DSP--LAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 689 ~sp--l~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+.. |...++..+..+.|.|.++++++||++
T Consensus 216 ~dd~tL~a~ll~F~~~~~e~g~larleeky~g 247 (473)
T COG4623 216 DDDSTLSAALLDFLNEAKEDGLLARLEEKYLG 247 (473)
T ss_pred CchHHHHHHHHHHHHHhhcchHHHHHHHHHhc
Confidence 654 999999999999999999999999997
No 107
>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=99.19 E-value=4.5e-10 Score=116.72 Aligned_cols=203 Identities=25% Similarity=0.343 Sum_probs=151.8
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
+++.+|||+.++.....+...+...++|+|++.+..+... .+++++++.+++..++.++++++.+.+|+++++++.+.
T Consensus 57 ~~~d~ii~~~~~~~~~~~~~~~~~~~ip~v~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~i~~~~ 134 (269)
T cd01391 57 QGVDGIIGPPSSSSALAVVELAAAAGIPVVSLDATAPDLT--GYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDD 134 (269)
T ss_pred cCCCEEEecCCCHHHHHHHHHHHHcCCcEEEecCCCCccC--CCceEEEEcCCcHHHHHHHHHHHHHhCCceEEEEecCC
Confidence 4789999999888777688889999999999877765554 57899999999999999999999999999999999877
Q ss_pred -CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC-CceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 83 -DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM-ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 83 -~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~-~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
.++....+.+.+++++.|.++......+.. .+.++......+++. ++++|++.++ ..+..+++++.+.|+.+.++.
T Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~i~~~~~-~~a~~~~~~~~~~g~~~~~~~ 212 (269)
T cd01391 135 GAYGRERLEGFKAALKKAGIEVVAIEYGDLD-TEKGFQALLQLLKAAPKPDAIFACND-EMAAGALKAAREAGLTPGDIS 212 (269)
T ss_pred cchhhHHHHHHHHHHHhcCcEEEeccccCCC-ccccHHHHHHHHhcCCCCCEEEEcCc-hHHHHHHHHHHHcCCCCCCCE
Confidence 677888999999999999877654444422 225677777777776 6888888777 889999999999998755677
Q ss_pred EEEeCCCcccCCCCCCCChhhHhhcccceEEEecCCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHH
Q 003275 161 WIATDWLPSVLDSTEPVDIDTMNLLQGVVALRHHTPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWL 234 (834)
Q Consensus 161 wi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~ 234 (834)
|+..+....... .......++.++....+..+. ..++.+...+||++.+
T Consensus 213 ii~~~~~~~~~~-------~~~~~~~~~~ti~~~~~~~~~------------------~~~~~~~~~~~~a~~~ 261 (269)
T cd01391 213 IIGFDGSPAALL-------AAGEAGPGLTTVAQPFPGDDP------------------DQPDYPAALGYDAVLL 261 (269)
T ss_pred EEeccccccccc-------ccccccceEEecccCCCCCCC------------------CCCCccccceeeeeee
Confidence 777765543321 011233455555554443322 2345566677887765
No 108
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=98.98 E-value=8.1e-09 Score=106.88 Aligned_cols=199 Identities=16% Similarity=0.147 Sum_probs=139.9
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
.+|+||+ .+.+.|+. +.+...++.+.+++++|.++ ++... .+|+.++..+..|++|+++.+.
T Consensus 32 ~~l~vg~--~~~~~~~~--------~~~~~~~l~~~l~~~~g~~v--~~~~~------~~~~~~~~~l~~g~~Di~~~~~ 93 (254)
T TIGR01098 32 KELNFGI--LPGENASN--------LTRRWEPLADYLEKKLGIKV--QLFVA------TDYSAVIEAMRFGRVDIAWFGP 93 (254)
T ss_pred CceEEEE--CCCCCHHH--------HHHHHHHHHHHHHHHhCCcE--EEEeC------CCHHHHHHHHHcCCccEEEECc
Confidence 5799999 34444432 23456799999999999874 44432 5699999999999999998665
Q ss_pred eeec---CceeeEEecceeeec------eEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCC
Q 003275 454 TIVT---NRTKLVDFTQPYMES------GLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEF 524 (834)
Q Consensus 454 ~i~~---~r~~~vdfs~p~~~~------~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~ 524 (834)
.... +|....+|+.||... ...+++++..
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~------------------------------------------ 131 (254)
T TIGR01098 94 SSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADS------------------------------------------ 131 (254)
T ss_pred HHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCC------------------------------------------
Confidence 4332 566667788876543 2355555443
Q ss_pred CCCCCcchhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCe
Q 003275 525 RGPPSQQLVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPI 604 (834)
Q Consensus 525 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v 604 (834)
+|++++||. |++|
T Consensus 132 -----------------------------------------------------------------~i~~~~dL~--gk~I 144 (254)
T TIGR01098 132 -----------------------------------------------------------------PIKSLKDLK--GKTF 144 (254)
T ss_pred -----------------------------------------------------------------CCCChHHhc--CCEE
Confidence 688999995 8889
Q ss_pred eEee-Cchh-----hHHHHhhhcccc----cceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCC---ccEE
Q 003275 605 GVQD-GSFA-----WNYLVDELKIAE----SRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTN---CEFR 671 (834)
Q Consensus 605 ~~~~-~s~~-----~~~l~~~~~~~~----~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~---~~l~ 671 (834)
++.. ++.. ..++.+..+.+. .++....+..+.+++|.+ |++|+.+.+.+....+.++.. .++.
T Consensus 145 ~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~----G~~Da~~~~~~~~~~~~~~~~~~~~~~~ 220 (254)
T TIGR01098 145 AFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVAN----GKVDAATNNSSAIGRLKKRGPSDMKKVR 220 (254)
T ss_pred EeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHc----CCCCeEEecHHHHHHHHHhCccchhheE
Confidence 9874 3321 233433333221 345556667889999999 999999999888877665522 2578
Q ss_pred EeCCcccccceEEEEcCC-Cc-chHHHHHHHHhh
Q 003275 672 TVGQEFTKSGWGFAFQRD-SP-LAIDLSTAILQL 703 (834)
Q Consensus 672 ~v~~~~~~~~~~~~~~k~-sp-l~~~~~~~i~~l 703 (834)
++.+.....+++++++|+ .+ +++.+|++|..+
T Consensus 221 ~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 221 VIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred EEEecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 887666666789999999 44 999999999764
No 109
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.80 E-value=3.2e-08 Score=103.29 Aligned_cols=164 Identities=20% Similarity=0.221 Sum_probs=131.8
Q ss_pred CChHHHHHHHHhCcccEEeeeeeeecCceeeEEecce--eeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHH
Q 003275 432 PIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQP--YMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFV 509 (834)
Q Consensus 432 ~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p--~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~ 509 (834)
.+|.++...|.+|++|+++++..++.+|.+.++|+.| |....+++++|...
T Consensus 51 ~~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~--------------------------- 103 (287)
T PRK00489 51 LRPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDS--------------------------- 103 (287)
T ss_pred ECcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCC---------------------------
Confidence 4589999999999999999999999999888999988 77778888888765
Q ss_pred HhhhheeecccCCCCCCCCCcchhhHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeeccc
Q 003275 510 GAVVWILEHRFNNEFRGPPSQQLVTIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTS 589 (834)
Q Consensus 510 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~ 589 (834)
T Consensus 104 -------------------------------------------------------------------------------- 103 (287)
T PRK00489 104 -------------------------------------------------------------------------------- 103 (287)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCChhhhhcCCCCeeEeeCchhhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCcc
Q 003275 590 QIEGIDSLISSTEPIGVQDGSFAWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCE 669 (834)
Q Consensus 590 ~i~s~~dL~~~~~~v~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~ 669 (834)
++++++||. |+++++..+.....++.+ .+.. .+++.+.+..|. ++.. |..|++++.......+.+. +
T Consensus 104 ~i~sl~DL~--Gk~ia~~~~~~~~~~l~~-~gi~-~~iv~~~gs~ea--a~~~----G~aDaivd~~~~~~~l~~~---~ 170 (287)
T PRK00489 104 DWQGVEDLA--GKRIATSYPNLTRRYLAE-KGID-AEVVELSGAVEV--APRL----GLADAIVDVVSTGTTLRAN---G 170 (287)
T ss_pred CCCChHHhC--CCEEEEcCcHHHHHHHHH-cCCc-eEEEECCCchhh--hhcC----CcccEEEeeHHHHHHHHHC---C
Confidence 678899996 889999888888888854 3442 456667666664 5555 8999999887777665543 4
Q ss_pred EEEeCCcccccceEEEEcC--CCc-chHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 670 FRTVGQEFTKSGWGFAFQR--DSP-LAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 670 l~~v~~~~~~~~~~~~~~k--~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+.++ +.+.....+++.+| .+| ..+.+|..+.++ .|.+..+.+||+.
T Consensus 171 L~~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~g~l~a~~~k~~~ 219 (287)
T PRK00489 171 LKIV-EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--QGVLRARESKYLM 219 (287)
T ss_pred CEEE-EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--HHHHHhhceEEEE
Confidence 6666 45566678999998 666 888999999999 5999999999997
No 110
>PF10613 Lig_chan-Glu_bd: Ligated ion channel L-glutamate- and glycine-binding site; InterPro: IPR019594 This entry, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine [, ]. It is found in association with IPR001320 from INTERPRO. ; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 4E0W_A 3S9E_A 3QXM_B 2F34_A 3C34_B 3S2V_A 3GBB_B 2F36_D 4E0X_A 1TXF_A ....
Probab=98.71 E-value=8.7e-09 Score=78.62 Aligned_cols=47 Identities=21% Similarity=0.460 Sum_probs=37.2
Q ss_pred CCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCC-----CCCCChHHHHHHHHh
Q 003275 395 SPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNG-----KRNPIYNDIVQQVAL 443 (834)
Q Consensus 395 ~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~-----~~n~s~~~~~~~l~~ 443 (834)
++.++.|||+||+++|++.+||+ |++....++ ++|++|+|++++|.+
T Consensus 14 g~~~~eGyciDll~~la~~l~F~--y~i~~~~Dg~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 14 GNDRYEGYCIDLLEELAEELNFT--YEIYLVPDGKYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp GGGGEESHHHHHHHHHHHHHT-E--EEEEE-TTS--EEBETTSEBEHHHHHHHT
T ss_pred CCccEEEEHHHHHHHHHHHcCCe--EEEEECCCCCCcCcCCCCcCcCHHHHhcC
Confidence 46789999999999999999999 555544443 368999999999874
No 111
>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown.; PDB: 3CKM_A.
Probab=98.59 E-value=1.9e-06 Score=97.30 Aligned_cols=252 Identities=15% Similarity=0.209 Sum_probs=134.1
Q ss_pred CCCcEEEECCCChhhHHHHHHhhcc--CCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNE--LNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIF 79 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~--~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~ 79 (834)
.+|+..||||..=.....++..... ..||++.....+.. .. -+.++...-+....+..+|+.+..-|+++..+|+
T Consensus 276 ~~ga~~ViGPL~k~~V~~l~~~~~~~~~~vp~LaLN~~~~~-~~--~~~l~~f~LspEdEA~q~A~~a~~~g~~~alvl~ 352 (536)
T PF04348_consen 276 ADGADFVIGPLLKSNVEALAQLPQLQAQPVPVLALNQPDNS-QA--PPNLYQFGLSPEDEARQAAQKAFQDGYRRALVLA 352 (536)
T ss_dssp HTT--EEE---SHHHHHHHHH-GG-GGTT-EEEES---TT-------TTEEE----HHHHHHHHHHHHHHTT--S-EEEE
T ss_pred HcCCCEEEcCCCHHHHHHHHhcCcccccCCceeeccCCCcc-cC--ccceEEEeCCcHHHHHHHHHHHHhcCCCCEEEEc
Confidence 3689999999988888777766543 58999998665543 11 2455666666677789999999999999999999
Q ss_pred EcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 80 VDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 80 ~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
.++++|....+.|.+.+++.|+.+.....+. ...++...++.-.+...|.|++.+.+..++.|-....-. . ..+-
T Consensus 353 p~~~~g~R~~~aF~~~W~~~gg~~~~~~~~~---~~~~~~~~i~~r~r~d~D~ifl~a~~~~ar~ikP~l~~~-~-a~~l 427 (536)
T PF04348_consen 353 PQNAWGQRMAEAFNQQWQALGGQVAEVSYYG---SPADLQAAIQPRRRQDIDAIFLVANPEQARLIKPQLDFH-F-AGDL 427 (536)
T ss_dssp ESSHHHHHHHHHHHHHHHHHHSS--EEEEES---STTHHHHHHHHS--TT--EEEE---HHHHHHHHHHHTT--T--TT-
T ss_pred CCChHHHHHHHHHHHHHHHcCCCceeeEecC---CHHHHHHHHhhcCCCCCCEEEEeCCHHHHHHHhhhcccc-c-CCCC
Confidence 9999999999999999999988876666665 236888888866667789999999999888877665421 1 1122
Q ss_pred EEEEeCCCcccCCCCCCCChhhHhhcccceEEEe-c--CCCChhHHHHHHHHHhhhcCCCCCCCccchhHHHhhHHHHHH
Q 003275 160 VWIATDWLPSVLDSTEPVDIDTMNLLQGVVALRH-H--TPDTDLKKNFISRWKNLKYKENSPSGFNSYALYAYDSVWLVA 236 (834)
Q Consensus 160 vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~~-~--~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~YDav~~la 236 (834)
-.+.++..... ..++.....++|+..+.. + .+..+..+.+...|.... .......+.+|||..++.
T Consensus 428 PvyatS~~~~g-----~~~~~~~~dL~gv~f~d~Pwll~~~~~~~~~~~~~~~~~~------~~~~RL~AlG~DA~~L~~ 496 (536)
T PF04348_consen 428 PVYATSRSYSG-----SPNPSQDRDLNGVRFSDMPWLLDPNSPLRQQLAALWPNAS------NSLQRLYALGIDAYRLAP 496 (536)
T ss_dssp EEEE-GGG--H-----HT-HHHHHHTTT-EEEE-GGGG---SHHHHHHH-HHTTT-------HHHHHHHHHHHHHHHHHH
T ss_pred CEEEeccccCC-----CCCcchhhhhcCCEEeccccccCCCchHHHHHHhhccCCc------cHHHHHHHHHHHHHHHHH
Confidence 22233221111 112455678899988753 2 223333344444443211 111223345566543332
Q ss_pred HHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceeeEEEccCCCCCCCcEEEEE
Q 003275 237 HALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGEIRFDADKNLVNPAYDVLN 312 (834)
Q Consensus 237 ~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~i~Fd~~g~~~~~~~~I~~ 312 (834)
+ +. -++.+....+.|.||.+++|++|. +.-...-..
T Consensus 497 ~-l~--------------------------------------~l~~~~~~~~~G~TG~L~~~~~g~-i~R~l~wa~ 532 (536)
T PF04348_consen 497 R-LP--------------------------------------QLRQFPGYRLDGLTGQLSLDEDGR-IERQLSWAQ 532 (536)
T ss_dssp T-HH--------------------------------------HHHHSTT--EEETTEEEEE-TT-B-EEEE-EEEE
T ss_pred H-HH--------------------------------------HHhhCCCCcccCCceeEEECCCCe-EEEeeccee
Confidence 1 11 123334456899999999999885 434333333
No 112
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=98.19 E-value=2.4e-05 Score=82.50 Aligned_cols=116 Identities=17% Similarity=0.213 Sum_probs=75.3
Q ss_pred CCCChhhhhcCCCCeeEe-eCchhhH-----HHHhhhccccc---ceEecC-CHHHHHHHHhcCCCCCceEEEEechhhH
Q 003275 590 QIEGIDSLISSTEPIGVQ-DGSFAWN-----YLVDELKIAES---RLVKLK-NMEEYSIALARGPKGGGVAAIVDELPYI 659 (834)
Q Consensus 590 ~i~s~~dL~~~~~~v~~~-~~s~~~~-----~l~~~~~~~~~---~~~~~~-~~~~~~~~l~~~~~~g~~~a~~~~~~~~ 659 (834)
+|++++||. |++|++. .++.... .+.+..+.... ..+.+. +..+.+++|.. |++|+.+.+.+.+
T Consensus 126 ~i~sl~DL~--Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~----G~vDa~~~~~~~~ 199 (288)
T TIGR03431 126 PIKSLEDLK--GKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVAN----GTVDAATTNDENL 199 (288)
T ss_pred CCCcHHHhC--CCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHc----CCCCeEeccHHHH
Confidence 689999995 8889986 3432221 22222232211 123444 67889999999 9999999988877
Q ss_pred HHHhhcCC----ccEEEeCCcccccceEEEEcCCC-c-chHHHHHHHHhhhccccHHH
Q 003275 660 ELFMSKTN----CEFRTVGQEFTKSGWGFAFQRDS-P-LAIDLSTAILQLSENGDLQK 711 (834)
Q Consensus 660 ~~~~~~~~----~~l~~v~~~~~~~~~~~~~~k~s-p-l~~~~~~~i~~l~e~G~~~~ 711 (834)
..+..+.. .++.++...-.....+++++++. + +.+.++++|..+.+++..+.
T Consensus 200 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~~ 257 (288)
T TIGR03431 200 DRMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKTDKACF 257 (288)
T ss_pred HHHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCCcHHHH
Confidence 77665322 12444432111224578889984 3 99999999999999966544
No 113
>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=97.75 E-value=0.00029 Score=72.86 Aligned_cols=153 Identities=12% Similarity=0.039 Sum_probs=107.4
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
+++.+||+...+.........+...++|+|.+.+..+. .+++++...++...+..+++.+...|-+++++|..+.
T Consensus 54 ~~~d~ii~~~~~~~~~~~~~~l~~~~ip~v~~~~~~~~-----~~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~ 128 (264)
T cd01537 54 RGVDGIIIAPSDLTAPTIVKLARKAGIPVVLVDRDIPD-----GDRVPSVGSDNEQAGYLAGEHLAEKGHRRIALLAGPL 128 (264)
T ss_pred cCCCEEEEecCCCcchhHHHHhhhcCCCEEEeccCCCC-----CcccceEecCcHHHHHHHHHHHHHhcCCcEEEEECCC
Confidence 46788887766655544567888899999998765543 2566778888888899999999888899999998654
Q ss_pred C--cccchHHHHHHHHhcCC-cEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCCCCC
Q 003275 83 D--YGRNGISVLGDALSKKR-AKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g-~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~~~ 157 (834)
. ++....+.+.+.+++.| ..+....... .+..+....+.++.+.. +++++.. +...+..+++++.+.|+..+
T Consensus 129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~~~~~~g~~i~ 205 (264)
T cd01537 129 GSSTARERVAGFKDALKEAGPIEIVLVQEGD--WDAEKGYQAAEELLTAHPDPTAIFAA-NDDMALGALRALREAGLRVP 205 (264)
T ss_pred CCCcHHHHHHHHHHHHHHcCCcChhhhccCC--CCHHHHHHHHHHHHhcCCCCCEEEEc-CcHHHHHHHHHHHHhCCCCC
Confidence 4 66667899999998887 4433222222 23456667777777666 4555544 33567778899999998654
Q ss_pred CeEEEE
Q 003275 158 SYVWIA 163 (834)
Q Consensus 158 ~~vwi~ 163 (834)
+.+-++
T Consensus 206 ~~i~i~ 211 (264)
T cd01537 206 DDISVI 211 (264)
T ss_pred CCeEEE
Confidence 444444
No 114
>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=97.63 E-value=0.00053 Score=70.95 Aligned_cols=154 Identities=11% Similarity=-0.002 Sum_probs=102.9
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
+++.+||....+..+.. ...+...++|+|.+....+. +.+.....++...+..+++.+...|.+++++++.+.
T Consensus 54 ~~~d~iii~~~~~~~~~-~~~~~~~~ipvv~~~~~~~~------~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~ 126 (264)
T cd06267 54 RRVDGIILAPSRLDDEL-LEELAALGIPVVLVDRPLDG------LGVDSVGIDNRAGAYLAVEHLIELGHRRIAFIGGPP 126 (264)
T ss_pred cCcCEEEEecCCcchHH-HHHHHHcCCCEEEecccccC------CCCCEEeeccHHHHHHHHHHHHHCCCceEEEecCCC
Confidence 46777777666655555 66788999999998665432 344556677777788888888777999999998654
Q ss_pred C--cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 83 D--YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
. ++....+.+.+.+++.|..+.....+....+..+....+.++.... +++|+. .+...+..+++++++.|+..++
T Consensus 127 ~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~-~~~~~a~~~~~al~~~g~~~~~ 205 (264)
T cd06267 127 DLSTARERLEGYREALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIFA-ANDLMAIGALRALRELGLRVPE 205 (264)
T ss_pred ccchHHHHHHHHHHHHHHcCCCCCcceEEecccchhhHHHHHHHHHhcCCCCcEEEE-cCcHHHHHHHHHHHHhCCCCCC
Confidence 3 6667788899999888853322222222222355566677666555 555554 3455677888888998986444
Q ss_pred eEEEEe
Q 003275 159 YVWIAT 164 (834)
Q Consensus 159 ~vwi~~ 164 (834)
.+.+.+
T Consensus 206 ~i~i~~ 211 (264)
T cd06267 206 DVSVVG 211 (264)
T ss_pred ceEEEe
Confidence 444443
No 115
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=97.57 E-value=0.002 Score=66.80 Aligned_cols=146 Identities=12% Similarity=0.048 Sum_probs=97.8
Q ss_pred CCcEEEECCCCh-hhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEE
Q 003275 3 NEVVAAIGPQSS-GIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIF 79 (834)
Q Consensus 3 ~~V~aiiGp~~S-~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~ 79 (834)
.++.+||+...+ .....+...+...++|+|......+. .+.+....+++...+..+++.+... |-+++++|+
T Consensus 54 ~~vdgvi~~~~~~~~~~~~~~~l~~~~ip~V~~~~~~~~-----~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~ 128 (267)
T cd01536 54 QGVDGIIISPVDSAALTPALKKANAAGIPVVTVDSDIDG-----GNRLAYVGTDNYEAGRLAGEYLAKLLGGKGKVAIIE 128 (267)
T ss_pred cCCCEEEEeCCCchhHHHHHHHHHHCCCcEEEecCCCCc-----cceeEEEecCHHHHHHHHHHHHHHHhCCCceEEEEE
Confidence 367777754333 33334556677789999987654432 2345566777777788888888666 889999998
Q ss_pred EcC--CcccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHhhcCCceE-EEEEeChhhHHHHHHHHHhCCCC
Q 003275 80 VDD--DYGRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGANLMESRV-FVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 80 ~d~--~~g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~v-ivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
.++ .++....+.+.+++++. |.++....... .+..+....+.++.+..+++ .++.++...+..+++++++.|+.
T Consensus 129 ~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~i~~~~d~~a~~~~~~l~~~g~~ 206 (267)
T cd01536 129 GPPGSSNAQERVKGFRDALKEYPDIEIVAVQDGN--WDREKALQAMEDLLQANPDIDAIFAANDSMALGAVAALKAAGRK 206 (267)
T ss_pred cccccchHHHHHHHHHHHHHhCCCcEEEEEecCC--CcHHHHHHHHHHHHHhCCCccEEEEecCCchHHHHHHHHhcCCC
Confidence 654 47777889999999998 46655432222 23355667777776555433 23334446778899999999875
No 116
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=97.32 E-value=0.0024 Score=68.19 Aligned_cols=111 Identities=16% Similarity=0.181 Sum_probs=64.0
Q ss_pred CCCChhhhhcCCCCeeEeeCchhhHHHHh---hhcccccce-EecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhc
Q 003275 590 QIEGIDSLISSTEPIGVQDGSFAWNYLVD---ELKIAESRL-VKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSK 665 (834)
Q Consensus 590 ~i~s~~dL~~~~~~v~~~~~s~~~~~l~~---~~~~~~~~~-~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~ 665 (834)
+|++++||. |++|++..|+..+.++.. ..+.+...+ ..+.+..+..+++.+ |++|+++...++......+
T Consensus 120 ~i~s~~dL~--Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~----G~vDa~~~~ep~~~~~~~~ 193 (314)
T PRK11553 120 PIKTVADLK--GHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQ----GNVDAWAIWDPYYSAALLQ 193 (314)
T ss_pred CCCCHHHhC--CCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHc----CCCCEEEEcCcHHHHHHhc
Confidence 678999997 888999888766655433 223332222 234466788899998 9999998887877665554
Q ss_pred CCccEEEeCCcccccceEEEEcCCC--cchHHHHHHHHhhhcc
Q 003275 666 TNCEFRTVGQEFTKSGWGFAFQRDS--PLAIDLSTAILQLSEN 706 (834)
Q Consensus 666 ~~~~l~~v~~~~~~~~~~~~~~k~s--pl~~~~~~~i~~l~e~ 706 (834)
..-++...++.+...+..++..+.. ...+.+++.+..+.+.
T Consensus 194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~~l~a~~~A 236 (314)
T PRK11553 194 GGVRVLKDGTDLNQTGSFYLAARPYAEKNGAFIQQVLATLTEA 236 (314)
T ss_pred CCcEEeecCcccCcCceEEEEcHHHHHHCHHHHHHHHHHHHHH
Confidence 2223333333333233233333221 1444555555554444
No 117
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=97.26 E-value=0.003 Score=64.70 Aligned_cols=122 Identities=20% Similarity=0.210 Sum_probs=75.8
Q ss_pred cCCCChhhhhcCCCCeeEeeCchh-----hHHHH-hhhcccc---cceEecCCHHHHHHHHhcCCCCCceEEEEechhhH
Q 003275 589 SQIEGIDSLISSTEPIGVQDGSFA-----WNYLV-DELKIAE---SRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYI 659 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v~~~~~s~~-----~~~l~-~~~~~~~---~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~ 659 (834)
.+|++++||. |+++++...+.. ..... +..+++. -..+...+.+..+.+|.+ |++|+.+.....+
T Consensus 95 s~i~~l~dL~--Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~----G~~Da~~~~~~~~ 168 (243)
T PF12974_consen 95 SPITSLADLK--GKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLN----GKADAAAIPSDAF 168 (243)
T ss_dssp SS--SHHHHG--GSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHT----TSSSEEEEEHHHH
T ss_pred CCCCChhhcC--CCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHc----CCccEEEEechhH
Confidence 4799999996 889998754422 22222 2334442 133455688899999999 9999998887777
Q ss_pred HHHhhcC---CccEEEeCCcccccceEEEEcCCCc--chHHHHHHHHhhhccccHHHHHHhh
Q 003275 660 ELFMSKT---NCEFRTVGQEFTKSGWGFAFQRDSP--LAIDLSTAILQLSENGDLQKIHNKW 716 (834)
Q Consensus 660 ~~~~~~~---~~~l~~v~~~~~~~~~~~~~~k~sp--l~~~~~~~i~~l~e~G~~~~i~~kw 716 (834)
+.+...+ ..+++++...-......++..++-| .++.+-.+++.+..+..-.++.+.+
T Consensus 169 ~~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~~~~~~~l~~~ 230 (243)
T PF12974_consen 169 ERLEAEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKDPEGKAILDAF 230 (243)
T ss_dssp HHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSSHHHHHHHHHT
T ss_pred HHHHHccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCChhhHHHHHhc
Confidence 7665542 1257777644333456677777766 8999999999999865555555544
No 118
>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=97.16 E-value=0.009 Score=62.25 Aligned_cols=146 Identities=12% Similarity=0.026 Sum_probs=96.2
Q ss_pred CCcEEEECCCChhh-HHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEE
Q 003275 3 NEVVAAIGPQSSGI-AHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIF 79 (834)
Q Consensus 3 ~~V~aiiGp~~S~~-~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~ 79 (834)
++|.+||....+.. .......+...++|+|......+ . +.+.+..+++...+..+++.+... |-+++++|.
T Consensus 59 ~~vdgiIi~~~~~~~~~~~l~~~~~~~iPvv~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~ 132 (272)
T cd06300 59 QGVDAIIINPASPTALNPVIEEACEAGIPVVSFDGTVT---T---PCAYNVNEDQAEFGKQGAEWLVKELGGKGNVLVVR 132 (272)
T ss_pred cCCCEEEEeCCChhhhHHHHHHHHHCCCeEEEEecCCC---C---CceeEecCCHHHHHHHHHHHHHHHcCCCceEEEEE
Confidence 47778887544433 23345667778999998754321 1 446678888888888899888665 778999997
Q ss_pred Ec--CCcccchHHHHHHHHhcCC-cEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 80 VD--DDYGRNGISVLGDALSKKR-AKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 80 ~d--~~~g~~~~~~l~~~l~~~g-~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
.+ ...+....+.+.+++++++ +.+...... ..+..+....+.++.+..+++-.+.+..+.+..+++++++.|+..
T Consensus 133 ~~~~~~~~~~R~~g~~~a~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~l~~~~~~~~i~~~~d~A~g~~~al~~~g~~~ 210 (272)
T cd06300 133 GLAGHPVDEDRYAGAKEVLKEYPGIKIVGEVYG--DWDQAVAQKAVADFLASNPDVDGIWTQGGDAVGAVQAFEQAGRDI 210 (272)
T ss_pred CCCCCcchHHHHHHHHHHHHHCCCcEEEeecCC--CCCHHHHHHHHHHHHHhCCCcCEEEecCCCcHHHHHHHHHcCCCC
Confidence 43 3345667788999999887 776532222 223355566777776555443333333222888999999999844
No 119
>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=97.05 E-value=0.0077 Score=62.44 Aligned_cols=151 Identities=13% Similarity=0.095 Sum_probs=94.7
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc-
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD- 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d- 81 (834)
+++.+||....+.........+...++|+|......+ ..++++ ..++...+..+++.+...|.+++++|..+
T Consensus 54 ~~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~~~~~~----~~~~~v---~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~ 126 (266)
T cd06282 54 QRVDGLILTVADAATSPALDLLDAERVPYVLAYNDPQ----PGRPSV---SVDNRAAARDVAQALAALGHRRIAMLAGRL 126 (266)
T ss_pred cCCCEEEEecCCCCchHHHHHHhhCCCCEEEEeccCC----CCCCEE---eeCcHHHHHHHHHHHHHcCcccEEEecccc
Confidence 4677777533333223355677888999988754322 233433 35667778888888887899999999743
Q ss_pred --CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHh-hcC-CceEEEEEeChhhHHHHHHHHHhCCCCCC
Q 003275 82 --DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGA-NLM-ESRVFVVHVNPDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 82 --~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l-~~~-~~~vivl~~~~~~~~~i~~~a~~~g~~~~ 157 (834)
++++....+.+.++++++|+.+......+ .+..+....+.++ ++. .+++|+. ++...+..+++++++.|+..+
T Consensus 127 ~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~~p 203 (266)
T cd06282 127 AASDRARQRYAGYRAAMRAAGLAPLPPVEIP--FNTAALPSALLALLTAHPAPTAIFC-SNDLLALAVIRALRRLGLRVP 203 (266)
T ss_pred ccCchHHHHHHHHHHHHHHcCCCCCccccCC--CcHHHHHHHHHHHhcCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCC
Confidence 34566778999999999987643322222 1222233344443 333 3566555 556667889999999998654
Q ss_pred CeEEEE
Q 003275 158 SYVWIA 163 (834)
Q Consensus 158 ~~vwi~ 163 (834)
+-+-+.
T Consensus 204 ~di~v~ 209 (266)
T cd06282 204 DDLSVV 209 (266)
T ss_pred CceEEE
Confidence 444333
No 120
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=97.05 E-value=0.0089 Score=63.38 Aligned_cols=70 Identities=20% Similarity=0.172 Sum_probs=48.4
Q ss_pred cCCCChhhhhcCCCCeeEeeCchhhHHHHh---hhccccc--ceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHh
Q 003275 589 SQIEGIDSLISSTEPIGVQDGSFAWNYLVD---ELKIAES--RLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFM 663 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v~~~~~s~~~~~l~~---~~~~~~~--~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~ 663 (834)
..|++++||. |++||+..++..+.++.. ..+++.. +++.+ +..+...++.+ |++|+++...++.....
T Consensus 90 s~I~s~~DLk--GK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~----G~vDa~~~~~p~~~~~~ 162 (300)
T TIGR01729 90 SGIEKPEDLK--GKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNL-KPPQIVAAWQR----GDIDAAYVWPPALSELL 162 (300)
T ss_pred CCCCChhHcC--CCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEec-CcHHHHHHHHc----CCcCEEEEecHHHHHHH
Confidence 3689999997 999999877655443322 2344322 23333 56788999998 99999998888776555
Q ss_pred hc
Q 003275 664 SK 665 (834)
Q Consensus 664 ~~ 665 (834)
.+
T Consensus 163 ~~ 164 (300)
T TIGR01729 163 KS 164 (300)
T ss_pred hc
Confidence 44
No 121
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=96.96 E-value=0.019 Score=61.90 Aligned_cols=242 Identities=14% Similarity=0.154 Sum_probs=142.8
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
++|+.-|+||..-.....+..-.. ..+|++....++..- ..+-..-...+....++..|+.+-.-|-|...++...
T Consensus 317 q~G~~~VVGPLlK~nVe~L~~~~q-~~i~vLALN~~~n~r---~~~~~cyfaLSPEDEa~~AA~~l~~qG~R~plvlvPr 392 (604)
T COG3107 317 QDGADFVVGPLLKPNVEALLASNQ-QPIPVLALNQPENSR---NPAQLCYFALSPEDEARDAANHLWDQGKRNPLVLVPR 392 (604)
T ss_pred hcCCcEEeccccchhHHHHHhCcC-CCCceeeecCCcccc---CcccceeeecChhHHHHHHHHHHHHccccCceEEecc
Confidence 468899999999888888755444 778888765443222 2233333334444457888899988999999999999
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHH-----------------------HHhhcCC-ceEEEEEe
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLL-----------------------VGANLME-SRVFVVHV 137 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l-----------------------~~l~~~~-~~vivl~~ 137 (834)
+++|+...++|.+++++.|+..+....+-. ..++..-+ ..+.+.. .|.|++..
T Consensus 393 ~~lG~Rv~~AF~~~Wq~~gg~~v~~~~fg~---~~~l~~~i~~~a~ir~~~~p~~~~~~~g~~~~p~~~~d~iDaVyivA 469 (604)
T COG3107 393 NDLGDRVANAFNQEWQKLGGGTVLQQKFGS---TSELRQGINDGAGIRLTGLPADLTTTNGLQTPPLDDQDTIDAVYIVA 469 (604)
T ss_pred hHHHHHHHHHHHHHHHHhcCCchhHhhcCc---HHHHHhhcccccceeecCCccchhcccCCCCCCcccccccceEEEEe
Confidence 999999999999999999885444433321 11111111 1112222 67888888
Q ss_pred ChhhHHHHHHHHHhCCCCCCCeEEEEeCCCcccCCCCCCCChhhHhhcccceEEE-e--cCCCChhHHHHHHHHHhhhcC
Q 003275 138 NPDTGLTIFSVAKSLGMTAGSYVWIATDWLPSVLDSTEPVDIDTMNLLQGVVALR-H--HTPDTDLKKNFISRWKNLKYK 214 (834)
Q Consensus 138 ~~~~~~~i~~~a~~~g~~~~~~vwi~~~~~~~~~~~~~~~~~~~~~~~~Gv~~~~-~--~~~~~~~~~~F~~~~~~~~~~ 214 (834)
.++++..|--...-.+.....-++..+. ... .. ..|+....++|+..-. | ..+..|.+++....|...
T Consensus 470 tp~el~~IKP~ia~~~~~~~~p~yaSSr-~~~--gT---~~P~~~~~m~GiqysdiP~l~~~~~p~~qq~a~~~p~~--- 540 (604)
T COG3107 470 TPSELALIKPMIAMANGSDSPPLYASSR-SSQ--GT---NGPDFRLEMEGIQYSDIPWLAQPNPPLMQQAAAAWPND--- 540 (604)
T ss_pred cchhHhHHhhHHHhhcCCCCcceeeecc-ccc--cC---CCccHHHhccCccccCCchhcCCCchHHHHHHHhcCCc---
Confidence 8777766544444333222111222221 110 11 1245567788875432 1 224556666666666432
Q ss_pred CCCCCCccchhHHHhhHHHHHHHHHHHHHhcCCCccccCCCCCCCCCCCCccCCCccccCchHHHHHHHHhcccccceee
Q 003275 215 ENSPSGFNSYALYAYDSVWLVAHALDALLNEGGKFTFSNDPKLHDTNGSMLNLSSLRVFDGGQQFLQTLLRMNFTGLSGE 294 (834)
Q Consensus 215 ~~~~~~~~~~~~~~YDav~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~l~~~~f~g~tG~ 294 (834)
|-.+.++|.+++.-.-... + .+ ++.....+.+|+||.
T Consensus 541 --------------~sl~RLyAmGvDAwrLan~-------------------------f---~e-lrqV~G~~i~G~TG~ 577 (604)
T COG3107 541 --------------YSLARLYAMGVDAWRLANH-------------------------F---SE-LRQVPGYQIDGLTGT 577 (604)
T ss_pred --------------hHHHHHHHhcchHHHHHHH-------------------------h---HH-hhcCCCcccccccce
Confidence 4456677777765321100 0 01 122333468899999
Q ss_pred EEEccCCC
Q 003275 295 IRFDADKN 302 (834)
Q Consensus 295 i~Fd~~g~ 302 (834)
++.|++..
T Consensus 578 Lsad~~c~ 585 (604)
T COG3107 578 LSADPDCV 585 (604)
T ss_pred eecCCCce
Confidence 99998874
No 122
>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=96.84 E-value=0.034 Score=57.98 Aligned_cols=145 Identities=10% Similarity=-0.013 Sum_probs=90.2
Q ss_pred CCcEE-EECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEE
Q 003275 3 NEVVA-AIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIF 79 (834)
Q Consensus 3 ~~V~a-iiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~ 79 (834)
++|.| |+.|..+.........+.+.++|+|.+....+ ....+ .+..++...+..+++.+... |.++++++.
T Consensus 56 ~~vdgiIi~~~~~~~~~~~~~~~~~~~iPvV~~~~~~~---~~~~~---~V~~d~~~~g~~~~~~l~~~~~g~~~i~~l~ 129 (275)
T cd06320 56 KGYKGLLFSPISDVNLVPAVERAKKKGIPVVNVNDKLI---PNATA---FVGTDNKANGVRGAEWIIDKLAEGGKVAIIE 129 (275)
T ss_pred hCCCEEEECCCChHHhHHHHHHHHHCCCeEEEECCCCC---Cccce---EEecCcHHHHHHHHHHHHHHhCCCceEEEEe
Confidence 46666 56776555444455667788999998754321 11112 24566666688888887655 889999987
Q ss_pred EcC--CcccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEE-eChhhHHHHHHHHHhCCCC
Q 003275 80 VDD--DYGRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVH-VNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 80 ~d~--~~g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~-~~~~~~~~i~~~a~~~g~~ 155 (834)
... .......+.+.++++++ |+.+..... ...+..+....+.++.+..+++-.+. .+...+..+++++++.|..
T Consensus 130 ~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~~~~~al~~~g~~ 207 (275)
T cd06320 130 GKAGAFAAEQRTEGFTEAIKKASGIEVVASQP--ADWDREKAYDVATTILQRNPDLKAIYCNNDTMALGVVEAVKNAGKQ 207 (275)
T ss_pred CCCCCccHHHHHHHHHHHHhhCCCcEEEEecC--CCccHHHHHHHHHHHHHhCCCccEEEECCchhHHHHHHHHHhcCCC
Confidence 533 23345568899999999 887754321 12223444556666554444433333 3455666788888988874
No 123
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=96.75 E-value=0.044 Score=56.76 Aligned_cols=144 Identities=15% Similarity=0.106 Sum_probs=87.0
Q ss_pred CCcEE-EECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEE
Q 003275 3 NEVVA-AIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIF 79 (834)
Q Consensus 3 ~~V~a-iiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~ 79 (834)
+++.| |++|..+.........+...++|+|......+ ..+.+-.+..++...+..+++.+... |-+++++++
T Consensus 54 ~~~dgii~~~~~~~~~~~~l~~l~~~~ipvv~~~~~~~-----~~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~l~ 128 (268)
T cd06323 54 RGVDAIIINPTDSDAVVPAVKAANEAGIPVFTIDREAN-----GGEVVSQIASDNVAGGKMAAEYLVKLLGGKGKVVELQ 128 (268)
T ss_pred cCCCEEEEcCCChHHHHHHHHHHHHCCCcEEEEccCCC-----CCceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEe
Confidence 35666 66665555444444556678999998755332 11223345555555677788887665 778999997
Q ss_pred Ec--CCcccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 80 VD--DDYGRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 80 ~d--~~~g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
.+ ..++....+.+.++++++ |+.+....... .+..+....+.++.+.. +++ ++..+...+..+++++++.|.
T Consensus 129 ~~~~~~~~~~r~~g~~~~l~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~~l~~~g~ 205 (268)
T cd06323 129 GIPGASAARERGKGFHEVVDKYPGLKVVASQPAD--FDRAKGLNVMENILQAHPDIKG-VFAQNDEMALGAIEALKAAGK 205 (268)
T ss_pred CCCCCccHHHHHHHHHHHHHhCCCcEEEecccCC--CCHHHHHHHHHHHHHHCCCcCE-EEEcCCchHHHHHHHHHHcCC
Confidence 53 345666788999999985 77765322111 22233334454544333 444 333445556678888899887
No 124
>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=96.73 E-value=0.04 Score=57.47 Aligned_cols=147 Identities=10% Similarity=0.065 Sum_probs=88.6
Q ss_pred CCcEEE-ECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc------CCeEE
Q 003275 3 NEVVAA-IGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY------GWREV 75 (834)
Q Consensus 3 ~~V~ai-iGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~------~W~~v 75 (834)
+++.+| ++|..+.....+...+...++|+|.+.... . ...++..+.+++..-+..+++++... |-+++
T Consensus 54 ~~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~~---~--~~~~~~~v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i 128 (277)
T cd06319 54 KGVSGIIISPTNSSAAVTLLKLAAQAKIPVVIADIGA---E--GGDYVSYIKSDNYEGAYDLGKFLAAAMKAQGWADGKV 128 (277)
T ss_pred cCCCEEEEcCCchhhhHHHHHHHHHCCCCEEEEecCC---C--CCceEEEEeeccHHHHHHHHHHHHHHHHhhCCCCCcE
Confidence 456655 577666555566677888899999864321 1 11233345556555566677665443 66899
Q ss_pred EEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEE-EEEeChhhHHHHHHHHHhC
Q 003275 76 IAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVF-VVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 76 ~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vi-vl~~~~~~~~~i~~~a~~~ 152 (834)
+++..+ ...+....+.+.+.+++.|+.+.... ...+.+..+....+.++.+..++.- ++..+...+..+++++++.
T Consensus 129 ~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~g~~~al~~~ 207 (277)
T cd06319 129 GMVAIPQKRKNGQKRTKGFKEAMKEAGCDLAGIR-QQKDFSYQETFDYTNDLLTANPDIRAIWLQGSDRYQGALDAIATA 207 (277)
T ss_pred EEEeccCCCccHHHHHHHHHHHHHhcCCceEeec-cCCCCCHHHHHHHHHHHHHhCCCCCEEEECCCccchHHHHHHHHc
Confidence 998743 34466778899999999988754221 1112222333445555544444432 3334455567899999999
Q ss_pred CCC
Q 003275 153 GMT 155 (834)
Q Consensus 153 g~~ 155 (834)
|+.
T Consensus 208 g~~ 210 (277)
T cd06319 208 GKT 210 (277)
T ss_pred CCC
Confidence 985
No 125
>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=96.60 E-value=0.022 Score=59.06 Aligned_cols=133 Identities=16% Similarity=0.110 Sum_probs=85.1
Q ss_pred HHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc---CCcccchHHHHHHHHh
Q 003275 21 SHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD---DDYGRNGISVLGDALS 97 (834)
Q Consensus 21 ~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d---~~~g~~~~~~l~~~l~ 97 (834)
...+...++|+|......+ ....++ ...++...+..+++.+...|.+++++|... +.++......|.++++
T Consensus 71 ~~~l~~~~iPvv~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~ 144 (268)
T cd06273 71 LDLLARRGVPYVATWNYSP---DSPYPC---VGFDNREAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAALA 144 (268)
T ss_pred HHHHHhCCCCEEEEcCCCC---CCCCCE---EEeChHHHHHHHHHHHHHCCCCeEEEEeccccCCccHHHHHHHHHHHHH
Confidence 3456778999998754322 122333 345677778888888877799999999743 2345667889999999
Q ss_pred cCCcEEEeeecCCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 98 KKRAKISYKAPFSPGASRSAINSLLVGANL--MESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 98 ~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~--~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
++++.+.....+....+..+....+.++.+ ..+++|+. ++...+..+++++++.|+..++.+
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~~~~a~~~~~~l~~~g~~~p~~i 208 (268)
T cd06273 145 EAGLELPELWQVEAPYSIADGRAALRQLLEQPPRPTAVIC-GNDVLALGALYEARRLGLSVPEDL 208 (268)
T ss_pred HcCCCCCHHHeeeCCCcHHHHHHHHHHHHcCCCCCCEEEE-cChHHHHHHHHHHHHcCCCCCCce
Confidence 988654322222212222333445555543 34666665 566678888999999998654443
No 126
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=96.46 E-value=0.033 Score=58.27 Aligned_cols=143 Identities=13% Similarity=0.095 Sum_probs=92.5
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC----CCCCceEEccCChHHHHHHHHHHHHHc--CCeEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS----LQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVI 76 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~----~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~ 76 (834)
++|.+||+..++. ...+ .....++|+|.++..++.... ...+....+..++...+..+++++... |.++++
T Consensus 59 ~~vd~iI~~~~~~-~~~~--~~~~~~iPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~i~ 135 (281)
T cd06325 59 DKPDLIVAIATPA-AQAA--ANATKDIPIVFTAVTDPVGAGLVKSLEKPGGNVTGVSDLVPVETQLELLKKLLPDAKTVG 135 (281)
T ss_pred cCCCEEEEcCcHH-HHHH--HHcCCCCCEEEEecCCccccccccccccCCCceeCeecccchHHHHHHHHHHCCCCcEEE
Confidence 4788888865432 2222 255679999988654432111 111112223445666677788888765 999999
Q ss_pred EEEEcC-CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 77 AIFVDD-DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 77 iI~~d~-~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
+++.+. .++....+.+.+++++.|+++.... .. +..+....++++... +++|++..+ ..+..+++++.+.|+
T Consensus 136 ~l~~~~~~~~~~r~~g~~~~~~~~g~~~~~~~-~~---~~~~~~~~~~~~~~~-~dai~~~~d-~~a~~~~~~~~~~~~ 208 (281)
T cd06325 136 VLYNPSEANSVVQVKELKKAAAKLGIEVVEAT-VS---SSNDVQQAAQSLAGK-VDAIYVPTD-NTVASAMEAVVKVAN 208 (281)
T ss_pred EEeCCCCccHHHHHHHHHHHHHhCCCEEEEEe-cC---CHHHHHHHHHHhccc-CCEEEEcCc-hhHHhHHHHHHHHHH
Confidence 998654 3677778999999999998876532 21 335667777777643 577666544 466678888888775
No 127
>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=96.41 E-value=0.041 Score=57.10 Aligned_cols=156 Identities=13% Similarity=0.087 Sum_probs=93.6
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
+++.|||....+.......+.+...++|+|......+. ...++ ...++...+..+++.+...|.+++++|..+.
T Consensus 55 ~~vdgiii~~~~~~~~~~~~~~~~~~ipvv~i~~~~~~---~~~~~---V~~d~~~~g~~a~~~l~~~g~~~i~~i~~~~ 128 (270)
T cd01545 55 SRVDGVILTPPLSDNPELLDLLDEAGVPYVRIAPGTPD---PDSPC---VRIDDRAAAREMTRHLIDLGHRRIAFIAGPP 128 (270)
T ss_pred CCCCEEEEeCCCCCccHHHHHHHhcCCCEEEEecCCCC---CCCCe---EEeccHHHHHHHHHHHHHCCCceEEEEeCCC
Confidence 46888877544433344456677789999987654332 12233 2345666677888888778999999998654
Q ss_pred Ccc--cchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 83 DYG--RNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANL--MESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 83 ~~g--~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~--~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
.+. ......+.+++++.|+.+..........+..+-...+.++.+ ..+++|+ .++...+..+++++++.|...++
T Consensus 129 ~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~-~~~d~~a~~~~~~~~~~g~~~p~ 207 (270)
T cd01545 129 DHRASAERLEGYRDALAEAGLPLDPELVAQGDFTFESGLEAAEALLALPDRPTAIF-ASNDDMAAGVLAVAHRRGLRVPD 207 (270)
T ss_pred CchhHHHHHHHHHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHhCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCC
Confidence 432 344678899998888765210111111111222234444433 3456665 45567788999999999986443
Q ss_pred -eEEEEeC
Q 003275 159 -YVWIATD 165 (834)
Q Consensus 159 -~vwi~~~ 165 (834)
...+..|
T Consensus 208 ~i~vig~d 215 (270)
T cd01545 208 DLSVVGFD 215 (270)
T ss_pred ceEEEEEC
Confidence 3344444
No 128
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=96.34 E-value=0.11 Score=53.97 Aligned_cols=156 Identities=15% Similarity=0.068 Sum_probs=92.2
Q ss_pred CCcEEEE-CCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEE
Q 003275 3 NEVVAAI-GPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIF 79 (834)
Q Consensus 3 ~~V~aii-Gp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~ 79 (834)
.+|.++| .|..+.....+...+...++|+|......+.. .+.+..+..++...+..+++.+... +=+++++|.
T Consensus 55 ~~vdgiii~~~~~~~~~~~~~~l~~~~iPvv~~~~~~~~~----~~~~~~V~~d~~~~g~~~~~~l~~~~~~~~~i~~i~ 130 (272)
T cd06301 55 QGVDAIIVVPVDTAATAPIVKAANAAGIPLVYVNRRPENA----PKGVAYVGSDEVVAGRLQAEYVADKLGGKGNVAILM 130 (272)
T ss_pred cCCCEEEEecCchhhhHHHHHHHHHCCCeEEEecCCCCCC----CCeeEEEecChHHHHHHHHHHHHHHhCCCccEEEEE
Confidence 3566664 66555544555566788999999875432211 1234456677777788888887544 446999887
Q ss_pred EcC--CcccchHHHHHHHHhcCC-cEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 80 VDD--DYGRNGISVLGDALSKKR-AKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 80 ~d~--~~g~~~~~~l~~~l~~~g-~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
... .......+.+.+++++.| +.+... .....+.......+.++.+. .+++| ++.+...+..+++.+++.|.
T Consensus 131 ~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~~l~~~g~ 207 (272)
T cd06301 131 GPLGQSAQIDRTKGVEEVLAKYPDIKVVEE--QTANWSRAEAMDLMENWLSSGGKIDAV-VANNDEMALGAIMALKAAGK 207 (272)
T ss_pred CCCCCccHHHHHHHHHHHHHHCCCcEEEec--CCCCccHHHHHHHHHHHHHhCCCCCEE-EECCCchHHHHHHHHHHcCC
Confidence 543 234455788999999887 444321 11112222223444444332 34554 44455667788999999998
Q ss_pred CCCCeEEEEeC
Q 003275 155 TAGSYVWIATD 165 (834)
Q Consensus 155 ~~~~~vwi~~~ 165 (834)
.+.+...+..+
T Consensus 208 ~~~di~ivg~d 218 (272)
T cd06301 208 SDKDVPVAGID 218 (272)
T ss_pred CCCCcEEEeeC
Confidence 74354445444
No 129
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=96.30 E-value=0.091 Score=54.66 Aligned_cols=112 Identities=21% Similarity=0.189 Sum_probs=75.1
Q ss_pred ccCCCChhhhhcCCCCeeEeeCchhhH------HHHhhhcccc---cceEecCC-HHHHHHHHhcCCCCCceEEEEechh
Q 003275 588 TSQIEGIDSLISSTEPIGVQDGSFAWN------YLVDELKIAE---SRLVKLKN-MEEYSIALARGPKGGGVAAIVDELP 657 (834)
Q Consensus 588 ~~~i~s~~dL~~~~~~v~~~~~s~~~~------~l~~~~~~~~---~~~~~~~~-~~~~~~~l~~~~~~g~~~a~~~~~~ 657 (834)
.++|++++||. |+++++..-+.... +|.++.+.+. -.-+.|.. -+..+.+|.+ |++|+......
T Consensus 133 ds~i~sl~dlk--gk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~a~~aV~n----G~vDva~~~~~ 206 (299)
T COG3221 133 DSPIKSLEDLK--GKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDAAVLAVAN----GQVDVAAVNSS 206 (299)
T ss_pred CCCcchHHHhc--CCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHHHHHHHHc----CCceEEeccHH
Confidence 46899999997 99999875332222 2222222221 11223444 7788999999 99998888776
Q ss_pred hHHHHhhcCC----ccEEEeCCcccccceEEEEcCCCc--chHHHHHHHHhhhc
Q 003275 658 YIELFMSKTN----CEFRTVGQEFTKSGWGFAFQRDSP--LAIDLSTAILQLSE 705 (834)
Q Consensus 658 ~~~~~~~~~~----~~l~~v~~~~~~~~~~~~~~k~sp--l~~~~~~~i~~l~e 705 (834)
....+..... .++.++...-...+..++++++-| +++.+-.+++.+.+
T Consensus 207 ~~~~~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 207 ARGLLKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred HHhhhhhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHHhcCc
Confidence 6665543322 257777654444556788888877 99999999999987
No 130
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=96.27 E-value=0.016 Score=59.67 Aligned_cols=72 Identities=26% Similarity=0.244 Sum_probs=48.6
Q ss_pred cCCCChhhhhc-----CCCCeeE-eeCchhhHHHH---hhhcccc---cceEecCCHHHHHHHHhcCCCCCceEEEEech
Q 003275 589 SQIEGIDSLIS-----STEPIGV-QDGSFAWNYLV---DELKIAE---SRLVKLKNMEEYSIALARGPKGGGVAAIVDEL 656 (834)
Q Consensus 589 ~~i~s~~dL~~-----~~~~v~~-~~~s~~~~~l~---~~~~~~~---~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~ 656 (834)
+.+++++||.+ .|++|++ ..|+...-.+. ++.+++. -+++.++. .+..++++. |++|+++...
T Consensus 104 ~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~----g~iDa~~~~e 178 (252)
T PF13379_consen 104 SDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRA----GEIDAAVLWE 178 (252)
T ss_dssp STTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHT----TS-SEEEEET
T ss_pred CCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhC----CCcCEEEecC
Confidence 47899999943 3778998 45664433332 2344444 45666666 999999999 9999999999
Q ss_pred hhHHHHhhc
Q 003275 657 PYIELFMSK 665 (834)
Q Consensus 657 ~~~~~~~~~ 665 (834)
|+......+
T Consensus 179 P~~~~~~~~ 187 (252)
T PF13379_consen 179 PFASQAEAK 187 (252)
T ss_dssp THHHHHHHT
T ss_pred CHHHHHHhc
Confidence 998877766
No 131
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=96.25 E-value=0.092 Score=54.61 Aligned_cols=149 Identities=9% Similarity=0.031 Sum_probs=84.7
Q ss_pred CCcEEE-ECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEc-cCChHHHHHHHHHHHHHc--CCeEEEEE
Q 003275 3 NEVVAA-IGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRT-TQSDYYQMHAVADLVEYY--GWREVIAI 78 (834)
Q Consensus 3 ~~V~ai-iGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~-~ps~~~q~~aia~ll~~~--~W~~v~iI 78 (834)
++|.+| +.|..+.........+...++|+|......+ ..+.++++.. .+++...+...++.+... |-++++++
T Consensus 55 ~~vdgiii~~~~~~~~~~~l~~~~~~~iPvV~~~~~~~---~~~~~~v~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l 131 (275)
T cd06317 55 QKVDGIILWPTDGQAYIPGLRKAKQAGIPVVITNSNIS---EKGFEFIKSFTGPDDISQGERSAEAMCKALGGKGQIVVI 131 (275)
T ss_pred cCCCEEEEecCCccccHHHHHHHHHCCCcEEEeCCCCC---CCccchhhhhccccHHHHHHHHHHHHHHHcCCCceEEEE
Confidence 466666 4454444434445666788999998654321 2233544333 344555666667776444 67899999
Q ss_pred EEcCCc--ccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhh-c--CCceEEEEEeChhhHHHHHHHHHhCC
Q 003275 79 FVDDDY--GRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGAN-L--MESRVFVVHVNPDTGLTIFSVAKSLG 153 (834)
Q Consensus 79 ~~d~~~--g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~-~--~~~~vivl~~~~~~~~~i~~~a~~~g 153 (834)
..+.++ +....+.+.++++++|..+..........+..+....+.++- + ..+++|++ ++...+..+++++++.|
T Consensus 132 ~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~-~~d~~a~g~~~~l~~~g 210 (275)
T cd06317 132 AGQPGNGTAIERQKGFEDELAEVCPGVEVLDTQPADWDREKAQVAMEALITKFGDDIDGVYA-GDDNMARGALNAAKEAG 210 (275)
T ss_pred ecCCCCchHHHHHHHHHHHHHhhCCCCEEEeccCCCCCHHHHHHHHHHHHHhCCCCccEEEE-CCCcHHHHHHHHHHhcC
Confidence 754433 334468899999998643322222221112122223334332 2 23567664 44455788999999999
Q ss_pred CC
Q 003275 154 MT 155 (834)
Q Consensus 154 ~~ 155 (834)
+.
T Consensus 211 ~~ 212 (275)
T cd06317 211 LA 212 (275)
T ss_pred Cc
Confidence 75
No 132
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=96.21 E-value=0.087 Score=56.07 Aligned_cols=68 Identities=15% Similarity=0.190 Sum_probs=49.6
Q ss_pred CCChhhhhcCCCCeeEeeCchhhHHHHh---hhcccc--cceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhc
Q 003275 591 IEGIDSLISSTEPIGVQDGSFAWNYLVD---ELKIAE--SRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSK 665 (834)
Q Consensus 591 i~s~~dL~~~~~~v~~~~~s~~~~~l~~---~~~~~~--~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~ 665 (834)
|+|++||. |++|++..|+..+-++.+ ..+++. -+++.. +..+...++.+ |++||.+...|+......+
T Consensus 98 i~svaDLK--GKkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~-~~~d~~aAl~~----G~VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 98 GKSLADLK--GQKVNLVELSVSHYLLARALESVGLSEKDVKVVNT-SDADIVAAFIT----KDVTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred CCCHHHcC--CCEEeccCCChHHHHHHHHHHHcCCCHHHeEEEeC-ChHHHHHHHhc----CCCcEEEEcCchHHHHHhC
Confidence 89999998 999999999876654443 233432 344445 45778899999 9999999888887655443
No 133
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=96.14 E-value=0.15 Score=52.87 Aligned_cols=147 Identities=12% Similarity=0.150 Sum_probs=91.5
Q ss_pred CCcEEEECCC-ChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHH-cCCeEEEEEEE
Q 003275 3 NEVVAAIGPQ-SSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEY-YGWREVIAIFV 80 (834)
Q Consensus 3 ~~V~aiiGp~-~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~-~~W~~v~iI~~ 80 (834)
.++.+||... ...........+...++|+|......+... ..+.+..+..++...+..+++.+.. .|-++++++..
T Consensus 56 ~~vdgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~~~~~~--~~~~~~~V~~d~~~~g~~~~~~l~~~~g~~~i~~i~g 133 (271)
T cd06312 56 AKPDGIVVTIPDPDALDPAIKRAVAAGIPVISFNAGDPKYK--ELGALAYVGQDEYAAGEAAGERLAELKGGKNVLCVIH 133 (271)
T ss_pred hCCCEEEEeCCChHHhHHHHHHHHHCCCeEEEeCCCCCccc--cccceEEeccChHHHHHHHHHHHHHhcCCCeEEEEec
Confidence 3566666533 323233444556778999998754322211 1234566778888899999999888 89899998874
Q ss_pred c--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 81 D--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 81 d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
+ +..+....+.+.++++++++.+.. +....+..+....++++.+. .+++|+. .+...+..+++.+++.|+.
T Consensus 134 ~~~~~~~~~r~~g~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~~aI~~-~~d~~a~g~~~al~~~g~~ 208 (271)
T cd06312 134 EPGNVTLEDRCAGFADGLGGAGITEEV---IETGADPTEVASRIAAYLRANPDVDAVLT-LGAPSAAPAAKALKQAGLK 208 (271)
T ss_pred CCCCccHHHHHHHHHHHHHhcCceeeE---eecCCCHHHHHHHHHHHHHhCCCccEEEE-eCCccchHHHHHHHhcCCC
Confidence 3 334556788999999988875432 11112223344445554333 3455444 4455677888889998875
No 134
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=96.05 E-value=0.13 Score=53.45 Aligned_cols=156 Identities=13% Similarity=-0.000 Sum_probs=90.0
Q ss_pred CCcEEEECC-CChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHH--cCCeEEEEEE
Q 003275 3 NEVVAAIGP-QSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEY--YGWREVIAIF 79 (834)
Q Consensus 3 ~~V~aiiGp-~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~--~~W~~v~iI~ 79 (834)
.++.+||.. ..+.....+...+...++|+|......+. +.+..+..++...+..+++.+.. .|-++++++.
T Consensus 54 ~~vdgii~~~~~~~~~~~~i~~~~~~~ipvV~~~~~~~~------~~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~ 127 (273)
T cd06305 54 QKVDAIIIQHGRAEVLKPWVKRALDAGIPVVAFDVDSDN------PKVNNTTQDDYSLARLSLDQLVKDLGGKGNVGYVN 127 (273)
T ss_pred cCCCEEEEecCChhhhHHHHHHHHHcCCCEEEecCCCCC------CccceeeechHHHHHHHHHHHHHHhCCCCCEEEEE
Confidence 467777664 33333344445567889999987543221 22334556777778888888755 5889999887
Q ss_pred Ec-CCcccchHHHHHHHHhcCC-cEEEeeecCCCCCChHHHHHHHHHhhcCCceE---EEEEeChhhHHHHHHHHHhCCC
Q 003275 80 VD-DDYGRNGISVLGDALSKKR-AKISYKAPFSPGASRSAINSLLVGANLMESRV---FVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 80 ~d-~~~g~~~~~~l~~~l~~~g-~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~v---ivl~~~~~~~~~i~~~a~~~g~ 154 (834)
.. ..........+.+.+++.+ ..+..........+..+....++++....+++ .|++.+...+..++.++++.|.
T Consensus 128 ~~~~~~~~~R~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~~d~~a~g~~~~l~~~g~ 207 (273)
T cd06305 128 VAGFPPLDRRYDVWQAVLKAYPGIKEVAELGDVSNNTAQDAAAQVEAVLKKYPKGGIDAIWAAWDEFAKGAKQALDEAGR 207 (273)
T ss_pred ccCCchHHHHHHHHHHHHHHCCCcEEecccccccccchhHHHHHHHHHHHHCCCcccCeEEEcChhhhHHHHHHHHHcCC
Confidence 43 2233344667888888877 55443221111112233444555554444433 2333455577788889999997
Q ss_pred CCCCeEEEEeC
Q 003275 155 TAGSYVWIATD 165 (834)
Q Consensus 155 ~~~~~vwi~~~ 165 (834)
.. +...+..+
T Consensus 208 ~~-di~iig~d 217 (273)
T cd06305 208 TD-EIKIYGVD 217 (273)
T ss_pred CC-CceEEEec
Confidence 53 33344443
No 135
>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=95.90 E-value=0.091 Score=54.40 Aligned_cols=153 Identities=14% Similarity=0.104 Sum_probs=92.8
Q ss_pred CCcEEEE--CCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 3 NEVVAAI--GPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 3 ~~V~aii--Gp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
.++.||| ++..+ ..+...+...++|+|.+....+ ....++ ..+++...+..+++.+...|-+++++|..
T Consensus 54 ~~vdgiii~~~~~~---~~~~~~l~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~l~~ 124 (268)
T cd06298 54 KQVDGIIFMGGKIS---EEHREEFKRSPTPVVLAGSVDE---DNELPS---VNIDYKKAAFEATELLIKNGHKKIAFISG 124 (268)
T ss_pred hcCCEEEEeCCCCc---HHHHHHHhcCCCCEEEEccccC---CCCCCE---EEECcHHHHHHHHHHHHHcCCceEEEEeC
Confidence 3566666 43222 2344556677999998755322 112232 45566667777888887778899999974
Q ss_pred cC---CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCC-ceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 81 DD---DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLME-SRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 81 d~---~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~-~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
+. ..+....+.+.++++++|+.+..........+.......+.++.+.. +++|+. ++...+..+++++++.|+..
T Consensus 125 ~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~v 203 (268)
T cd06298 125 PLEDSINGDERLAGYKEALSEANIEFDESLIFEGDYTYESGYELAEELLEDGKPTAAFV-TDDELAIGILNAAQDAGLKV 203 (268)
T ss_pred CcccccchhHHHHHHHHHHHHcCCCCCHHHeEeCCCChhHHHHHHHHHhcCCCCCEEEE-cCcHHHHHHHHHHHHcCCCC
Confidence 33 35677789999999998876422111111112223334455555444 677665 45555778999999999865
Q ss_pred CCe-EEEEeC
Q 003275 157 GSY-VWIATD 165 (834)
Q Consensus 157 ~~~-vwi~~~ 165 (834)
++. .++..|
T Consensus 204 p~di~vvg~d 213 (268)
T cd06298 204 PEDFEIIGFN 213 (268)
T ss_pred ccceEEEeec
Confidence 443 444444
No 136
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=95.71 E-value=0.81 Score=44.74 Aligned_cols=182 Identities=14% Similarity=0.138 Sum_probs=113.7
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+.+++.. ++..++++.|.+|++|++++........ + -..|+....+++++++
T Consensus 19 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~---~-~~~~l~~~~~~~~~~~ 86 (209)
T PF03466_consen 19 SLLPPLLAEFRERHP-NIRIEIRE-------GDSDELIEALRSGELDLAITFGPPPPPG---L-ESEPLGEEPLVLVVSP 86 (209)
T ss_dssp HTHHHHHHHHHHHST-TEEEEEEE-------ESHHHHHHHHHTTSSSEEEESSSSSSTT---E-EEEEEEEEEEEEEEET
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEe-------ccchhhhHHHhcccccEEEEEeeccccc---c-ccccccceeeeeeeec
Confidence 445788888888776 35566654 5578999999999999998866553222 2 2567788899999987
Q ss_pred CCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcchhhHHHHHHHHhhccCCCcccccchhhhH
Q 003275 481 QKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQLVTIFWFSFSTMFFSHRENTVSSLGRVVL 560 (834)
Q Consensus 481 ~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~~~ 560 (834)
..+...
T Consensus 87 ~~pl~~-------------------------------------------------------------------------- 92 (209)
T PF03466_consen 87 DHPLAQ-------------------------------------------------------------------------- 92 (209)
T ss_dssp TSGGGT--------------------------------------------------------------------------
T ss_pred cccccc--------------------------------------------------------------------------
Confidence 762211
Q ss_pred HHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeE-eeCchhhHHHHh---hhcccccceEecCCHHHH
Q 003275 561 IVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGV-QDGSFAWNYLVD---ELKIAESRLVKLKNMEEY 636 (834)
Q Consensus 561 ~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~-~~~s~~~~~l~~---~~~~~~~~~~~~~~~~~~ 636 (834)
...+ +++||. +.++.. ..+......+.+ ..+........+++.+..
T Consensus 93 ---------------------------~~~i-~~~dL~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 142 (209)
T PF03466_consen 93 ---------------------------KKPI-TLEDLA--DYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESI 142 (209)
T ss_dssp ---------------------------TSSS-SGGGGT--TSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHH
T ss_pred ---------------------------cccc-hhhhhh--hccccccccccccccccccccccccccccccccccchhhh
Confidence 1234 888887 455444 334434444432 234444455668899999
Q ss_pred HHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCC-cccccceEEEEcCCCcchHHHHHHHHhhh
Q 003275 637 SIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQ-EFTKSGWGFAFQRDSPLAIDLSTAILQLS 704 (834)
Q Consensus 637 ~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~-~~~~~~~~~~~~k~spl~~~~~~~i~~l~ 704 (834)
...+.. |..-+++.+ ................+.. .+. ..+.++.+++.+....+...+..+.
T Consensus 143 ~~~v~~----g~gi~~~p~-~~~~~~~~~~~l~~~~~~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~l~ 205 (209)
T PF03466_consen 143 LSLVAS----GDGIAILPD-SLAQDELESGELVFLPLPDPPLP-RPIYLVWRKDRPLSPAIQWFIDLLR 205 (209)
T ss_dssp HHHHHT----TSEBEEEEH-HHHHHHHHCTTEEEEEESSSTEE-EEEEEEEETTGTTHHHHHHHHHHHH
T ss_pred cccccc----ccceeecCc-ccccccccCCCEEEEECCCCCCc-eEEEEEEECCCCCCHHHHHHHHHHH
Confidence 999998 555555544 3333333332333334444 444 7788888888776666666655544
No 137
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=95.68 E-value=0.093 Score=54.29 Aligned_cols=150 Identities=13% Similarity=0.081 Sum_probs=87.8
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
+++.|||...+..........+...++|+|.+....+. ...+ ....++...+..+++.+...|-++++++..+.
T Consensus 54 ~~vdgiii~~~~~~~~~~~~~~~~~~ipvV~~~~~~~~---~~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~l~~~~ 127 (268)
T cd06289 54 HGVAGIILCPAAGTSPDLLKRLAESGIPVVLVAREVAG---APFD---YVGPDNAAGARLATEHLISLGHRRIAFIGGLE 127 (268)
T ss_pred cCCCEEEEeCCCCccHHHHHHHHhcCCCEEEEeccCCC---CCCC---EEeecchHHHHHHHHHHHHCCCCCEEEecCCc
Confidence 46777766544333333456677889999987543221 1222 24455666777788887777889999887432
Q ss_pred --CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 83 --DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 83 --~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
.......+.|.+.+++.|..+.....++...+.......+.++... .+++|+ +.+...+..+++++++.|+..++
T Consensus 128 ~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~-~~~~~~a~~~~~al~~~g~~~p~ 206 (268)
T cd06289 128 DSSTRRERLAGYRAALAEAGLPFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTAIV-CFNDLVAFGAMSGLRRAGLTPGR 206 (268)
T ss_pred cccchHHHHHHHHHHHHHcCCCCCchhEEecCcchhhHHHHHHHHHcCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCc
Confidence 3455668899999988875322111111111222333444444333 345544 34455577789999999986543
Q ss_pred e
Q 003275 159 Y 159 (834)
Q Consensus 159 ~ 159 (834)
.
T Consensus 207 d 207 (268)
T cd06289 207 D 207 (268)
T ss_pred c
Confidence 3
No 138
>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=95.64 E-value=0.15 Score=52.62 Aligned_cols=153 Identities=11% Similarity=0.086 Sum_probs=90.6
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
+++.+||...+...... ...+...++|+|.+....+ ...+++ ...++...+..+++.+...|-++++++....
T Consensus 58 ~~vdgiii~~~~~~~~~-~~~~~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~ 130 (268)
T cd06271 58 GLVDGVIISRTRPDDPR-VALLLERGFPFVTHGRTEL---GDPHPW---VDFDNEAAAYQAVRRLIALGHRRIALLNPPE 130 (268)
T ss_pred CCCCEEEEecCCCCChH-HHHHHhcCCCEEEECCcCC---CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEecCcc
Confidence 35777776433322222 3455678999998754322 123344 3356666677788888777999999987443
Q ss_pred --CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 83 --DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 83 --~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
..+....+.+.++++++|..+.....+....+.......+.++... .+++|+.. +...+..+++++++.|+..++
T Consensus 131 ~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~~vp~ 209 (268)
T cd06271 131 DLTFAQHRRAGYRRALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIVCS-SELMALGVLAALAEAGLRPGR 209 (268)
T ss_pred ccchHHHHHHHHHHHHHHhCCCCCCceEEeCCCChHHHHHHHHHHHhCCCCCCEEEEc-CcHHHHHHHHHHHHhCCCCCc
Confidence 2344567889999999887542111111112223333445554332 35665554 456677899999999987655
Q ss_pred eEEEE
Q 003275 159 YVWIA 163 (834)
Q Consensus 159 ~vwi~ 163 (834)
.+-+.
T Consensus 210 ~i~ii 214 (268)
T cd06271 210 DVSVV 214 (268)
T ss_pred ceeEE
Confidence 44444
No 139
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=95.56 E-value=0.92 Score=43.26 Aligned_cols=70 Identities=16% Similarity=0.222 Sum_probs=47.6
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+..++++.+.+..+ .+++++.. .+..+++..|.+|++|++++...... ..++ ..++....+++++++
T Consensus 13 ~~l~~~i~~~~~~~p-~i~i~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~~~---~~~~-~~~l~~~~~~~~~~~ 80 (197)
T cd05466 13 YLLPPLLAAFRQRYP-GVELSLVE-------GGSSELLEALLEGELDLAIVALPVDD---PGLE-SEPLFEEPLVLVVPP 80 (197)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEE-------CChHHHHHHHHcCCceEEEEcCCCCC---Ccce-EeeeeccceEEEecC
Confidence 455677777777765 35566654 44678999999999999987554322 2233 456667788888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (197)
T cd05466 81 DH 82 (197)
T ss_pred CC
Confidence 65
No 140
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=95.40 E-value=0.21 Score=52.38 Aligned_cols=71 Identities=18% Similarity=0.218 Sum_probs=48.4
Q ss_pred cCCCChhhhhcCCCCeeEeeCchhhHHHHh---hhcccccce-EecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhh
Q 003275 589 SQIEGIDSLISSTEPIGVQDGSFAWNYLVD---ELKIAESRL-VKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMS 664 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v~~~~~s~~~~~l~~---~~~~~~~~~-~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~ 664 (834)
.+|++++||. |++|++..++.....+.. ..+++...+ ..+.+..+..+++.+ |++|+++...++......
T Consensus 91 ~~i~s~~dL~--Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~----g~vda~~~~~p~~~~~~~ 164 (288)
T TIGR01728 91 SPIRTVADLK--GKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAA----GQVDAWAIWEPWGSALVE 164 (288)
T ss_pred CCCCCHHHcC--CCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHC----CCCCEEEeccchHhHHhh
Confidence 4788999997 888998877644443322 234433222 223456788899998 899999998888776655
Q ss_pred c
Q 003275 665 K 665 (834)
Q Consensus 665 ~ 665 (834)
+
T Consensus 165 ~ 165 (288)
T TIGR01728 165 E 165 (288)
T ss_pred c
Confidence 4
No 141
>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=95.39 E-value=0.99 Score=46.74 Aligned_cols=154 Identities=8% Similarity=-0.012 Sum_probs=87.7
Q ss_pred CcEEEEC-CCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEEE
Q 003275 4 EVVAAIG-PQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIFV 80 (834)
Q Consensus 4 ~V~aiiG-p~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~~ 80 (834)
++.+||- +........+...+...++|+|......+ + ..+ +--+..++...+..+++++... |.+++++|..
T Consensus 57 ~vdgvii~~~~~~~~~~~l~~~~~~~ipvV~~~~~~~---~-~~~-~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~~ 131 (273)
T cd06310 57 GPDAILLAPTDAKALVPPLKEAKDAGIPVVLIDSGLN---S-DIA-VSFVATDNVAAGKLAAEALAELLGKKGKVAVISF 131 (273)
T ss_pred CCCEEEEcCCChhhhHHHHHHHHHCCCCEEEecCCCC---C-Ccc-eEEEeeChHHHHHHHHHHHHHHcCCCceEEEEeC
Confidence 5666654 32222223444555678999998743211 1 011 1224455556667788887665 8999999975
Q ss_pred cCCc--ccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHhhcCCceE-EEEEeChhhHHHHHHHHHhCCCCC
Q 003275 81 DDDY--GRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGANLMESRV-FVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 81 d~~~--g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~v-ivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
..++ .....+.+.+++++. |+.+... .....+..+-...+.++....+++ .|++.+...+..+++.+++.|+.
T Consensus 132 ~~~~~~~~~r~~gf~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~d~~a~g~~~~l~~~g~~- 208 (273)
T cd06310 132 VPGSSTTDQREEGFLEGLKEYPGIEIVAT--QYSDSDYAKALDITEDLLTANPDLKGIFGANEGSAVGAARAVRQAGKA- 208 (273)
T ss_pred CCCCccHHHHHHHHHHHHHhCCCcEEEec--ccCCcCHHHHHHHHHHHHHhCCCceEEEecCchhHHHHHHHHHhcCCC-
Confidence 4333 334578889999988 8766431 111112223334555554333332 33444566788899999999985
Q ss_pred CCeEEEEeC
Q 003275 157 GSYVWIATD 165 (834)
Q Consensus 157 ~~~vwi~~~ 165 (834)
.+...+..|
T Consensus 209 ~di~vig~d 217 (273)
T cd06310 209 GKVKVVGFD 217 (273)
T ss_pred CCeEEEEeC
Confidence 444444444
No 142
>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=95.35 E-value=0.22 Score=53.52 Aligned_cols=132 Identities=12% Similarity=0.068 Sum_probs=83.1
Q ss_pred HHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC--C-cccchHHHHHHHH
Q 003275 20 ISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD--D-YGRNGISVLGDAL 96 (834)
Q Consensus 20 ~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~--~-~g~~~~~~l~~~l 96 (834)
+...+...++|+|......+ ...+++ ...++..-+..+++.+...|.++++++..+. . .+....+.+.+++
T Consensus 130 ~~~~l~~~~iPvV~~~~~~~---~~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~~R~~Gf~~~l 203 (329)
T TIGR01481 130 LREEFSRSPVPVVLAGTVDK---ENELPS---VNIDYKQATKEAVGELIAKGHKSIAFVGGPLSDSINGEDRLEGYKEAL 203 (329)
T ss_pred HHHHHHhcCCCEEEEecCCC---CCCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEecCcccccchHHHHHHHHHHH
Confidence 34455667999997654321 122332 4455666667777888778999999996432 2 3466788999999
Q ss_pred hcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 97 SKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 97 ~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
+++|+.+..........+..+-...+.++.+..+++|+. .+...+..+++++++.|+..++
T Consensus 204 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~p~ai~~-~~d~~A~g~~~al~~~g~~vP~ 264 (329)
T TIGR01481 204 NKAGIQFGEDLVCEGKYSYDAGYKAFAELKGSLPTAVFV-ASDEMAAGILNAAMDAGIKVPE 264 (329)
T ss_pred HHcCCCCCcceEEecCCChHHHHHHHHHHhCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCC
Confidence 999876432111111112233344556665556777665 4556788899999999986543
No 143
>PF09084 NMT1: NMT1/THI5 like; InterPro: IPR015168 This entry is found in the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [, , ]. They are regulated by thiamine []. ; PDB: 2X26_A 3E4R_A 3KSJ_A 3KSX_A 3UIF_A 4DDD_A 1US4_A 1US5_A 3IX1_B 2X7P_A ....
Probab=95.32 E-value=0.13 Score=51.45 Aligned_cols=59 Identities=27% Similarity=0.276 Sum_probs=38.6
Q ss_pred cCCCChhhhhcCCCCeeEeeCchhhHHHH---hhhcccccceEecC-CHHHHHHHHhcCCCCCceEEEE
Q 003275 589 SQIEGIDSLISSTEPIGVQDGSFAWNYLV---DELKIAESRLVKLK-NMEEYSIALARGPKGGGVAAIV 653 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v~~~~~s~~~~~l~---~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~g~~~a~~ 653 (834)
..|++++||. |++|++..++.....+. +..+++.+.+.... +..+...+|.+ |++|+.+
T Consensus 83 s~i~~~~DLk--GK~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~----g~vDa~~ 145 (216)
T PF09084_consen 83 SGIKSPADLK--GKKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLS----GQVDAAI 145 (216)
T ss_dssp TS-SSGGGGT--TSEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHT----TSSSEEE
T ss_pred CCCCCHHHhC--CCEEEEecCcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhc----CCCCEEE
Confidence 3699999997 99999999765444332 23455444443322 35667679998 8999888
No 144
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=95.31 E-value=0.71 Score=47.90 Aligned_cols=156 Identities=11% Similarity=0.047 Sum_probs=93.2
Q ss_pred CcEEE-ECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEEE
Q 003275 4 EVVAA-IGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIFV 80 (834)
Q Consensus 4 ~V~ai-iGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~~ 80 (834)
++.+| +.|..+.........+...++|+|......+. ....+++.++.+++...+..+++.+... |-++++++..
T Consensus 55 ~vdgiIi~~~~~~~~~~~i~~~~~~~iPvV~~~~~~~~--~~~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~ 132 (273)
T cd06309 55 GVDVIILAPVVETGWDPVLKEAKAAGIPVILVDRGVDV--KDDSLYVTFIGSDFVEEGRRAADWLAKATGGKGNIVELQG 132 (273)
T ss_pred CCCEEEEcCCccccchHHHHHHHHCCCCEEEEecCcCC--ccCcceeeEecCChHHHHHHHHHHHHHHcCCCceEEEEeC
Confidence 45544 44544443334445677889999987643221 1112456778888888888888888665 8889999975
Q ss_pred cCC--cccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 81 DDD--YGRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGANLM---ESRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 81 d~~--~g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~~---~~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
+.+ ......+.+.++++++ +.++... .....+..+....+.++.+. .+++| +..+...+..+++++++.|+
T Consensus 133 ~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~aI-~~~~d~~a~g~~~a~~~~g~ 209 (273)
T cd06309 133 TVGSSVAIDRKKGFAEVIKKYPNMKIVAS--QTGDFTRAKGKEVMEALLKAHGDDIDAV-YAHNDEMALGAIQAIKAAGK 209 (273)
T ss_pred CCCCchHHHHHHHHHHHHHHCCCCEEeec--cCCcccHHHHHHHHHHHHHhCCCCccEE-EECCcHHHHHHHHHHHHcCC
Confidence 432 2234578889999987 4554421 11111223333444554433 34544 33455566678899999998
Q ss_pred CCCCeEEEEe
Q 003275 155 TAGSYVWIAT 164 (834)
Q Consensus 155 ~~~~~vwi~~ 164 (834)
..++-+-+.+
T Consensus 210 ~ip~di~iig 219 (273)
T cd06309 210 KPGKDIKIVS 219 (273)
T ss_pred CCCCCeEEEe
Confidence 7554444443
No 145
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=95.29 E-value=0.1 Score=55.88 Aligned_cols=61 Identities=18% Similarity=0.098 Sum_probs=39.9
Q ss_pred cCCCChhhhhcCCCCeeEeeC-chhhHH---HHhhhcccccc--eEecCCHHHHHHHHhcCCCCCceEEEEec
Q 003275 589 SQIEGIDSLISSTEPIGVQDG-SFAWNY---LVDELKIAESR--LVKLKNMEEYSIALARGPKGGGVAAIVDE 655 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v~~~~~-s~~~~~---l~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~g~~~a~~~~ 655 (834)
.++++++||. ++++++... +..... +.+..++.... .+.+.+..+...+|.+ |++|+++..
T Consensus 131 ~~i~sl~dL~--gk~v~~~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~----G~vDa~~~~ 197 (320)
T TIGR02122 131 SGIKTVADLK--GKRVAVGAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKD----GKIDAAFYT 197 (320)
T ss_pred CCCCcHHHcC--CCEEecCCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHC----CCccEEEEe
Confidence 4688999997 677776533 322211 22234443322 3567788899999998 999999887
No 146
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=95.23 E-value=0.81 Score=48.18 Aligned_cols=144 Identities=13% Similarity=0.110 Sum_probs=84.1
Q ss_pred CcE-EEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHH-cCCe-EEEEEEE
Q 003275 4 EVV-AAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEY-YGWR-EVIAIFV 80 (834)
Q Consensus 4 ~V~-aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~-~~W~-~v~iI~~ 80 (834)
++. +|++|..+.........+...++|+|.+....+ ..+.+....+++..-+..+++.+.. .|.+ +++++..
T Consensus 82 ~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~~~-----~~~~~~~V~~D~~~~g~~~~~~l~~~~~~~~~i~~~~~ 156 (295)
T PRK10653 82 GTKILLINPTDSDAVGNAVKMANQANIPVITLDRGAT-----KGEVVSHIASDNVAGGKMAGDFIAKKLGEGAKVIQLEG 156 (295)
T ss_pred CCCEEEEcCCChHHHHHHHHHHHHCCCCEEEEccCCC-----CCceeeEEccChHHHHHHHHHHHHHHhCCCceEEEEEc
Confidence 454 566776555544555677788999998753221 1122344556555556778877644 4543 5555553
Q ss_pred cC--CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEE-EEEeChhhHHHHHHHHHhCCC
Q 003275 81 DD--DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVF-VVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 81 d~--~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vi-vl~~~~~~~~~i~~~a~~~g~ 154 (834)
+. .......+.+.+++++.|+.+.... ....+..+....+.++.+..++.- +++.+...+..+++++++.|+
T Consensus 157 ~~~~~~~~~R~~gf~~al~~~g~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~A~g~l~al~~~G~ 231 (295)
T PRK10653 157 IAGTSAARERGEGFKQAVAAHKFNVLASQ--PADFDRTKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGK 231 (295)
T ss_pred cCCCccHHHHHHHHHHHHhhCCCEEEEec--CCCCCHHHHHHHHHHHHHhCCCcCEEEECCChhHHHHHHHHHHcCC
Confidence 32 2344667899999999998764321 111222334445556654444433 333445566678999999997
No 147
>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=95.18 E-value=0.26 Score=50.87 Aligned_cols=147 Identities=11% Similarity=0.022 Sum_probs=85.7
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc-
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD- 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d- 81 (834)
.+|.|||......... ..... ..++|+|......+ . +.+.....++...+..+++.+...|.++++++..+
T Consensus 54 ~~vdgiii~~~~~~~~-~~~~~-~~~ipvv~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~~ 125 (267)
T cd06284 54 KQADGIILLDGSLPPT-ALTAL-AKLPPIVQACEYIP---G---LAVPSVSIDNVAAARLAVDHLISLGHRRIALITGPR 125 (267)
T ss_pred cCCCEEEEecCCCCHH-HHHHH-hcCCCEEEEecccC---C---CCcceEEecccHHHHHHHHHHHHcCCceEEEEcCCc
Confidence 4677777632222222 22333 34999997642211 1 22233556667777888888877899999999754
Q ss_pred -CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 82 -DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 82 -~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
+..+....+.|.++++++|+.+..........+..+....+.++.+. .+++|+.. +...+..+++++++.|+..++
T Consensus 126 ~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~~~~a~g~~~al~~~g~~~p~ 204 (267)
T cd06284 126 DNPLARDRLEGYRQALAEAGLPADEELIQEGDFSLESGYAAARRLLALPDRPTAIFCF-SDEMAIGAISALKELGLRVPE 204 (267)
T ss_pred cchhHHHHHHHHHHHHHHcCCCCCcceEEeCCCChHHHHHHHHHHHhCCCCCcEEEEc-CcHHHHHHHHHHHHcCCCCcc
Confidence 34566678899999999885432111111111223334445554333 35665554 555677888999999976443
No 148
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=94.95 E-value=1.2 Score=43.31 Aligned_cols=70 Identities=13% Similarity=0.162 Sum_probs=48.4
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. ++.+++..+|.+|++|+++...... ...+ .+.|.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~v~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~---~~~l-~~~~l~~~~~~~v~~~ 80 (201)
T cd08459 13 YFLPRLLAALREVAP-GVRIETVR-------LPVDELEEALESGEIDLAIGYLPDL---GAGF-FQQRLFRERYVCLVRK 80 (201)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe-------cCccCHHHHhhCCCceEEEEcCCCC---cccc-eEEEeecCceEEEEcC
Confidence 455678888888875 34566653 4567889999999999998643221 1223 3568888888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (201)
T cd08459 81 DH 82 (201)
T ss_pred CC
Confidence 65
No 149
>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=94.89 E-value=1.4 Score=45.82 Aligned_cols=145 Identities=12% Similarity=0.054 Sum_probs=86.3
Q ss_pred CcEE-EECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEEE
Q 003275 4 EVVA-AIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIFV 80 (834)
Q Consensus 4 ~V~a-iiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~~ 80 (834)
+|.+ ||-|..+.........+...++|+|.+....+ ....+.+....+++...+..+++.+... |.+++++|..
T Consensus 55 ~vdgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~~~---~~~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~g 131 (272)
T cd06313 55 GWDFIAVDPLGIGTLTEAVQKAIARGIPVIDMGTLIA---PLQINVHSFLAPDNYFMGASVAQALCNAMGGKGKIAMLQG 131 (272)
T ss_pred CCCEEEEcCCChHHhHHHHHHHHHCCCcEEEeCCCCC---CCCCceEEEECCCcHHHHHHHHHHHHHHcCCCceEEEEEC
Confidence 4433 34444444344444555667999998755332 1111223345677777788888887666 8899999975
Q ss_pred cCC--cccchHHHHHHHHhcCC-cEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 81 DDD--YGRNGISVLGDALSKKR-AKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 81 d~~--~g~~~~~~l~~~l~~~g-~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
+.. ......+.+.+.+++.+ .++... .....+.......+.++.+.. +++| ++.+...+..+++.+++.|+
T Consensus 132 ~~~~~~~~~R~~gf~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~nd~~a~g~~~al~~~g~ 207 (272)
T cd06313 132 ALGHTGAQGRAQGFNDVIKKYPDIEVVDE--QPANWDVSKAARIWETWLTKYPQLDGA-FCHNDSMALAAYQIMKAAGR 207 (272)
T ss_pred CCCCcchhHHHHHHHHHHHhCCCCEEEec--cCCCCCHHHHHHHHHHHHHhCCCCCEE-EECCCcHHHHHHHHHHHcCC
Confidence 432 23456888999998875 555431 121222233344555544333 4553 34556677788999999897
No 150
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=94.82 E-value=3.2 Score=39.70 Aligned_cols=70 Identities=14% Similarity=0.144 Sum_probs=48.3
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. .+..++.+.+.+|++|+++...... ...+ -+.++....+++++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~ 80 (197)
T cd08440 13 TLLPPVLAAFRRRHP-GIRVRLRD-------VSAEQVIEAVRSGEVDFGIGSEPEA---DPDL-EFEPLLRDPFVLVCPK 80 (197)
T ss_pred hHHHHHHHHHHHhCC-CcEEEEEe-------CChHHHHHHHHcCCccEEEEeCCCC---CCCe-eEEEeecccEEEEecC
Confidence 555788888888775 34566653 4578899999999999998643221 1222 2457777888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (197)
T cd08440 81 DH 82 (197)
T ss_pred CC
Confidence 55
No 151
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=94.77 E-value=0.28 Score=50.46 Aligned_cols=150 Identities=10% Similarity=0.075 Sum_probs=93.3
Q ss_pred CCcEEE-ECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc-CC-eEEEEEE
Q 003275 3 NEVVAA-IGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY-GW-REVIAIF 79 (834)
Q Consensus 3 ~~V~ai-iGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~-~W-~~v~iI~ 79 (834)
+++.|| +.|..+........-+...+||+|++... .....+......+++...+..+++++... +- .+++++.
T Consensus 54 ~~~d~Iiv~~~~~~~~~~~l~~~~~~gIpvv~~d~~----~~~~~~~~~~v~~d~~~~G~~~a~~l~~~~~~~~~v~~~~ 129 (257)
T PF13407_consen 54 QGVDGIIVSPVDPDSLAPFLEKAKAAGIPVVTVDSD----EAPDSPRAAYVGTDNYEAGKLAAEYLAEKLGAKGKVLILS 129 (257)
T ss_dssp TTESEEEEESSSTTTTHHHHHHHHHTTSEEEEESST----HHTTSTSSEEEEE-HHHHHHHHHHHHHHHHTTTEEEEEEE
T ss_pred hcCCEEEecCCCHHHHHHHHHHHhhcCceEEEEecc----ccccccceeeeeccHHHHHHHHHHHHHHHhccCceEEecc
Confidence 345444 47777666667777788889999997554 11223455667778888899999997443 32 6777775
Q ss_pred EcCCc--ccchHHHHHHHHhc-CCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 80 VDDDY--GRNGISVLGDALSK-KRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 80 ~d~~~--g~~~~~~l~~~l~~-~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
...++ .....+.+.+.+++ .++++..... ....+..+....+.++....+-..|+.++...+..+.++..+.|+.+
T Consensus 130 ~~~~~~~~~~r~~g~~~~l~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~l~~~~~~~i~~~~~~~~~g~~~al~~~g~~~ 208 (257)
T PF13407_consen 130 GSPGNPNTQERLEGFRDALKEYPGVEIVDEYE-YTDWDPEDARQAIENLLQANPVDAIIACNDGMALGAAQALQQAGRAG 208 (257)
T ss_dssp SSTTSHHHHHHHHHHHHHHHHCTTEEEEEEEE-ECTTSHHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHHHHHHTTCTT
T ss_pred CCCCchHHHHHHHHHHHHHhhcceeeeeeeee-ccCCCHHHHHHHHHHhhhcCCceEEEeCCChHHHHHHHHHHHcCCcc
Confidence 44332 33467888888888 4666665222 22234455555555554444322335566777778999999999844
Q ss_pred C
Q 003275 157 G 157 (834)
Q Consensus 157 ~ 157 (834)
.
T Consensus 209 ~ 209 (257)
T PF13407_consen 209 K 209 (257)
T ss_dssp T
T ss_pred c
Confidence 3
No 152
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=94.69 E-value=3 Score=39.85 Aligned_cols=70 Identities=17% Similarity=0.133 Sum_probs=47.6
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. ++..++...+.+|++|+++.... .....+ ...+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~ 80 (193)
T cd08442 13 VRLPPLLAAYHARYP-KVDLSLST-------GTTGALIQAVLEGRLDGAFVAGP---VEHPRL-EQEPVFQEELVLVSPK 80 (193)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCccEEEEeCC---CCCCCc-EEEEeecCcEEEEecC
Confidence 455788888888775 34566654 55778999999999999986422 111222 2456677778888776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (193)
T cd08442 81 GH 82 (193)
T ss_pred CC
Confidence 54
No 153
>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=94.60 E-value=0.47 Score=48.98 Aligned_cols=150 Identities=12% Similarity=0.050 Sum_probs=87.1
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
.++.|||--...... .....+...++|+|......+ . +.......+....+..+++.+...|-+++++|..+.
T Consensus 54 ~~vdgiii~~~~~~~-~~~~~~~~~~ipvv~~~~~~~---~---~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~ 126 (268)
T cd01575 54 RRPAGLILTGLEHTE-RTRQLLRAAGIPVVEIMDLPP---D---PIDMAVGFSHAEAGRAMARHLLARGYRRIGFLGARM 126 (268)
T ss_pred cCCCEEEEeCCCCCH-HHHHHHHhcCCCEEEEecCCC---C---CCCCeEEeCcHHHHHHHHHHHHHCCCCcEEEecCCC
Confidence 356665542221122 233445567999998643211 1 112234556677788888888888999999998654
Q ss_pred --CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 83 --DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 83 --~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
.......+.+.+.+++.|.............+.......+.++.+. .+++|+. ++...+..+++.+++.|...++
T Consensus 127 ~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~~p~ 205 (268)
T cd01575 127 DDTRAQQRLEGFRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFC-SNDDLALGALFECQRRGISVPE 205 (268)
T ss_pred CcccHHHHHHHHHHHHHHcCCCCCceeEeccCCCHHHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHhCCCCCc
Confidence 3444557889999998886322211111112223334455555433 3566554 4555677889999999976544
Q ss_pred eE
Q 003275 159 YV 160 (834)
Q Consensus 159 ~v 160 (834)
.+
T Consensus 206 di 207 (268)
T cd01575 206 DI 207 (268)
T ss_pred ce
Confidence 44
No 154
>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=94.60 E-value=0.38 Score=49.70 Aligned_cols=134 Identities=10% Similarity=-0.009 Sum_probs=82.5
Q ss_pred hccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHhcCCc
Q 003275 24 VNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDALSKKRA 101 (834)
Q Consensus 24 ~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l~~~g~ 101 (834)
....++|+|......+. ..+ ..+.+++...+..+++.+...|-+++++|..+.. ......+.+.+.++++|+
T Consensus 74 ~~~~~ipvv~~~~~~~~---~~~---~~v~~d~~~~~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~ 147 (269)
T cd06288 74 PELLSVPTVLLNCYDAD---GAL---PSVVPDEEQGGYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQALAEAGI 147 (269)
T ss_pred HHhcCCCEEEEecccCC---CCC---CeEEEccHHHHHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHHHHcCC
Confidence 34578999987543221 122 2355677777888888887779999999975432 334567889999999886
Q ss_pred EEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEEe
Q 003275 102 KISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIAT 164 (834)
Q Consensus 102 ~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~~ 164 (834)
.+..........+..+....+.++.+. .+++|+. .+...+..+++++++.|+..++-+.+.+
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~vp~di~v~g 211 (269)
T cd06288 148 PFDPDLVVHGDWSADDGYEAAAALLDLDDRPTAIFC-GNDRMAMGAYQALLERGLRIPQDVSVVG 211 (269)
T ss_pred CCCHHHeEeCCCChHHHHHHHHHHHhCCCCCCEEEE-eCcHHHHHHHHHHHHcCCCCcccceEEe
Confidence 532111111111223333445555443 3566644 5566777899999999987555555554
No 155
>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=94.51 E-value=0.46 Score=49.38 Aligned_cols=136 Identities=10% Similarity=0.064 Sum_probs=82.2
Q ss_pred HHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHhc
Q 003275 21 SHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDALSK 98 (834)
Q Consensus 21 ~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l~~ 98 (834)
...+...++|+|.+....+. .. +....+++...+..+++.+...|.+++++|..+.. .+....+.+.+++++
T Consensus 80 ~~~~~~~~ipvV~~~~~~~~---~~---~~~V~~d~~~~g~~~a~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~ 153 (275)
T cd06295 80 PERLAETGLPFVVWGRPLPG---QP---YCYVGSDNVGGGRLATEHLLARGRRRIAFLGGPQDMPEGEERLEGYREALAE 153 (275)
T ss_pred HHHHHhCCCCEEEECCccCC---CC---CCEEEECcHHHHHHHHHHHHHCCCCeEEEEcCCCCcchhHHHHHHHHHHHHH
Confidence 34566789999987653322 22 23355667777888888888889999999875432 344567889999998
Q ss_pred CCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 99 KRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 99 ~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
.|..+..........+.......+.++... .+++|+.. +...+..+++.+++.|...++-+.+.
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~~~~a~g~~~~l~~~g~~ip~~i~ii 219 (275)
T cd06295 154 AGLPLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVFAA-SDLMALGALRALREAGRRVPEDVAVV 219 (275)
T ss_pred cCCCCChhhEEeccCCHHHHHHHHHHHHhCCCCCCEEEEC-CcHHHHHHHHHHHHhCCCCccceEEE
Confidence 875432211112112223333444444333 34655544 44566778888899998544444333
No 156
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=94.35 E-value=4.4 Score=38.83 Aligned_cols=70 Identities=16% Similarity=0.196 Sum_probs=47.4
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+.+.+.. ++-.+++.+|.+|++|+++....... ..+ .+.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~~~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~~~---~~~-~~~~l~~~~~~~v~~~ 80 (201)
T cd08420 13 YLLPRLLARFRKRYP-EVRVSLTI-------GNTEEIAERVLDGEIDLGLVEGPVDH---PDL-IVEPFAEDELVLVVPP 80 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCccEEEecCCCCC---cce-EEEeecCccEEEEecC
Confidence 455788888888765 34455553 44678899999999999987443222 222 2467777788888776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (201)
T cd08420 81 DH 82 (201)
T ss_pred CC
Confidence 55
No 157
>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=94.28 E-value=1.9 Score=45.03 Aligned_cols=162 Identities=10% Similarity=0.029 Sum_probs=87.3
Q ss_pred CcEEEEC-CCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHH----HcCC--eEEE
Q 003275 4 EVVAAIG-PQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVE----YYGW--REVI 76 (834)
Q Consensus 4 ~V~aiiG-p~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~----~~~W--~~v~ 76 (834)
++.+||= |..+.........+...++|+|.+....+.......+.+-....+....+...++.+. ..|+ ++++
T Consensus 54 ~~dgiii~~~~~~~~~~~~~~~~~~~iPvV~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~~~~~g~~~~~i~ 133 (289)
T cd01540 54 GAKGFVICVPDVKLGPAIVAKAKAYNMKVVAVDDRLVDADGKPMEDVPHVGMSATKIGEQVGEAIADEMKKRGWDPKEVG 133 (289)
T ss_pred CCCEEEEccCchhhhHHHHHHHHhCCCeEEEecCCCcccCCCccccceEecCCHHHHHHHHHHHHHHHHHhhcCCCcceE
Confidence 4544442 2223334455566778999999875432211100111222344556655566655543 3577 7888
Q ss_pred EEE-Ec--CCcccchHHHHHHHHhcCCcEEEeeecCCCC-CChHHHHHHHHHhhcCC--ceE-EEEEeChhhHHHHHHHH
Q 003275 77 AIF-VD--DDYGRNGISVLGDALSKKRAKISYKAPFSPG-ASRSAINSLLVGANLME--SRV-FVVHVNPDTGLTIFSVA 149 (834)
Q Consensus 77 iI~-~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~-~~~~~~~~~l~~l~~~~--~~v-ivl~~~~~~~~~i~~~a 149 (834)
+|. .. ........+.+.+++++.|+........... .+...-...+.++.... ++. .|++.+...+..+++++
T Consensus 134 ~i~~~~~~~~~~~~R~~G~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~~d~~a~g~~~al 213 (289)
T cd01540 134 ALRITYDELDTAKPRTDGALEALKAPGFPEANIFQAPQKTTDTEGAFDAAASTLTKNPNVKNWIIYGLNDETVLGAVRAT 213 (289)
T ss_pred EEEecCCCCcchhhHHHHHHHHHhcCCCCcceEecccccCcchhhHHHHHHHHHHhCCCcCeeEEEeCCcHHHHHHHHHH
Confidence 875 22 2345667889999999888653211111111 11122233444544333 343 45556667788899999
Q ss_pred HhCCCCCCCeEEEEeC
Q 003275 150 KSLGMTAGSYVWIATD 165 (834)
Q Consensus 150 ~~~g~~~~~~vwi~~~ 165 (834)
++.|..+.....+..+
T Consensus 214 ~~~g~~~~di~vig~d 229 (289)
T cd01540 214 EQSGIAAADVIGVGIN 229 (289)
T ss_pred HHcCCCCcceEEEecC
Confidence 9999874344444444
No 158
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=94.25 E-value=3.7 Score=39.86 Aligned_cols=73 Identities=16% Similarity=0.185 Sum_probs=49.5
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.++.+ .+++++.. ++.+++++.|.+|++|++++.......-...+. +.+..+..+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~ 83 (202)
T cd08468 13 AVMPRLMARLEELAP-SVRLNLVH-------AEQKLPLDALLAGEIDFALGYSHDDGAEPRLIE-ERDWWEDTYVVIASR 83 (202)
T ss_pred HHhHHHHHHHHhhCC-CCEEEEEE-------CChHhHHHHHHCCCccEEEecccccccCCCCEE-EEEEecCcEEEEEeC
Confidence 456788899988875 34566664 567899999999999999874322110012233 357777788888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
+.
T Consensus 84 ~h 85 (202)
T cd08468 84 DH 85 (202)
T ss_pred CC
Confidence 65
No 159
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=94.22 E-value=4.7 Score=38.57 Aligned_cols=70 Identities=16% Similarity=0.126 Sum_probs=48.5
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+..++++.+.+..+ .+.+++.. ++..++...|.+|++|+++....... ..+ -..++....+++++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~L~~~~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~v~~~ 80 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVE-------YGGKKVEQAVLNGELDVGITVLPVDE---EEF-DSQPLCNEPLVAVLPR 80 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEE-------cCcHHHHHHHHcCCCCEEEEeccccc---CCc-eeEEeccccEEEEecC
Confidence 456788899988875 45566654 45788999999999999986443221 222 2456677788888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (197)
T cd08438 81 GH 82 (197)
T ss_pred CC
Confidence 65
No 160
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=94.19 E-value=4.2 Score=39.03 Aligned_cols=71 Identities=11% Similarity=0.052 Sum_probs=49.3
Q ss_pred eeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEe
Q 003275 400 KGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAP 479 (834)
Q Consensus 400 ~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~ 479 (834)
..+-.+++..+.+..+ .+.+++.. ++..+++.+|.+|++|+++...... ...+ .+.|+....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~~~---~~~~-~~~~l~~~~~~~~~~ 79 (198)
T cd08412 12 PYYLPGLLRRFREAYP-GVEVRVVE-------GNQEELEEGLRSGELDLALTYDLDL---PEDI-AFEPLARLPPYVWLP 79 (198)
T ss_pred hhhhHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEcCCCC---Cccc-ceeeeeccceEEEec
Confidence 3566788888888876 34566654 5578899999999999998633221 2222 247777888888877
Q ss_pred cCC
Q 003275 480 VQK 482 (834)
Q Consensus 480 ~~~ 482 (834)
...
T Consensus 80 ~~~ 82 (198)
T cd08412 80 ADH 82 (198)
T ss_pred CCC
Confidence 655
No 161
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=94.19 E-value=0.66 Score=50.05 Aligned_cols=132 Identities=8% Similarity=-0.001 Sum_probs=80.3
Q ss_pred HHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHH
Q 003275 19 VISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDAL 96 (834)
Q Consensus 19 ~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l 96 (834)
.....+...++|+|...... ....+++ ...++...+..+++.+...|.+++++|..+.. ......+.+.+++
T Consensus 135 ~~~~~l~~~~iPvV~~~~~~---~~~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~al 208 (342)
T PRK10014 135 DLREMAEEKGIPVVFASRAS---YLDDVDT---VRPDNMQAAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATL 208 (342)
T ss_pred HHHHHHhhcCCCEEEEecCC---CCCCCCE---EEeCCHHHHHHHHHHHHHCCCCEEEEEcCCcccccHHHHHHHHHHHH
Confidence 44456677899999864321 1122332 45566667788888888889999999864432 2334678899999
Q ss_pred hcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCC
Q 003275 97 SKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 97 ~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~ 157 (834)
++.|+.+.....+....+.......+.++.+. .+++|+ +.+...+..+++.+.+.|+..+
T Consensus 209 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~A~g~~~~l~~~g~~vp 270 (342)
T PRK10014 209 LKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVV-CYNETIAMGAWFGLLRAGRQSG 270 (342)
T ss_pred HHcCCCCCcceEecCCCChHHHHHHHHHHHcCCCCCCEEE-ECCcHHHHHHHHHHHHcCCCCC
Confidence 99987543211111111222333444454433 345554 4556677788889999998654
No 162
>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=94.17 E-value=0.67 Score=47.74 Aligned_cols=152 Identities=11% Similarity=0.064 Sum_probs=85.4
Q ss_pred CcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC-
Q 003275 4 EVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD- 82 (834)
Q Consensus 4 ~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~- 82 (834)
+|.+||=-........ ...+.+.++|+|......+ ....+++ ..++..-+..+++.+...|-++|++|....
T Consensus 55 ~vdgiIi~~~~~~~~~-~~~l~~~~ipvV~~~~~~~---~~~~~~v---~~d~~~~~~~~~~~l~~~g~~~I~~i~~~~~ 127 (265)
T cd06299 55 RVDGIIVVPHEQSAEQ-LEDLLKRGIPVVFVDREIT---GSPIPFV---TSDPQPGMTEAVSLLVALGHKKIGYISGPQD 127 (265)
T ss_pred CCCEEEEcCCCCChHH-HHHHHhCCCCEEEEecccC---CCCCCEE---EECcHHHHHHHHHHHHHcCCCcEEEEeCCCC
Confidence 5555553222222223 3555667999998765322 2233443 234444455566777677889999986433
Q ss_pred -CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 83 -DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 83 -~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
.......+.+.++++++|+.+.............+....+.++.+..+++|+. ++...+..+++++++.|+..++-+.
T Consensus 128 ~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~av~~-~~d~~a~gv~~al~~~g~~vp~dv~ 206 (265)
T cd06299 128 TSTGRERLEAFRQACASLGLEVNEDLVVLGGYSQESGYAGATKLLDQGATAIIA-GDSMMTIGAIRAIHDAGLVIGEDIS 206 (265)
T ss_pred cccHHHHHHHHHHHHHHCCCCCChHhEEecCcchHHHHHHHHHHHcCCCCEEEE-cCcHHHHHHHHHHHHhCCCCCccee
Confidence 23445567899999998854321111111111223334455554444776544 5556678889999999987554444
Q ss_pred EE
Q 003275 162 IA 163 (834)
Q Consensus 162 i~ 163 (834)
+.
T Consensus 207 v~ 208 (265)
T cd06299 207 LI 208 (265)
T ss_pred EE
Confidence 44
No 163
>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=94.12 E-value=0.79 Score=47.24 Aligned_cols=135 Identities=13% Similarity=0.086 Sum_probs=81.4
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cc-cchHHHHHHHHhc
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YG-RNGISVLGDALSK 98 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g-~~~~~~l~~~l~~ 98 (834)
..+...++|+|.+....+ ....+ ....++...+..+++.+...|-++++++..... .. ......+.+.+++
T Consensus 72 ~~~~~~~ipvV~~~~~~~---~~~~~---~v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~~~ 145 (267)
T cd06283 72 QRLAKNGKPVVLVDRKIP---ELGVD---TVTLDNYEAAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEALAE 145 (267)
T ss_pred HHHhcCCCCEEEEcCCCC---CCCCC---EEEeccHHHHHHHHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHHHH
Confidence 445677999998754322 11223 234556667788888887889999999975432 11 2457888999988
Q ss_pred CCcEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 99 KRAKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 99 ~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
.|.............+..+....+.++.+.. +++|+.. +...+..+++.+++.|+..++-+-+.
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~vp~di~v~ 211 (267)
T cd06283 146 HGIGVNEELIEIDDEDADELDERLRQLLNKPKKKTAIFAA-NGLILLEVLKALKELGIRIPEDVGLI 211 (267)
T ss_pred cCCCCCcceeEecccchHHHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCccceEEE
Confidence 8743221111111112244455666665443 4555543 45566788999999998655444444
No 164
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=94.12 E-value=4.1 Score=39.11 Aligned_cols=70 Identities=23% Similarity=0.296 Sum_probs=48.2
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. ++..+++.+|.+|++|+++..... ....+. ..+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 80 (198)
T cd08421 13 EFLPEDLASFLAAHP-DVRIDLEE-------RLSADIVRAVAEGRADLGIVAGNV---DAAGLE-TRPYRTDRLVVVVPR 80 (198)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------cCcHHHHHHHhcCCceEEEEecCC---CCCCcE-EEEeecCcEEEEeCC
Confidence 344678888888765 34566653 457889999999999999864322 222333 467778888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (198)
T cd08421 81 DH 82 (198)
T ss_pred CC
Confidence 65
No 165
>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=94.06 E-value=0.66 Score=47.80 Aligned_cols=141 Identities=13% Similarity=0.060 Sum_probs=83.7
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
.+|.+||--.+.... .+...+...++|+|.+....+ . +.+.....++...+..+++.+...|-++++++..+.
T Consensus 53 ~~vdgiii~~~~~~~-~~~~~~~~~~ipvV~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~ 125 (266)
T cd06278 53 YRVDGVIVTSGTLSS-ELAEECRRNGIPVVLINRYVD---G---PGVDAVCSDNYEAGRLAAELLLAKGCRRIAFIGGPA 125 (266)
T ss_pred cCCCEEEEecCCCCH-HHHHHHhhcCCCEEEECCccC---C---CCCCEEEEChHHHHHHHHHHHHHCCCceEEEEcCCC
Confidence 456666543222222 234556678999998754322 1 122346667777888888888777889999998543
Q ss_pred C--cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCC
Q 003275 83 D--YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLG 153 (834)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g 153 (834)
. ......+.+.+.+++.|..+... ... ..+..+....+.++.+. .+++|+.. +...+..+++.+++.+
T Consensus 126 ~~~~~~~R~~gf~~~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~~l~~~~ 197 (266)
T cd06278 126 DTSTSRERERGFRDALAAAGVPVVVE-EAG-DYSYEGGYEAARRLLASRPRPDAIFCA-NDLLAIGVMDAARQEG 197 (266)
T ss_pred cccchHHHHHHHHHHHHHcCCChhhh-ccC-CCCHHHHHHHHHHHHhcCCCCCEEEEc-CcHHHHHHHHHHHHhc
Confidence 3 44556788999999888764321 111 11223334445554433 34555443 4445667777777653
No 166
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=94.04 E-value=3.8 Score=43.34 Aligned_cols=70 Identities=9% Similarity=0.097 Sum_probs=49.0
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
++-..++..+.+..+ .+.+.+.. .+-++++++|.+|++|+++........ . -.+.|+....+++++++
T Consensus 104 ~~~~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~---~-l~~~~l~~~~~~~~~~~ 171 (305)
T PRK11151 104 YLLPHIIPMLHQTFP-KLEMYLHE-------AQTHQLLAQLDSGKLDCAILALVKESE---A-FIEVPLFDEPMLLAVYE 171 (305)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEEecCCCCC---C-eEEEEeccCcEEEEecC
Confidence 444677777777665 35566653 456889999999999999874432222 1 24578888899999876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 172 ~h 173 (305)
T PRK11151 172 DH 173 (305)
T ss_pred CC
Confidence 65
No 167
>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=94.01 E-value=2.1 Score=44.17 Aligned_cols=143 Identities=15% Similarity=0.096 Sum_probs=82.9
Q ss_pred CCcEEEEC-CCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEE
Q 003275 3 NEVVAAIG-PQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIF 79 (834)
Q Consensus 3 ~~V~aiiG-p~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~ 79 (834)
.++.++|- |..+.........+...++|+|.+....+ ..+.+....+++...+...++++... |-+++++++
T Consensus 54 ~~vdgiii~~~~~~~~~~~~~~~~~~~ipvV~~~~~~~-----~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~ 128 (267)
T cd06322 54 KKVDAIVLSPVDSKGIRAAIAKAKKAGIPVITVDIAAE-----GVAVVSHVATDNYAGGVLAGELAAKVLNGKGQVAIID 128 (267)
T ss_pred cCCCEEEEcCCChhhhHHHHHHHHHCCCCEEEEcccCC-----CCceEEEEecChHHHHHHHHHHHHHHhCCCceEEEEe
Confidence 35665544 44333323334556678999998753211 11223345566666677777777554 778999987
Q ss_pred EcC-CcccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 80 VDD-DYGRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 80 ~d~-~~g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
..+ .......+.+++++++. |+.+.... . ..+.+.....+.++... .+++|+ .++...+..+++++++.|.
T Consensus 129 ~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~al~~~g~ 203 (267)
T cd06322 129 YPTVQSVVDRVRGFKEALADYPNIKIVAVQ-P--GITRAEALTAAQNILQANPDLDGIF-AFGDDAALGAVSAIKAAGR 203 (267)
T ss_pred cCCCccHHHHHHHHHHHHHhCCCcEEEEec-C--CCChHHHHHHHHHHHHhCCCCCEEE-EcCCcHHHHHHHHHHHCCC
Confidence 432 23344578899999998 88764221 1 11222333344444332 355443 3445567788889899897
No 168
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=94.01 E-value=0.66 Score=50.07 Aligned_cols=136 Identities=7% Similarity=0.051 Sum_probs=80.6
Q ss_pred Hhhcc-CCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc--CCcccchHHHHHHHHhc
Q 003275 22 HVVNE-LNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD--DDYGRNGISVLGDALSK 98 (834)
Q Consensus 22 ~~~~~-~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d--~~~g~~~~~~l~~~l~~ 98 (834)
..+.. .++|+|.+....+ +..++.+ ..+++...+...++.+...|-+++++|..+ +.......+.+.+++++
T Consensus 132 ~~l~~~~~iPvV~~d~~~~---~~~~~~~--v~~d~~~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~ 206 (341)
T PRK10703 132 AMLEEYRHIPMVVMDWGEA---KADFTDA--IIDNAFEGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEE 206 (341)
T ss_pred HHHHhcCCCCEEEEecccC---CcCCCCe--EEECcHHHHHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHHHHHHH
Confidence 34444 6999998754321 1121222 344444556777777776788999998643 33445567899999999
Q ss_pred CCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 99 KRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 99 ~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
+|+.+........+.+..+....+.++.+. .+++|+. ++...+..+++++++.|...++-+.++
T Consensus 207 ~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~nd~~a~g~~~al~~~g~~ip~dv~vv 272 (341)
T PRK10703 207 ANIKVPEEWIVQGDFEPESGYEAMQQILSQKHRPTAVFC-GGDIMAMGAICAADEMGLRVPQDISVI 272 (341)
T ss_pred cCCCCChHHeEeCCCCHHHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 997654321111111223334455555433 3566554 455667789999999997655444444
No 169
>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=94.00 E-value=0.99 Score=46.48 Aligned_cols=134 Identities=11% Similarity=0.049 Sum_probs=80.3
Q ss_pred hhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHhcCC
Q 003275 23 VVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDALSKKR 100 (834)
Q Consensus 23 ~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l~~~g 100 (834)
.+...++|+|.+....+ ....++ ...++..-+..+++.+...|-++++++..+.. ......+.+.+.++++|
T Consensus 73 ~~~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~ 146 (264)
T cd06274 73 LCQKAGLPVVALDRPGD---PSRFPS---VVSDNRDGAAELTRELLAAPPEEVLFLGGLPELSPSRERLAGFRQALADAG 146 (264)
T ss_pred HHHhcCCCEEEecCccC---CCCCCE---EEEccHHHHHHHHHHHHHCCCCcEEEEeCCCcccchHHHHHHHHHHHHHcC
Confidence 45667899998754322 222333 34455555677788777788899999875432 34456789999999988
Q ss_pred cEEEeeecCCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 101 AKISYKAPFSPGASRSAINSLLVGANLM---ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 101 ~~I~~~~~~~~~~~~~~~~~~l~~l~~~---~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
..+..........+...-...+.++.+. .+++|+.. +...+..+++++++.|+..++-+-|+
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~~-~d~~A~g~~~al~~~g~~ip~dv~v~ 211 (264)
T cd06274 147 LPVQPDWIYAEGYSPESGYQLMAELLARLGRLPRALFTT-SYTLLEGVLRFLRERPGLAPSDLRIA 211 (264)
T ss_pred CCCCcceeecCCCChHHHHHHHHHHHccCCCCCcEEEEc-ChHHHHHHHHHHHHcCCCCCcceEEE
Confidence 5432111111112222333444444332 35665544 55667789999999998755555544
No 170
>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=93.95 E-value=0.84 Score=47.13 Aligned_cols=134 Identities=7% Similarity=-0.073 Sum_probs=80.0
Q ss_pred hhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHhcCC
Q 003275 23 VVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD--DYGRNGISVLGDALSKKR 100 (834)
Q Consensus 23 ~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~--~~g~~~~~~l~~~l~~~g 100 (834)
+....++|+|......+ ...+++ ...++...+..+++.+...|-+++++|.... .......+.+.+.+++.|
T Consensus 74 l~~~~~ipvV~i~~~~~---~~~~~~---V~~d~~~~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~ 147 (269)
T cd06275 74 LERYRHIPMVVMDWGPE---DDFADK---IQDNSEEGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAG 147 (269)
T ss_pred HHhcCCCCEEEEecccC---CCCCCe---EeeCcHHHHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHcC
Confidence 33456999998754322 122333 4455666677778888778999999987432 234455788999999888
Q ss_pred cEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 101 AKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 101 ~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
+.+..........+.......++++.+.. +++|+ +++...+..+++.+++.|...++-+-++
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~vp~di~vv 211 (269)
T cd06275 148 LPVNPGWIVEGDFECEGGYEAMQRLLAQPKRPTAVF-CGNDLMAMGALCAAQEAGLRVPQDLSII 211 (269)
T ss_pred CCCCHHHhccCCCChHHHHHHHHHHHcCCCCCcEEE-ECChHHHHHHHHHHHHcCCCCCcceEEE
Confidence 76532111111112233344555554443 45433 3455667788889999887655444444
No 171
>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=93.90 E-value=2.2 Score=44.50 Aligned_cols=112 Identities=11% Similarity=0.022 Sum_probs=68.5
Q ss_pred EEccCChHHHHHHHHHHHHH--cCCeEEEEEEEcC-CcccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHh
Q 003275 50 LRTTQSDYYQMHAVADLVEY--YGWREVIAIFVDD-DYGRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGA 125 (834)
Q Consensus 50 ~r~~ps~~~q~~aia~ll~~--~~W~~v~iI~~d~-~~g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l 125 (834)
-....++..-+..+++.+.. .|-+++++|.... ..+....+.+.++++++ |+.+... +....+..+....+.++
T Consensus 107 ~~V~~d~~~~g~~~~~~L~~~~~g~~~i~~l~~~~~~~~~~R~~gf~~al~~~~~~~~~~~--~~~~~~~~~~~~~~~~~ 184 (280)
T cd06303 107 LYVGFDHAAGARLLADYFIKRYPNHARYAMLYFSPGYISTARGDTFIDCVHARNNWTLTSE--FYTDATRQKAYQATSDI 184 (280)
T ss_pred eEeCCCHHHHHHHHHHHHHHhcCCCcEEEEEECCCCcchhHHHHHHHHHHHhCCCceEEEe--ecCCCCHHHHHHHHHHH
Confidence 34556666677778887766 7889999996532 33445678899999988 7664332 22122223333445554
Q ss_pred hcCC--ceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 126 NLME--SRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 126 ~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
.+.. +++|+ +.+...+..+++++++.|+. .+...+..+
T Consensus 185 l~~~~~~~ai~-~~nd~~A~g~l~al~~~G~~-~dv~vvg~d 224 (280)
T cd06303 185 LSNNPDVDFIY-ACSTDIALGASDALKELGRE-DDILINGWG 224 (280)
T ss_pred HHhCCCCcEEE-ECCcHHHHHHHHHHHHcCCC-CCcEEEecC
Confidence 4333 45544 45566777899999999985 343344433
No 172
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=93.89 E-value=5.3 Score=38.42 Aligned_cols=72 Identities=19% Similarity=0.234 Sum_probs=48.0
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-..++..+.+..+ .+.+++.. .+..++..+|.+|++|++++..... .....+ .+.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~-~~~~l~~~~~~~v~~~ 82 (201)
T cd08418 13 TLMPAVINRFKEQFP-DVQISIYE-------GQLSSLLPELRDGRLDFAIGTLPDE-MYLKEL-ISEPLFESDFVVVARK 82 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CcHHHHHHHHHcCCCcEEEEecCCC-CCCcce-eEEeecCCceEEEeCC
Confidence 455778888888775 45566654 5578999999999999998743221 111223 3466677788888776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 83 ~~ 84 (201)
T cd08418 83 DH 84 (201)
T ss_pred CC
Confidence 54
No 173
>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=93.88 E-value=0.73 Score=47.60 Aligned_cols=139 Identities=13% Similarity=0.114 Sum_probs=81.0
Q ss_pred HHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCCc--ccchHHHHHHHHhc
Q 003275 21 SHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDDY--GRNGISVLGDALSK 98 (834)
Q Consensus 21 ~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~~--g~~~~~~l~~~l~~ 98 (834)
...+...++|+|.+....+. ....++ +..++...+..+++.+...|-++++++..+..+ .....+.|.+++++
T Consensus 76 ~~~~~~~~ipvV~~~~~~~~--~~~~~~---v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~ 150 (270)
T cd06294 76 IDYLKEEKFPFVVIGKPEDD--KENITY---VDNDNIQAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALED 150 (270)
T ss_pred HHHHHhcCCCEEEECCCCCC--CCCCCe---EEECcHHHHHHHHHHHHHcCCccEEEecCCcccHHHHHHHHHHHHHHHH
Confidence 34456779999987543211 012222 344566667777888777788999999754332 33457889999999
Q ss_pred CCcEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCCCCCCeE-EEEeC
Q 003275 99 KRAKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV-WIATD 165 (834)
Q Consensus 99 ~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v-wi~~~ 165 (834)
.|+.+..........+.......+.++.+.. +++|+. .+...+..+++++++.|+..++-+ ++..+
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~iP~dv~vig~d 219 (270)
T cd06294 151 HGIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIVA-TDDLLALGVLKVLNELGLKVPEDLSIIGFN 219 (270)
T ss_pred cCCCCCcceEEecCCchHHHHHHHHHHHhCCCCCCEEEE-CChHHHHHHHHHHHHcCCCCCcceEEEeeC
Confidence 8853211111111112233344555554333 555544 455678889999999998654433 44433
No 174
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=93.88 E-value=2.6 Score=43.69 Aligned_cols=154 Identities=8% Similarity=-0.022 Sum_probs=83.1
Q ss_pred CcEEEE-CCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc-CC--eEEEEEE
Q 003275 4 EVVAAI-GPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY-GW--REVIAIF 79 (834)
Q Consensus 4 ~V~aii-Gp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~-~W--~~v~iI~ 79 (834)
++.||| .|..+.........+.+.++|+|.+....+. ... +..+..++...+...++++... |. +++++|.
T Consensus 58 ~vdgiii~~~~~~~~~~~i~~~~~~~ipvV~~~~~~~~--~~~---~~~V~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~ 132 (275)
T cd06307 58 RSDGVALVAPDHPQVRAAVARLAAAGVPVVTLVSDLPG--SPR---AGYVGIDNRAAGRTAAWLIGRFLGRRPGKVAVLA 132 (275)
T ss_pred cCCEEEEeCCCcHHHHHHHHHHHHCCCcEEEEeCCCCC--Cce---eeEEccChHHHHHHHHHHHHHHhCCCCCeEEEEe
Confidence 444443 4433332223345566689999987542211 111 1224455555566666766443 53 6999887
Q ss_pred EcCC--cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 80 VDDD--YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANL--MESRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 80 ~d~~--~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~--~~~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
.+.. ......+.+.+++++.+..+..........+..+....+.++.+ ..+++|+...+. +..+++++++.|+.
T Consensus 133 ~~~~~~~~~~R~~gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~--~~g~~~al~~~g~~ 210 (275)
T cd06307 133 GSHRFRGHEEREMGFRSVLREEFPGLRVLETLEGLDDPARAYEATRKLLARHPDLVGIYNAGGG--NRGVIRALREAGRA 210 (275)
T ss_pred cCCCCcchHHHHHHHHHHHHhhCCCcEEEeeccCCCChHHHHHHHHHHHHhCCCceEEEECCCC--hHHHHHHHHHcCCC
Confidence 5432 33455788999998877544322222212222333345555433 245666665543 46899999999974
Q ss_pred CCCeEEEEeC
Q 003275 156 AGSYVWIATD 165 (834)
Q Consensus 156 ~~~~vwi~~~ 165 (834)
.+...+..|
T Consensus 211 -~di~Ivg~d 219 (275)
T cd06307 211 -GKVVFVGHE 219 (275)
T ss_pred -CCcEEEEec
Confidence 344444433
No 175
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=93.82 E-value=6.3 Score=37.85 Aligned_cols=70 Identities=14% Similarity=0.184 Sum_probs=47.1
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. .+-.++...|.+|++|+++..... ....+ -+.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~-~~~~l~~~~~~~~~~~ 80 (198)
T cd08433 13 VLAVPLLRAVRRRYP-GIRLRIVE-------GLSGHLLEWLLNGRLDLALLYGPP---PIPGL-STEPLLEEDLFLVGPA 80 (198)
T ss_pred hcchHHHHHHHHHCC-CcEEEEEe-------cCcHHHHHHHhCCCCcEEEEeCCC---CCCCe-eEEEeccccEEEEecC
Confidence 455678888888775 44566653 345788999999999999863322 11222 3567777888888776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (198)
T cd08433 81 DA 82 (198)
T ss_pred CC
Confidence 55
No 176
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=93.78 E-value=5.6 Score=38.77 Aligned_cols=72 Identities=10% Similarity=0.081 Sum_probs=49.3
Q ss_pred eeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEe
Q 003275 400 KGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAP 479 (834)
Q Consensus 400 ~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~ 479 (834)
..+-.+++..+.+..+ .+.+++... ++.++++++|.+|++|++++...... ..++ ..|+.+..++++++
T Consensus 12 ~~~~~~~l~~~~~~~P-~~~v~~~~~------~~~~~l~~~L~~g~lDl~i~~~~~~~---~~l~-~~~l~~~~~~lv~~ 80 (203)
T cd08463 12 ALFLPELVARFRREAP-GARLEIHPL------GPDFDYERALASGELDLVIGNWPEPP---EHLH-LSPLFSDEIVCLMR 80 (203)
T ss_pred HHHhHHHHHHHHHHCC-CCEEEEEeC------CcchhHHHHHhcCCeeEEEeccccCC---CCcE-EeEeecCceEEEEe
Confidence 3566788999988776 344665531 34678999999999999987422211 2232 36777888888888
Q ss_pred cCC
Q 003275 480 VQK 482 (834)
Q Consensus 480 ~~~ 482 (834)
+..
T Consensus 81 ~~h 83 (203)
T cd08463 81 ADH 83 (203)
T ss_pred CCC
Confidence 766
No 177
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR 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 wh
Probab=93.76 E-value=0.78 Score=47.07 Aligned_cols=149 Identities=15% Similarity=0.099 Sum_probs=89.8
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc-
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD- 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d- 81 (834)
+++.++|....... ..+...+...++|+|......+ ..+ .+..+....+..+++.+...|-++++++...
T Consensus 54 ~~~dgii~~~~~~~-~~~~~~~~~~~ipvv~~~~~~~-----~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~v~~~~ 124 (259)
T cd01542 54 QKVDGIILLATTIT-DEHREAIKKLNVPVVVVGQDYP-----GIS---SVVYDDYGAGYELGEYLAQQGHKNIAYLGVSE 124 (259)
T ss_pred cCCCEEEEeCCCCC-HHHHHHHhcCCCCEEEEeccCC-----CCC---EEEECcHHHHHHHHHHHHHcCCCcEEEEcCCc
Confidence 46666665433222 2344556667899998754221 222 2455667778888888877888999988632
Q ss_pred C--CcccchHHHHHHHHhcCCc-EEEeeecCCCCCChHHHHHHHHHhhcCC-ceEEEEEeChhhHHHHHHHHHhCCCCCC
Q 003275 82 D--DYGRNGISVLGDALSKKRA-KISYKAPFSPGASRSAINSLLVGANLME-SRVFVVHVNPDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 82 ~--~~g~~~~~~l~~~l~~~g~-~I~~~~~~~~~~~~~~~~~~l~~l~~~~-~~vivl~~~~~~~~~i~~~a~~~g~~~~ 157 (834)
+ ..+....+.+.+.+++.|. .+.. .....+.......+.++.+.. +++|+... ...+..+++.+++.|+..+
T Consensus 125 ~~~~~~~~r~~gf~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~~i~~~~-d~~a~g~~~~l~~~g~~vp 200 (259)
T cd01542 125 SDIAVGILRKQGYLDALKEHGICPPNI---VETDFSYESAYEAAQELLEPQPPDAIVCAT-DTIALGAMKYLQELGRRIP 200 (259)
T ss_pred ccchhHHHHHHHHHHHHHHcCCChHHe---eeccCchhhHHHHHHHHhcCCCCCEEEEcC-cHHHHHHHHHHHHcCCCCC
Confidence 2 2334567889999998887 2111 111111223334455554443 56655544 5567789999999998766
Q ss_pred CeEEEEe
Q 003275 158 SYVWIAT 164 (834)
Q Consensus 158 ~~vwi~~ 164 (834)
+-+.+.+
T Consensus 201 ~di~v~g 207 (259)
T cd01542 201 EDISVAG 207 (259)
T ss_pred CceEEEe
Confidence 6666654
No 178
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=93.72 E-value=3.7 Score=43.61 Aligned_cols=85 Identities=18% Similarity=0.133 Sum_probs=54.9
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
.++|+||+... ....+-.+++..+.++.+ .+.+.+.. ++...++..|.+|++|+++..
T Consensus 92 ~g~l~Ig~~~~--------------~~~~~l~~~l~~~~~~~p-~i~l~~~~-------~~~~~~~~~L~~g~~D~~i~~ 149 (313)
T PRK12684 92 QGNLTIATTHT--------------QARYALPAAIKEFKKRYP-KVRLSILQ-------GSPTQIAEMVLHGQADLAIAT 149 (313)
T ss_pred CCeEEEEechH--------------HHHHHhHHHHHHHHHHCC-CceEEEEe-------CChHHHHHHHHCCCcCEEEee
Confidence 36799998321 112444778888887765 34466553 457889999999999999864
Q ss_pred eeeecCceeeEEecceeeeceEEEEEecCC
Q 003275 453 ITIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 453 ~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
-..... ..+ -+.|+....++++++...
T Consensus 150 ~~~~~~--~~l-~~~~l~~~~~~~v~~~~~ 176 (313)
T PRK12684 150 EAIADY--KEL-VSLPCYQWNHCVVVPPDH 176 (313)
T ss_pred cCCCCC--CCc-eEEEeccceEEEEeCCCC
Confidence 221111 112 256777788888887665
No 179
>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=93.69 E-value=1.2 Score=45.98 Aligned_cols=131 Identities=11% Similarity=-0.001 Sum_probs=80.3
Q ss_pred HHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHhc
Q 003275 21 SHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDALSK 98 (834)
Q Consensus 21 ~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l~~ 98 (834)
...+...++|+|.+....+ ...+++ ...++...+..+++.+...|-+++++|..+.. ......+.+.+.+++
T Consensus 71 ~~~~~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~ 144 (268)
T cd06270 71 LIELAAQVPPLVLINRHIP---GLADRC---IWLDNEQGGYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAE 144 (268)
T ss_pred HHHHhhCCCCEEEEeccCC---CCCCCe---EEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHH
Confidence 3445677999998754332 112232 45667777888888887789999999875432 233457788999998
Q ss_pred CCcEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 99 KRAKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 99 ~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
+|..+..........+..+....+.++.+.. +++|+ .++...+..+++.+++.|+..++
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~ip~ 205 (268)
T cd06270 145 AGIALDESLIIEGDFTEEGGYAAMQELLARGAPFTAVF-CANDEMAAGAISALREHGISVPQ 205 (268)
T ss_pred cCCCCCcceEEECCCCHHHHHHHHHHHHhCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCC
Confidence 8865421111111122234445555554443 45544 34455677889999999986544
No 180
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=93.68 E-value=6 Score=41.82 Aligned_cols=86 Identities=17% Similarity=0.136 Sum_probs=55.2
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
++||||+... -...+-.+++..+.+..+ .+.+.+.. ++...++..|.+|++|+++...
T Consensus 95 g~l~ig~~~~--------------~~~~~~~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 152 (305)
T CHL00180 95 GTLIIGASQT--------------TGTYLMPRLIGLFRQRYP-QINVQLQV-------HSTRRIAWNVANGQIDIAIVGG 152 (305)
T ss_pred ceEEEEEcCc--------------chHhHHHHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHcCCccEEEEcC
Confidence 5799998321 112345677788877765 24455543 4578899999999999998632
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCC
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
......... -.+.++....++++++...
T Consensus 153 ~~~~~~~~~-~~~~~l~~~~~~~v~~~~~ 180 (305)
T CHL00180 153 EVPTELKKI-LEITPYVEDELALIIPKSH 180 (305)
T ss_pred ccCcccccc-eeEEEeccCcEEEEECCCC
Confidence 221111111 2357778888888888765
No 181
>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=93.62 E-value=0.86 Score=46.86 Aligned_cols=133 Identities=15% Similarity=0.107 Sum_probs=80.7
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHhcC
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDALSKK 99 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l~~~ 99 (834)
..+...++|+|.+....+ ..+++ +..++...+..+++.+...|-++++++..... ........+.+++++.
T Consensus 68 ~~~~~~~ipvV~~~~~~~----~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~ 140 (261)
T cd06272 68 LYKIKLAIPVVSYGVDYD----LKYPI---VNVDNEKAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDEN 140 (261)
T ss_pred HHHHHcCCCEEEEcccCC----CCCCE---EEEChHHHHHHHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHHHc
Confidence 445578899998754322 12233 45567777788888887789999999975433 3344578899999998
Q ss_pred CcEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEE
Q 003275 100 RAKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWI 162 (834)
Q Consensus 100 g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi 162 (834)
|+.+..........+.......+.++.+.. +++ |++++...+..+++.+++.|+..++-+-+
T Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~~l~~~g~~vp~dv~v 204 (261)
T cd06272 141 GISISDSHIDVDGLSAEGGDNAAKKLLKESDLPTA-IICGSYDIALGVLSALNKQGISIPEDIEI 204 (261)
T ss_pred CCCCCHHHeeeCCCCHHHHHHHHHHHHcCCCCCCE-EEECCcHHHHHHHHHHHHhCCCCCCceEE
Confidence 864322111111112233344555554443 455 44455566778899999999865544333
No 182
>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=93.61 E-value=0.91 Score=46.80 Aligned_cols=135 Identities=12% Similarity=0.102 Sum_probs=82.3
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHhcC
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD--DYGRNGISVLGDALSKK 99 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~--~~g~~~~~~l~~~l~~~ 99 (834)
..+...++|++.+....+ ..++ ...++..-+..+++.+...|-++++++..+. ..+....+.+.+.+++.
T Consensus 72 ~~~~~~~iPvv~~~~~~~-----~~~~---V~~d~~~ag~~a~~~L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~ 143 (265)
T cd06285 72 DELTRRGVPFVLVLRHAG-----TSPA---VTGDDVLGGRLATRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEA 143 (265)
T ss_pred HHHHHcCCCEEEEccCCC-----CCCE---EEeCcHHHHHHHHHHHHHCCCccEEEEeCCcccccHHHHHHHHHHHHHHc
Confidence 445667999998754321 2233 3445666677788888778999999997543 24456688899999998
Q ss_pred CcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCC-CeEEEEeC
Q 003275 100 RAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAG-SYVWIATD 165 (834)
Q Consensus 100 g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~-~~vwi~~~ 165 (834)
|+.+.....+....+.......+.++... .+++| ++.+...+..+++.+++.|+..+ ....+.-|
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~g~~~~l~~~g~~~p~di~iig~d 211 (265)
T cd06285 144 GIEVPPERIVYSGFDIEGGEAAAEKLLRSDSPPTAI-FAVNDFAAIGVMGAARDRGLRVPDDVALVGYN 211 (265)
T ss_pred CCCCChhhEEeCCCCHHHHHHHHHHHHcCCCCCCEE-EEcCcHHHHHHHHHHHHcCCCCCcceEEEeec
Confidence 87643211111111223333445555433 34554 44466677889999999998643 33344433
No 183
>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=93.50 E-value=0.77 Score=47.52 Aligned_cols=149 Identities=7% Similarity=-0.009 Sum_probs=85.3
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
.+|.+||--.+......+...+.+.++|+|......+ . ..++ ...++..-+..+++.+...|-++++++....
T Consensus 54 ~~vdgii~~~~~~~~~~~~~~~~~~~ipvV~i~~~~~--~--~~~~---V~~d~~~~g~~a~~~l~~~G~~~i~~l~~~~ 126 (269)
T cd06281 54 RRMDGIIIAPGDERDPELVDALASLDLPIVLLDRDMG--G--GADA---VLFDHAAGMRQAVEYLISLGHRRIALVGGGS 126 (269)
T ss_pred cCCCEEEEecCCCCcHHHHHHHHhCCCCEEEEecccC--C--CCCE---EEECcHHHHHHHHHHHHHCCCcEEEEecCcc
Confidence 3566666422222234455566778999998765332 1 2232 3444444456667777667999999886432
Q ss_pred --CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 83 --DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANL--MESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 83 --~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~--~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
..+....+.+.++++++|+.+.......... .......+.++.. ..+++|+. .+...+..+++++++.|+..++
T Consensus 127 ~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~ip~ 204 (269)
T cd06281 127 NTRPGRERLEGYKAAFAAAGLPPDPALVRLSTP-AASGFDATRALLALPDRPTAIIA-GGTQVLVGVLRALREAGLRIPR 204 (269)
T ss_pred ccccHHHHHHHHHHHHHHcCCCCCHHHeecCcH-HHHHHHHHHHHHcCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCCc
Confidence 2334556889999999887542111111111 1222334444432 34677653 4556677889999999986554
Q ss_pred eE
Q 003275 159 YV 160 (834)
Q Consensus 159 ~v 160 (834)
-+
T Consensus 205 dv 206 (269)
T cd06281 205 DL 206 (269)
T ss_pred ce
Confidence 43
No 184
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=93.46 E-value=6.7 Score=41.70 Aligned_cols=207 Identities=12% Similarity=0.089 Sum_probs=124.4
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
+.||||++.. -...+-.+++..+.+..+ .+.+.+.. ++.++++++|.+|++|+++...
T Consensus 93 g~lrIg~~~~--------------~~~~~l~~~l~~f~~~~P-~i~l~l~~-------~~~~~~~~~L~~g~~Dl~i~~~ 150 (316)
T PRK12679 93 GVLTIATTHT--------------QARYSLPEVIKAFRELFP-EVRLELIQ-------GTPQEIATLLQNGEADIGIASE 150 (316)
T ss_pred ceEEEEechH--------------hhhcchHHHHHHHHHHCC-CeEEEEec-------CCHHHHHHHHHcCCCCEEEecc
Confidence 6799999321 113555778888888765 34455543 4577899999999999998633
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcchh
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQLV 533 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~ 533 (834)
... .. ..+. +.++....+++++++..+...
T Consensus 151 ~~~-~~-~~l~-~~~l~~~~~~~v~~~~hpl~~----------------------------------------------- 180 (316)
T PRK12679 151 RLS-ND-PQLV-AFPWFRWHHSLLVPHDHPLTQ----------------------------------------------- 180 (316)
T ss_pred cCC-CC-CCce-EEEccCCcEEEEecCCCcccc-----------------------------------------------
Confidence 211 11 2233 357778888888876653211
Q ss_pred hHHHHHHHHhhccCCCcccccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCC-eeEeeCchh
Q 003275 534 TIFWFSFSTMFFSHRENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEP-IGVQDGSFA 612 (834)
Q Consensus 534 ~~~~~~~~~l~~~~~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~-v~~~~~s~~ 612 (834)
...-+++||. +.+ +....+...
T Consensus 181 -------------------------------------------------------~~~i~~~~L~--~~~~i~~~~~~~~ 203 (316)
T PRK12679 181 -------------------------------------------------------ITPLTLESIA--KWPLITYRQGITG 203 (316)
T ss_pred -------------------------------------------------------CCCCCHHHHh--CCCeEEecCCCcH
Confidence 1223677776 333 333334322
Q ss_pred ----hHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeC--CcccccceEEEE
Q 003275 613 ----WNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVG--QEFTKSGWGFAF 686 (834)
Q Consensus 613 ----~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~--~~~~~~~~~~~~ 686 (834)
..++. ..+.........++.....+.+.. |..-+++... +... . + ...+..+. .......+.++.
T Consensus 204 ~~~~~~~~~-~~~~~~~~~~~~~s~~~~~~~v~~----g~Gi~~lp~~-~~~~-~-~-~~~L~~~~~~~~~~~~~~~l~~ 274 (316)
T PRK12679 204 RSRIDDAFA-RKGLLADIVLSAQDSDVIKTYVAL----GLGIGLVAEQ-SSGE-Q-E-ESNLIRLDTRHLFDANTVWLGL 274 (316)
T ss_pred HHHHHHHHH-HcCCCceEEEEeccHHHHHHHHHc----CCcEEEeccc-cccc-c-c-CCcEEEEECcccCCCceEEEEE
Confidence 23332 234444445566788888888888 4444444433 2222 2 1 22344443 233345688889
Q ss_pred cCCCcchHHHHHHHHhhhccccHHHHHHhhcC
Q 003275 687 QRDSPLAIDLSTAILQLSENGDLQKIHNKWLT 718 (834)
Q Consensus 687 ~k~spl~~~~~~~i~~l~e~G~~~~i~~kw~~ 718 (834)
+++.+....+...+..+.+.--++.|+++-+.
T Consensus 275 ~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~ 306 (316)
T PRK12679 275 KRGQLQRNYVWRFLELCNAGLSVEDIKRQVME 306 (316)
T ss_pred eCCchhhHHHHHHHHHHhcccCHHHHHHHHhh
Confidence 99988888888888777776667788777654
No 185
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=93.45 E-value=1.2 Score=47.86 Aligned_cols=145 Identities=12% Similarity=0.065 Sum_probs=95.2
Q ss_pred CcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc--
Q 003275 4 EVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD-- 81 (834)
Q Consensus 4 ~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d-- 81 (834)
+|.+||=-. ..........+...++|+|......+ +.. +-....++..-+..+++.+...|-+++++|...
T Consensus 114 ~vdGiIi~~-~~~~~~~~~~l~~~~~P~V~i~~~~~---~~~---~~~V~~Dn~~~~~~a~~~L~~~G~~~i~~i~~~~~ 186 (333)
T COG1609 114 RVDGLILLG-ERPNDSLLELLAAAGIPVVVIDRSPP---GLG---VPSVGIDNFAGAYLATEHLIELGHRRIAFIGGPLD 186 (333)
T ss_pred CCCEEEEec-CCCCHHHHHHHHhcCCCEEEEeCCCc---cCC---CCEEEEChHHHHHHHHHHHHHCCCceEEEEeCCCc
Confidence 455544332 23334445566677999998765444 222 233456777788888999999999999999975
Q ss_pred CCcccchHHHHHHHHhcCCcEE--EeeecCCCCCChHHHHHHHHHhhcCC---ceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 82 DDYGRNGISVLGDALSKKRAKI--SYKAPFSPGASRSAINSLLVGANLME---SRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I--~~~~~~~~~~~~~~~~~~l~~l~~~~---~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
...+....+.+.+++++.|+.. .....-. .+..+-...+.++.... +++| ++++...|..+++++++.|...
T Consensus 187 ~~~~~~R~~Gf~~al~~~~~~~~~~~i~~~~--~~~~~g~~~~~~ll~~~~~~ptAi-f~~nD~~Alg~l~~~~~~g~~v 263 (333)
T COG1609 187 SSASRERLEGYRAALREAGLPINPEWIVEGD--FSEESGYEAAERLLARGEPRPTAI-FCANDLMALGALRALRELGLRV 263 (333)
T ss_pred cccHhHHHHHHHHHHHHCCCCCCcceEEecC--CChHHHHHHHHHHHhcCCCCCcEE-EEcCcHHHHHHHHHHHHcCCCC
Confidence 4456777899999999999875 2221111 12344445555555432 5564 4566678999999999999876
Q ss_pred CC
Q 003275 157 GS 158 (834)
Q Consensus 157 ~~ 158 (834)
++
T Consensus 264 P~ 265 (333)
T COG1609 264 PE 265 (333)
T ss_pred CC
Confidence 54
No 186
>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=93.43 E-value=3 Score=43.01 Aligned_cols=138 Identities=14% Similarity=0.107 Sum_probs=83.4
Q ss_pred HHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEEEcCCc--ccchHHHHHHH
Q 003275 20 ISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIFVDDDY--GRNGISVLGDA 95 (834)
Q Consensus 20 ~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~~d~~~--g~~~~~~l~~~ 95 (834)
....+...++|+|.+....+ +. .+...+..++...+...++.+... |-+++++|..+... .....+.+.++
T Consensus 73 ~~~~~~~~~ipvV~~~~~~~---~~--~~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~g~~~~ 147 (270)
T cd06308 73 VVEEAYRAGIPVILLDRKIL---SD--KYTAYIGADNYEIGRQAGEYIANLLPGKGNILEIWGLEGSSPAIERHDGFKEA 147 (270)
T ss_pred HHHHHHHCCCCEEEeCCCCC---Cc--cceEEeecCcHHHHHHHHHHHHHHcCCCceEEEEECCCCCchHHHHHHHHHHH
Confidence 33445678999998754221 11 223345667777778888887664 88999999744332 33457889999
Q ss_pred HhcC-CcEEEeeecCCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEEeCC
Q 003275 96 LSKK-RAKISYKAPFSPGASRSAINSLLVGANL--MESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIATDW 166 (834)
Q Consensus 96 l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~--~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~~~~ 166 (834)
++++ |+++.... ....+..+....+.++.+ ..+++| +..+...+..+++++++.|+. .+...+..|.
T Consensus 148 l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~aI-~~~~d~~a~g~~~al~~~g~~-~dv~vvg~d~ 217 (270)
T cd06308 148 LSKYPKIKIVAQQ--DGDWLKEKAEEKMEELLQANPDIDLV-YAHNDPMALGAYLAAKRAGRE-KEIKFIGIDG 217 (270)
T ss_pred HHHCCCCEEEEec--CCCccHHHHHHHHHHHHHhCCCCcEE-EeCCcHHHHHHHHHHHHcCCC-CCcEEEEecC
Confidence 9998 88765321 111122222333444432 235654 344566777899999999986 4445555443
No 187
>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=93.39 E-value=1.6 Score=45.11 Aligned_cols=153 Identities=9% Similarity=0.027 Sum_probs=88.6
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
.++.+||--.+......+..+. ..++|+|......+ +...+ ...+++...+..+++.+...|-+++++|..+.
T Consensus 54 ~~~dgiii~~~~~~~~~~~~~~-~~~~pvV~i~~~~~---~~~~~---~V~~d~~~~~~~~~~~L~~~G~~~i~~i~~~~ 126 (269)
T cd06293 54 NHVDGLIFVTNRPDDGALAKLI-NSYGNIVLVDEDVP---GAKVP---KVFCDNEQGGRLATRHLARAGHRRIAFVGGPD 126 (269)
T ss_pred CCCCEEEEeCCCCCHHHHHHHH-hcCCCEEEECCCCC---CCCCC---EEEECCHHHHHHHHHHHHHCCCceEEEEecCc
Confidence 3566666432221222233333 34799998764332 11122 35567777888888888888999999997543
Q ss_pred C--cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 83 D--YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANL--MESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 83 ~--~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~--~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
. ......+.+.+++++.|..+..........+..+....+.++.+ ..+++|+. ++...+..+++++++.|...++
T Consensus 127 ~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~vp~ 205 (269)
T cd06293 127 ALISARERYAGYREALAEAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDPPTAIFA-ASDEIAIGLLEVLRERGLSIPG 205 (269)
T ss_pred ccccHHHHHHHHHHHHHHcCCCCChheEEecCCCHHHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCcc
Confidence 3 23345788999999888643211111111122233344555433 33566554 4556677889999999986555
Q ss_pred eEEEE
Q 003275 159 YVWIA 163 (834)
Q Consensus 159 ~vwi~ 163 (834)
-+-|.
T Consensus 206 di~i~ 210 (269)
T cd06293 206 DMSLV 210 (269)
T ss_pred ceEEE
Confidence 45544
No 188
>cd06324 PBP1_ABC_sugar_binding_like_13 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 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=93.37 E-value=1.7 Score=46.00 Aligned_cols=158 Identities=14% Similarity=0.072 Sum_probs=89.5
Q ss_pred CcEEEE-CCCChhhHHHHHHhhccCCccEEecccCCCCCC-----C--CCC-CceEEccCChHHHHHHHHHHHHHcCCeE
Q 003275 4 EVVAAI-GPQSSGIAHVISHVVNELNVPLLSFGATDPTLT-----S--LQY-PYFLRTTQSDYYQMHAVADLVEYYGWRE 74 (834)
Q Consensus 4 ~V~aii-Gp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls-----~--~~~-p~~~r~~ps~~~q~~aia~ll~~~~W~~ 74 (834)
+|.+|| .|... ....+...+...++|+|.+....+... . ..+ +++-...+++...+..+++.+...|-++
T Consensus 58 ~vdgiIi~~~~~-~~~~~~~~~~~~giPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~g~~~ 136 (305)
T cd06324 58 KPDALIFTNEKS-VAPELLRLAEGAGVKLFLVNSGLTEAQARELGPPREKFPDWLGQLLPNDEEAGYLMAEALISQARSV 136 (305)
T ss_pred CCCEEEEcCCcc-chHHHHHHHHhCCCeEEEEecCCCcchhhcccccccccCceeeeeccCcHHHHHHHHHHHHHHhhcc
Confidence 565544 33322 233334566778999998765432211 0 111 2344566777777888888886666553
Q ss_pred --------EEEEEEcC--CcccchHHHHHHHHhcCC-cEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhh
Q 003275 75 --------VIAIFVDD--DYGRNGISVLGDALSKKR-AKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDT 141 (834)
Q Consensus 75 --------v~iI~~d~--~~g~~~~~~l~~~l~~~g-~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~ 141 (834)
++++..+. .......+.++++++++| ..+.. .+....+.......+.++.+. .+++|+ +.+...
T Consensus 137 ~~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~g~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~ 213 (305)
T cd06324 137 QAPGGRIDLLAISGDPTTPAAILREAGLRRALAEHPDVRLRQ--VVYAGWSEDEAYEQAENLLKRYPDVRLIW-AANDQM 213 (305)
T ss_pred cCCCCceeEEEEeCCCCChHHHHHHHHHHHHHHHCCCceEee--eecCCCCHHHHHHHHHHHHHHCCCccEEE-ECCchH
Confidence 66665332 233456788999999887 43322 122122223334455555433 356554 445667
Q ss_pred HHHHHHHHHhCCCCCCCe-EEEEeC
Q 003275 142 GLTIFSVAKSLGMTAGSY-VWIATD 165 (834)
Q Consensus 142 ~~~i~~~a~~~g~~~~~~-vwi~~~ 165 (834)
+..+++++++.|+..++- ..+..|
T Consensus 214 A~g~~~al~~~g~~vp~di~vig~D 238 (305)
T cd06324 214 AFGALRAAKEAGRKPGRDVLFGGVN 238 (305)
T ss_pred HHHHHHHHHHcCCCcCCCEEEEecC
Confidence 788999999999865433 344433
No 189
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=93.33 E-value=6.3 Score=37.67 Aligned_cols=71 Identities=13% Similarity=0.074 Sum_probs=49.5
Q ss_pred eeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEe
Q 003275 400 KGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAP 479 (834)
Q Consensus 400 ~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~ 479 (834)
..+-.+++..+.+..+ .+++++.. ++..++..++.+|++|+++...... ...+ .+.|+....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~ 79 (196)
T cd08415 12 LSLLPRAIARFRARHP-DVRISLHT-------LSSSTVVEAVLSGQADLGLASLPLD---HPGL-ESEPLASGRAVCVLP 79 (196)
T ss_pred ccccHHHHHHHHHHCC-CcEEEEEe-------cchHHHHHHHHcCCccEEEEeCCCC---CCcc-eeeeecccceEEEEc
Confidence 3556788999888775 34566654 4578899999999999998643322 1122 467777888888887
Q ss_pred cCC
Q 003275 480 VQK 482 (834)
Q Consensus 480 ~~~ 482 (834)
+..
T Consensus 80 ~~~ 82 (196)
T cd08415 80 PGH 82 (196)
T ss_pred CCC
Confidence 654
No 190
>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=93.29 E-value=1 Score=46.52 Aligned_cols=155 Identities=10% Similarity=0.050 Sum_probs=89.0
Q ss_pred CCcEEEE-CCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAI-GPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aii-Gp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
+++.+|| .|.... . .....+...++|+|.+....+. ....++ ..+++...+..+++.+...|.++++++..+
T Consensus 54 ~~~dgiii~~~~~~-~-~~~~~~~~~~ipvV~i~~~~~~--~~~~~~---v~~d~~~~~~~a~~~l~~~g~~~i~~i~~~ 126 (270)
T cd06296 54 RRTDGVILVTPELT-S-AQRAALRRTGIPFVVVDPAGDP--DADVPS---VGATNWAGGLAATEHLLELGHRRIGFITGP 126 (270)
T ss_pred cCCCEEEEecCCCC-h-HHHHHHhcCCCCEEEEecccCC--CCCCCE---EEeCcHHHHHHHHHHHHHcCCCcEEEEcCC
Confidence 3566554 332222 2 2345567789999987653211 112232 555666677777888777799999998743
Q ss_pred C--CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCC
Q 003275 82 D--DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 82 ~--~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~ 157 (834)
. .......+.|.+++++.|+.+..........+.+.....+.++... .+++|+ +.+...+..+++.+++.|...+
T Consensus 127 ~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~~p 205 (270)
T cd06296 127 PDLLCSRARLDGYRAALAEAGIPVDPALVREGDFSTESGFRAAAELLALPERPTAIF-AGNDLMALGVYEAARERGLRIP 205 (270)
T ss_pred CcchhHHHHHHHHHHHHHHcCCCCChHHheeCCCCHHHHHHHHHHHHhCCCCCcEEE-EcCcHHHHHHHHHHHHhCCCCC
Confidence 2 2344567889999998876543211111111223333444444333 345544 3455667788999999998644
Q ss_pred C-eEEEEeC
Q 003275 158 S-YVWIATD 165 (834)
Q Consensus 158 ~-~vwi~~~ 165 (834)
+ ...+..+
T Consensus 206 ~~i~v~~~d 214 (270)
T cd06296 206 EDLSVVGFD 214 (270)
T ss_pred CceEEEEEC
Confidence 4 3444444
No 191
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=93.27 E-value=3.5 Score=42.68 Aligned_cols=145 Identities=12% Similarity=0.051 Sum_probs=81.9
Q ss_pred CcEEEE-CCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEEE
Q 003275 4 EVVAAI-GPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIFV 80 (834)
Q Consensus 4 ~V~aii-Gp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~~ 80 (834)
++.+|| .|............+...+||+|.+....+ ... .......+++...+...++++... |-++++++..
T Consensus 60 ~vDgiii~~~~~~~~~~~i~~~~~~gIpvV~~d~~~~---~~~-~~~~~V~~d~~~~g~~aa~~l~~~~~g~~~i~~~~g 135 (274)
T cd06311 60 KIDALVILPFESAPLTQPVAKAKKAGIFVVVVDRGLS---SPG-AQDLYVAGDNYGMGRVAGEYIATKLGGNGNIVVLRG 135 (274)
T ss_pred CCCEEEEeCCCchhhHHHHHHHHHCCCeEEEEcCCCC---CCc-ccceEEcCCcHHHHHHHHHHHHHHhCCCCeEEEEEC
Confidence 454443 343333322333445678999998754221 111 111235666666777788887655 7889998874
Q ss_pred cC-CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 81 DD-DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 81 d~-~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
+. .......+.+.+.+++.++++... .....+.......+.++... .+++|+. .+...+..+++++++.|..
T Consensus 136 ~~~~~~~~R~~gf~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~ 210 (274)
T cd06311 136 IPTPIDNERVDAFDAAIAKYPIKILDR--QYANWNRDDAFSVMQDLLTKFPKIDAVWA-HDDDMAVGVLAAIKQAGRT 210 (274)
T ss_pred CCCcchhHHHHHHHHHHhhCCcEEEec--cCCCCcHHHHHHHHHHHHHhCCCcCEEEE-CCCcHHHHHHHHHHHcCCC
Confidence 33 223345788999999988766532 22122222333444444332 3455444 3445577888899988875
No 192
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=93.25 E-value=1.5 Score=44.14 Aligned_cols=132 Identities=9% Similarity=0.065 Sum_probs=92.8
Q ss_pred HHHHhhccCCccEEecccCCCCCCC--CC-CCce--EEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHH
Q 003275 19 VISHVVNELNVPLLSFGATDPTLTS--LQ-YPYF--LRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLG 93 (834)
Q Consensus 19 ~~~~~~~~~~vP~Is~~at~~~ls~--~~-~p~~--~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~ 93 (834)
+.+.+....++=.|.|++|+.++-. .+ ..-. -++..+-..-..|+.+-++++|-++++++.. |-....+.+.
T Consensus 62 aa~~ll~~a~~dvi~~~cTsgs~~~G~~~~~~~i~~~~~g~p~tt~~~A~~~AL~alg~~RIalvTP---Y~~~v~~~~~ 138 (239)
T TIGR02990 62 AAALILPDEELDVVAYSCTSASVVIGDDEVTRAINAAKPGTPVVTPSSAAVDGLAALGVRRISLLTP---YTPETSRPMA 138 (239)
T ss_pred HHHHhcCCCCCCEEEEccchhheecCHHHHHHHHHhcCCCCCeeCHHHHHHHHHHHcCCCEEEEECC---CcHHHHHHHH
Confidence 3344445568888999999876631 00 0000 0122233445678888899999999999984 7778899999
Q ss_pred HHHhcCCcEEEeeecCCCC-------CChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHh-CC
Q 003275 94 DALSKKRAKISYKAPFSPG-------ASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKS-LG 153 (834)
Q Consensus 94 ~~l~~~g~~I~~~~~~~~~-------~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~-~g 153 (834)
+.+++.|++|+....+... .+...+...+.++...++|.|++.|..-.+..++.++.+ +|
T Consensus 139 ~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aDAifisCTnLrt~~vi~~lE~~lG 206 (239)
T TIGR02990 139 QYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDADALFLSCTALRAATCAQRIEQAIG 206 (239)
T ss_pred HHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCCEEEEeCCCchhHHHHHHHHHHHC
Confidence 9999999999876544432 244667777777777889999999988778888877754 45
No 193
>cd06321 PBP1_ABC_sugar_binding_like_11 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=93.25 E-value=3.3 Score=42.77 Aligned_cols=147 Identities=12% Similarity=-0.004 Sum_probs=84.8
Q ss_pred EECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEEEcC-Cc
Q 003275 8 AIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIFVDD-DY 84 (834)
Q Consensus 8 iiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~~d~-~~ 84 (834)
|+.|............+...++|+|......+ . . ...+..++...+..+++.+... |.+++++|..+. ..
T Consensus 62 Ii~~~~~~~~~~~i~~~~~~~ipvv~~~~~~~---~-~---~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~g~~~~~ 134 (271)
T cd06321 62 LLNAVDSKGIAPAVKRAQAAGIVVVAVDVAAE---G-A---DATVTTDNVQAGEISCQYLADRLGGKGNVAILNGPPVSA 134 (271)
T ss_pred EEeCCChhHhHHHHHHHHHCCCeEEEecCCCC---C-c---cceeeechHHHHHHHHHHHHHHhCCCceEEEEeCCCCch
Confidence 34454333223333445667999999865332 1 1 1235667777788888888766 999999997542 23
Q ss_pred ccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEE
Q 003275 85 GRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVW 161 (834)
Q Consensus 85 g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vw 161 (834)
.....+.+.+++++. ++++... ......+...-...+.++.+. .+++|+. .+...+..+++++++.|+ .+..+
T Consensus 135 ~~~R~~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~--~di~v 210 (271)
T cd06321 135 VLDRVAGCKAALAKYPGIKLLSD-DQNGKGSRDGGLRVMQGLLTRFPKLDGVFA-INDPTAIGADLAAKQAGR--NDIKI 210 (271)
T ss_pred HHHHHHHHHHHHHhCCCcEEEee-ecCCCCChhhHHHHHHHHHHhCCCCCEEEE-CCchhHHHHHHHHHHcCC--CCcEE
Confidence 445578889999988 6653221 111111112222344444333 3566444 455567778889999887 34455
Q ss_pred EEeC
Q 003275 162 IATD 165 (834)
Q Consensus 162 i~~~ 165 (834)
+..+
T Consensus 211 ~g~d 214 (271)
T cd06321 211 TSVD 214 (271)
T ss_pred EEec
Confidence 5544
No 194
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member 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. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=93.16 E-value=3.7 Score=43.33 Aligned_cols=153 Identities=12% Similarity=0.072 Sum_probs=79.6
Q ss_pred CcEE-EECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCe-------
Q 003275 4 EVVA-AIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWR------- 73 (834)
Q Consensus 4 ~V~a-iiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~------- 73 (834)
+|.+ |+.|..+.........+...++|+|......+.......+-+..+.+++...+...++++... |-+
T Consensus 57 ~vdgiii~~~~~~~~~~~~~~~~~~giPvV~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~a~~l~~~~~~~~~~~~~~~ 136 (303)
T cd01539 57 GVDLLAVNLVDPTAAQTVINKAKQKNIPVIFFNREPEEEDIKSYDKAYYVGTDAEQSGILQGKLIADYWNANKDALDKNG 136 (303)
T ss_pred CCCEEEEecCchhhHHHHHHHHHHCCCCEEEeCCCCcccccccccccceeeecHHHHHHHHHHHHHHHhhccccccccCC
Confidence 4544 344544443344545567789999987543221111111223345666666667777776443 211
Q ss_pred ----EEEEEEEcCC--cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHH
Q 003275 74 ----EVIAIFVDDD--YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM---ESRVFVVHVNPDTGLT 144 (834)
Q Consensus 74 ----~v~iI~~d~~--~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~---~~~vivl~~~~~~~~~ 144 (834)
.++++..+.. ......+.+.++++++|..+..........+.......+.++... .+++|+. .+...+..
T Consensus 137 ~g~~~i~~~~g~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~~ai~~-~~d~~a~g 215 (303)
T cd01539 137 DGIIQYVMLKGEPGHPDAIARTKYSIETLNDAGIKTEELASDTANWDRAQAKDKMDALLLKYGDKIEAVIA-NNDAMALG 215 (303)
T ss_pred CCceEEEEEEcCCCCchhhhhhhhHHHHHHhcCCCeEEEEeecCCCCHHHHHHHHHHHHHhcCCCccEEEE-CCchHHHH
Confidence 2344443322 223457788999998887653222222222223333344554332 2455443 44556667
Q ss_pred HHHHHHhCCCCCC
Q 003275 145 IFSVAKSLGMTAG 157 (834)
Q Consensus 145 i~~~a~~~g~~~~ 157 (834)
+++++++.|...+
T Consensus 216 ~~~al~~~g~~~p 228 (303)
T cd01539 216 AIEALQKYGYNKG 228 (303)
T ss_pred HHHHHHHcCCCcC
Confidence 8888888887654
No 195
>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=93.06 E-value=1.8 Score=44.45 Aligned_cols=149 Identities=10% Similarity=0.052 Sum_probs=86.9
Q ss_pred CCcEEEE-CCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc
Q 003275 3 NEVVAAI-GPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD 81 (834)
Q Consensus 3 ~~V~aii-Gp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d 81 (834)
+++.|+| -+..... ..+.. ....++|+|......+ ...+ ....++...+..+++.+...|-++|+++..+
T Consensus 55 ~~vdgiii~~~~~~~-~~~~~-~~~~~ipvv~~~~~~~----~~~~---~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~ 125 (264)
T cd01574 55 QRVDGVIVNAPLDDA-DAALA-AAPADVPVVFVDGSPS----PRVS---TVSVDQEGGARLATEHLLELGHRTIAHVAGP 125 (264)
T ss_pred cCCCEEEEeCCCCCh-HHHHH-HHhcCCCEEEEeccCC----CCCC---EEEeCcHHHHHHHHHHHHHCCCCEEEEEecC
Confidence 3566665 2322222 23333 3467899999764321 1222 3556667778888888878898999988654
Q ss_pred CCc--ccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCC-ceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 82 DDY--GRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLME-SRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 82 ~~~--g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~-~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
... .....+.+.+++++.|+.+... +....+.......+.++.+.. +++|+. ++...+..+++++++.|...++
T Consensus 126 ~~~~~~~~r~~gf~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~ai~~-~~d~~a~g~~~~~~~~g~~ip~ 202 (264)
T cd01574 126 EEWLSARARLAGWRAALEAAGIAPPPV--LEGDWSAESGYRAGRELLREGDPTAVFA-ANDQMALGVLRALHELGLRVPD 202 (264)
T ss_pred CccchHHHHHHHHHHHHHHCCCCccee--eecCCCHHHHHHHHHHHHhCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCcc
Confidence 332 2345678899998888765422 211112233344455554333 565444 4556778889999998875443
Q ss_pred eEEEE
Q 003275 159 YVWIA 163 (834)
Q Consensus 159 ~vwi~ 163 (834)
-+-+.
T Consensus 203 ~i~ii 207 (264)
T cd01574 203 DVSVV 207 (264)
T ss_pred ceEEe
Confidence 33333
No 196
>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=92.96 E-value=1.7 Score=44.91 Aligned_cols=136 Identities=15% Similarity=0.063 Sum_probs=81.7
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHhcC
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD--DYGRNGISVLGDALSKK 99 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~--~~g~~~~~~l~~~l~~~ 99 (834)
..+...++|+|.+....+. ...+++ ...++...+..+++.+...|-+++++|.... .......+.+.++++++
T Consensus 77 ~~~~~~~ipvV~i~~~~~~--~~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~ 151 (273)
T cd06292 77 ERLAERGLPVVLVNGRAPP--PLKVPH---VSTDDALAMRLAVRHLVALGHRRIGFASGPGRTVPRRRKIAGFRAALEEA 151 (273)
T ss_pred HHHHhCCCCEEEEcCCCCC--CCCCCE---EEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHc
Confidence 3456779999987653322 012332 4556777778888888778999999887442 23445678899999998
Q ss_pred CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 100 RAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 100 g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
|+.......+....+.......+.++....+++|+. ++...+..+++.+++.|+..++-+-+.
T Consensus 152 ~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~ai~~-~~d~~a~g~~~~l~~~g~~ip~di~ii 214 (273)
T cd06292 152 GLEPPEALVARGMFSVEGGQAAAVELLGSGPTAIVA-ASDLMALGAIRAARRRGLRVPEDVSVV 214 (273)
T ss_pred CCCCChhheEeCCCCHHHHHHHHHHHhcCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcceEEE
Confidence 853211111111112222334444544444776554 455667788899999998655444444
No 197
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=92.91 E-value=8 Score=40.55 Aligned_cols=83 Identities=14% Similarity=0.097 Sum_probs=56.3
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
++++||++.. ....+-.+++..+.+..+ .+.+++.. .+...++.+|.+|++|+++...
T Consensus 91 ~~i~I~~~~~--------------~~~~~l~~~l~~~~~~~p-~~~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 148 (296)
T PRK11242 91 GSLRLAMTPT--------------FTAYLIGPLIDAFHARYP-GITLTIRE-------MSQERIEALLADDELDVGIAFA 148 (296)
T ss_pred eEEEEEeccc--------------hhhhhhHHHHHHHHHHCC-CCEEEEEe-------CCHHHHHHHHHCCCCcEEEEec
Confidence 5789998321 113445788888888765 45566653 4578899999999999998643
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCC
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
.. +...+ .+.++....+++++++..
T Consensus 149 ~~---~~~~l-~~~~l~~~~~~~~~~~~~ 173 (296)
T PRK11242 149 PV---HSPEI-EAQPLFTETLALVVGRHH 173 (296)
T ss_pred CC---CCcce-eEEEeeeccEEEEEcCCC
Confidence 22 22222 357777888888888765
No 198
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate
Probab=92.84 E-value=4.5 Score=38.94 Aligned_cols=70 Identities=17% Similarity=0.160 Sum_probs=47.5
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++.+.. .+...+...|.+|++|+++..... ....+ -..|+....++++++.
T Consensus 13 ~~~~~~i~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~-~~~~l~~~~~~~v~~~ 80 (200)
T cd08417 13 LLLPPLLARLRQEAP-GVRLRFVP-------LDRDDLEEALESGEIDLAIGVFPE---LPPGL-RSQPLFEDRFVCVARK 80 (200)
T ss_pred HHHHHHHHHHHhhCC-CeEEEecc-------CCHHHHHHHHHcCCCCEEEeeccc---CCCcc-chhhhhcCceEEEecC
Confidence 455677888887764 33455543 557889999999999999864322 22222 2467778888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (200)
T cd08417 81 DH 82 (200)
T ss_pred CC
Confidence 55
No 199
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=92.73 E-value=8.3 Score=40.83 Aligned_cols=84 Identities=17% Similarity=0.133 Sum_probs=55.4
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
+.|+||++.. -...+-.+++..+.+..+ .+.+++.. ++.+.++..|.+|++|++++..
T Consensus 93 g~l~Ig~~~~--------------~~~~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~ 150 (309)
T PRK12682 93 GTLTIATTHT--------------QARYVLPRVVAAFRKRYP-KVNLSLHQ-------GSPDEIARMVISGEADIGIATE 150 (309)
T ss_pred CeEEEeeCch--------------HHHHHHHHHHHHHHHhCC-CeEEEEec-------CCHHHHHHHHHcCCccEEEecC
Confidence 5689998311 113455788888888765 34455543 4568899999999999998643
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCC
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
... ....++ +.|+....++++++...
T Consensus 151 ~~~--~~~~l~-~~~l~~~~~~~~~~~~~ 176 (309)
T PRK12682 151 SLA--DDPDLA-TLPCYDWQHAVIVPPDH 176 (309)
T ss_pred ccc--CCCcce-EEEeeeeeEEEEecCCC
Confidence 211 112233 45788888888887765
No 200
>cd08411 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repre
Probab=92.69 E-value=7.6 Score=37.31 Aligned_cols=70 Identities=10% Similarity=0.136 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. ++..+++..|.+|++|+++...... ...+ -..++.+..++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~ 81 (200)
T cd08411 14 YLLPRLLPALRQAYP-KLRLYLRE-------DQTERLLEKLRSGELDAALLALPVD---EPGL-EEEPLFDEPFLLAVPK 81 (200)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEe-------CcHHHHHHHHHcCCccEEEEeccCC---CCCc-eEEEeeccceEEEecC
Confidence 355788888888765 34466553 5578899999999999998643221 1222 2456677778888776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 82 ~~ 83 (200)
T cd08411 82 DH 83 (200)
T ss_pred CC
Confidence 55
No 201
>cd06316 PBP1_ABC_sugar_binding_like_7 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=92.65 E-value=4.6 Score=42.36 Aligned_cols=157 Identities=14% Similarity=0.067 Sum_probs=85.6
Q ss_pred CcEEE-ECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEEE
Q 003275 4 EVVAA-IGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIFV 80 (834)
Q Consensus 4 ~V~ai-iGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~~ 80 (834)
++.+| +.|........+...+...++|+|.+....+.... .-+++.-+..++..-+..+++++... |-++++++..
T Consensus 56 ~~dgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~~~~~~~-~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~ 134 (294)
T cd06316 56 KPDIIISIPVDPVSTAAAYKKVAEAGIKLVFMDNVPSGLEH-GKDYAGIVTDDNYGNGQIAADALAKALPGKGKVGLIYH 134 (294)
T ss_pred CCCEEEEcCCCchhhhHHHHHHHHcCCcEEEecCCCccccc-CcceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEeC
Confidence 44433 44433322234445566789999987654332221 11233335556666677888887665 7789999975
Q ss_pred cCCc--ccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCC
Q 003275 81 DDDY--GRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 81 d~~~--g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~ 156 (834)
+.+. .....+.+.+.+++++..+......... +.......++++... .+++|+. .+...+..+++.+++.|+
T Consensus 135 ~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~-- 210 (294)
T cd06316 135 GADYFVTNQRDQGFKETIKKNYPDITIVAEKGID-GPSKAEDIANAMLTQNPDLKGIYA-VWDVPAEGVIAALRAAGR-- 210 (294)
T ss_pred CCCcccHHHHHHHHHHHHHHhCCCcEEEeecCCc-chhHHHHHHHHHHHhCCCeeEEEe-CCCchhHHHHHHHHHcCC--
Confidence 4333 3344688888888665332211111111 112223344444333 3455444 455678889999999987
Q ss_pred CCeEEEEeC
Q 003275 157 GSYVWIATD 165 (834)
Q Consensus 157 ~~~vwi~~~ 165 (834)
.+...+..+
T Consensus 211 ~di~vvg~d 219 (294)
T cd06316 211 DDIKVTTVD 219 (294)
T ss_pred CCceEEEeC
Confidence 333444444
No 202
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=92.59 E-value=4.5 Score=39.23 Aligned_cols=70 Identities=14% Similarity=0.097 Sum_probs=48.0
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
++-.+++..+.++.+ .++++... ++..+++++|.+|++|++++..... ...+.. .+..+..+++++++
T Consensus 13 ~~l~~~l~~f~~~~P-~i~l~i~~-------~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~lv~~~ 80 (200)
T cd08465 13 LVLPALMRQLRAEAP-GIDLAVSQ-------ASREAMLAQVADGEIDLALGVFPEL---PEELHA-ETLFEERFVCLADR 80 (200)
T ss_pred HhhhHHHHHHHHHCC-CcEEEEec-------CChHhHHHHHHCCCccEEEeccccC---CcCeeE-EEeeeccEEEEEeC
Confidence 556788888877765 35566553 5688999999999999998643222 122333 46677788888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~h 82 (200)
T cd08465 81 AT 82 (200)
T ss_pred CC
Confidence 54
No 203
>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T
Probab=92.50 E-value=6.2 Score=38.16 Aligned_cols=69 Identities=14% Similarity=0.123 Sum_probs=45.8
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-..++..+.+..+ .+.++... ++. ++++.|.+|++|++++.-.... ..+. ..|+....++++++.
T Consensus 13 ~~l~~~i~~~~~~~P-~i~l~i~~-------~~~-~~~~~l~~g~~D~~i~~~~~~~---~~~~-~~~l~~~~~~~v~~~ 79 (200)
T cd08462 13 VLLPPVIERVAREAP-GVRFELLP-------PDD-QPHELLERGEVDLLIAPERFMS---DGHP-SEPLFEEEFVCVVWA 79 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEec-------CCh-hHHHHHhcCCeeEEEecCCCCC---CCce-eeeeeccceEEEEcC
Confidence 344677788877775 34466553 344 8999999999999986432211 2232 447777888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 80 ~h 81 (200)
T cd08462 80 DN 81 (200)
T ss_pred CC
Confidence 65
No 204
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=92.45 E-value=9.7 Score=36.49 Aligned_cols=70 Identities=10% Similarity=0.010 Sum_probs=47.3
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. ++..++..++.+|++|+++....... ..+. +.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~~~~---~~~~-~~~l~~~~~~~v~~~ 80 (199)
T cd08426 13 ELLPSLIARFRQRYP-GVFFTVDV-------ASTADVLEAVLSGEADIGLAFSPPPE---PGIR-VHSRQPAPIGAVVPP 80 (199)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEe-------CCcHHHHHHHHCCCccEEEecCCCCC---CCeE-EEeeccCcEEEEecC
Confidence 445678888887765 34455543 45688999999999999986432221 2222 467778888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~h 82 (199)
T cd08426 81 GH 82 (199)
T ss_pred CC
Confidence 55
No 205
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=92.37 E-value=10 Score=35.98 Aligned_cols=70 Identities=16% Similarity=0.192 Sum_probs=47.0
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-..++..+.+..+ .+++++.. ++...++.++.+|++|+++...... ...+. +.++....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~l~-~~~l~~~~~~~v~~~ 80 (195)
T cd08434 13 SLVPDLIRAFRKEYP-NVTFELHQ-------GSTDELLDDLKNGELDLALCSPVPD---EPDIE-WIPLFTEELVLVVPK 80 (195)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEec-------CcHHHHHHHHHcCCccEEEEccCCC---CCCee-EEEeecceEEEEecC
Confidence 455677888887764 24455553 4567889999999999998643222 22333 467777888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (195)
T cd08434 81 DH 82 (195)
T ss_pred CC
Confidence 65
No 206
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=92.35 E-value=11 Score=40.00 Aligned_cols=84 Identities=17% Similarity=0.112 Sum_probs=54.0
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
++|+||+... . ...+-..++..+.+..+ .+.+.+.. +++++++..|.+|++|++++..
T Consensus 93 g~l~Ig~~~~--~------------~~~~l~~~i~~f~~~~P-~i~l~~~~-------~~~~~~~~~L~~~~~D~~i~~~ 150 (309)
T PRK12683 93 GHLTVATTHT--Q------------ARYALPKVVRQFKEVFP-KVHLALRQ-------GSPQEIAEMLLNGEADIGIATE 150 (309)
T ss_pred ceEEEEeccc--h------------HHHHHHHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHcCCccEEEecC
Confidence 6799998321 1 12344567888877764 34466554 5689999999999999988632
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCC
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
... ....+.+ .|+....+++++++..
T Consensus 151 ~~~--~~~~l~~-~~l~~~~~~~v~~~~h 176 (309)
T PRK12683 151 ALD--REPDLVS-FPYYSWHHVVVVPKGH 176 (309)
T ss_pred CCC--CCCCceE-EEcccCeEEEEecCCC
Confidence 211 1122333 4677778888887665
No 207
>cd06318 PBP1_ABC_sugar_binding_like_9 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=92.35 E-value=6.6 Score=40.73 Aligned_cols=147 Identities=15% Similarity=0.060 Sum_probs=82.1
Q ss_pred CcEEEE-CCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHH-cCCe--EEEEEE
Q 003275 4 EVVAAI-GPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEY-YGWR--EVIAIF 79 (834)
Q Consensus 4 ~V~aii-Gp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~-~~W~--~v~iI~ 79 (834)
++.+|| .+..+.........+...++|+|.+....+ . ..+.+-.+..++...+..+++.+.. .|-+ +++++.
T Consensus 55 ~~Dgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~~~---~-~~~~~~~v~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~ 130 (282)
T cd06318 55 GVNVLIINPVDPEGLVPAVAAAKAAGVPVVVVDSSIN---L-EAGVVTQVQSSNAKNGNLVGEWVVGELGDKPMKIILLS 130 (282)
T ss_pred CCCEEEEecCCccchHHHHHHHHHCCCCEEEecCCCC---C-CcCeEEEEecCcHHHHHHHHHHHHHHhCCCCceEEEEE
Confidence 444433 443333223344555678999998764321 1 0122344666777778888888754 6754 888886
Q ss_pred Ec--CCcccchHHHHHHHHhcCCcE------EEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHH
Q 003275 80 VD--DDYGRNGISVLGDALSKKRAK------ISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVA 149 (834)
Q Consensus 80 ~d--~~~g~~~~~~l~~~l~~~g~~------I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a 149 (834)
.+ ...+....+.+.++++++|.. +..........+..+....+.++... .+++|+. .+...+..+++++
T Consensus 131 ~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al 209 (282)
T cd06318 131 GDAGNLVGQARRDGFLLGVSEAQLRKYGKTNFTIVAQGYGDWTREGGLKAMEDLLVAHPDINVVYS-ENDDMALGAMRVL 209 (282)
T ss_pred CCCCCchHhHHHHhHHHHHhhCcccccccCCeEEEecCCCCCCHHHHHHHHHHHHHhCCCcCEEEE-CCcchHHHHHHHH
Confidence 43 334566778899999988642 11111011111222333344444322 3455444 4445677888999
Q ss_pred HhCCCC
Q 003275 150 KSLGMT 155 (834)
Q Consensus 150 ~~~g~~ 155 (834)
++.|+.
T Consensus 210 ~~~g~~ 215 (282)
T cd06318 210 AEAGKT 215 (282)
T ss_pred HHcCCC
Confidence 999974
No 208
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=92.28 E-value=9.2 Score=36.87 Aligned_cols=71 Identities=17% Similarity=0.069 Sum_probs=48.9
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. +....+.+.|.+|++|+++...... ....+. +.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~~-~~~l~~~~~~~v~~~ 81 (198)
T cd08413 13 YVLPPVIAAFRKRYP-KVKLSLHQ-------GTPSQIAEMVLKGEADIAIATEALD--DHPDLV-TLPCYRWNHCVIVPP 81 (198)
T ss_pred hhccHHHHHHHHhCC-ceEEEEEe-------CCHHHHHHHHHcCCCCEEEEccCCC--CCCCcE-EEEeeeeeEEEEecC
Confidence 455788888888876 34566654 5578899999999999998632221 112232 477778888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 82 ~h 83 (198)
T cd08413 82 GH 83 (198)
T ss_pred CC
Confidence 65
No 209
>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=92.21 E-value=1.8 Score=44.84 Aligned_cols=135 Identities=13% Similarity=0.036 Sum_probs=81.6
Q ss_pred HHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC--C------cccchHH
Q 003275 19 VISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD--D------YGRNGIS 90 (834)
Q Consensus 19 ~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~--~------~g~~~~~ 90 (834)
.....+...++|+|...... ...++ ..+++..-+..+++.+... .+++++|..+. . .+....+
T Consensus 69 ~~~~~l~~~~iPvv~~~~~~-----~~~~~---v~~d~~~~g~~a~~~L~~~-~~~i~~i~~~~~~~~~~~~~~~~~R~~ 139 (269)
T cd06297 69 RLAERRLPTERPVVLVDAEN-----PRFDS---FYLDNRLGGRLAGAYLADF-PGRIGAITVEEEPDRAFRRTVFAERRA 139 (269)
T ss_pred HHHHHHhhcCCCEEEEccCC-----CCCCE---EEECcHHHHHHHHHHHHHh-CCceEEEeCccccccccccccHHHHHH
Confidence 33445567899999875422 12233 3456666677777776555 68999886432 2 3455688
Q ss_pred HHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 91 VLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 91 ~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
.+++++++.|+++.....+....+..+....+.++.+. .+++|+.. +...+..+++.+++.|...++-+-++
T Consensus 140 gf~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~vP~di~vv 213 (269)
T cd06297 140 GFQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLLEKASPPLAVFAS-ADQQALGALQEAVELGLTVGEDVRVV 213 (269)
T ss_pred HHHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHcCCCCCcEEEEc-CcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 99999999887643211111111223344556665443 34555544 55577789999999998655555444
No 210
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=92.20 E-value=6.6 Score=41.98 Aligned_cols=85 Identities=16% Similarity=0.086 Sum_probs=54.9
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
.++|+||++.. + ...+-.+++..+.+..+ .+++++.. ++.++++.+|.+|++|+++..
T Consensus 92 ~g~l~Ig~~~~--~------------~~~~l~~~l~~f~~~~P-~i~i~i~~-------~~~~~~~~~L~~g~iDl~i~~ 149 (324)
T PRK12681 92 KGSLYIATTHT--Q------------ARYALPPVIKGFIERYP-RVSLHMHQ-------GSPTQIAEAAAKGNADFAIAT 149 (324)
T ss_pred CCeEEEEechh--H------------HHHhhHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCCCEEEec
Confidence 46899999321 1 12455677888877765 45566654 568899999999999999863
Q ss_pred eeeecCceeeEEecceeeeceEEEEEecCC
Q 003275 453 ITIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 453 ~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
... .....+. ..|+....++++++...
T Consensus 150 ~~~--~~~~~l~-~~~l~~~~~~~v~~~~h 176 (324)
T PRK12681 150 EAL--HLYDDLI-MLPCYHWNRSVVVPPDH 176 (324)
T ss_pred Ccc--cCCCCeE-EEEeccceeEEEeCCCC
Confidence 211 1112232 35666777777777654
No 211
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=92.18 E-value=3.4 Score=44.13 Aligned_cols=130 Identities=8% Similarity=0.030 Sum_probs=79.5
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHhcC
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDALSKK 99 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l~~~ 99 (834)
..+...++|+|......+ ...+++ ...++...+..+++.+...|-++|++|..... .+....+.+.++++++
T Consensus 135 ~~l~~~~iPvV~v~~~~~---~~~~~~---V~~d~~~~~~~a~~~L~~~G~r~I~~i~~~~~~~~~~~R~~Gf~~al~~~ 208 (328)
T PRK11303 135 QRLQNDGLPIIALDRALD---REHFTS---VVSDDQDDAEMLAESLLKFPAESILLLGALPELSVSFEREQGFRQALKDD 208 (328)
T ss_pred HHHHhcCCCEEEECCCCC---CCCCCE---EEeCCHHHHHHHHHHHHHCCCCeEEEEeCccccccHHHHHHHHHHHHHHc
Confidence 334567899998654221 222333 34566666777788877778899999975432 3455678999999999
Q ss_pred CcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 100 RAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 100 g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|+.+... .....+..+-...+.++.+. .+++|+.. +...+..+++++.+.|+..++-+
T Consensus 209 g~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~A~g~~~al~~~g~~vP~di 268 (328)
T PRK11303 209 PREVHYL--YANSFEREAGAQLFEKWLETHPMPDALFTT-SYTLLQGVLDVLLERPGELPSDL 268 (328)
T ss_pred CCCceEE--EeCCCChHHHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCCce
Confidence 8754322 11111222333445555433 35665554 44567788889899998655444
No 212
>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=92.16 E-value=1.4 Score=45.91 Aligned_cols=139 Identities=11% Similarity=0.067 Sum_probs=90.3
Q ss_pred HHHHHhhccCCccEEecccCCCCCCCC-CCCceEEccCChHHHHHHHHHHHHHcCCeE-EEEEEEcCCc--ccchHHHHH
Q 003275 18 HVISHVVNELNVPLLSFGATDPTLTSL-QYPYFLRTTQSDYYQMHAVADLVEYYGWRE-VIAIFVDDDY--GRNGISVLG 93 (834)
Q Consensus 18 ~~~~~~~~~~~vP~Is~~at~~~ls~~-~~p~~~r~~ps~~~q~~aia~ll~~~~W~~-v~iI~~d~~~--g~~~~~~l~ 93 (834)
..+..+.+. ++|+|...... ... .+|++ ..++..-+..+++.+...|-++ |+++..+.+. .....+.+.
T Consensus 70 ~~l~~~~~~-~iPvV~~~~~~---~~~~~~~~V---~~D~~~a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~ 142 (279)
T PF00532_consen 70 EELRRLIKS-GIPVVLIDRYI---DNPEGVPSV---YIDNYEAGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYR 142 (279)
T ss_dssp HHHHHHHHT-TSEEEEESS-S---CTTCTSCEE---EEEHHHHHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHH
T ss_pred HHHHHHHHc-CCCEEEEEecc---CCcccCCEE---EEcchHHHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHH
Confidence 455556666 99999865432 111 33443 2345566667778888889999 9999976543 455677899
Q ss_pred HHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceE-EEEEeChhhHHHHHHHHHhCC-CCCCCeEEEE
Q 003275 94 DALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRV-FVVHVNPDTGLTIFSVAKSLG-MTAGSYVWIA 163 (834)
Q Consensus 94 ~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~v-ivl~~~~~~~~~i~~~a~~~g-~~~~~~vwi~ 163 (834)
++++++|+++..........+..+-...++++.+..|++ .|++++...+..+++++++.| ...+.-+-+.
T Consensus 143 ~Al~~~Gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~p~idai~~~nd~~A~ga~~~l~~~gr~~ip~di~~~ 214 (279)
T PF00532_consen 143 DALKEAGLPIDEEWIFEGDFDYESGYEAARELLESHPDIDAIFCANDMMAIGAIRALRERGRLKIPEDIVSG 214 (279)
T ss_dssp HHHHHTTSCEEEEEEEESSSSHHHHHHHHHHHHHTSTT-SEEEESSHHHHHHHHHHHHHTT-TCTTTEEEEC
T ss_pred HHHHHcCCCCCcccccccCCCHHHHHHHHHHHHhhCCCCEEEEEeCHHHHHHHHHHHHHcCCcccChhheee
Confidence 999999996544443332233344445566666665651 345567778889999999999 7666555333
No 213
>cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar bindi
Probab=92.15 E-value=2.6 Score=43.63 Aligned_cols=135 Identities=9% Similarity=0.010 Sum_probs=80.3
Q ss_pred HHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC-------cccchHHHHH
Q 003275 21 SHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD-------YGRNGISVLG 93 (834)
Q Consensus 21 ~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~-------~g~~~~~~l~ 93 (834)
...+...++|++...... .+..+++ ...++...+..+++.+...|-++++++..+.. ..+...+.+.
T Consensus 67 ~~~~~~~~~pvV~~~~~~---~~~~~~~---v~~D~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~R~~gf~ 140 (270)
T cd01544 67 LAKLAKLNPNLVFVDSNP---APDGFDS---VVPDFEQAVEKALDYLLELGHTRIGFIGGEEKTTDGHEYIEDPRETAFR 140 (270)
T ss_pred HHHHHhhCCCEEEECCCC---CCCCCCE---EEECHHHHHHHHHHHHHHcCCCcEEEECCCcccccccchhhhHHHHHHH
Confidence 344566789999875322 2223343 55567777788888887789999999975432 3445578899
Q ss_pred HHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC----CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 94 DALSKKRAKISYKAPFSPGASRSAINSLLVGANLM----ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 94 ~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~----~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
++++++|.. .....+....+..+....++++.+. .+++|+ +++...+..+++.+++.|+..++-+-|.
T Consensus 141 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~vp~di~v~ 212 (270)
T cd01544 141 EYMKEKGLY-DPELIYIGDFTVESGYQLMKEALKSLGDNLPTAFF-IASDPMAIGALRALQEAGIKVPEDVSVI 212 (270)
T ss_pred HHHHHcCCC-ChheEeeCCCCHHHHHHHHHHHHhccCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 999988841 1000111111222223334443322 245544 4567778889999999998655433333
No 214
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=92.13 E-value=2 Score=44.89 Aligned_cols=154 Identities=14% Similarity=0.055 Sum_probs=89.3
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
.++.+||--...... .....+...++|+|.+....+ .. +-....++...+..+++.+...|-++++++..+.
T Consensus 55 ~~~dgiii~~~~~~~-~~~~~~~~~~ipvV~~~~~~~----~~---~~~v~~d~~~~g~~~~~~L~~~g~~~i~~i~~~~ 126 (283)
T cd06279 55 ALVDGFIVYGVPRDD-PLVAALLRRGLPVVVVDQPLP----PG---VPSVGIDDRAAAREAARHLLDLGHRRIGILGLRL 126 (283)
T ss_pred cCCCEEEEeCCCCCh-HHHHHHHHcCCCEEEEecCCC----CC---CCEEeeCcHHHHHHHHHHHHHcCCCcEEEecCcc
Confidence 456666653322222 334456778999998754321 11 2235566777788888888888999999997532
Q ss_pred -------------------CcccchHHHHHHHHhcCCcEEEeeecCC-CCCChHHHHHHHHHhhcCC--ceEEEEEeChh
Q 003275 83 -------------------DYGRNGISVLGDALSKKRAKISYKAPFS-PGASRSAINSLLVGANLME--SRVFVVHVNPD 140 (834)
Q Consensus 83 -------------------~~g~~~~~~l~~~l~~~g~~I~~~~~~~-~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~ 140 (834)
.......+.+.+++++.|++......+. ...+.......+.++.... +++|+ +++..
T Consensus 127 ~~~~~~~~~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~ 205 (283)
T cd06279 127 GRDRNTGRVTDERLASATFSVARERLEGYLEALEEAGIDISDVPIWEIPENDRASGEEAARELLDASPRPTAIL-CMSDV 205 (283)
T ss_pred cccccccccccccccccccccHHHHHHHHHHHHHHcCCCCChheEEecCCCchHHHHHHHHHHHcCCCCCcEEE-ECCcH
Confidence 1233457888999998885432111111 1112233445555554433 45544 44556
Q ss_pred hHHHHHHHHHhCCCCCCCe-EEEEeC
Q 003275 141 TGLTIFSVAKSLGMTAGSY-VWIATD 165 (834)
Q Consensus 141 ~~~~i~~~a~~~g~~~~~~-vwi~~~ 165 (834)
.+..+++++++.|+..++- ..+..|
T Consensus 206 ~a~gv~~al~~~g~~ip~di~vig~d 231 (283)
T cd06279 206 LALGALQVARELGLRVPEDLSVVGFD 231 (283)
T ss_pred HHHHHHHHHHHcCCCCCCceEEeeeC
Confidence 7778899999999864433 334433
No 215
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=92.06 E-value=6.3 Score=40.63 Aligned_cols=124 Identities=11% Similarity=-0.018 Sum_probs=77.0
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCC-----eEEEEEEEcCC--cccchHHHHHH
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGW-----REVIAIFVDDD--YGRNGISVLGD 94 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W-----~~v~iI~~d~~--~g~~~~~~l~~ 94 (834)
..+...++|+|......+ +. ...-....++...+..+++++...+- ++++++....+ ......+.+.+
T Consensus 75 ~~~~~~giPvV~~~~~~~---~~--~~~~~V~~d~~~~g~~~~~~l~~~g~~~~~~~~i~~l~g~~~~~~~~~R~~g~~~ 149 (268)
T cd06306 75 LQQVAASIPVIALVNDIN---SP--DITAKVGVSWYEMGYQAGEYLAQRHPKGSKPAKVAWFPGPKGAGWVKAVEKGFRD 149 (268)
T ss_pred HHHHHCCCCEEEeccCCC---Cc--ceeEEecCChHHHHHHHHHHHHHHhhcCCCCceEEEEeCCCCCchHHHHHHHHHH
Confidence 445678999998643211 11 11223566666777888888766665 89999875332 34556788999
Q ss_pred HHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 95 ALSKKRAKISYKAPFSPGASRSAINSLLVGANL--MESRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 95 ~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~--~~~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
++++.++++... .....+...-...+.++.+ ..+++|+. ....+..+++.+++.|+
T Consensus 150 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~--~d~~a~~~~~~l~~~g~ 207 (268)
T cd06306 150 ALAGSAIEISAI--KYGDTGKEVQRKLVEEALEAHPDIDYIVG--SAVAAEAAVGILRQRGL 207 (268)
T ss_pred HHhhcCcEEeee--ccCCccHHHHHHHHHHHHHhCCCcCEEee--cchhhhHHHHHHHhcCC
Confidence 999999877542 1111122333344454432 34577654 36677888889999886
No 216
>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=91.95 E-value=2.5 Score=43.48 Aligned_cols=126 Identities=10% Similarity=0.021 Sum_probs=75.8
Q ss_pred CCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc--CCcccchHHHHHHHHhcCCcEEE
Q 003275 27 LNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD--DDYGRNGISVLGDALSKKRAKIS 104 (834)
Q Consensus 27 ~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~ 104 (834)
.++|+|......+ ....++ ...++..-+..+++.+...|-+++++|..+ +.......+.+.+.+++.|+.+.
T Consensus 76 ~~iPvV~i~~~~~---~~~~~~---V~~d~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~ 149 (265)
T cd06290 76 EEIPVLAVGRRVP---GPGAAS---IAVDNFQGGYLATQHLIDLGHRRIAHITGPRGHIDARDRLAGYRKALEEAGLEVQ 149 (265)
T ss_pred cCCCEEEECCCcC---CCCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEeCccccchhhHHHHHHHHHHHHcCCCCC
Confidence 4899998765322 112233 445666677778887776788999998754 23344567888999988876543
Q ss_pred eeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCe
Q 003275 105 YKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY 159 (834)
Q Consensus 105 ~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~ 159 (834)
....+....+.......+.++.+. .+++|+ +++...+..+++.+++.|+..++.
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~aii-~~~~~~a~~~~~~l~~~g~~ip~d 205 (265)
T cd06290 150 PDLIVQGDFEEESGLEAVEELLQRGPDFTAIF-AANDQTAYGARLALYRRGLRVPED 205 (265)
T ss_pred HHHEEecCCCHHHHHHHHHHHHcCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCcc
Confidence 211111111122223445555433 356554 456667888899999999865443
No 217
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=91.91 E-value=2.3 Score=45.43 Aligned_cols=130 Identities=7% Similarity=-0.001 Sum_probs=76.4
Q ss_pred CCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc--CCcccchHHHHHHHHhcCCcEEE
Q 003275 27 LNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD--DDYGRNGISVLGDALSKKRAKIS 104 (834)
Q Consensus 27 ~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~ 104 (834)
.++|+|....... ...+ . ....++..-+..+++.+...|-+++++|..+ ........+.+.++++++|+.+.
T Consensus 135 ~~iPvV~i~~~~~---~~~~-~--~v~~d~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~ 208 (327)
T PRK10423 135 PSVPTVMMDWAPF---DGDS-D--LIQDNSLLGGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIP 208 (327)
T ss_pred CCCCEEEECCccC---CCCC-C--EEEEChHHHHHHHHHHHHHcCCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCCC
Confidence 4899998753211 1111 1 2334444456777788878899999998643 23445567899999999987542
Q ss_pred eeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 105 YKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 105 ~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
....+....+...-...+.++.+. .+++|+. ++...+..+++.+++.|+..++-+-++
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~A~g~~~~l~~~g~~vP~dvsvi 268 (327)
T PRK10423 209 DGYEVTGDFEFNGGFDAMQQLLALPLRPQAVFT-GNDAMAVGVYQALYQAGLSVPQDIAVI 268 (327)
T ss_pred cceEEeCCCChHHHHHHHHHHhcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 211111111112223444555433 3555444 456677889999999998765544444
No 218
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=91.87 E-value=5.2 Score=41.37 Aligned_cols=142 Identities=13% Similarity=0.096 Sum_probs=90.7
Q ss_pred cEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCC--C--CCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEE
Q 003275 5 VVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTS--L--QYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAI 78 (834)
Q Consensus 5 V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~--~--~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI 78 (834)
-++|++- .+..+.++.. +...+|+|-.+.|||.-.. . .-|---=|.-||..-...-.+++++. +-++++++
T Consensus 89 ~dviv~i-~tp~Aq~~~s--~~~~iPVV~aavtd~v~a~Lv~~~~~pg~NvTGvsD~~~v~q~i~lik~~~Pnak~Igv~ 165 (322)
T COG2984 89 PDVIVAI-ATPAAQALVS--ATKTIPVVFAAVTDPVGAKLVKSLEQPGGNVTGVSDLLPVAQQIELIKALLPNAKSIGVL 165 (322)
T ss_pred CcEEEec-CCHHHHHHHH--hcCCCCEEEEccCchhhccCCccccCCCCceeecCCcchHHHHHHHHHHhCCCCeeEEEE
Confidence 3444443 3344444432 2233999987777765332 1 11223335566666555566666654 78999999
Q ss_pred EEcC-CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh---hhHHHHHHHHHhCCC
Q 003275 79 FVDD-DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP---DTGLTIFSVAKSLGM 154 (834)
Q Consensus 79 ~~d~-~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~---~~~~~i~~~a~~~g~ 154 (834)
|.-+ +.....++.|+..+++.|++|.- ..++ +..|+...++.+. -++|+|++.++. .....+++.|.+.+.
T Consensus 166 Y~p~E~ns~~l~eelk~~A~~~Gl~vve-~~v~---~~ndi~~a~~~l~-g~~d~i~~p~dn~i~s~~~~l~~~a~~~ki 240 (322)
T COG2984 166 YNPGEANSVSLVEELKKEARKAGLEVVE-AAVT---SVNDIPRAVQALL-GKVDVIYIPTDNLIVSAIESLLQVANKAKI 240 (322)
T ss_pred eCCCCcccHHHHHHHHHHHHHCCCEEEE-EecC---cccccHHHHHHhc-CCCcEEEEecchHHHHHHHHHHHHHHHhCC
Confidence 9654 47788899999999999999874 3343 2246666666654 668999998775 355567777777664
No 219
>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=91.60 E-value=3.6 Score=42.31 Aligned_cols=153 Identities=9% Similarity=0.072 Sum_probs=89.1
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
.+|.|||=...+. .....+...++|+|.+....+. +.+-++..++...+..+++.+...|-++++++....
T Consensus 49 ~~vdGiI~~~~~~---~~~~~l~~~~~PvV~~~~~~~~------~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~ 119 (265)
T cd01543 49 WQGDGIIARIDDP---EMAEALQKLGIPVVDVSGSREK------PGIPRVTTDNAAIGRMAAEHFLERGFRHFAFYGLPG 119 (265)
T ss_pred cccceEEEECCCH---HHHHHHhhCCCCEEEEeCccCC------CCCCEEeeCHHHHHHHHHHHHHHCCCcEEEEEcCCC
Confidence 3677666432222 1224455679999987543221 123346667777788888888888999999887443
Q ss_pred C-cccchHHHHHHHHhcCCcEEEeeec--CCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCC-
Q 003275 83 D-YGRNGISVLGDALSKKRAKISYKAP--FSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTA- 156 (834)
Q Consensus 83 ~-~g~~~~~~l~~~l~~~g~~I~~~~~--~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~- 156 (834)
. ......+.+.+++++.|..+..... .....+..+-...+.++-+. .+++| ++++...+..+++.+++.|+..
T Consensus 120 ~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~g~~~~l~~~g~~vp 198 (265)
T cd01543 120 ARWSDEREEAFRQLVAEAGYECSFFYRGLSTDAQSWEEEQEELAQWLQSLPKPVGI-FACTDARARQLLEACRRAGIAVP 198 (265)
T ss_pred CHHHHHHHHHHHHHHHHcCCccccccCccccccccHHHHHHHHHHHHhcCCCCcEE-EecChHHHHHHHHHHHHhCCCCC
Confidence 3 2234467899999999876521111 11011112223344444322 35554 4456667788899999999853
Q ss_pred CCeEEEEeC
Q 003275 157 GSYVWIATD 165 (834)
Q Consensus 157 ~~~vwi~~~ 165 (834)
++...+..|
T Consensus 199 ~di~vigfd 207 (265)
T cd01543 199 EEVAVLGVD 207 (265)
T ss_pred CceEEEeeC
Confidence 344455544
No 220
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=91.58 E-value=4 Score=39.44 Aligned_cols=70 Identities=13% Similarity=0.144 Sum_probs=48.1
Q ss_pred eeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEe
Q 003275 400 KGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAP 479 (834)
Q Consensus 400 ~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~ 479 (834)
..+-.+++..+.++.+ .++++... ++. .++++|.+|++|++++..... ...+. ..|+.+..++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~v~l~~-------~~~-~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~~ 78 (200)
T cd08460 12 AAFGPALLAAVAAEAP-GVRLRFVP-------ESD-KDVDALREGRIDLEIGVLGPT---GPEIR-VQTLFRDRFVGVVR 78 (200)
T ss_pred HHHHHHHHHHHHHHCC-CCEEEEec-------Cch-hHHHHHHCCCccEEEecCCCC---Ccchh-eeeeeccceEEEEe
Confidence 3566788888888875 45566653 345 788999999999998633221 12233 47777888888887
Q ss_pred cCC
Q 003275 480 VQK 482 (834)
Q Consensus 480 ~~~ 482 (834)
...
T Consensus 79 ~~h 81 (200)
T cd08460 79 AGH 81 (200)
T ss_pred CCC
Confidence 665
No 221
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=91.51 E-value=9.4 Score=36.65 Aligned_cols=70 Identities=16% Similarity=0.172 Sum_probs=48.7
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.++.+ .+.+++.. ++...+..+|.+|++|+++..... ....+ -+.|+....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~lv~~~ 80 (200)
T cd08466 13 LLLPRLLARLKQLAP-NISLRESP-------SSEEDLFEDLRLQEVDLVIDYVPF---RDPSF-KSELLFEDELVCVARK 80 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEec-------CchHhHHHHHHcCCccEEEecccC---CCCCc-eeeeecccceEEEEeC
Confidence 455788888888775 45566653 567889999999999999863221 11222 3467778888888886
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (200)
T cd08466 81 DH 82 (200)
T ss_pred CC
Confidence 65
No 222
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=91.50 E-value=20 Score=37.40 Aligned_cols=83 Identities=17% Similarity=0.152 Sum_probs=53.5
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
+.++||++.. ....+-.+++..+.+..+ .+.+.+.. +...+++..|.+|++|+++...
T Consensus 89 g~l~i~~~~~--------------~~~~~~~~~l~~~~~~~P-~i~i~v~~-------~~~~~~~~~l~~g~~Di~i~~~ 146 (290)
T PRK10837 89 GALRIYASST--------------IGNYILPAMIARYRRDYP-QLPLELSV-------GNSQDVINAVLDFRVDIGLIEG 146 (290)
T ss_pred CeEEEEecch--------------hHhhhhHHHHHHHHHHCC-CceEEEEE-------CCHHHHHHHHHhCCceEEEecC
Confidence 5789998421 112445678888888764 34455553 4577899999999999998632
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCC
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
.... ..+ ...|+....+++++++..
T Consensus 147 ~~~~---~~~-~~~~l~~~~~~lv~~~~h 171 (290)
T PRK10837 147 PCHS---PEL-ISEPWLEDELVVFAAPDS 171 (290)
T ss_pred CCCC---Cce-eEEEeecceEEEEEcCCC
Confidence 2211 122 235667778888887655
No 223
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=91.48 E-value=2.5 Score=45.61 Aligned_cols=111 Identities=9% Similarity=-0.000 Sum_probs=67.8
Q ss_pred ccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC-
Q 003275 52 TTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM- 128 (834)
Q Consensus 52 ~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~- 128 (834)
...++..-+..+++.+...|-+++++|..+.. ......+.+.++++++|+.+..........+...-...+.++.+.
T Consensus 156 V~~Dn~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 235 (343)
T PRK10727 156 IALDDRYGAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPANDRLVTFGEPDESGGEQAMTELLGRG 235 (343)
T ss_pred EEECcHHHHHHHHHHHHHCCCccEEEEeCCccccchHHHHHHHHHHHHHCCCCCChhhEEeCCCChhHHHHHHHHHHhCC
Confidence 34556666666777777789999999975432 345567899999999987542211111111112222344454333
Q ss_pred -CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 129 -ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 129 -~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
.+++|+ +.+...+..+++++++.|+..++-+-|+
T Consensus 236 ~~~~ai~-~~nD~~A~g~~~al~~~G~~vP~disVi 270 (343)
T PRK10727 236 RNFTAVA-CYNDSMAAGAMGVLNDNGIDVPGEISLI 270 (343)
T ss_pred CCCCEEE-EcCcHHHHHHHHHHHHcCCCCCcceeEE
Confidence 356554 4556678889999999998765444433
No 224
>cd08425 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold. CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding
Probab=91.44 E-value=12 Score=35.74 Aligned_cols=70 Identities=11% Similarity=0.080 Sum_probs=47.8
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-..++..+.+..+ .+.+++.. ....++...|.+|++|+++...... ...+ ...++....+++++++
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~ 81 (197)
T cd08425 14 YLIGPLIDRFHARYP-GIALSLRE-------MPQERIEAALADDRLDLGIAFAPVR---SPDI-DAQPLFDERLALVVGA 81 (197)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEE-------CcHHHHHHHHHcCCccEEEEecCCC---CCCc-EEEEeccccEEEEecC
Confidence 344688888888765 45566654 4467899999999999998643222 1222 3466777788888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
+.
T Consensus 82 ~~ 83 (197)
T cd08425 82 TH 83 (197)
T ss_pred CC
Confidence 65
No 225
>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=91.43 E-value=2.8 Score=43.23 Aligned_cols=146 Identities=12% Similarity=0.077 Sum_probs=82.7
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD 82 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~ 82 (834)
.+|.+||-...... .....+...++|+|......+ ....++ ...++...+...++.+...|.++++++..+.
T Consensus 57 ~~vdgiii~~~~~~--~~~~~l~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~ 128 (268)
T cd06277 57 GKVDGIILLGGIST--EYIKEIKELGIPFVLVDHYIP---NEKADC---VLTDNYSGAYAATEYLIEKGHRKIGFVGDPL 128 (268)
T ss_pred CCCCEEEEeCCCCh--HHHHHHhhcCCCEEEEccCCC---CCCCCE---EEecchHHHHHHHHHHHHCCCCcEEEECCCC
Confidence 45666664222221 224556677999998754322 122233 3345555566667777777999999997654
Q ss_pred Cc--ccchHHHHHHHHhcCCcEEEeeecCCC-CCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 83 DY--GRNGISVLGDALSKKRAKISYKAPFSP-GASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 83 ~~--g~~~~~~l~~~l~~~g~~I~~~~~~~~-~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
.. .....+.|.+++++.|+.+........ ......+...+.++. ..+++|+. .+...+..+++++++.|+..++
T Consensus 129 ~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~ai~~-~~d~~a~g~~~a~~~~g~~~p~ 205 (268)
T cd06277 129 YSPSFEERYEGYKKALLDHGIPFNEDYDITEKEEDEEDIGKFIDELK-PLPTAFFC-SNDGVAFLLIKVLKEMGIRVPE 205 (268)
T ss_pred CCcchHHHHHHHHHHHHHcCCCCCcceEEEcchhHHHHHHHHHhcCC-CCCCEEEE-CCcHHHHHHHHHHHHcCCCCCC
Confidence 32 234567899999998876432111110 111223333333322 23565444 4555667788888888986443
No 226
>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=91.26 E-value=3.6 Score=42.28 Aligned_cols=127 Identities=11% Similarity=0.069 Sum_probs=76.0
Q ss_pred hhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC---CcccchHHHHHHHHhcC
Q 003275 23 VVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD---DYGRNGISVLGDALSKK 99 (834)
Q Consensus 23 ~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~---~~g~~~~~~l~~~l~~~ 99 (834)
.+...++|+|......+ ...++ ...++...+..+++.+...|.++++++.... .......+.+.++++++
T Consensus 70 ~~~~~gipvv~~~~~~~----~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~ 142 (265)
T cd06291 70 EYENIDLPIVSFDRYLS----ENIPI---VSSDNYEGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKEN 142 (265)
T ss_pred HHhcCCCCEEEEeCCCC----CCCCe---EeechHHHHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHHHc
Confidence 33567899998765432 12232 4455566677788888777999999986433 23445678899999988
Q ss_pred CcEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCCCCCC
Q 003275 100 RAKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGMTAGS 158 (834)
Q Consensus 100 g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~~~~ 158 (834)
|+.+... ......+..+....+.++.+.. +++|+. .+...+..+++.+++.|...++
T Consensus 143 ~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~al~~~g~~vp~ 201 (265)
T cd06291 143 GLEVRII-EIQENFDDAEKKEEIKELLEEYPDIDGIFA-SNDLTAILVLKEAQQRGIRVPE 201 (265)
T ss_pred CCCCChh-eeeccccchHHHHHHHHHHhCCCCCCEEEE-CChHHHHHHHHHHHHcCCCCCc
Confidence 8754221 1111111122233444443333 455444 3445677889999999976443
No 227
>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=91.21 E-value=4.1 Score=42.14 Aligned_cols=134 Identities=9% Similarity=0.048 Sum_probs=81.4
Q ss_pred hhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHhcCC
Q 003275 23 VVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD--DYGRNGISVLGDALSKKR 100 (834)
Q Consensus 23 ~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~--~~g~~~~~~l~~~l~~~g 100 (834)
.+...++|+|......+. ...+++ ...++...+..+++.+...|-+++++|.... .........+.+++++.|
T Consensus 74 ~l~~~~iPvV~i~~~~~~--~~~~~~---V~~d~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g 148 (269)
T cd06287 74 RLRQRGIPVVSIGRPPGD--RTDVPY---VDLQSAATARMLLEHLRAQGARQIALIVGSARRNSYLEAEAAYRAFAAEHG 148 (269)
T ss_pred HHHHcCCCEEEeCCCCCC--CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEEeCCcccccHHHHHHHHHHHHHHcC
Confidence 345679999987543210 122333 3345666667777888888999999996432 334456788999999988
Q ss_pred cEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 101 AKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 101 ~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
+..... ......+..+-...++++.+. .+++|+ +.+...+..+++.+++.|+..+.-+=|+
T Consensus 149 ~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~A~gvl~al~~~gl~vP~dvsvi 211 (269)
T cd06287 149 MPPVVL-RVDEAGGEEAGYAACAQLLAQHPDLDALC-VPVDAFAVGAVRAATELGRAVPDQLRVV 211 (269)
T ss_pred CCccee-EecCCCChHHHHHHHHHHHhCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 753211 111111223333455555433 356655 4466778889999999998766544443
No 228
>PF07885 Ion_trans_2: Ion channel; InterPro: IPR013099 This entry includes the two membrane helix type ion channels found in bacteria []. ; PDB: 1KKD_A 2A0L_A 1ORQ_C 3UKM_C 1LNQ_E 3OUS_A 3LDC_A 3LDD_A 3RBZ_A 3LDE_A ....
Probab=91.12 E-value=0.22 Score=40.56 Aligned_cols=55 Identities=18% Similarity=0.391 Sum_probs=45.5
Q ss_pred CCcchhhHHHHHHHHhhccC--CCcccccchhhhHHHHHHHHHHhhhccccceeeEE
Q 003275 528 PSQQLVTIFWFSFSTMFFSH--RENTVSSLGRVVLIVWLFVVLIINSSYTASLTSIL 582 (834)
Q Consensus 528 ~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~L 582 (834)
...++..++|+++.++...| .-.|.+..+|++.+.+.++++.+.....+.+++.+
T Consensus 21 ~~~~~~da~yfs~~t~tTvGyGDi~p~t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l 77 (79)
T PF07885_consen 21 EKWSFIDALYFSFVTITTVGYGDIVPQTPAGRIFTIIYMLIGIFLFALFLSVLASVL 77 (79)
T ss_dssp STTSHHHHHHHHHHHHTT---SSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHhcccCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35679999999999998665 55899999999999999999999988888776654
No 229
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=90.84 E-value=8.8 Score=36.81 Aligned_cols=70 Identities=11% Similarity=0.012 Sum_probs=46.2
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
++-..++..+.+..+ .+++++.. ++...+...|.+|++|+++..... . ...+ -+.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~--~-~~~~-~~~~l~~~~~~~v~~~ 80 (200)
T cd08464 13 WLAPPLLAALRAEAP-GVRLVFRQ-------VDPFNVGDMLDRGEIDLAIGVFGE--L-PAWL-KREVLYTEGYACLFDP 80 (200)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CCcccHHHHHhcCcccEEEecCCC--C-cccc-eeeeecccceEEEEeC
Confidence 555778888888765 34566653 446678899999999999863321 1 1222 3467777777777765
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (200)
T cd08464 81 QQ 82 (200)
T ss_pred CC
Confidence 54
No 230
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=90.79 E-value=14 Score=38.75 Aligned_cols=86 Identities=13% Similarity=0.130 Sum_probs=56.3
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
.+.|+||++.. . ...+-.+++..+.+..+ .+.+.+.. .+...++.++.+|++|++++.
T Consensus 92 ~~~l~I~~~~~---~-----------~~~~~~~~l~~~~~~~P-~~~i~~~~-------~~~~~~~~~l~~g~~D~~i~~ 149 (300)
T TIGR02424 92 GPTVRIGALPT---V-----------AARLMPEVVKRFLARAP-RLRVRIMT-------GPNAYLLDQLRVGALDLVVGR 149 (300)
T ss_pred CceEEEecccH---H-----------HHhhhHHHHHHHHHhCC-CcEEEEEe-------CchHHHHHHHHCCCCCEEEEe
Confidence 46799998321 1 12344677888887776 45566654 457889999999999999864
Q ss_pred eeeecCceeeEEecceeeeceEEEEEecCC
Q 003275 453 ITIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 453 ~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
.... .....+ ...|.....+++++++..
T Consensus 150 ~~~~-~~~~~~-~~~~l~~~~~~~~~~~~h 177 (300)
T TIGR02424 150 LGAP-ETMQGL-SFEHLYNEPVVFVVRAGH 177 (300)
T ss_pred cCCc-ccccce-eeeeecCCceEEEEcCCC
Confidence 4321 111222 345777788888887655
No 231
>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=90.69 E-value=3.2 Score=42.91 Aligned_cols=135 Identities=14% Similarity=0.173 Sum_probs=81.3
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC-CcccchHHHHHHHHhcCC
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD-DYGRNGISVLGDALSKKR 100 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~-~~g~~~~~~l~~~l~~~g 100 (834)
..+...++|+|......+. .. +..+..++...+..+++.+...|.++++++...+ ..+....+.+.+.+++.|
T Consensus 77 ~~~~~~~ipvV~~~~~~~~---~~---~~~V~~D~~~~g~~~~~~l~~~G~~~i~~l~~~~~~~~~~r~~g~~~~l~~~~ 150 (273)
T cd01541 77 LKLEKLGIPYVFINASYEE---LN---FPSLVLDDEKGGYKATEYLIELGHRKIAGIFKADDLQGVKRMKGFIKAYREHG 150 (273)
T ss_pred HHHHHCCCCEEEEecCCCC---CC---CCEEEECcHHHHHHHHHHHHHcCCcCEEEecCCCcccHHHHHHHHHHHHHHcC
Confidence 3456779999987543221 11 2235566777778888888888999999887432 234455778899998888
Q ss_pred cEEEeee--cCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 101 AKISYKA--PFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 101 ~~I~~~~--~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
..+.... ..............+.++.+. .+++| ++.+...+..+++++++.|+..++-+-|.
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~av-~~~~d~~a~g~~~al~~~g~~~p~dv~vv 216 (273)
T cd01541 151 IPFNPSNVITYTTEEKEEKLFEKIKEILKRPERPTAI-VCYNDEIALRVIDLLKELGLKIPEDISVV 216 (273)
T ss_pred CCCChHHEEeccccchhhHHHHHHHHHHcCCCCCCEE-EEcCcHHHHHHHHHHHHcCCCCCCcEEEE
Confidence 6432111 111111112334445554433 35655 44556677789999999998655544444
No 232
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=90.63 E-value=10 Score=39.55 Aligned_cols=147 Identities=9% Similarity=0.001 Sum_probs=81.8
Q ss_pred CCcEEEE-CCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc------CCeEE
Q 003275 3 NEVVAAI-GPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY------GWREV 75 (834)
Q Consensus 3 ~~V~aii-Gp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~------~W~~v 75 (834)
.++.+|| .|..+.........+...++|+|......+. ...++. +..++...+..+++.+... |-+++
T Consensus 54 ~~vdgiii~~~~~~~~~~~l~~l~~~~ipvV~~~~~~~~---~~~~~~--v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i 128 (288)
T cd01538 54 KGVDVLVIAPVDGEALASAVEKAADAGIPVIAYDRLILN---SNVDYY--VSFDNEKVGELQGQALVDGLGAKGKPPGNI 128 (288)
T ss_pred cCCCEEEEecCChhhHHHHHHHHHHCCCCEEEECCCCCC---CCcceE--EEeChHHHHHHHHHHHHHHHhhcCCCCceE
Confidence 3455444 4433333334445566789999987654321 122222 3445555666667666444 88899
Q ss_pred EEEEEcCC--cccchHHHHHHHHhcCC----cEEEeeecCCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHHHH
Q 003275 76 IAIFVDDD--YGRNGISVLGDALSKKR----AKISYKAPFSPGASRSAINSLLVGANLM---ESRVFVVHVNPDTGLTIF 146 (834)
Q Consensus 76 ~iI~~d~~--~g~~~~~~l~~~l~~~g----~~I~~~~~~~~~~~~~~~~~~l~~l~~~---~~~vivl~~~~~~~~~i~ 146 (834)
+++..+.. ......+.|.+++++.+ +.+... ......+...-...+.++.+. .+++|+. .+...+..++
T Consensus 129 ~~l~g~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~I~~-~~d~~a~g~~ 206 (288)
T cd01538 129 ELIAGSPTDNNAKLFFNGAMSVLKPLIDSGKITIVGE-VATPDWDPETAQKRMENALTANYNKVDGVLA-ANDGTAGGAI 206 (288)
T ss_pred EEEECCCCCchHHHHHHHHHHHHHhccccCCeeEEec-cccCCCCHHHHHHHHHHHHHhCCCCccEEEe-CCcHHHHHHH
Confidence 98875432 23345778899999887 444322 112122222233444444333 3455444 3456677888
Q ss_pred HHHHhCCCCC
Q 003275 147 SVAKSLGMTA 156 (834)
Q Consensus 147 ~~a~~~g~~~ 156 (834)
.++++.|+..
T Consensus 207 ~al~~~g~~~ 216 (288)
T cd01538 207 AALKAAGLAG 216 (288)
T ss_pred HHHHHcCCCC
Confidence 8999988764
No 233
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=90.50 E-value=14 Score=38.81 Aligned_cols=145 Identities=7% Similarity=-0.076 Sum_probs=80.2
Q ss_pred CcEEEEC-CCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc-CC-eEEEEEEE
Q 003275 4 EVVAAIG-PQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY-GW-REVIAIFV 80 (834)
Q Consensus 4 ~V~aiiG-p~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~-~W-~~v~iI~~ 80 (834)
++.|||= +..+.........+...++|+|.+....+. + . .-+.....++...+..+++.+... +- ++++++..
T Consensus 56 ~~DgiIi~~~~~~~~~~~~~~~~~~~iPvV~v~~~~~~--~-~-~~~~~v~~D~~~~g~~a~~~l~~~~~~~~~I~~l~g 131 (298)
T cd06302 56 GVDAIAVVPNDPDALEPVLKKAREAGIKVVTHDSDVQP--D-N-RDYDIEQADNKAIGETLMDSLAEQMGGKGEYAIFVG 131 (298)
T ss_pred CCCEEEEecCCHHHHHHHHHHHHHCCCeEEEEcCCCCC--C-c-ceeEEeccCHHHHHHHHHHHHHHHcCCCCEEEEEeC
Confidence 4544443 333332233444567789999987543211 0 1 112334566777778888887555 43 68998875
Q ss_pred cCC--cccchHHHHHHHHhcCC---cEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCC
Q 003275 81 DDD--YGRNGISVLGDALSKKR---AKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLG 153 (834)
Q Consensus 81 d~~--~g~~~~~~l~~~l~~~g---~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g 153 (834)
+.. ......+.+.++++++| .++.. ......+...-...+.++.+. .+++|+. .+...+..+++++++.|
T Consensus 132 ~~~~~~~~~R~~Gf~~~l~~~g~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~D~~A~g~~~al~~~g 208 (298)
T cd06302 132 SLTATNQNAWIDAAKAYQKEKYYPMLELVD--RQYGDDDADKSYQTAQELLKAYPDLKGIIG-PTSVGIPGAARAVEEAG 208 (298)
T ss_pred CCCCcchHHHHHHHHHHHhhcCCCCeEEeC--cccCCCCHHHHHHHHHHHHHhCCCceEEEE-CCCcchhHHHHHHHhcC
Confidence 432 23345688999999887 23221 112112222222334444332 3444443 44567888999999999
Q ss_pred CC
Q 003275 154 MT 155 (834)
Q Consensus 154 ~~ 155 (834)
+.
T Consensus 209 ~~ 210 (298)
T cd06302 209 LK 210 (298)
T ss_pred CC
Confidence 75
No 234
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=90.39 E-value=17 Score=34.86 Aligned_cols=69 Identities=12% Similarity=0.146 Sum_probs=45.3
Q ss_pred eeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecC
Q 003275 402 YCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQ 481 (834)
Q Consensus 402 ~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~ 481 (834)
+-..++..+.+..+ .+.++... ++...+..+|.+|++|+++..-... ...+ -..++....++++++..
T Consensus 14 ~~~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~~ 81 (198)
T cd08441 14 WLMPVLDQFRERWP-DVELDLSS-------GFHFDPLPALLRGELDLVITSDPLP---LPGI-AYEPLFDYEVVLVVAPD 81 (198)
T ss_pred hhHHHHHHHHHhCC-CeEEEEEe-------CCchhHHHHHHcCCceEEEecCCcC---CCCc-EEEEccCCcEEEEEcCC
Confidence 44678888888775 24455553 4567899999999999998632221 1222 24566777777777765
Q ss_pred C
Q 003275 482 K 482 (834)
Q Consensus 482 ~ 482 (834)
.
T Consensus 82 ~ 82 (198)
T cd08441 82 H 82 (198)
T ss_pred C
Confidence 4
No 235
>PRK09701 D-allose transporter subunit; Provisional
Probab=90.31 E-value=18 Score=38.30 Aligned_cols=131 Identities=13% Similarity=0.019 Sum_probs=77.2
Q ss_pred HhhccCCccEEecccCCCC--CCCCCCCceEEccCChHHHHHHHHHHHHH-cCC--eEEEEEEEcC--CcccchHHHHHH
Q 003275 22 HVVNELNVPLLSFGATDPT--LTSLQYPYFLRTTQSDYYQMHAVADLVEY-YGW--REVIAIFVDD--DYGRNGISVLGD 94 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~--ls~~~~p~~~r~~ps~~~q~~aia~ll~~-~~W--~~v~iI~~d~--~~g~~~~~~l~~ 94 (834)
..+...++|++.+....+. +....-....-+..++...+...++.+.. .|- ++++++..+. .......+.+.+
T Consensus 101 ~~~~~~giPvV~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~aa~~L~~~~g~~~~~i~~l~g~~~~~~~~~R~~Gf~~ 180 (311)
T PRK09701 101 ARAWKKGIYLVNLDEKIDMDNLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATE 180 (311)
T ss_pred HHHHHCCCcEEEeCCCCCcccccccCCceEEEeccchHHHHHHHHHHHHHHhCCCCCEEEEEECCCCCccHHHHHHHHHH
Confidence 3345689999988643321 11111112233566777778888887744 453 7898886443 334456788999
Q ss_pred HHhcCC-cEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 95 ALSKKR-AKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 95 ~l~~~g-~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
++++.| +++..... ...+..+-...+.++.+. .+++ |++.+...+..+++++++.|..
T Consensus 181 al~~~~~~~~~~~~~--~~~~~~~~~~~~~~ll~~~~~~~~-I~~~~d~~A~g~~~al~~~G~~ 241 (311)
T PRK09701 181 AFKKASQIKLVASQP--ADWDRIKALDVATNVLQRNPNIKA-IYCANDTMAMGVAQAVANAGKT 241 (311)
T ss_pred HHHhCCCcEEEEecC--CCCCHHHHHHHHHHHHHhCCCCCE-EEECCcchHHHHHHHHHHcCCC
Confidence 998887 76543211 112222334445555433 3454 4455566788899999998874
No 236
>PRK09526 lacI lac repressor; Reviewed
Probab=90.27 E-value=4.6 Score=43.42 Aligned_cols=128 Identities=9% Similarity=-0.013 Sum_probs=77.6
Q ss_pred cCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHhcCCcEE
Q 003275 26 ELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD--DYGRNGISVLGDALSKKRAKI 103 (834)
Q Consensus 26 ~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~--~~g~~~~~~l~~~l~~~g~~I 103 (834)
..++|++.+... + ....+ ....++..-+..+++.+...|-+++++|..+. .........+.+++++.|+.+
T Consensus 142 ~~~iPvV~~d~~-~---~~~~~---~V~~d~~~~~~~a~~~L~~~G~~~I~~l~g~~~~~~~~~R~~Gf~~al~~~gi~~ 214 (342)
T PRK09526 142 CADVPCLFLDVS-P---QSPVN---SVSFDPEDGTRLGVEHLVELGHQRIALLAGPESSVSARLRLAGWLEYLTDYQLQP 214 (342)
T ss_pred cCCCCEEEEecc-C---CCCCC---EEEECcHHHHHHHHHHHHHCCCCeEEEEeCCCccccHHHHHHHHHHHHHHcCCCc
Confidence 358999976432 1 11222 34556666677788888778999999997532 233455788999999998764
Q ss_pred EeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 104 SYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 104 ~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
... +....+..+-...+.++... .+++|+ +++...+..+++++++.|+..++-+-|+
T Consensus 215 ~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~A~g~~~al~~~g~~vP~disvi 273 (342)
T PRK09526 215 IAV--REGDWSAMSGYQQTLQMLREGPVPSAIL-VANDQMALGVLRALHESGLRVPGQISVI 273 (342)
T ss_pred ceE--EeCCCchHHHHHHHHHHhcCCCCCcEEE-EcCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 321 11111212222334444333 356554 4555677889999999998765544333
No 237
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=90.21 E-value=1.1 Score=46.20 Aligned_cols=103 Identities=14% Similarity=0.075 Sum_probs=61.8
Q ss_pred cCCCChhhhhcCCCCeeEeeCchhhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCc
Q 003275 589 SQIEGIDSLISSTEPIGVQDGSFAWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNC 668 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~ 668 (834)
.+|++++||. |+++.+..++.....++. ++ ...+ +.+..|.+.+|++ |.+|+++.....+..+--.+..
T Consensus 126 ~~i~s~~Dl~--G~kir~~~~~~~~~~~~~-~G---a~~v-~~~~~e~~~aL~~----G~vDg~~~~~~~~~~~~~~ev~ 194 (257)
T TIGR00787 126 KPITKPEDLK--GLKIRIPNSPMNEAQFKA-LG---ANPE-PMAFSEVYTALQT----GVVDGQENPLSNVYSSKFYEVQ 194 (257)
T ss_pred CccCChHHhC--CCEEecCCCHHHHHHHHH-cC---Cccc-ccCHHHHHHHHHc----CCcccccCCHHHHhhcchhhhc
Confidence 5799999997 999999877766777753 43 2233 5578899999999 8999988764443221111122
Q ss_pred cEEEeCCcccccceEEEEcCCC--cchHHHHHHHHhh
Q 003275 669 EFRTVGQEFTKSGWGFAFQRDS--PLAIDLSTAILQL 703 (834)
Q Consensus 669 ~l~~v~~~~~~~~~~~~~~k~s--pl~~~~~~~i~~l 703 (834)
++..... .......+.+.++. .|-+....+|...
T Consensus 195 ~y~~~~~-~~~~~~~~~~n~~~~~~L~~e~q~~i~~a 230 (257)
T TIGR00787 195 KYLSMTN-HGYLGYLVVVNKAFWKSLPPDLQAVVKEA 230 (257)
T ss_pred chheecC-CcccceEEEEeHHHHhcCCHHHHHHHHHH
Confidence 3222222 22344556666642 2545544444443
No 238
>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.
Probab=90.17 E-value=4.4 Score=41.77 Aligned_cols=144 Identities=13% Similarity=0.003 Sum_probs=76.6
Q ss_pred CCcEEEECCCChhhHHHHHHhhccC-CccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHH-cCCeEEEEEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNEL-NVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEY-YGWREVIAIFV 80 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~-~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~-~~W~~v~iI~~ 80 (834)
.+|.+||--. +...........++ ++|++......+.. +.+-+...++..-+..++.++.. .|-+++++|..
T Consensus 56 ~~vdgiI~~~-~~~~~~~~~~~~~~~~~PiV~i~~~~~~~-----~~~~~v~~d~~~a~~~a~~ll~~~~G~~~I~~i~~ 129 (265)
T cd06354 56 AGYDLIVGVG-FLLADALKEVAKQYPDQKFAIIDAVVDDP-----PNVASIVFKEEEGSFLAGYLAALMTKTGKVGFIGG 129 (265)
T ss_pred CCCCEEEEcC-cchHHHHHHHHHHCCCCEEEEEecccCCC-----CcEEEEEecchhHHHHHHHHHHhhcCCCeEEEEec
Confidence 3566666421 12223445555555 89999865422110 11222333444334444455554 38899999975
Q ss_pred cCC-cccchHHHHHHHHhcCC---cEEEeeecCCCCCC-hHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCC
Q 003275 81 DDD-YGRNGISVLGDALSKKR---AKISYKAPFSPGAS-RSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLG 153 (834)
Q Consensus 81 d~~-~g~~~~~~l~~~l~~~g---~~I~~~~~~~~~~~-~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g 153 (834)
+.. ......+.+.+.+++.| ..+..........+ ..+-...+.++.+..+++|+. .+...+..+++++++.|
T Consensus 130 ~~~~~~~~r~~gf~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~pdaI~~-~nd~~A~gv~~al~~~g 206 (265)
T cd06354 130 MDIPLIRRFEAGFEAGVKYVNPGVPDIEVLVQYAGSFNDPAKGKEIAQAMYDQGADVIFA-AAGGTGNGVFQAAKEAG 206 (265)
T ss_pred ccChHHHHHHHHHHHHHHHHhccCCCceEEEEEcCcccCHHHHHHHHHHHHHCCCcEEEE-CCCCCchHHHHHHHhcC
Confidence 422 11222367888888888 54322111111111 123334555655445786544 45667778889999888
No 239
>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=90.15 E-value=4.7 Score=43.06 Aligned_cols=134 Identities=7% Similarity=0.019 Sum_probs=79.2
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHhcC
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDALSKK 99 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l~~~ 99 (834)
..+...++|+|......+ +..+++ +..++..-+..+++.+...|-+++++|..... ......+.+.++++++
T Consensus 134 ~~l~~~~iPvV~~~~~~~---~~~~~~---V~~dn~~~~~~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~ 207 (327)
T TIGR02417 134 QKLQNEGLPVVALDRSLD---DEHFCS---VISDDVDAAAELIERLLSQHADEFWYLGAQPELSVSRDRLAGFRQALKQA 207 (327)
T ss_pred HHHHhcCCCEEEEccccC---CCCCCE---EEeCcHHHHHHHHHHHHHCCCCeEEEEeCcccchhHHHHHHHHHHHHHHc
Confidence 344567899998754322 122333 34455555666677777788899999975432 3445678899999998
Q ss_pred CcEEEeeecCCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHHHHHHHHhCCCCCCCe-EEEEeC
Q 003275 100 RAKISYKAPFSPGASRSAINSLLVGANLM---ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSY-VWIATD 165 (834)
Q Consensus 100 g~~I~~~~~~~~~~~~~~~~~~l~~l~~~---~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~-vwi~~~ 165 (834)
|+.+... +....+..+-...+.++.+. .+++|+.. +...+..+++++++.| ..++- ..+..|
T Consensus 208 ~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~~Ai~~~-~D~~A~g~~~al~~~g-~vP~dvsvigfd 273 (327)
T TIGR02417 208 TLEVEWV--YGGNYSRESGYQMFAKLCARLGRLPQALFTT-SYTLLEGVLDYMLERP-LLDSQLHLATFG 273 (327)
T ss_pred CCChHhE--EeCCCChHHHHHHHHHHHhcCCCCCcEEEEc-CcHHHHHHHHHHHHcC-CCCCcceEEEEC
Confidence 8753211 11111222233445555432 35665554 4566788999999999 55543 344433
No 240
>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=90.01 E-value=17 Score=37.48 Aligned_cols=142 Identities=14% Similarity=0.130 Sum_probs=77.3
Q ss_pred CcEEEE-CCCChhh-HHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc--CCeEEEEEE
Q 003275 4 EVVAAI-GPQSSGI-AHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY--GWREVIAIF 79 (834)
Q Consensus 4 ~V~aii-Gp~~S~~-~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~ 79 (834)
+|.++| .|..... ...+..+ .+ ++|+|......+. ...++ -...++..-+..+++.+... +-.+++++.
T Consensus 55 ~vDgiIi~~~~~~~~~~~l~~~-~~-~ipvV~~~~~~~~--~~~~~---~V~~D~~~~g~~a~~~l~~~~~~g~~~~~~~ 127 (271)
T cd06314 55 GVDGIAISPIDPKAVIPALNKA-AA-GIKLITTDSDAPD--SGRYV---YIGTDNYAAGRTAGEIMKKALPGGGKVAIFV 127 (271)
T ss_pred CCCEEEEecCChhHhHHHHHHH-hc-CCCEEEecCCCCc--cceeE---EEccChHHHHHHHHHHHHHHcCCCCEEEEEe
Confidence 454444 4443332 2333333 45 9999987542211 11112 24455666677777777553 234566665
Q ss_pred EcC--CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 80 VDD--DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 80 ~d~--~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
.+. .......+.+.+++++.|+++.... . ...+..+....+.++.+. .+++|+. .+...+..++.++++.|..
T Consensus 128 ~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~l~~~~~~~~i~~-~~d~~a~~~~~al~~~g~~ 204 (271)
T cd06314 128 GSLGADNAKERIQGIKDAIKDSKIEIVDTR-G-DEEDFAKAKSNAEDALNAHPDLKCMFG-LYAYNGPAIAEAVKAAGKL 204 (271)
T ss_pred cCCCCCCHHHHHHHHHHHHhcCCcEEEEEe-c-CccCHHHHHHHHHHHHHhCCCccEEEe-cCCccHHHHHHHHHHcCCC
Confidence 432 2344567889999999998765421 1 111223344455555433 3455543 3445556678888888875
No 241
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=89.99 E-value=17 Score=34.93 Aligned_cols=71 Identities=8% Similarity=0.013 Sum_probs=48.5
Q ss_pred eeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEe
Q 003275 400 KGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAP 479 (834)
Q Consensus 400 ~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~ 479 (834)
..+-.+++..+.+..+ .+++++.. ++..++.+.|.+|++|+++..... . ...+. ..+.....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~--~-~~~~~-~~~l~~~~~~~v~~ 79 (200)
T cd08467 12 VALLPRLAPRLRERAP-GLDLRLCP-------IGDDLAERGLEQGTIDLAVGRFAV--P-PDGLV-VRRLYDDGFACLVR 79 (200)
T ss_pred HHHHHHHHHHHHhhCC-CCEEEEec-------CCcccHHHHhhCCCcCEEEecCCC--C-Cccce-eEEeeeccEEEEEc
Confidence 3555788888888776 35566654 456789999999999999863221 1 12233 46777888888887
Q ss_pred cCC
Q 003275 480 VQK 482 (834)
Q Consensus 480 ~~~ 482 (834)
+..
T Consensus 80 ~~h 82 (200)
T cd08467 80 HGH 82 (200)
T ss_pred CCC
Confidence 655
No 242
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=89.83 E-value=23 Score=37.88 Aligned_cols=84 Identities=11% Similarity=0.009 Sum_probs=56.9
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
+.||||+... ....+-.++++.+.+..+ .+.+.+.. ++.++++++|.+|++|+++...
T Consensus 93 g~lrIg~~~~--------------~~~~~l~~~l~~f~~~~P-~v~i~l~~-------~~~~~~~~~l~~g~~Dl~i~~~ 150 (327)
T PRK12680 93 GQLTLTTTHT--------------QARFVLPPAVAQIKQAYP-QVSVHLQQ-------AAESAALDLLGQGDADIAIVST 150 (327)
T ss_pred eEEEEEecch--------------hHHHhhHHHHHHHHHHCC-CcEEEEEe-------CChHHHHHHHHCCCCcEEEEec
Confidence 5799999322 113445788888888887 34566654 5578999999999999998632
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCC
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
.... ..... ..|+....++++++...
T Consensus 151 ~~~~--~~~~~-~~~l~~~~~~l~~~~~h 176 (327)
T PRK12680 151 AGGE--PSAGI-AVPLYRWRRLVVVPRGH 176 (327)
T ss_pred CCCC--CCcce-EEEeeccceEEEEeCCC
Confidence 2111 11222 47888888888888665
No 243
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=89.68 E-value=2.5 Score=45.11 Aligned_cols=66 Identities=21% Similarity=0.187 Sum_probs=45.3
Q ss_pred CCCChhhhhcCCCCeeEeeCchhhHHHH---hhhcccccce--EecCCHHHHHHHHhcCCCCCceEEEEechhhHHHH
Q 003275 590 QIEGIDSLISSTEPIGVQDGSFAWNYLV---DELKIAESRL--VKLKNMEEYSIALARGPKGGGVAAIVDELPYIELF 662 (834)
Q Consensus 590 ~i~s~~dL~~~~~~v~~~~~s~~~~~l~---~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~ 662 (834)
.|++++||. |++|++..++.....+. +..+++.+.+ +.+ ...+...++.+ |.+|+++...++....
T Consensus 113 ~I~s~~DLk--GK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~Al~~----G~VDAa~~~~p~~~~~ 183 (320)
T PRK11480 113 TISKPEDLI--GKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNL-QPPAIIAAWQR----GDIDGAYVWAPAVNAL 183 (320)
T ss_pred CCCChHHcC--CCEEecCCCCchHHHHHHHHHHcCCCHhheEEEEC-CcHHHHHHHHc----CCcCEEEEcchHHHHH
Confidence 699999997 99999987664443322 2344444333 333 46788899998 9999988877776544
No 244
>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=89.68 E-value=5.4 Score=40.76 Aligned_cols=123 Identities=11% Similarity=0.045 Sum_probs=74.9
Q ss_pred cEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHhcCCcEEEeee
Q 003275 30 PLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD--DYGRNGISVLGDALSKKRAKISYKA 107 (834)
Q Consensus 30 P~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~--~~g~~~~~~l~~~l~~~g~~I~~~~ 107 (834)
|++......+ ...+ ...+++...+..+++.+...|-+++++|..+. .......+.+.+++++.|+.+....
T Consensus 79 pvv~~~~~~~----~~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~ 151 (260)
T cd06286 79 PIVLCEEYDS----KNIS---SVYIDHYEAFYEALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTPDEEW 151 (260)
T ss_pred CEEEEecccC----CCCC---EEEECChHHHHHHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCCCChHh
Confidence 8887543211 1223 35556667777888888888999999997542 3445567899999999886542211
Q ss_pred cCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 108 PFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 108 ~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
.+....+..+....+.++.+. .+++|+ +++...+..+++.+++.|+..++-+
T Consensus 152 i~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~ip~di 205 (260)
T cd06286 152 IFEGCFTIEDGERIGHQLLKMKDRPDAIF-TGSDEVAAGIITEAKKQGIRVPEDL 205 (260)
T ss_pred eEeCCCCHHHHHHHHHHHHcCCCCCCEEE-EcchHHHHHHHHHHHHcCCCCCcce
Confidence 111111223334445555443 456544 5566677889999999998644333
No 245
>PF13377 Peripla_BP_3: Periplasmic binding protein-like domain; PDB: 3K9C_B 3BIL_B 3JVD_B 1ZAY_A 1VPW_A 1DBQ_A 2PUA_A 1QQA_A 1PNR_A 1JHZ_A ....
Probab=89.61 E-value=1.2 Score=41.64 Aligned_cols=98 Identities=13% Similarity=0.149 Sum_probs=64.1
Q ss_pred HHHHHHcCCeEEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHH-HHhhcCCceEEEEEeChh
Q 003275 64 ADLVEYYGWREVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLL-VGANLMESRVFVVHVNPD 140 (834)
Q Consensus 64 a~ll~~~~W~~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l-~~l~~~~~~vivl~~~~~ 140 (834)
++.+...|-+++++|..+ +.+.....+.+.+++++.|+........... ...+..... ..+++..+++|++ ++..
T Consensus 1 ~~~L~~~G~r~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~pdaii~-~~~~ 78 (160)
T PF13377_consen 1 VDYLIERGHRRIAFIGGPPNSSVSRERLEGFREALKEHGIEFEELIFFSDD-DSEDAREAQLLWLRRLRPDAIIC-SNDR 78 (160)
T ss_dssp HHHHHHTT-SSEEEEESSTTSHHHHHHHHHHHHHHHHTTSEEEGEEEEESS-SHHHHHHHHHHHHHTCSSSEEEE-SSHH
T ss_pred ChHHHHCCCCeEEEEecCCCChhHHHHHHHHHHHHHHCCCCCCeeEeecCC-cchhHHHHHHHHHhcCCCcEEEE-cCHH
Confidence 456778899999999933 3455566889999999999986654444433 222222222 2344346676555 7788
Q ss_pred hHHHHHHHHHhCCCCCCCeEEEE
Q 003275 141 TGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 141 ~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
.+..+++.+.+.|+..+.-+-++
T Consensus 79 ~a~~~~~~l~~~g~~vP~di~vv 101 (160)
T PF13377_consen 79 LALGVLRALRELGIRVPQDISVV 101 (160)
T ss_dssp HHHHHHHHHHHTTSCTTTTSEEE
T ss_pred HHHHHHHHHHHcCCcccccccEE
Confidence 89999999999998655433333
No 246
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=89.57 E-value=14 Score=39.90 Aligned_cols=149 Identities=9% Similarity=0.007 Sum_probs=83.9
Q ss_pred CcEEEE-CCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc-----CCeEEEE
Q 003275 4 EVVAAI-GPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY-----GWREVIA 77 (834)
Q Consensus 4 ~V~aii-Gp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~-----~W~~v~i 77 (834)
+|.||| .|.......... .+.+.++|+|.+..... .. . .......++...+...++.+... |-+++++
T Consensus 104 ~vdgIIl~~~~~~~~~~~l-~~~~~giPvV~~~~~~~--~~-~--~~~~V~~D~~~~g~~aa~~L~~~~~~~~g~~~i~~ 177 (343)
T PRK10936 104 GADAILLGAVTPDGLNPDL-ELQAANIPVIALVNGID--SP-Q--VTTRVGVSWYQMGYQAGRYLAQWHPKGSKPLNVAL 177 (343)
T ss_pred CCCEEEEeCCChHHhHHHH-HHHHCCCCEEEecCCCC--Cc-c--ceEEEecChHHHHHHHHHHHHHHHHhcCCCceEEE
Confidence 454443 454433322222 45678999997633211 11 1 12235566677777777776443 4689998
Q ss_pred EEEcC--CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHhCC
Q 003275 78 IFVDD--DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANL--MESRVFVVHVNPDTGLTIFSVAKSLG 153 (834)
Q Consensus 78 I~~d~--~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~--~~~~vivl~~~~~~~~~i~~~a~~~g 153 (834)
+..+. .......+.+.+.+++.|+++.... .. ..+...-...++++.+ ..+++|+ +....+..+++.+++.|
T Consensus 178 i~g~~~~~~~~~R~~Gf~~~l~~~~i~~~~~~-~~-~~~~~~~~~~~~~~l~~~~~~~ai~--~~d~~A~ga~~al~~~g 253 (343)
T PRK10936 178 LPGPEGAGGSKAVEQGFRAAIAGSDVRIVDIA-YG-DNDKELQRNLLQELLERHPDIDYIA--GSAVAAEAAIGELRGRN 253 (343)
T ss_pred EECCCCCchHHHHHHHHHHHHhcCCCEEEEee-cC-CCcHHHHHHHHHHHHHhCCCccEEE--eCCHHHHHHHHHHHhcC
Confidence 87432 2333457889999998898875421 11 1122223334444433 2357765 44566777888889988
Q ss_pred CCCCCeEEEEe
Q 003275 154 MTAGSYVWIAT 164 (834)
Q Consensus 154 ~~~~~~vwi~~ 164 (834)
+ ++.+.|++
T Consensus 254 ~--~~di~Vvg 262 (343)
T PRK10936 254 L--TDKIKLVS 262 (343)
T ss_pred C--CCCeEEEE
Confidence 7 34455543
No 247
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=89.55 E-value=17 Score=34.69 Aligned_cols=70 Identities=14% Similarity=0.067 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+.+++.. ++.+.+...+.+|++|+++..... ....+ -+.++....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Di~i~~~~~---~~~~~-~~~~l~~~~~~lv~~~ 80 (198)
T cd08461 13 AILPPLLAALRQEAP-GVRVAIRD-------LESDNLEAQLERGEVDLALTTPEY---APDGL-RSRPLFEERYVCVTRR 80 (198)
T ss_pred HHhHHHHHHHHHHCC-CcEEEEee-------CCcccHHHHHhcCCCcEEEecCcc---CCccc-eeeeeecCcEEEEEcC
Confidence 455788888888775 34455543 345678999999999999863221 11222 2567778888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (198)
T cd08461 81 GH 82 (198)
T ss_pred CC
Confidence 54
No 248
>PF13531 SBP_bac_11: Bacterial extracellular solute-binding protein; PDB: 2HXW_B 3FJG_C 3FJM_B 3FJ7_B 3FIR_B 3AXF_C 1WOD_A 1AMF_A 3R26_A 1SBP_A ....
Probab=89.36 E-value=5.8 Score=39.86 Aligned_cols=198 Identities=17% Similarity=0.092 Sum_probs=115.0
Q ss_pred eeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhC-cccEEeeeeeeecCce---eeEE--ecceeeec
Q 003275 399 VKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALN-KFDAAVGDITIVTNRT---KLVD--FTQPYMES 472 (834)
Q Consensus 399 ~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g-~~D~~~~~~~i~~~r~---~~vd--fs~p~~~~ 472 (834)
..+..-++.+...+..++++++.+. .-..+..+|..| ++|+.+.+-....++. ..++ -..|+..+
T Consensus 9 ~~~~~~~l~~~f~~~~g~~v~v~~~---------~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~ 79 (230)
T PF13531_consen 9 LAPALEELAEAFEKQPGIKVEVSFG---------GSGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLARS 79 (230)
T ss_dssp GHHHHHHHHHHHHHHHCEEEEEEEE---------CHHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEEE
T ss_pred HHHHHHHHHHHHHhccCCeEEEEEC---------ChHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCcccccccC
Confidence 3455667888888888877555553 356788888877 6899877543221211 2333 57888889
Q ss_pred eEEEEEecCCCCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcchhhHHHHHHHHhhccCCCccc
Q 003275 473 GLVVVAPVQKLKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQLVTIFWFSFSTMFFSHRENTV 552 (834)
Q Consensus 473 ~~~~vv~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 552 (834)
.+++++++..+
T Consensus 80 ~~vl~~~~~~~--------------------------------------------------------------------- 90 (230)
T PF13531_consen 80 PLVLAVPKGNP--------------------------------------------------------------------- 90 (230)
T ss_dssp EEEEEEETTST---------------------------------------------------------------------
T ss_pred ceEEEeccCcc---------------------------------------------------------------------
Confidence 99999988771
Q ss_pred ccchhhhHHHHHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCc------hhhHHHHhhh-----c
Q 003275 553 SSLGRVVLIVWLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGS------FAWNYLVDEL-----K 621 (834)
Q Consensus 553 s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s------~~~~~l~~~~-----~ 621 (834)
..+.+++||.+.+.++++.... .....+.+.- .
T Consensus 91 ------------------------------------~~~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~~g~~~~~~ 134 (230)
T PF13531_consen 91 ------------------------------------KGIRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAAAGGQELLD 134 (230)
T ss_dssp ------------------------------------TSTTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHHHTHCHHHH
T ss_pred ------------------------------------cccCCHHHHhhccCEEEecCcccChhhHHHHHHHHHcccHHHHH
Confidence 2567788887666677776421 1122222110 0
Q ss_pred ccccceE-ecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCccc--ccceEEEEcCCCcchHHHHH
Q 003275 622 IAESRLV-KLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQEFT--KSGWGFAFQRDSPLAIDLST 698 (834)
Q Consensus 622 ~~~~~~~-~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~~--~~~~~~~~~k~spl~~~~~~ 698 (834)
.-..++. ..++..+....+.+ |+.|+.+.......+.-....-.+..+.+... ...+.+++.++++-.+.-..
T Consensus 135 ~l~~~~~~~~~~~~~~~~~v~~----g~~d~~~~~~s~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~a~~ 210 (230)
T PF13531_consen 135 ALQKNIVQYVPSTSQVLSAVAS----GEADAGIVYESQAIFARQGDPLSYVYPPDGVNSPPIDYPIAILKNAPHPEAARA 210 (230)
T ss_dssp HHHHTEEEEESSHHHHHHHHHT----TSSSEEEEEHHHHHHCTSHTTEEEEE-STTTSSSEEEEEEEEBTTCTTHHHHHH
T ss_pred HHHHhCcccccchHHHHHHHHc----CCCcceeeHHHHHHHhhcCCCeEEEECCchhcCCCEEEEEEEecCCCCHHHHHH
Confidence 0012333 45677888899988 88998887655553221111123444444444 24578888888876666666
Q ss_pred HHHhhhccccHHHHHHh
Q 003275 699 AILQLSENGDLQKIHNK 715 (834)
Q Consensus 699 ~i~~l~e~G~~~~i~~k 715 (834)
.+.-|... .-+++..+
T Consensus 211 f~~~L~s~-~~q~~l~~ 226 (230)
T PF13531_consen 211 FIDFLLSP-EGQQILAK 226 (230)
T ss_dssp HHHHHTSH-HHHHHHHH
T ss_pred HHHHHCCH-HHHHHHHH
Confidence 66555543 34444443
No 249
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=89.34 E-value=20 Score=34.03 Aligned_cols=70 Identities=19% Similarity=0.200 Sum_probs=47.2
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+...++..+.+..+ .+.+++.. +....+..+|.+|++|+++....... .. -.+.++....++++++.
T Consensus 12 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~-~~~~~l~~~~~~~~~~~ 79 (197)
T cd08419 12 YFAPRLLGAFCRRHP-GVEVSLRV-------GNREQVLERLADNEDDLAIMGRPPED---LD-LVAEPFLDNPLVVIAPP 79 (197)
T ss_pred hHhhHHHHHHHHHCC-CceEEEEE-------CCHHHHHHHHhcCCccEEEecCCCCC---CC-eEEEEeccCCEEEEecC
Confidence 456778888888764 34466553 45778999999999999986432211 11 23567777888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 80 ~~ 81 (197)
T cd08419 80 DH 81 (197)
T ss_pred CC
Confidence 55
No 250
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=88.90 E-value=23 Score=34.05 Aligned_cols=72 Identities=15% Similarity=0.120 Sum_probs=49.0
Q ss_pred eeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEe
Q 003275 400 KGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAP 479 (834)
Q Consensus 400 ~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~ 479 (834)
.++-.+++..+.+..+ .+.++... ++...+++.|.+|++|+++..-... ....+ .+.++....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~~~~ 80 (198)
T cd08444 12 RYALPWVVQAFKEQFP-NVHLVLHQ-------GSPEEIASMLANGQADIGIATEALE--NHPEL-VSFPYYDWHHHIIVP 80 (198)
T ss_pred hhhhhHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHCCCccEEEeccccC--CCcCc-EEeeccccceeEEec
Confidence 3566788888888875 34566554 5578899999999999998632211 11222 356777788888887
Q ss_pred cCC
Q 003275 480 VQK 482 (834)
Q Consensus 480 ~~~ 482 (834)
+..
T Consensus 81 ~~h 83 (198)
T cd08444 81 VGH 83 (198)
T ss_pred CCC
Confidence 665
No 251
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=88.88 E-value=22 Score=33.87 Aligned_cols=73 Identities=14% Similarity=0.044 Sum_probs=48.5
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeee--cCceeeEEecceeeeceEEEEE
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIV--TNRTKLVDFTQPYMESGLVVVA 478 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~--~~r~~~vdfs~p~~~~~~~~vv 478 (834)
.+-.+++..+.+..+ .+++.+.. ++...+..++.+|++|+++...... ......+ .+.+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~ 83 (200)
T cd08423 13 ALLPPALAALRARHP-GLEVRLRE-------AEPPESLDALRAGELDLAVVFDYPVTPPPDDPGL-TRVPLLDDPLDLVL 83 (200)
T ss_pred HhhhHHHHHHHHhCC-CCeEEEEe-------CCHHHHHHHHhcCCccEEEEeccccccCCCCCCc-EEEEeccCcEEEEe
Confidence 445778888888875 44566654 4567899999999999998642111 0112222 35677788888888
Q ss_pred ecCC
Q 003275 479 PVQK 482 (834)
Q Consensus 479 ~~~~ 482 (834)
+...
T Consensus 84 ~~~~ 87 (200)
T cd08423 84 PADH 87 (200)
T ss_pred cCCC
Confidence 7665
No 252
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=88.80 E-value=22 Score=37.71 Aligned_cols=69 Identities=10% Similarity=0.116 Sum_probs=46.6
Q ss_pred eeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecC
Q 003275 402 YCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQ 481 (834)
Q Consensus 402 ~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~ 481 (834)
+-.+++..+.+..+ .+.++... ..-.++...|.+|++|+++..-.. ....+. +.++....++++++..
T Consensus 103 ~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~L~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~lv~~~~ 170 (317)
T PRK15421 103 WLTPALENFHKNWP-QVEMDFKS-------GVTFDPQPALQQGELDLVMTSDIL---PRSGLH-YSPMFDYEVRLVLAPD 170 (317)
T ss_pred HHHHHHHHHHHHCC-CceEEEEe-------CccHHHHHHHHCCCcCEEEecCcc---cCCCce-EEEeccceEEEEEcCC
Confidence 34677888877765 34566553 345788999999999999864322 122333 3777788888888766
Q ss_pred C
Q 003275 482 K 482 (834)
Q Consensus 482 ~ 482 (834)
.
T Consensus 171 h 171 (317)
T PRK15421 171 H 171 (317)
T ss_pred C
Confidence 5
No 253
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=88.72 E-value=7.8 Score=41.76 Aligned_cols=111 Identities=7% Similarity=-0.073 Sum_probs=68.0
Q ss_pred ccCChHHHHHHHHHHHHHcCCeEEEEEEEcC--CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC-
Q 003275 52 TTQSDYYQMHAVADLVEYYGWREVIAIFVDD--DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM- 128 (834)
Q Consensus 52 ~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~--~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~- 128 (834)
...++..-+..+++.+...|-+++++|.... ..+....+.+.++++++|+.+..........+...-...+.++.+.
T Consensus 156 V~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 235 (346)
T PRK10401 156 VCLDNVSGARMATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWMSALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGRN 235 (346)
T ss_pred EEECcHHHHHHHHHHHHHCCCCeEEEEeCCCcCcchHHHHHHHHHHHHHcCCCCChhheecCCCChHHHHHHHHHHHcCC
Confidence 3345555566677777778999999997443 3455678899999999987543211111111112222344454332
Q ss_pred -CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 129 -ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 129 -~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
.+++|+. .+...+..+++++++.|+..++-+-+.
T Consensus 236 ~~~~ai~~-~nd~~A~g~~~al~~~G~~vP~disvi 270 (346)
T PRK10401 236 LQLTAVFA-YNDNMAAGALTALKDNGIAIPLHLSII 270 (346)
T ss_pred CCCcEEEE-CCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 3566554 566677889999999998765444433
No 254
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=88.68 E-value=0.56 Score=49.16 Aligned_cols=90 Identities=17% Similarity=0.121 Sum_probs=57.1
Q ss_pred ccCCCChhhhhcCCCCeeEeeCchhhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCC
Q 003275 588 TSQIEGIDSLISSTEPIGVQDGSFAWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTN 667 (834)
Q Consensus 588 ~~~i~s~~dL~~~~~~v~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~ 667 (834)
..+|++++||. |.++.+..+.....+++ .++.. -+.. ...|.+.+|++ |.+|+.......+...--.+.
T Consensus 125 ~~pi~s~~Dlk--G~kiR~~~~~~~~~~~~-~lGa~---pv~i-p~~evy~aLq~----G~vDg~~~~~~~~~~~~~~ev 193 (286)
T PF03480_consen 125 KKPIRSPEDLK--GLKIRVPGSPVMSDFFE-ALGAS---PVPI-PWSEVYQALQQ----GVVDGAENSASSIYSLGLYEV 193 (286)
T ss_dssp SS--SSGGGGT--TEEEEETSSHHHHHHHH-HCTSE---EEE--TGGGHHHHHHT----TSSSEEEEEHHHHHHTTGGGT
T ss_pred ccCCccHhhHh--hCeEEecCCHHHHHHHH-HcCCe---eecC-cHHHHHHHHhc----CCcCeEecCHHHHHhcChhhh
Confidence 36899999997 88888876666666664 45433 3333 56789999999 999999987666533222224
Q ss_pred ccEEEeCCcccccceEEEEcCC
Q 003275 668 CEFRTVGQEFTKSGWGFAFQRD 689 (834)
Q Consensus 668 ~~l~~v~~~~~~~~~~~~~~k~ 689 (834)
+++..... ....++.+++.+.
T Consensus 194 ~~y~~~~~-~~~~~~~~~~n~~ 214 (286)
T PF03480_consen 194 AKYFTDTN-HGWSPYAVIMNKD 214 (286)
T ss_dssp SSEEEEEE-EEEEEEEEEEEHH
T ss_pred CCeeEeec-ccCcceEEEEcHH
Confidence 55544433 3445566777654
No 255
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=88.65 E-value=23 Score=34.75 Aligned_cols=70 Identities=11% Similarity=0.059 Sum_probs=48.1
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+..+++..+.+..+ .+++++.. .+..++.+.|.+|++|++++.... ....+. ..|.....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~Di~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~ 80 (221)
T cd08469 13 VLLPALVRRLETEAP-GIDLRIRP-------VTRLDLAEQLDLGRIDLVIGIFEQ---IPPRFR-RRTLFDEDEVWVMRK 80 (221)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEee-------CChhhHHHHHHCCCccEEEecCCC---CCccce-eeeeeccceEEEEeC
Confidence 445678888887765 34566553 456789999999999999874321 122333 467778888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (221)
T cd08469 81 DH 82 (221)
T ss_pred CC
Confidence 65
No 256
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=88.61 E-value=20 Score=37.88 Aligned_cols=71 Identities=15% Similarity=0.267 Sum_probs=48.8
Q ss_pred eeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecC
Q 003275 402 YCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQ 481 (834)
Q Consensus 402 ~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~ 481 (834)
+-.+++..+.+..+ .+++.+.. ++..+++.+|.+|++|+++........ ... -...|+....+++++++.
T Consensus 111 ~l~~~l~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~-~~~-l~~~~l~~~~~~lv~~~~ 180 (312)
T PRK10341 111 FMSDMINKFKEVFP-KAQVSMYE-------AQLSSFLPAIRDGRLDFAIGTLSNEMK-LQD-LHVEPLFESEFVLVASKS 180 (312)
T ss_pred hHHHHHHHHHHhCC-CCEEEEEe-------CCHHHHHHHHHcCCCcEEEecCCcccc-cCC-eeEEEEecccEEEEEcCC
Confidence 44688888888765 35566664 557899999999999999864322111 111 235778888888888766
Q ss_pred C
Q 003275 482 K 482 (834)
Q Consensus 482 ~ 482 (834)
.
T Consensus 181 ~ 181 (312)
T PRK10341 181 R 181 (312)
T ss_pred C
Confidence 5
No 257
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=88.55 E-value=5.9 Score=42.40 Aligned_cols=134 Identities=10% Similarity=0.031 Sum_probs=79.3
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC-CcccchHHHHHHHHhcCC
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD-DYGRNGISVLGDALSKKR 100 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~-~~g~~~~~~l~~~l~~~g 100 (834)
..+...++|+|....... . .... ....++..-+..+++.+...|-+++++|.... .........+.++++++|
T Consensus 136 ~~l~~~~iPvV~~~~~~~---~-~~~~--~V~~Dn~~~~~~a~~~L~~~Gh~~I~~i~~~~~~~~~~R~~Gf~~al~~~g 209 (331)
T PRK14987 136 KMIEVAGIPVVELMDSQS---P-CLDI--AVGFDNFEAARQMTTAIIARGHRHIAYLGARLDERTIIKQKGYEQAMLDAG 209 (331)
T ss_pred HHHHhCCCCEEEEecCCC---C-CCCc--eEEeCcHHHHHHHHHHHHHCCCceEEEEcCCCcccHHHHHHHHHHHHHHcC
Confidence 445677999997532111 1 1112 24556666677778888888999999996432 223345788999999988
Q ss_pred cEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 101 AKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 101 ~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
+... ...+....+...-...+.++.+. .+++|+. ++...+..+++++++.|+..++-+-|+
T Consensus 210 ~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~nD~~A~g~~~al~~~g~~vP~disvi 272 (331)
T PRK14987 210 LVPY-SVMVEQSSSYSSGIELIRQARREYPQLDGVFC-TNDDLAVGAAFECQRLGLKVPDDMAIA 272 (331)
T ss_pred CCcc-ceeecCCCChhhHHHHHHHHHhcCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCccEEE
Confidence 6311 11111111112223344554433 3566554 556678888999999998766555444
No 258
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=88.30 E-value=19 Score=38.02 Aligned_cols=70 Identities=13% Similarity=0.087 Sum_probs=45.4
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+...++..+.+..+ .+.+.+.. +....+...|.+|++|+++..-.... ..+ ...|+.+..++++++.
T Consensus 105 ~~~~~~l~~~~~~~p-~i~l~~~~-------~~~~~~~~~l~~g~~Di~i~~~~~~~---~~~-~~~~l~~~~~~lv~~~ 172 (305)
T PRK11233 105 SLTMPLLQAVRAEFP-GIVLYLHE-------NSGATLNEKLMNGQLDMAVIYEHSPV---AGL-SSQPLLKEDLFLVGTQ 172 (305)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEE-------CCcHHHHHHHHCCCCCEEEEcCCcCC---CCc-EEEEEeeeeEEEEEcC
Confidence 344567888887764 34455543 44678999999999999986322211 122 3457778888888765
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 173 ~~ 174 (305)
T PRK11233 173 DC 174 (305)
T ss_pred cc
Confidence 53
No 259
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT. Members of this family are the periplasmic protein TorT which, together with the the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase, and shows homology to a periplasmic D-ribose binding protein.
Probab=88.13 E-value=14 Score=38.78 Aligned_cols=127 Identities=11% Similarity=-0.033 Sum_probs=72.5
Q ss_pred CCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHH-cC----CeEEEEEEEcC--CcccchHHHHHHHHhcC
Q 003275 27 LNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEY-YG----WREVIAIFVDD--DYGRNGISVLGDALSKK 99 (834)
Q Consensus 27 ~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~-~~----W~~v~iI~~d~--~~g~~~~~~l~~~l~~~ 99 (834)
.++|+|.+....+ .. ..+-.+..++..-+..+++.+.. +. -+++++|.... .......+.+.+++++.
T Consensus 80 ~~iPvV~~~~~~~---~~--~~~~~V~~D~~~~g~~~~~~L~~~~~~~~g~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~ 154 (295)
T TIGR02955 80 KSIPVFALVNQID---SN--QVKGRVGVDWYQMGYQAGEYLAQRHPKGSGPTTLAWLPGPKNRGGTKPVTQGFRAALEGS 154 (295)
T ss_pred cCCCEEEEecCCC---cc--ceeEEEeecHHHHHHHHHHHHHHhcccCCCCeeEEEEeCCCcCCchhHHHHHHHHHHhcC
Confidence 4899987532211 11 11233455666666777776654 21 34699987543 33455688999999999
Q ss_pred CcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEEe
Q 003275 100 RAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIAT 164 (834)
Q Consensus 100 g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~~ 164 (834)
|+++... .....+..+-...++++.+. .+++| +++...+..+++++++.|. ++-+.+.+
T Consensus 155 g~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~d~i--~~~d~~a~g~l~al~~~g~--~~dv~vvg 215 (295)
T TIGR02955 155 DVEISAI--LWADNDKELQRNLLQDLLKKHPDIDYL--VGSAVAAEAAISELRSLHM--TQQIKLVS 215 (295)
T ss_pred CcEEEEE--ecCCCcHHHHHHHHHHHHHhCCCcCEE--EeccHHHHHHHHHHHhhCc--cCCeEEEE
Confidence 9877532 22112223333444554332 35654 4566667888888888776 33454444
No 260
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=88.03 E-value=22 Score=37.98 Aligned_cols=149 Identities=11% Similarity=-0.022 Sum_probs=76.9
Q ss_pred CcEEEEC-CCChhhHHHHHHhhccCCccEEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHc-----------
Q 003275 4 EVVAAIG-PQSSGIAHVISHVVNELNVPLLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYY----------- 70 (834)
Q Consensus 4 ~V~aiiG-p~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~----------- 70 (834)
+|.+||= |..+.........+...++|+|.+....+ ... ...+-...+..++..-+..+++++..+
T Consensus 81 ~vdgiIi~~~~~~~~~~~l~~l~~~giPvV~vd~~~~-~~~~~~~~~~~~V~~D~~~ag~~a~~~l~~~~~~~~~~~~~~ 159 (330)
T PRK15395 81 GVKALAINLVDPAAAPTVIEKARGQDVPVVFFNKEPS-RKALDSYDKAYYVGTDSKESGIIQGDLIAKHWKANPAWDLNK 159 (330)
T ss_pred CCCEEEEeccCHHHHHHHHHHHHHCCCcEEEEcCCcc-ccccccccceeEEccChHHHHHHHHHHHHHHHhhccccccCC
Confidence 5555442 32333333334556778999999865321 111 111112234555555566555554332
Q ss_pred -CCeEEEEEEEcC--CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC----CceEEEEEeChhhHH
Q 003275 71 -GWREVIAIFVDD--DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM----ESRVFVVHVNPDTGL 143 (834)
Q Consensus 71 -~W~~v~iI~~d~--~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~----~~~vivl~~~~~~~~ 143 (834)
|-..+++|.... .......+.+.++++++|+.+..........+..+-...+.++.+. .+++|+ +++...+.
T Consensus 160 ~g~~~i~~i~g~~~~~~~~~R~~G~~~al~~~g~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~ai~-~~~d~~A~ 238 (330)
T PRK15395 160 DGKIQYVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVI-ANNDAMAM 238 (330)
T ss_pred CCceEEEEEecCCCCchHHHHHHHHHHHHHhcCCCeeeeecccCCcCHHHHHHHHHHHHhhCcCCCeeEEE-ECCchHHH
Confidence 333445454322 2334457889999998887654321111111222223444554332 345444 44566778
Q ss_pred HHHHHHHhCCC
Q 003275 144 TIFSVAKSLGM 154 (834)
Q Consensus 144 ~i~~~a~~~g~ 154 (834)
.+++++++.|+
T Consensus 239 gvl~al~~~Gl 249 (330)
T PRK15395 239 GAVEALKAHNK 249 (330)
T ss_pred HHHHHHHhcCC
Confidence 89999999987
No 261
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=88.00 E-value=9.5 Score=39.04 Aligned_cols=121 Identities=12% Similarity=0.064 Sum_probs=67.7
Q ss_pred cCCCChhhhhcCCCCeeEeeCchhhHH----HHhhhcc--------------------cccceEecCCHHHHHHHHhcCC
Q 003275 589 SQIEGIDSLISSTEPIGVQDGSFAWNY----LVDELKI--------------------AESRLVKLKNMEEYSIALARGP 644 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v~~~~~s~~~~~----l~~~~~~--------------------~~~~~~~~~~~~~~~~~l~~~~ 644 (834)
..++|++||. .|.+|++..+...... |. ..++ ..-+++.+ ...+...++.+
T Consensus 106 ~~~~sl~dlk-~G~~IAip~d~~n~~raL~~L~-~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel-~~~~~~~al~~-- 180 (258)
T TIGR00363 106 KKIKNVNELQ-DGAKVAVPNDPTNLGRALLLLQ-KQGLIKLKDGNGLLPTVLDIVENPKKLNITEL-ETSQLPRALDD-- 180 (258)
T ss_pred cCCCCHHHcC-CCCEEEEeCCcchHHHHHHHHH-HcCCceecCCCCCcCChhhhhcCCCCCEEEEc-CHHHHHHHhhc--
Confidence 5899999995 4889999876543333 32 2222 11233444 44567788887
Q ss_pred CCCceEEEEechhhHHHHhhcCCccEEEeCCcccccceEEEEcCCCcchHHHHHHHHhhhccccHHHHHHhh
Q 003275 645 KGGGVAAIVDELPYIELFMSKTNCEFRTVGQEFTKSGWGFAFQRDSPLAIDLSTAILQLSENGDLQKIHNKW 716 (834)
Q Consensus 645 ~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~~~~~i~~l~e~G~~~~i~~kw 716 (834)
|++|+.+...++....-.+...+-......-...--.++++.+.-=.+.+...+..+++...-+.|.++|
T Consensus 181 --g~vDaa~v~~~~~~~agl~~~~~~i~~e~~~~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 250 (258)
T TIGR00363 181 --PKVDLAVINTTYAGQVGLNPQDDGVFVEDKDSPYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAAQKHF 250 (258)
T ss_pred --ccccEEEEChHHHHHcCCCcCcCceeecCCCCCeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 8999999887776544222011111111111111234555555334566666666666666566666654
No 262
>PRK09492 treR trehalose repressor; Provisional
Probab=87.92 E-value=8 Score=40.96 Aligned_cols=137 Identities=13% Similarity=0.076 Sum_probs=80.9
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc-
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD- 81 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d- 81 (834)
.+|.++|--..+... .......++|++...... ..++ ....++...+..+++.+...|-++++++...
T Consensus 117 ~~vdgiIi~~~~~~~---~~~l~~~~~pvv~i~~~~-----~~~~---~V~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~ 185 (315)
T PRK09492 117 RNVDGVILFGFTGIT---EEMLAPWQDKLVLLARDA-----KGFS---SVCYDDEGAIKLLMQRLYDQGHRHISYLGVDH 185 (315)
T ss_pred cCCCEEEEeCCCccc---HHHHHhcCCCEEEEeccC-----CCCc---EEEECcHHHHHHHHHHHHHcCCCeEEEEcCCc
Confidence 356666643222111 123334567877654311 1222 3445666667777788777899999999632
Q ss_pred C--CcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 82 D--DYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 82 ~--~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
. ..+....+.+.+++++.|+.+... .. ..+...-...+.++....+++|+. .+...+..+++++++.|+
T Consensus 186 ~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~-~~~~~~~~~~~~~~l~~~~~ai~~-~~D~~A~g~~~al~~~g~ 256 (315)
T PRK09492 186 SDVTTGKRRHQAYLAFCKQHKLTPVAA--LG-GLSMQSGYELVAKVLTPETTALVC-ATDTLALGASKYLQEQGR 256 (315)
T ss_pred ccchhHHHHHHHHHHHHHHcCCCceee--cC-CCCchHHHHHHHHHhhcCCCEEEE-cCcHHHHHHHHHHHHcCC
Confidence 2 234567889999999999865421 11 111122233444544456777664 445677889999999997
No 263
>cd08443 PBP2_CysB The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding speci
Probab=87.75 E-value=27 Score=33.55 Aligned_cols=72 Identities=15% Similarity=0.085 Sum_probs=48.6
Q ss_pred eeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEe
Q 003275 400 KGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAP 479 (834)
Q Consensus 400 ~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~ 479 (834)
..+-.+++..+.+..+ .+.+++.. ++...+...+.+|++|+++...... ....+ .+.++....++++++
T Consensus 12 ~~~l~~~l~~f~~~~P-~~~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~ 80 (198)
T cd08443 12 RYVLPPVIKGFIERYP-RVSLQMHQ-------GSPTQIAEMVSKGLVDFAIATEALH--DYDDL-ITLPCYHWNRCVVVK 80 (198)
T ss_pred eeECcHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHCCCccEEEEecccc--ccCCc-eEeeeeeceEEEEEc
Confidence 4566788888888765 34455553 5577899999999999998632211 11223 246777888888887
Q ss_pred cCC
Q 003275 480 VQK 482 (834)
Q Consensus 480 ~~~ 482 (834)
...
T Consensus 81 ~~h 83 (198)
T cd08443 81 RDH 83 (198)
T ss_pred CCC
Confidence 665
No 264
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=87.41 E-value=27 Score=33.18 Aligned_cols=70 Identities=11% Similarity=0.023 Sum_probs=47.8
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. +....+++++.+|++|+++...... ...+ -+.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~~~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~ 80 (196)
T cd08456 13 SFLPRAIKAFLQRHP-DVTISIHT-------RDSPTVEQWLSAQQCDLGLVSTLHE---PPGI-ERERLLRIDGVCVLPP 80 (196)
T ss_pred hhHHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEEecCCC---CCCe-eEEEeeccCeEEEecC
Confidence 455788888888875 45566654 4567889999999999998633221 1122 2556777788887776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (196)
T cd08456 81 GH 82 (196)
T ss_pred CC
Confidence 54
No 265
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=87.36 E-value=26 Score=37.16 Aligned_cols=82 Identities=12% Similarity=0.100 Sum_probs=54.5
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
.++|+||+... . ...+-..++..+.+..+ ++.++.. ..+++++.|.+|++|++++.
T Consensus 116 ~~~l~Ig~~~~--~------------~~~~l~~~l~~f~~~~P-~i~i~~~---------~~~~~~~~l~~g~~Dl~i~~ 171 (317)
T PRK11482 116 QRTITIATTPS--V------------GALVMPVIYQAIKTHYP-QLLLRNI---------PISDAENQLSQFQTDLIIDT 171 (317)
T ss_pred CceEEEEecHH--H------------HHHHHHHHHHHHHHHCC-CCEEEEe---------cchhHHHHHHCCCcCEEEec
Confidence 35899999321 1 12345778888888776 4444432 25688999999999999865
Q ss_pred eeeecCceeeEEecceeeeceEEEEEecCC
Q 003275 453 ITIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 453 ~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
.... ...+. +.|+....++++++...
T Consensus 172 ~~~~---~~~~~-~~~l~~~~~~lv~~~~h 197 (317)
T PRK11482 172 HSCS---NRTIQ-HHVLFTDNVVLVCRQGH 197 (317)
T ss_pred cCCC---CCceE-EEEEecCcEEEEEeCCC
Confidence 4322 22333 46788888888888766
No 266
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=87.35 E-value=29 Score=36.40 Aligned_cols=85 Identities=14% Similarity=0.054 Sum_probs=53.8
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
+.++||+... + ...+..+++..+.++.+ .+.+.... ++..++++.|.+|++|++++..
T Consensus 92 g~l~Ig~~~~--~------------~~~~l~~~l~~~~~~~p-~i~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~ 149 (300)
T PRK11074 92 GQLSIAVDNI--V------------RPDRTRQLIVDFYRHFD-DVELIIRQ-------EVFNGVWDALADGRVDIAIGAT 149 (300)
T ss_pred ceEEEEEcCc--c------------chhHHHHHHHHHHHhCC-CceEEEEe-------hhhhHHHHHHHCCCCCEEEecC
Confidence 6899998322 1 12344678888887776 34455543 4567899999999999999743
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCC
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
..... ...+ -+.++....+++++++..
T Consensus 150 ~~~~~-~~~l-~~~~l~~~~~~~v~~~~h 176 (300)
T PRK11074 150 RAIPV-GGRF-AFRDMGMLSWACVVSSDH 176 (300)
T ss_pred ccCCc-cccc-ceeecccceEEEEEcCCC
Confidence 21111 1111 245667777888887665
No 267
>TIGR01256 modA molybdenum ABC transporter, periplasmic molybdate-binding protein. The model describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represent hydrophylioc periplasmic-binding protein in gram-negative organisms and its counterpart in gram-positive organisms is a lipoprotein. The other components of the system include the ModB, an integral membrane protein and ModC the ATP-binding subunit. Invariably almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.
Probab=86.95 E-value=11 Score=37.38 Aligned_cols=72 Identities=14% Similarity=0.058 Sum_probs=41.0
Q ss_pred eEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCc-ccccceEEEEcCCCcchHHHHHHHHhhh
Q 003275 627 LVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQE-FTKSGWGFAFQRDSPLAIDLSTAILQLS 704 (834)
Q Consensus 627 ~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~-~~~~~~~~~~~k~spl~~~~~~~i~~l~ 704 (834)
+....+..+..+.+.+ |++++.+........ .+.......++.. .....+++++.|+++-.+.-.+.|.-|.
T Consensus 132 ~~~~~~~~~~~~~~~~----Ge~~~~~~~~~~~~~--~~~~~~~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl~ 204 (216)
T TIGR01256 132 LVYGEDVRQALQFVET----GNAPAGIVALSDVIP--SKKVGSVATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYLK 204 (216)
T ss_pred eeecCcHHHHHHHHHc----CCCCEEeeehhhhcc--cCCccEEEEeCccccCCccccEEEEECCCChHHHHHHHHHHc
Confidence 3334566788888888 899987765432211 1212333344433 2234578999998876555444454443
No 268
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=86.95 E-value=17 Score=37.60 Aligned_cols=121 Identities=12% Similarity=0.101 Sum_probs=62.4
Q ss_pred cCCCChhhhhcCCCCeeEeeCchhhH----HHHhhhcc--------------------cccceEecCCHHHHHHHHhcCC
Q 003275 589 SQIEGIDSLISSTEPIGVQDGSFAWN----YLVDELKI--------------------AESRLVKLKNMEEYSIALARGP 644 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v~~~~~s~~~~----~l~~~~~~--------------------~~~~~~~~~~~~~~~~~l~~~~ 644 (834)
..|+|++||. .|.+|++........ +|. ..++ ..-++++. ...+...++.+
T Consensus 119 ~~i~si~DL~-~Gk~IAip~d~~n~~r~L~lL~-~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~-~~~~~~~al~~-- 193 (271)
T PRK11063 119 KKIKSLDELQ-DGSQVAVPNDPTNLGRSLLLLQ-KVGLIKLKDGVGLLPTVLDIVENPKNLKIVEL-EAPQLPRSLDD-- 193 (271)
T ss_pred cCCCCHHHhc-CCCEEEecCCCccHHHHHHHHH-HCCCEEecCCCCCCCCHHHHhcCCCCCEEEEC-cHHHHHHhccc--
Confidence 5799999996 488899886332211 221 1111 12334444 45577777877
Q ss_pred CCCceEEEEechhhHHHHhhcCCccEEEeCCcccccceEEEEcCCCcchHHHHHHHHhhhccccHHHHHHhh
Q 003275 645 KGGGVAAIVDELPYIELFMSKTNCEFRTVGQEFTKSGWGFAFQRDSPLAIDLSTAILQLSENGDLQKIHNKW 716 (834)
Q Consensus 645 ~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~~~~~i~~l~e~G~~~~i~~kw 716 (834)
|++|+++...++....-.+...+-......-..+--.+++++..--.+.+...+.-++....-+.|.++|
T Consensus 194 --g~vDaa~i~~~~a~~a~~~~~~~~l~~e~~~~~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i~~~~ 263 (271)
T PRK11063 194 --AQIALAVINTTYASQIGLTPAKDGIFVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAANKVF 263 (271)
T ss_pred --ccccEEEEChHHHHHcCCCCCCCeeEECCCCCCeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 8999999888877653222111211222111111234556554333344444444444444444555554
No 269
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=86.84 E-value=29 Score=36.41 Aligned_cols=86 Identities=8% Similarity=0.050 Sum_probs=57.0
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
.++|+||++.. -...+-.+++..+.+..+ .+++.+.. ++..++..+|.+|++|+++..
T Consensus 94 ~g~l~I~~~~~--------------~~~~~l~~~l~~~~~~~p-~i~~~~~~-------~~~~~~~~~l~~g~~Di~i~~ 151 (302)
T PRK09791 94 AGQINIGMGAS--------------IARSLMPAVISRFHQQHP-QVKVRIME-------GQLVSMINELRQGELDFTINT 151 (302)
T ss_pred ceEEEEEechH--------------HHHhhhHHHHHHHHHHCC-CeEEEEEe-------CChHHHHHHHHCCCccEEEEe
Confidence 36899999422 113455778888887776 44555543 457899999999999998863
Q ss_pred eeeecCceeeEEecceeeeceEEEEEecCC
Q 003275 453 ITIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 453 ~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
..... ....+. ..|+....+++++++..
T Consensus 152 ~~~~~-~~~~~~-~~~l~~~~~~l~~~~~~ 179 (302)
T PRK09791 152 YYQGP-YDHEFT-FEKLLEKQFAVFCRPGH 179 (302)
T ss_pred cCCcc-ccccee-EEEeccceEEEEEcCCC
Confidence 21111 112243 36888889999988766
No 270
>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type I periplasmic sugar-binding protein-like fold.
Probab=86.68 E-value=12 Score=38.37 Aligned_cols=143 Identities=10% Similarity=-0.015 Sum_probs=77.0
Q ss_pred CcEEEECCCChhhHHHHHHhhccC-CccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHc-CCeEEEEEEEc
Q 003275 4 EVVAAIGPQSSGIAHVISHVVNEL-NVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYY-GWREVIAIFVD 81 (834)
Q Consensus 4 ~V~aiiGp~~S~~~~~~~~~~~~~-~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~-~W~~v~iI~~d 81 (834)
+|.+||=...+ ....+....++. ++|++......+. ....+ ....++..-+..++.++... |-+++++|..+
T Consensus 56 ~vdgiii~~~~-~~~~~~~~~~~~~~ipvv~~~~~~~~--~~~~~---~v~~d~~~~~~~a~~l~~~~~g~~~I~~i~~~ 129 (260)
T cd06304 56 GYDLIFGVGFG-FMDAVEKVAKEYPDVKFAIIDGVVDA--PPNVA---SYVFREYEGSYLAGVLAALMTKTGKVGFVGGM 129 (260)
T ss_pred CCCEEEECCcc-hhHHHHHHHHHCCCCEEEEecCccCC--CCCee---eeecchHHHHHHHHHHHHHhccCCceEEEecc
Confidence 45555432222 223444555444 7898876442211 01112 22333433344444555544 88999999753
Q ss_pred C-CcccchHHHHHHHHhcCCcEEEeeecCCCCCC-hHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCC
Q 003275 82 D-DYGRNGISVLGDALSKKRAKISYKAPFSPGAS-RSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLG 153 (834)
Q Consensus 82 ~-~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~-~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g 153 (834)
. .......+.|.++++++|..+..........+ ..+-...++++.+..+++| ++.+...+..++.++++.|
T Consensus 130 ~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ai-~~~~d~~A~gv~~al~~~g 202 (260)
T cd06304 130 PIPEVNRFINGFAAGAKSVNPDITVLVIYTGSFFDPAKGKEAALALIDQGADVI-FAAAGGTGPGVIQAAKEAG 202 (260)
T ss_pred ccHHHHHHHHHHHHHHHHhCCCcEEEEEEecCccCcHHHHHHHHHHHhCCCCEE-EEcCCCCchHHHHHHHHcC
Confidence 2 22334577899999998864332111111111 1233445566555557775 5566677778999999888
No 271
>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=86.53 E-value=12 Score=38.34 Aligned_cols=129 Identities=12% Similarity=0.132 Sum_probs=79.4
Q ss_pred ccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC-CcccchHHHHHHHHhcCCcEE
Q 003275 25 NELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD-DYGRNGISVLGDALSKKRAKI 103 (834)
Q Consensus 25 ~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~-~~g~~~~~~l~~~l~~~g~~I 103 (834)
...++|+|......+ ...++++ ..++..-+..+++.+...|-++++++..+. .........+.++++++|+..
T Consensus 74 ~~~~iPvV~~~~~~~---~~~~~~v---~~d~~~~g~~a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~~~~~~~ 147 (263)
T cd06280 74 LRLSFPVVLIDRAGP---AGRVDAV---VLDNRAAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAP 147 (263)
T ss_pred HhcCCCEEEECCCCC---CCCCCEE---EECcHHHHHHHHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHHHcCCCC
Confidence 456899998754432 2233443 345666677777888788989999887532 233455788999999888764
Q ss_pred EeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEE
Q 003275 104 SYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIA 163 (834)
Q Consensus 104 ~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~ 163 (834)
... ... .+..+....+.++... .+++| ++.+...+..+++.+++.|+..++-+.+.
T Consensus 148 ~~~-~~~--~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~g~~~~l~~~g~~~p~di~ii 205 (263)
T cd06280 148 DAR-FVA--PTAEAAEAALAAWLAAPERPEAL-VASNGLLLLGALRAVRAAGLRIPQDLALA 205 (263)
T ss_pred Chh-hcc--cCHHHHHHHHHHHhcCCCCCcEE-EECCcHHHHHHHHHHHHcCCCCCCcEEEE
Confidence 321 112 1223333344444333 35554 44566678889999999998655444443
No 272
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=86.43 E-value=15 Score=38.86 Aligned_cols=70 Identities=11% Similarity=0.199 Sum_probs=48.8
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
++-.+++..+.+..+ .+.+++.. ++...++.+|.+|++|+++...... ...+. ..++....++++++.
T Consensus 125 ~~l~~~l~~f~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Di~i~~~~~~---~~~l~-~~~l~~~~~~lv~~~ 192 (314)
T PRK09508 125 RLTSQIYNRIEQIAP-NIHVVFKS-------SLNQNIEHQLRYQETEFVISYEEFD---RPEFT-SVPLFKDELVLVASK 192 (314)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEe-------CcchhHHHHHhcCCccEEEecCCCC---ccccc-eeeeecCceEEEEcC
Confidence 466888889888875 34566653 4568899999999999998743221 12232 346777888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 193 ~h 194 (314)
T PRK09508 193 NH 194 (314)
T ss_pred CC
Confidence 65
No 273
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=86.29 E-value=31 Score=32.79 Aligned_cols=72 Identities=13% Similarity=0.147 Sum_probs=47.9
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+.+++.. ++..++.+++.+|++|+++...... .+...+ ...|+....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~-~~~~~~-~~~~l~~~~~~~~~~~ 82 (201)
T cd08435 13 VLLPPAIARLLARHP-RLTVRVVE-------GTSDELLEGLRAGELDLAIGRLADD-EQPPDL-ASEELADEPLVVVARP 82 (201)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHcCCccEEEEecCcc-cCCCCc-EEEEcccCcEEEEEeC
Confidence 344678888888766 45566553 4578899999999999998643211 112223 2457778888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 83 ~~ 84 (201)
T cd08435 83 GH 84 (201)
T ss_pred CC
Confidence 65
No 274
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=86.14 E-value=38 Score=35.99 Aligned_cols=155 Identities=12% Similarity=0.106 Sum_probs=92.0
Q ss_pred CCc-EEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHH-HHcCC-eEEEEEE
Q 003275 3 NEV-VAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLV-EYYGW-REVIAIF 79 (834)
Q Consensus 3 ~~V-~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll-~~~~W-~~v~iI~ 79 (834)
+++ ..+|.|..+........-+...+||+|.+....+.- .........+....+...++.+ ++++- -+++++.
T Consensus 90 ~~~daIiv~~~d~~~~~~~v~~a~~aGIpVv~~d~~~~~~----~~~~~~vg~dn~~~G~~~a~~l~~~~~~~g~v~~~~ 165 (322)
T COG1879 90 QGVDAIIINPVDPDALTPAVKKAKAAGIPVVTVDSDIPGP----GDRVAYVGSDNYKAGRLAAEYLAKALGGKGKVVVLV 165 (322)
T ss_pred cCCCEEEEcCCChhhhHHHHHHHHHCCCcEEEEecCCCCC----CceeEEEecCcHHHHHHHHHHHHHHhCCCCeEEEEe
Confidence 344 456788889999999999999999999976543322 1222233334455555556665 33432 2355555
Q ss_pred Ec--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhhHHHHHHHHHhCCCCC
Q 003275 80 VD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-PDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 80 ~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-~~~~~~i~~~a~~~g~~~ 156 (834)
.. ..........+.+.+.+.+.++........+.+.+.-.+....+....+++-.+++. ...+....+++++.|...
T Consensus 166 g~~~~~~~~~R~~G~~~~l~~~~~~~~v~~~~~~~~~~~~a~~~~~~~L~~~pdi~~i~~~~d~~a~ga~~A~~~~g~~~ 245 (322)
T COG1879 166 GSPGNSSAEERVKGFRDALKEHPPDIEVVDVQTGDWDRDKALEVMEDLLAANPDIDGIYAANDGMALGAIQALKAAGRKG 245 (322)
T ss_pred cCCCCchHHHHHhhHHHHHHhCCCcEEEeeccCCcccHHHHHHHHHHHHHhCCCceEEEECCchhHHHHHHHHHHcCCCC
Confidence 33 334455688999999998753222223332233344455566666667787666654 445556666777778654
Q ss_pred CCeEEEE
Q 003275 157 GSYVWIA 163 (834)
Q Consensus 157 ~~~vwi~ 163 (834)
.+.+.
T Consensus 246 --~v~v~ 250 (322)
T COG1879 246 --DVVVV 250 (322)
T ss_pred --ceEEE
Confidence 45555
No 275
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=85.86 E-value=6.1 Score=43.27 Aligned_cols=88 Identities=8% Similarity=0.026 Sum_probs=65.4
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe--C
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV--N 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~--~ 138 (834)
..+.+.++.+|.+++.+++.......+..+.+.+.|++.|+.+.....+.++.+.+++...+..+++.++|+||-.+ +
T Consensus 20 ~~l~~~~~~~g~~~~livt~~~~~~~g~~~~v~~~L~~~~i~~~~f~~v~~np~~~~v~~~~~~~~~~~~D~IiaiGGGS 99 (383)
T PRK09860 20 TDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGS 99 (383)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCCch
Confidence 45677888999999988875433344568899999999998765444555566678899999999999999999654 3
Q ss_pred hhhHHHHHHH
Q 003275 139 PDTGLTIFSV 148 (834)
Q Consensus 139 ~~~~~~i~~~ 148 (834)
.-|+.+.+..
T Consensus 100 ~iD~AK~ia~ 109 (383)
T PRK09860 100 PHDCAKGIAL 109 (383)
T ss_pred HHHHHHHHHH
Confidence 4466655544
No 276
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=85.41 E-value=25 Score=33.96 Aligned_cols=131 Identities=11% Similarity=0.041 Sum_probs=85.7
Q ss_pred HHHHHhhccCCccEEecccCCCCCCC-CCCCc--eEEc----cCChHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHH
Q 003275 18 HVISHVVNELNVPLLSFGATDPTLTS-LQYPY--FLRT----TQSDYYQMHAVADLVEYYGWREVIAIFVDDDYGRNGIS 90 (834)
Q Consensus 18 ~~~~~~~~~~~vP~Is~~at~~~ls~-~~~p~--~~r~----~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~ 90 (834)
...+..+...++-+|.|++|+.++.. .+|.- --|+ .-.-..-..|+++-++.++-+++.++. +|-.+..+
T Consensus 57 ~~aAl~Lada~vdvI~Y~CtsgS~i~G~~~d~ei~~~ie~~~~v~vvTts~Avv~aL~al~a~ri~vlT---PY~~evn~ 133 (238)
T COG3473 57 ERAALELADAGVDVIVYGCTSGSLIGGPGYDKEIAQRIEEAKGVPVVTTSTAVVEALNALGAQRISVLT---PYIDEVNQ 133 (238)
T ss_pred HHHHHhcCccccCEEEEeccceeeecCCchhHHHHHHHHhccCCceeechHHHHHHHHhhCcceEEEec---cchhhhhh
Confidence 33445566678999999999988764 33310 0000 000001235677788999999999998 46667778
Q ss_pred HHHHHHhcCCcEEEeeecCCCC-------CChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHh
Q 003275 91 VLGDALSKKRAKISYKAPFSPG-------ASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKS 151 (834)
Q Consensus 91 ~l~~~l~~~g~~I~~~~~~~~~-------~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~ 151 (834)
.-.+.++++|.+|+....+-.. ..+...-+.-.++...++|.|++.|..-.+..++....+
T Consensus 134 ~e~ef~~~~Gfeiv~~~~Lgi~dn~eigr~~P~~~y~lAk~~~~~~~DaiFiSCTnlRt~eii~~lE~ 201 (238)
T COG3473 134 REIEFLEANGFEIVDFKGLGITDNLEIGRQEPWAVYRLAKEVFTPDADAIFISCTNLRTFEIIEKLER 201 (238)
T ss_pred HHHHHHHhCCeEEEEeeccCCcccchhcccChHHHHHHHHHhcCCCCCeEEEEeeccccHHHHHHHHH
Confidence 8888999999999876544322 122344555666777889999999877666666655443
No 277
>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca
Probab=85.35 E-value=34 Score=32.38 Aligned_cols=70 Identities=13% Similarity=0.131 Sum_probs=47.5
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+..+++..+.+..+ .+.+.+.. ++..++..+|.+|++|+++...... ...+ -..|+....+++++++
T Consensus 13 ~~l~~~l~~~~~~~p-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~ 80 (197)
T cd08414 13 GLLPRLLRRFRARYP-DVELELRE-------MTTAEQLEALRAGRLDVGFVRPPPD---PPGL-ASRPLLREPLVVALPA 80 (197)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CChHHHHHHHHcCCccEEEEcCCCC---CCCe-eEEEEeeccEEEEecC
Confidence 445677888887765 34455553 4568899999999999998643222 1222 2467778888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (197)
T cd08414 81 DH 82 (197)
T ss_pred CC
Confidence 55
No 278
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=85.27 E-value=10 Score=40.42 Aligned_cols=131 Identities=10% Similarity=0.029 Sum_probs=76.0
Q ss_pred HhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHhcC
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDALSKK 99 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l~~~ 99 (834)
..+...++|++......+ ...+++ ...++..-+..+++.+...|.+++++|..+.. ........+.++++..
T Consensus 130 ~~l~~~~~pvV~~~~~~~---~~~~~~---V~~D~~~~~~~a~~~l~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~ 203 (327)
T PRK10339 130 AAASALTDNICFIDFHEP---GSGYDA---VDIDLARISKEIIDFYINQGVNRIGFIGGEDEPGKADIREVAFAEYGRLK 203 (327)
T ss_pred HHHHhcCCCEEEEeCCCC---CCCCCE---EEECHHHHHHHHHHHHHHCCCCeEEEeCCccccchhhHHHHHHHHHHHHc
Confidence 445667899997643221 122332 45566666677788887889999999964332 3344567888888888
Q ss_pred CcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 100 RAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 100 g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
|+ +.....+....+..+-...+.++.+. .+++|+ +++...+..+++++++.|...++-+
T Consensus 204 g~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~D~~A~g~~~al~~~g~~vP~di 264 (327)
T PRK10339 204 QV-VREEDIWRGGFSSSSGYELAKQMLAREDYPKALF-VASDSIAIGVLRAIHERGLNIPQDI 264 (327)
T ss_pred CC-CChhheeecCcChhHHHHHHHHHHhCCCCCCEEE-ECCcHHHHHHHHHHHHcCCCCCCce
Confidence 76 11101111111112223344444332 355544 4556678889999999998654433
No 279
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=85.21 E-value=34 Score=32.27 Aligned_cols=71 Identities=14% Similarity=0.075 Sum_probs=48.0
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ ++.+++.. ++..++.+++.+|++|+++..... .....+ ...+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~~~~~ 81 (194)
T cd08436 13 VDLPELLARFHRRHP-GVDIRLRQ-------AGSDDLLAAVREGRLDLAFVGLPE--RRPPGL-ASRELAREPLVAVVAP 81 (194)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CCHHHHHHHHHcCCccEEEEecCC--CCCCCc-EEEEeecceEEEEecC
Confidence 555778888888775 44566653 456789999999999999864332 112222 3466677788888776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 82 ~~ 83 (194)
T cd08436 82 DH 83 (194)
T ss_pred CC
Confidence 65
No 280
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=85.13 E-value=13 Score=35.36 Aligned_cols=99 Identities=8% Similarity=-0.012 Sum_probs=68.7
Q ss_pred HHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcC--CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEE
Q 003275 58 YQMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKK--RAKISYKAPFSPGASRSAINSLLVGANLMESRVFVV 135 (834)
Q Consensus 58 ~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~--g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl 135 (834)
.....+.+.+...++ +++++..+.+ .++.+...+++. |+.|+....-+ .+..+....++.|++++||+|++
T Consensus 35 dl~~~l~~~~~~~~~-~ifllG~~~~----~~~~~~~~l~~~yP~l~ivg~~~g~--f~~~~~~~i~~~I~~~~pdiv~v 107 (172)
T PF03808_consen 35 DLFPDLLRRAEQRGK-RIFLLGGSEE----VLEKAAANLRRRYPGLRIVGYHHGY--FDEEEEEAIINRINASGPDIVFV 107 (172)
T ss_pred HHHHHHHHHHHHcCC-eEEEEeCCHH----HHHHHHHHHHHHCCCeEEEEecCCC--CChhhHHHHHHHHHHcCCCEEEE
Confidence 345667777767775 6777776543 566666677666 77777644333 25578889999999999999999
Q ss_pred EeChhhHHHHHHHHHhCCCCCCCeEEEEeCC
Q 003275 136 HVNPDTGLTIFSVAKSLGMTAGSYVWIATDW 166 (834)
Q Consensus 136 ~~~~~~~~~i~~~a~~~g~~~~~~vwi~~~~ 166 (834)
.+..+.-..++...++.. ... +|+...+
T Consensus 108 glG~PkQE~~~~~~~~~l--~~~-v~i~vG~ 135 (172)
T PF03808_consen 108 GLGAPKQERWIARHRQRL--PAG-VIIGVGG 135 (172)
T ss_pred ECCCCHHHHHHHHHHHHC--CCC-EEEEECc
Confidence 988887777776666533 233 7777654
No 281
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=84.90 E-value=35 Score=32.22 Aligned_cols=72 Identities=17% Similarity=0.202 Sum_probs=47.7
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. ++.+.+++.+.+|++|+++..-... .....+ .+.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~-~~~~l~~~~~~~v~~~ 82 (195)
T cd08427 13 GLLPRALARLRRRHP-DLEVHIVP-------GLSAELLARVDAGELDAAIVVEPPF-PLPKDL-VWTPLVREPLVLIAPA 82 (195)
T ss_pred HHhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCCCEEEEcCCCC-ccccCc-eEEEcccCcEEEEECC
Confidence 455778888887775 34566654 5578999999999999998642211 101222 3466777888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 83 ~~ 84 (195)
T cd08427 83 EL 84 (195)
T ss_pred CC
Confidence 54
No 282
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=84.40 E-value=29 Score=37.20 Aligned_cols=146 Identities=8% Similarity=-0.034 Sum_probs=74.7
Q ss_pred CCcEEEEC-CCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHH-c--CCeEEEEE
Q 003275 3 NEVVAAIG-PQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEY-Y--GWREVIAI 78 (834)
Q Consensus 3 ~~V~aiiG-p~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~-~--~W~~v~iI 78 (834)
++|.||+= |..+........-+...+||+|++.+..+. +.. -+++-. .++...+..+++++.+ . +-.+++++
T Consensus 79 ~~vdgIiv~~~d~~al~~~l~~a~~~gIpVV~~d~~~~~--~~~-~~~V~~-~~~~~~G~~~~~~l~~~l~~g~gki~il 154 (336)
T PRK15408 79 QGYNAIIVSAVSPDGLCPALKRAMQRGVKVLTWDSDTKP--ECR-SYYINQ-GTPEQLGSMLVEMAAKQVGKDKAKVAFF 154 (336)
T ss_pred cCCCEEEEecCCHHHHHHHHHHHHHCCCeEEEeCCCCCC--ccc-eEEEec-CCHHHHHHHHHHHHHHhcCCCCCEEEEE
Confidence 45544443 544444455666677889999997653221 111 122211 2233556666666543 2 34688887
Q ss_pred EEcCC--cccchHHHHHHHHhcC--CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHHHhCC
Q 003275 79 FVDDD--YGRNGISVLGDALSKK--RAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDT-GLTIFSVAKSLG 153 (834)
Q Consensus 79 ~~d~~--~g~~~~~~l~~~l~~~--g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~-~~~i~~~a~~~g 153 (834)
..... ......+.+.+.+++. +++++... ....+...-....+.+.+..+++=.+.+.... +...++++++.|
T Consensus 155 ~g~~~~~~~~~r~~g~~~~l~~~~p~~~vv~~~--~~~~d~~~a~~~~~~lL~~~pdi~aI~~~~~~~~~Ga~~Al~~~g 232 (336)
T PRK15408 155 YSSPTVTDQNQWVKEAKAKIAKEHPGWEIVTTQ--FGYNDATKSLQTAEGILKAYPDLDAIIAPDANALPAAAQAAENLK 232 (336)
T ss_pred ECCCCCccHHHHHHHHHHHHHhhCCCCEEEeec--CCCCcHHHHHHHHHHHHHHCCCCcEEEECCCccHHHHHHHHHhCC
Confidence 64322 1223356677777543 56665322 11222233334555555555554444444333 345788888888
Q ss_pred C
Q 003275 154 M 154 (834)
Q Consensus 154 ~ 154 (834)
+
T Consensus 233 ~ 233 (336)
T PRK15408 233 R 233 (336)
T ss_pred C
Confidence 6
No 283
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=84.40 E-value=24 Score=33.93 Aligned_cols=70 Identities=6% Similarity=-0.019 Sum_probs=47.7
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .++++... ++.+.++++|.+|++|+++.... .. ...+ -+.++....++++++.
T Consensus 14 ~~l~~~l~~f~~~~P-~v~i~i~~-------~~~~~l~~~l~~g~~D~~~~~~~--~~-~~~~-~~~~l~~~~~~lv~~~ 81 (198)
T cd08486 14 RSLPLLLRAFLTSTP-TATVSLTH-------MTKDEQVEGLLAGTIHVGFSRFF--PR-HPGI-EIVNIAQEDLYLAVHR 81 (198)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEE-------CCHHHHHHHHHcCCceEEEecCC--CC-CCce-EEEEEeeccEEEEecC
Confidence 455778888887775 35566554 56889999999999999985321 11 1222 2456677788888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 82 ~h 83 (198)
T cd08486 82 SQ 83 (198)
T ss_pred CC
Confidence 54
No 284
>COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=84.30 E-value=9.6 Score=41.09 Aligned_cols=91 Identities=7% Similarity=-0.004 Sum_probs=72.7
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe--C
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV--N 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~--~ 138 (834)
..+.+.+..+|++++-+|....-...+..+.+.+.|++.|+.+.....+.++.+.+.+...+..+++.++|.||-.+ +
T Consensus 18 ~~l~~~~~~~g~~r~liVTd~~~~~~g~~~~v~~~L~~~~i~~~if~~v~p~P~~~~v~~~~~~~~~~~~D~iIalGGGS 97 (377)
T COG1454 18 KELGEEVKRLGAKRALIVTDRGLAKLGLLDKVLDSLDAAGIEYEVFDEVEPEPTIETVEAGAEVAREFGPDTIIALGGGS 97 (377)
T ss_pred HHHHHHHHhcCCCceEEEECCccccchhHHHHHHHHHhcCCeEEEecCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 56777788999999988886666667789999999999998876666677677778899999999999999999775 4
Q ss_pred hhhHHHHHHHHHh
Q 003275 139 PDTGLTIFSVAKS 151 (834)
Q Consensus 139 ~~~~~~i~~~a~~ 151 (834)
+-++.+.+....+
T Consensus 98 ~~D~AK~i~~~~~ 110 (377)
T COG1454 98 VIDAAKAIALLAE 110 (377)
T ss_pred HHHHHHHHHHHhh
Confidence 4566666655554
No 285
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=84.15 E-value=39 Score=32.03 Aligned_cols=72 Identities=10% Similarity=0.019 Sum_probs=48.0
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-..++..+.+..+ .+++++.. .+..++++.|.+|++|++++...... +...+ -..++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~-~~~~l~~~~~~~v~~~ 82 (197)
T cd08449 13 GGLGPALRRFKRQYP-NVTVRFHE-------LSPEAQKAALLSKRIDLGFVRFADTL-NDPPL-ASELLWREPMVVALPE 82 (197)
T ss_pred hhHHHHHHHHHHHCC-CeEEEEEE-------CCHHHHHHHHhCCCccEEEecccccC-CCCCc-eEEEEEEeeEEEEecC
Confidence 455788888888775 34566553 45788999999999999986433221 01122 2466777788888776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 83 ~~ 84 (197)
T cd08449 83 EH 84 (197)
T ss_pred CC
Confidence 54
No 286
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=84.12 E-value=43 Score=32.50 Aligned_cols=71 Identities=15% Similarity=0.258 Sum_probs=45.5
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .++++... ++..+++..|.+|++|+++........-... -...|+....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~-------~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~ 83 (204)
T cd08429 13 SIAYRLLEPAMDLHE-PIRLVCRE-------GKLEQLLADLALHRLDMVLADRPMPSSLDVK-GYSHRLGECGVSFFAAP 83 (204)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEecCCCccccchh-eeeccccccceEEEecC
Confidence 455778888887765 44566654 6789999999999999988533221110011 12457777777776554
No 287
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=84.10 E-value=60 Score=34.21 Aligned_cols=70 Identities=10% Similarity=0.045 Sum_probs=44.7
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .++++... .+-.++...|.+|++|+++...... ...+ ...+......+++++.
T Consensus 107 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~ 174 (309)
T PRK11013 107 SLLPGLCQPFLARYP-DVSLNIVP-------QESPLLEEWLSAQRHDLGLTETLHT---PAGT-ERTELLTLDEVCVLPA 174 (309)
T ss_pred hhHHHHHHHHHHHCC-CCeEEEEe-------CCHHHHHHHHHcCCCCEEEEcCCCC---CCCc-eeeeecceeEEEEEcC
Confidence 455788888888774 35566654 3456788999999999998643211 1112 2345556666777766
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 175 ~~ 176 (309)
T PRK11013 175 GH 176 (309)
T ss_pred CC
Confidence 55
No 288
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=83.84 E-value=39 Score=31.91 Aligned_cols=70 Identities=7% Similarity=-0.022 Sum_probs=48.1
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. ++..++..++.+|++|+++.... .....+ .+.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Di~i~~~~---~~~~~~-~~~~l~~~~~~~~~~~ 80 (197)
T cd08448 13 RGLPRILRAFRAEYP-GIEVALHE-------MSSAEQIEALLRGELDLGFVHSR---RLPAGL-SARLLHREPFVCCLPA 80 (197)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe-------CCHHHHHHHHHcCCcceEEEeCC---CCCcCc-eEEEEecCcEEEEeeC
Confidence 455788888888775 34566654 56788999999999999886322 111222 3467777888888776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~h 82 (197)
T cd08448 81 GH 82 (197)
T ss_pred CC
Confidence 54
No 289
>PRK15454 ethanol dehydrogenase EutG; Provisional
Probab=83.22 E-value=5.1 Score=44.03 Aligned_cols=88 Identities=5% Similarity=-0.084 Sum_probs=64.1
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP- 139 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~- 139 (834)
..+.++++.+|.+++.++........+..+.+.+.|++.|+.+.....+.++.+.+++...+...++.++|+||-.+.+
T Consensus 38 ~~l~~~~~~~g~~~~lvv~~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~P~~~~v~~~~~~~r~~~~D~IiavGGGS 117 (395)
T PRK15454 38 SSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLAVKGIAMTLWPCPVGEPCITDVCAAVAQLRESGCDGVIAFGGGS 117 (395)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCcCEEEEeCChH
Confidence 5567788889988887666444444456888999999999887654445555566788999999999999999987654
Q ss_pred -hhHHHHHHH
Q 003275 140 -DTGLTIFSV 148 (834)
Q Consensus 140 -~~~~~i~~~ 148 (834)
-|+.+.+..
T Consensus 118 ~iD~AKaia~ 127 (395)
T PRK15454 118 VLDAAKAVAL 127 (395)
T ss_pred HHHHHHHHHH
Confidence 355555433
No 290
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=83.10 E-value=31 Score=35.75 Aligned_cols=122 Identities=20% Similarity=0.210 Sum_probs=73.5
Q ss_pred cCCCChhhhhc----CC--CCeeEe-eCch---hhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhh
Q 003275 589 SQIEGIDSLIS----ST--EPIGVQ-DGSF---AWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPY 658 (834)
Q Consensus 589 ~~i~s~~dL~~----~~--~~v~~~-~~s~---~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~ 658 (834)
.+++|++||++ +. .++|.. .|+. ....+.+..+.. .+.++|+...+.+.+|.. |.+|+.+.....
T Consensus 88 sp~~t~~eli~~ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~-~~~Vpy~G~~~~~~allg----G~vd~~~~~~~~ 162 (274)
T PF03401_consen 88 SPYKTLEELIEYAKANPGKLTFGSSGPGSSDHLAAALLAKAAGIK-FTHVPYDGGAEALTALLG----GHVDAAFGSPGE 162 (274)
T ss_dssp SS-SSHHHHHHHHHCSCCC-EEEESSTTSHHHHHHHHHHHHHT----EEEE-SSHHHHHHHHHT----TSSSEEEEEHHH
T ss_pred CccccHHHHHHHHHhCCCCeEEEecCCCchHHHHHHHHHHHhCCc-eEEEEeCCccHHHHHHhC----CeeeEEeecHHH
Confidence 47888999864 22 245544 2332 223344555654 567899999999999998 999998887554
Q ss_pred HHHHhhcCCcc-EEEeC--------------Cc-c----cccceEEEEcCCCc--chHHHHHHHHhhhccccHHHHHHh
Q 003275 659 IELFMSKTNCE-FRTVG--------------QE-F----TKSGWGFAFQRDSP--LAIDLSTAILQLSENGDLQKIHNK 715 (834)
Q Consensus 659 ~~~~~~~~~~~-l~~v~--------------~~-~----~~~~~~~~~~k~sp--l~~~~~~~i~~l~e~G~~~~i~~k 715 (834)
..-+.+...-+ +.+.. +. + ....++++.|||-| .++.+..++.+..++..+++..++
T Consensus 163 ~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~ 241 (274)
T PF03401_consen 163 ALPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEK 241 (274)
T ss_dssp HHHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHH
T ss_pred HHHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 44443321211 22221 11 1 11235889999998 999999999999999887665554
No 291
>cd08457 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant h
Probab=82.87 E-value=44 Score=31.75 Aligned_cols=70 Identities=16% Similarity=0.151 Sum_probs=46.0
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. ++-.++...|.+|++|+++...... ...+. ..++.+..++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~~~ 80 (196)
T cd08457 13 GFLPRFLAAFLRLRP-NLHLSLMG-------LSSSQVLEAVASGRADLGIADGPLE---ERQGF-LIETRSLPAVVAVPM 80 (196)
T ss_pred cccHHHHHHHHHHCC-CeEEEEEe-------cCcHHHHHHHHcCCccEEEeccCCC---CCCcE-EEEeccCCeEEEeeC
Confidence 455788888888876 34555553 3356888999999999998643222 12222 356667777777765
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (196)
T cd08457 81 GH 82 (196)
T ss_pred CC
Confidence 54
No 292
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=82.76 E-value=18 Score=35.16 Aligned_cols=102 Identities=15% Similarity=0.128 Sum_probs=62.9
Q ss_pred cCCCChhhhhcCCCCe-eEeeCchhhHHHHhhh---cccccceEec----CCHHHHHHHHhcCCCCCceEEEEechhhHH
Q 003275 589 SQIEGIDSLISSTEPI-GVQDGSFAWNYLVDEL---KIAESRLVKL----KNMEEYSIALARGPKGGGVAAIVDELPYIE 660 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v-~~~~~s~~~~~l~~~~---~~~~~~~~~~----~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~ 660 (834)
..|.+++||.+.+.++ .-+.||-...+|...+ +++...+..| .+-.+...+|.. |..|+-+.......
T Consensus 81 ~~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~----G~AD~G~g~~~~A~ 156 (193)
T PF12727_consen 81 KGITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVAS----GKADAGIGIRAAAE 156 (193)
T ss_pred ccCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHc----CCCCEEeehHHHHH
Confidence 3799999998666553 3456777776665433 3444444433 466778888888 89999887655443
Q ss_pred HHhhcCCccEEEeCCcccccceEEEEcCCCcchHHHHHHHH
Q 003275 661 LFMSKTNCEFRTVGQEFTKSGWGFAFQRDSPLAIDLSTAIL 701 (834)
Q Consensus 661 ~~~~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~~~~~i~ 701 (834)
.+ . .-++.-+ ....|-+++++..-..+.+.+.|.
T Consensus 157 ~~--~-gL~Fvpl----~~E~~dlv~~~~~~~~~~vq~ll~ 190 (193)
T PF12727_consen 157 EF--Y-GLDFVPL----AEERYDLVIRREDLEDPAVQALLD 190 (193)
T ss_pred hh--c-CCCcEEc----cccceEEEEEhhHcCCHHHHHHHH
Confidence 21 1 2233333 335778888887655555555543
No 293
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=82.64 E-value=62 Score=33.27 Aligned_cols=69 Identities=16% Similarity=0.146 Sum_probs=46.6
Q ss_pred eeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecC
Q 003275 402 YCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQ 481 (834)
Q Consensus 402 ~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~ 481 (834)
+-.+++..+.+..+ .++++... ++..+++..|.+|++|+++........ .+ -..|+....++++++++
T Consensus 98 ~~~~~l~~~~~~~p-~v~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~---~~-~~~~l~~~~~~lv~s~~ 165 (279)
T TIGR03339 98 YVLDLVARFRQRYP-GIEVSVRI-------GNSQEVLQALQSYRVDVAVSSEVVDDP---RL-DRVVLGNDPLVAVVHRQ 165 (279)
T ss_pred HHHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEecccCCC---ce-EEEEcCCceEEEEECCC
Confidence 44677788887765 34455553 457889999999999999863332221 22 24667778888888766
Q ss_pred C
Q 003275 482 K 482 (834)
Q Consensus 482 ~ 482 (834)
.
T Consensus 166 ~ 166 (279)
T TIGR03339 166 H 166 (279)
T ss_pred C
Confidence 5
No 294
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=82.30 E-value=47 Score=31.61 Aligned_cols=72 Identities=6% Similarity=0.021 Sum_probs=48.9
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+.+++.. .+...+++.|.+|++|+++.... .......++ ..++.+..++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~l~-~~~l~~~~~~~~~~~ 82 (198)
T cd08437 13 YYFPKLAKDLIKTGL-MIQIDTYE-------GGSAELLEQLLQGDLDIALLGSL-TPLENSALH-SKIIKTQHFMIIVSK 82 (198)
T ss_pred HHhHHHHHHHHHhCC-ceEEEEEE-------cCHHHHHHHHHcCCCCEEEecCC-CCCCcccce-EEEeecceEEEEecC
Confidence 445788888888876 45566654 45788999999999999986321 111122233 467778888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 83 ~h 84 (198)
T cd08437 83 DH 84 (198)
T ss_pred CC
Confidence 65
No 295
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=81.52 E-value=12 Score=40.01 Aligned_cols=213 Identities=12% Similarity=0.021 Sum_probs=113.7
Q ss_pred HHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceee-EEecceeeeceEEEEEecCC
Q 003275 404 IDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKL-VDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 404 ~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~-vdfs~p~~~~~~~~vv~~~~ 482 (834)
..+-+.+.++.|-++.++..|-+ . -|.=..++++|..|.+||.+.+......+... --|+.||...+. .
T Consensus 47 ~~fa~~v~ekt~G~l~i~vfP~~--q-LG~~~~~ie~l~~G~id~~~~s~~~l~~~~P~~~v~~lPflf~d~-------~ 116 (332)
T COG1638 47 KKFAELVEEKTGGRLKIEVFPNS--Q-LGGEAEMIEQLRSGTLDIGVVSLGFLAGLVPEFGVFDLPFLFRDE-------E 116 (332)
T ss_pred HHHHHHHHHHhCCeEEEEECCCc--c-cCcHHHHHHHHhcCCeeEEeccchhhcccCCcceeecCCeeeCCH-------H
Confidence 45567788999999666666522 1 13457899999999999998877665554432 335666655322 1
Q ss_pred CCCCcceeccCCchhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcchhhHHHHHHHHhhccCCCcccccchhhhHHH
Q 003275 483 LKSSPWAFLKPFTIPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQLVTIFWFSFSTMFFSHRENTVSSLGRVVLIV 562 (834)
Q Consensus 483 ~~~~~~~~l~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~~~~~ 562 (834)
...+-++.++.=-+.-.+---++....+
T Consensus 117 ------~~~~~~~~~~g~~l~~~~e~~g~~~l~~---------------------------------------------- 144 (332)
T COG1638 117 ------HARRVLDSEFGEELLKSLEAKGLKGLAF---------------------------------------------- 144 (332)
T ss_pred ------HHHHHHccHHHHHHHHHHHHcCCEEEEE----------------------------------------------
Confidence 1111111222222222222111111000
Q ss_pred HHHHHHHhhhccccceeeEEEEeecccCCCChhhhhcCCCCeeEeeCchhhHHHHhhhcccccceEecCCHHHHHHHHhc
Q 003275 563 WLFVVLIINSSYTASLTSILTVQQLTSQIEGIDSLISSTEPIGVQDGSFAWNYLVDELKIAESRLVKLKNMEEYSIALAR 642 (834)
Q Consensus 563 w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s~~dL~~~~~~v~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~ 642 (834)
|. +=..-++.. ..+|.+.+||. |.++-+.........++ .++..+..+ ...|.+.+|++
T Consensus 145 -----------~~-~G~R~~t~~--k~PI~~peDlk--GlkiRv~~s~~~~~~~~-a~GA~P~pm----~f~Evy~aLqt 203 (332)
T COG1638 145 -----------WE-NGFRQFTSN--KRPIKTPEDLK--GLKIRVPQSPLLLAMFK-ALGANPTPM----PFAEVYTALQT 203 (332)
T ss_pred -----------ec-CceeeeecC--CCCCCChHHhC--CCeeecCCCHHHHHHHH-HcCCCCCCC----CHHHHHHHHHc
Confidence 00 000001111 24999999997 99999999888888774 455443333 67899999999
Q ss_pred CCCCCceEEEEechhhHHHHhhcCCc--cEEEeCCcccccceEEEEcCCCc--chHHHHHHHHhhhcc
Q 003275 643 GPKGGGVAAIVDELPYIELFMSKTNC--EFRTVGQEFTKSGWGFAFQRDSP--LAIDLSTAILQLSEN 706 (834)
Q Consensus 643 ~~~~g~~~a~~~~~~~~~~~~~~~~~--~l~~v~~~~~~~~~~~~~~k~sp--l~~~~~~~i~~l~e~ 706 (834)
|-+|+.-.....+. ..+-+- ++..... ....++.+.+.+..- |-+...++|++....
T Consensus 204 ----GvVDGqEnp~~~i~--~~k~~EVqky~t~tn-H~~~~~~~~~s~~~w~~L~~e~q~il~~aa~e 264 (332)
T COG1638 204 ----GVVDGQENPLSNIY--SAKLYEVQKYLTLTN-HIYLPLAVLVSKAFWDSLPEEDQTILLEAAKE 264 (332)
T ss_pred ----CCcccccCCHHHHh--hccHHHHhHHhhhcc-ccccceeeEEcHHHHhcCCHHHHHHHHHHHHH
Confidence 88887755543322 122000 1111111 112345555555422 666666666555444
No 296
>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom
Probab=81.47 E-value=49 Score=31.36 Aligned_cols=72 Identities=10% Similarity=0.093 Sum_probs=47.6
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
++-.+++..+.+..+ .+++++.. +...++..++.+|++|+++....... ....+ -+.++....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~l-~~~~l~~~~~~~v~~~ 82 (199)
T cd08416 13 NTVPRIIMGLKLRRP-ELDIELTL-------GSNKDLLKKLKDGELDAILVATPEGL-NDPDF-EVVPLFEDDIFLAVPA 82 (199)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEEE-------cCcHHHHHHHhCCCCCEEEEecCCcC-CCCCe-EEEEeecceEEEEECC
Confidence 556788888888775 34455553 44677899999999999987432100 11122 3567777888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 83 ~h 84 (199)
T cd08416 83 TS 84 (199)
T ss_pred CC
Confidence 55
No 297
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=81.35 E-value=51 Score=31.40 Aligned_cols=70 Identities=14% Similarity=0.128 Sum_probs=47.2
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.++.+ .++++... ++..++.+.|.+|++|+++....... ..+ -+.++.+..++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~v~~~ 80 (196)
T cd08458 13 SFMSGVIQTFIADRP-DVSVYLDT-------VPSQTVLELVSLQHYDLGISILAGDY---PGL-TTEPVPSFRAVCLLPP 80 (196)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEec-------cChHHHHHHHHcCCCCEEEEeccCCC---CCc-eEEEeccCceEEEecC
Confidence 345788888888876 44566653 45677899999999999987432221 122 2457777788888776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~h 82 (196)
T cd08458 81 GH 82 (196)
T ss_pred CC
Confidence 54
No 298
>cd08192 Fe-ADH7 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. NAD-dependent iron-containing alcohol dehydrogenase-like. Proteins in this family are NAD-dependent alcohol dehydrogenases which are involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. They catalyze the oxidation of beta-hydroxy CoA ester to beta-oxo CoA ester, which then be subject to CoA-dependent thiolysis to yield acetyl-CoA and 6-C8-SPC-CoA. The major laundry surfactant in worldwide use is commercial linear alkylbenzenesulfonate (LAS) which contains 20 congeners of linear alkanes (C10 to C13). LAS is fully biodegradable in oxic environments. Degradation involves microbial communities. Parvibaculum lavamentivorans DS-1T is a representative member of many heterotrophic, LAS-degrading communities, in which it catalyzes the first steps of LAS degradation. Strain DS-1T is a small heterotrophic bacterium able to omega-oxygenate the comm
Probab=81.25 E-value=13 Score=40.68 Aligned_cols=89 Identities=6% Similarity=-0.042 Sum_probs=65.3
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe--C
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV--N 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~--~ 138 (834)
..+.++++.+|.+++.+|+..........+.+.+.+++.|+++.....+..+.+.+++...+...+..++|+||-.+ +
T Consensus 13 ~~l~~~l~~~g~~~~liv~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGS 92 (370)
T cd08192 13 KELPAECAELGIKRPLIVTDPGLAALGLVARVLALLEDAGLAAALFDEVPPNPTEAAVEAGLAAYRAGGCDGVIAFGGGS 92 (370)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 45677788889999888875544444467889999999998875444455556668899999999999999998654 4
Q ss_pred hhhHHHHHHHH
Q 003275 139 PDTGLTIFSVA 149 (834)
Q Consensus 139 ~~~~~~i~~~a 149 (834)
.-|+.+++...
T Consensus 93 viD~aK~ia~~ 103 (370)
T cd08192 93 ALDLAKAVALM 103 (370)
T ss_pred HHHHHHHHHHH
Confidence 45666665444
No 299
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.
Probab=81.20 E-value=61 Score=34.03 Aligned_cols=132 Identities=8% Similarity=-0.069 Sum_probs=74.7
Q ss_pred HHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCe-EEEEEEEcC--CcccchHHHHH
Q 003275 17 AHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWR-EVIAIFVDD--DYGRNGISVLG 93 (834)
Q Consensus 17 ~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~-~v~iI~~d~--~~g~~~~~~l~ 93 (834)
.......+.+.++|+|.+....+ . .+....+..++..-+..+++.+...+-+ +++++..+. .......+.+.
T Consensus 68 ~~~~l~~~~~~~iPvV~~d~~~~---~--~~~~~~V~~d~~~~g~~~~~~L~~~g~~~~i~~i~g~~~~~~~~~R~~g~~ 142 (302)
T TIGR02634 68 LSNAVQEAKDEGIKVVAYDRLIN---D--ADIDFYLSFDNEKVGEMQARAVLEAAPKGNYFLMGGSPTDNNAKLLRGGQM 142 (302)
T ss_pred HHHHHHHHHHCCCeEEEecCcCC---C--CCccEEEecCHHHHHHHHHHHHHhhCCCCCEEEEeCCCCCcchHHHHHHHH
Confidence 34445556778999998754321 1 1122345566677778888888666545 677776432 22333457777
Q ss_pred HHHhcC----CcEEEeeecCCCCCChHHHHHHHHHhhc---CCceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 94 DALSKK----RAKISYKAPFSPGASRSAINSLLVGANL---MESRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 94 ~~l~~~----g~~I~~~~~~~~~~~~~~~~~~l~~l~~---~~~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
+.+++. ++.+... .........+....+.++.. ..+++|+. .+...+..+++++++.|+.
T Consensus 143 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ll~~~~~~~~aI~~-~~D~~A~g~~~al~~~g~~ 209 (302)
T TIGR02634 143 KVLQPAIDSGDIKIVGD-QWVDGWLPENALRIMENALTANDNKVDAVVA-SNDATAGGAIQALTAQGLA 209 (302)
T ss_pred HHHhhhccCCCeEEecC-cCCCCCCHHHHHHHHHHHHHhCCCCccEEEE-CCCchHHHHHHHHHHCCCC
Confidence 778764 3554322 11111122344455555543 23565544 4445677889999998873
No 300
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=81.17 E-value=77 Score=33.39 Aligned_cols=70 Identities=11% Similarity=0.140 Sum_probs=46.7
Q ss_pred eHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecCC
Q 003275 403 CIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 403 ~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
-.+++..+.++.+- +.+.+.. ++..++.+.|.+|++|++++... .......+ -..++....++++++...
T Consensus 108 l~~~l~~~~~~~P~-i~l~l~~-------~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l-~~~~l~~~~~~~v~~~~h 177 (308)
T PRK10094 108 VAQLLAWLNERYPF-TQFHISR-------QIYMGVWDSLLYEGFSLAIGVTG-TEALANTF-SLDPLGSVQWRFVMAADH 177 (308)
T ss_pred HHHHHHHHHHhCCC-cEEEEEe-------ehhhhHHHHHhCCCccEEEeccc-CccccCCe-eEEEecceeEEEEECCCC
Confidence 46788888887774 5566654 45678899999999999886321 11111223 345777788888887655
No 301
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=81.14 E-value=15 Score=35.80 Aligned_cols=108 Identities=18% Similarity=0.169 Sum_probs=65.1
Q ss_pred cCCCChhhhhcCCCCe-eEeeCchhhHHHHhh---hcccccceEecC----CHHHHHHHHhcCCCCCceEEEEechhhHH
Q 003275 589 SQIEGIDSLISSTEPI-GVQDGSFAWNYLVDE---LKIAESRLVKLK----NMEEYSIALARGPKGGGVAAIVDELPYIE 660 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v-~~~~~s~~~~~l~~~---~~~~~~~~~~~~----~~~~~~~~l~~~~~~g~~~a~~~~~~~~~ 660 (834)
..|++++||...+.++ --.+||-....+... .+.....+.-|. +-.....++.. |+.|+-++-..+.+
T Consensus 87 k~i~~~edl~~~d~~fVNR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~----G~AD~GvGlr~~A~ 162 (223)
T COG1910 87 KNISSLEDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVAS----GRADAGVGLRHAAE 162 (223)
T ss_pred CccccHHHHhhcCcEEEecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHc----CCCCccccHHHHHH
Confidence 4599999999655432 234677666655432 344445555553 33456667777 99999988554443
Q ss_pred HHhhcCCccEEEeCCcccccceEEEEcCCCcchHHHHHHHHhhhcccc
Q 003275 661 LFMSKTNCEFRTVGQEFTKSGWGFAFQRDSPLAIDLSTAILQLSENGD 708 (834)
Q Consensus 661 ~~~~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~~~~~i~~l~e~G~ 708 (834)
+..-+|..+ ....|-|+.+|+.-=.+.+...+..|...+.
T Consensus 163 ----~~gL~Fipl----~~E~YD~virke~~~~~~vr~fi~~L~s~~~ 202 (223)
T COG1910 163 ----KYGLDFIPL----GDEEYDFVIRKERLDKPVVRAFIKALKSEGF 202 (223)
T ss_pred ----HcCCceEEc----ccceEEEEEehhHccCHHHHHHHHHhccccc
Confidence 312344433 4557888999876555566666666655443
No 302
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=80.99 E-value=7.5 Score=41.71 Aligned_cols=71 Identities=25% Similarity=0.218 Sum_probs=49.1
Q ss_pred ccCCCChhhhhcCCCCeeEeeCch-hhHHHH---hhhcccccc--eEecCCHHHHHHHHhcCCCCCceEEEEechhhHHH
Q 003275 588 TSQIEGIDSLISSTEPIGVQDGSF-AWNYLV---DELKIAESR--LVKLKNMEEYSIALARGPKGGGVAAIVDELPYIEL 661 (834)
Q Consensus 588 ~~~i~s~~dL~~~~~~v~~~~~s~-~~~~l~---~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~ 661 (834)
..+|++++||. |+++|+..++. ....++ ...+++.+. ++.. ...+...++.. |.+|++....++...
T Consensus 125 ~~~i~~~adlk--Gk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~----g~vda~~~~ep~~~~ 197 (335)
T COG0715 125 DSGIKSVADLK--GKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNL-PPADAVAALAA----GQVDAFVVWEPWNAA 197 (335)
T ss_pred CCCcccccCCC--CceEEEeCCCchHHHHHHHHHHHcCCCcccceEEee-CcHHHHHHHhc----CCcceEEecCCchhh
Confidence 35888999996 99999998875 333332 233444433 3444 45588888888 999998888888776
Q ss_pred Hhhc
Q 003275 662 FMSK 665 (834)
Q Consensus 662 ~~~~ 665 (834)
...+
T Consensus 198 ~~~~ 201 (335)
T COG0715 198 AEGE 201 (335)
T ss_pred hhcc
Confidence 6555
No 303
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=80.91 E-value=27 Score=36.85 Aligned_cols=118 Identities=13% Similarity=0.021 Sum_probs=73.8
Q ss_pred ccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc---CCcccchHHHHHHHHhcCCc
Q 003275 25 NELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD---DDYGRNGISVLGDALSKKRA 101 (834)
Q Consensus 25 ~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d---~~~g~~~~~~l~~~l~~~g~ 101 (834)
...++|++...... ..++ ....++..-+..+++.+...|-+++++|..+ ...+....+.+.+++++.|+
T Consensus 133 ~~~~~p~V~i~~~~-----~~~~---~V~~D~~~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~~R~~gf~~a~~~~gi 204 (311)
T TIGR02405 133 ESWNHKAVVIARDT-----GGFS---SVCYDDYGAIELLMANLYQQGHRHISFLGVDPSDKTTGLMRHNAYLAYCESANL 204 (311)
T ss_pred HhcCCCEEEEecCC-----CCcc---EEEeCcHHHHHHHHHHHHHcCCCcEEEEccCcccchhHHHHHHHHHHHHHHcCC
Confidence 44577888765321 1222 2445666666777788877899999999732 23455678899999999998
Q ss_pred EEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 102 KISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 102 ~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
.... .....+..+....+.++.+.++++|+ +++...+..+++.+++.|.
T Consensus 205 ~~~~---~~~~~~~~~~~~~~~~~l~~~~tAi~-~~~D~~A~g~~~~l~~~g~ 253 (311)
T TIGR02405 205 EPIY---QTGQLSHESGYVLTDKVLKPETTALV-CATDTLALGAAKYLQELDR 253 (311)
T ss_pred Ccee---eeCCCCHHHHHHHHHHHHhcCCCEEE-ECCcHHHHHHHHHHHHcCC
Confidence 5321 11111222333344444334577664 5666678888999999885
No 304
>cd08190 HOT Hydroxyacid-oxoacid transhydrogenase (HOT) involved in gamma-hydroxybutyrate metabolism. Hydroxyacid-oxoacid transhydrogenase (HOT), also known as D-2-hydroxyglutarate transhydrogenase. It catalyzes the conversion of gamma-hydroxybutyrate (GHB) to succinic semialdehyde (SSA), coupled to the stoichiometric conversion of alpha-ketoglutarate to D-2-hydroxyglutarate in gamma-Hydroxybutyrate catabolism. Unlike many other alcohols, which are oxidized by NAD-linked dehydrogenases, gamma-hydroxybutyrate is metabolized to succinate semialdehyde by hydroxyacid-oxoacid transhydrogenase which does not require free NAD or NADP, but instead using alpha -ketoglutarate as an acceptor, converting it to d-2-hydroxyglutarate. Alpha-ketoglutarate serves as an intermediate acceptor to regenerate NAD(P) required for the oxidation of GHB. HOT also catalyzes the reversible oxidation of a hydroxyacid obligatorily coupled to the reduction of an oxoacid, and requires no cofactor. In mammals, the HOT
Probab=80.88 E-value=7.4 Score=43.14 Aligned_cols=87 Identities=11% Similarity=-0.018 Sum_probs=64.3
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.++++.+|.+++.+|+....+.....+.+.+.+++.|+++.....+..+.+.+.+...+..+++.++|+||-.+.
T Consensus 12 ~~l~~~l~~~g~~~vlivt~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 91 (414)
T cd08190 12 AEVGMDLKNLGARRVCLVTDPNLAQLPPVKVVLDSLEAAGINFEVYDDVRVEPTDESFKDAIAFAKKGQFDAFVAVGGGS 91 (414)
T ss_pred HHHHHHHHHcCCCeEEEEECcchhhcchHHHHHHHHHHcCCcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 456677888999999888865555445678899999999987764444555556678888899999999999987754
Q ss_pred hhhHHHHHH
Q 003275 139 PDTGLTIFS 147 (834)
Q Consensus 139 ~~~~~~i~~ 147 (834)
.-|+.+.+.
T Consensus 92 viD~AKaia 100 (414)
T cd08190 92 VIDTAKAAN 100 (414)
T ss_pred HHHHHHHHH
Confidence 345555543
No 305
>PRK10624 L-1,2-propanediol oxidoreductase; Provisional
Probab=80.62 E-value=7.7 Score=42.50 Aligned_cols=87 Identities=9% Similarity=0.076 Sum_probs=63.2
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.+.++.+|.+++.+|+....+-.+..+.+.+.+++.|+++.....+..+.+.+++...+..+++.++|+||-.+.
T Consensus 19 ~~l~~~~~~~g~~~~lvvtd~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 98 (382)
T PRK10624 19 GALTDEVKRRGFKKALIVTDKTLVKCGVVAKVTDVLDAAGLAYEIYDGVKPNPTIEVVKEGVEVFKASGADYLIAIGGGS 98 (382)
T ss_pred HHHHHHHHhcCCCEEEEEeCcchhhCcchHHHHHHHHHCCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCChH
Confidence 557778888999998888755444445788899999999987654444554555678888889999999999986644
Q ss_pred hhhHHHHHH
Q 003275 139 PDTGLTIFS 147 (834)
Q Consensus 139 ~~~~~~i~~ 147 (834)
.-|+.+.+.
T Consensus 99 ~iD~aK~ia 107 (382)
T PRK10624 99 PQDTCKAIG 107 (382)
T ss_pred HHHHHHHHH
Confidence 445555443
No 306
>PF00465 Fe-ADH: Iron-containing alcohol dehydrogenase ; InterPro: IPR001670 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of ethanol to acetaldehyde with the concomitant reduction of NAD. Currently three, structurally and catalytically, different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Iron-containing ADH's have been found in yeast (gene ADH4) [], as well as in Zymomonas mobilis (gene adhB) []. These two iron-containing ADH's are closely related to the following enzymes: Escherichia coli propanediol oxidoreductase (1.1.1.77 from EC) (gene fucO) [], an enzyme involved in the metabolism of fucose and which also seems to contain ferrous ion(s). Clostridium acetobutylicum NADPH- and NADH-dependent butanol dehydrogenases (1.1.1 from EC) (genes adh1, bdhA and bdhB) [], an enzyme which has activity using butanol and ethanol as substrates. E. coli adhE [], an iron-dependent enzyme which harbor three different activities: alcohol dehydrogenase, acetaldehyde dehydrogenase (acetylating) (1.2.1.10 from EC) and pyruvate-formate-lyase deactivase. Bacterial glycerol dehydrogenase (1.1.1.6 from EC) (gene gldA or dhaD) []. Clostridium kluyveri NAD-dependent 4-hydroxybutyrate dehydrogenase (4hbd) (1.1.1.61 from EC). Citrobacter freundii and Klebsiella pneumoniae 1,3-propanediol dehydrogenase (1.1.1.202 from EC) (gene dhaT). Bacillus methanolicus NAD-dependent methanol dehydrogenase (1.1.1.244 from EC) []. E. coli and Salmonella typhimurium ethanolamine utilization protein eutG. E. coli hypothetical protein yiaY. ; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 1RRM_A 2BL4_A 2BI4_A 3BFJ_R 1KQ3_A 1JQ5_A 1JPU_A 1JQA_A 3JZD_A 3UHJ_A ....
Probab=80.54 E-value=7 Score=42.59 Aligned_cols=89 Identities=8% Similarity=0.060 Sum_probs=67.6
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP- 139 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~- 139 (834)
..+.+.++.+| ++.+|+..........+.+.+.|++.|+++.....+....+..++...+..+++.++|+||-.+.+
T Consensus 12 ~~l~~~l~~~g--r~lvVt~~~~~~~~~~~~v~~~L~~~~i~~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 89 (366)
T PF00465_consen 12 EELGEELKRLG--RVLVVTDPSLSKSGLVDRVLDALEEAGIEVQVFDGVGPNPTLEDVDEAAEQARKFGADCIIAIGGGS 89 (366)
T ss_dssp GGHHHHHHCTT--EEEEEEEHHHHHHTHHHHHHHHHHHTTCEEEEEEEESSS-BHHHHHHHHHHHHHTTSSEEEEEESHH
T ss_pred HHHHHHHHhcC--CEEEEECchHHhCccHHHHHHHHhhCceEEEEEecCCCCCcHHHHHHHHHHHHhcCCCEEEEcCCCC
Confidence 44667778887 888888663334447899999999999998766666766777999999999999999999988765
Q ss_pred -hhHHHHHHHHHh
Q 003275 140 -DTGLTIFSVAKS 151 (834)
Q Consensus 140 -~~~~~i~~~a~~ 151 (834)
-++.+++.....
T Consensus 90 ~~D~aK~va~~~~ 102 (366)
T PF00465_consen 90 VMDAAKAVALLLA 102 (366)
T ss_dssp HHHHHHHHHHHHT
T ss_pred cCcHHHHHHhhcc
Confidence 356666655554
No 307
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=80.03 E-value=24 Score=33.59 Aligned_cols=99 Identities=13% Similarity=0.003 Sum_probs=64.9
Q ss_pred HHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcC--CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEE
Q 003275 57 YYQMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKK--RAKISYKAPFSPGASRSAINSLLVGANLMESRVFV 134 (834)
Q Consensus 57 ~~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~--g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~viv 134 (834)
......+.+.....+ .+++++....+ .++.+.+.+++. |+.|+....-+. ...+-...+.+|++++||+|+
T Consensus 32 ~dl~~~ll~~~~~~~-~~v~llG~~~~----~~~~~~~~l~~~yp~l~i~g~~~g~~--~~~~~~~i~~~I~~~~pdiv~ 104 (171)
T cd06533 32 SDLMPALLELAAQKG-LRVFLLGAKPE----VLEKAAERLRARYPGLKIVGYHHGYF--GPEEEEEIIERINASGADILF 104 (171)
T ss_pred HHHHHHHHHHHHHcC-CeEEEECCCHH----HHHHHHHHHHHHCCCcEEEEecCCCC--ChhhHHHHHHHHHHcCCCEEE
Confidence 344566667766666 56667775543 455555566655 778876433332 234445589999999999999
Q ss_pred EEeChhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 135 VHVNPDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 135 l~~~~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
+.+..+.-..++...++.. +.-+++...
T Consensus 105 vglG~PkQE~~~~~~~~~l---~~~v~~~vG 132 (171)
T cd06533 105 VGLGAPKQELWIARHKDRL---PVPVAIGVG 132 (171)
T ss_pred EECCCCHHHHHHHHHHHHC---CCCEEEEec
Confidence 9998888888877766544 233566644
No 308
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=79.69 E-value=12 Score=39.48 Aligned_cols=112 Identities=11% Similarity=0.026 Sum_probs=70.2
Q ss_pred ccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC--cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC-
Q 003275 52 TTQSDYYQMHAVADLVEYYGWREVIAIFVDDD--YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM- 128 (834)
Q Consensus 52 ~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~--~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~- 128 (834)
...++...+..+++.+...|-+++++|..+.. ......+.|.+.+++.|+++..........+.......+.++.+.
T Consensus 132 V~~Dn~~~g~~a~~~l~~~G~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 211 (309)
T PRK11041 132 VHIDNLTAAFEAVNYLHELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGITVDPQYIARGDFTFEAGAKALKQLLDLP 211 (309)
T ss_pred EEECcHHHHHHHHHHHHHcCCceEEEEeCCccccchHHHHHHHHHHHHHcCCCCCHHHeEeCCCCHHHHHHHHHHHHcCC
Confidence 44566667777778887779899999975433 234567889999999887653211111111223344555666543
Q ss_pred -CceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEEe
Q 003275 129 -ESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIAT 164 (834)
Q Consensus 129 -~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~~ 164 (834)
.+++|+. ++...+..+++++++.|+..+.-++|++
T Consensus 212 ~~~~ai~~-~~d~~a~gv~~al~~~g~~ip~di~vvg 247 (309)
T PRK11041 212 QPPTAVFC-HSDVMALGALSQAKRMGLRVPQDLSIIG 247 (309)
T ss_pred CCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 3677665 4556677888899999986544444443
No 309
>cd08193 HVD 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. 5-hydroxyvalerate dehydrogenase (HVD) is an iron-containing (type III) NAD-dependent alcohol dehydrogenase. It plays a role in the cyclopentanol metabolism biochemical pathway. It catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. This cyclopentanol (cpn) degradation pathway is present in some bacteria which can use cyclopentanol as sole carbon source. In Comamonas sp. strain NCIMB 9872, this enzyme is encoded by the CpnD gene.
Probab=79.62 E-value=8.6 Score=42.06 Aligned_cols=89 Identities=9% Similarity=0.053 Sum_probs=65.0
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.++++.++.+++.+|+..........+.+.+.+++.|+++.....+..+.+.+++...+..+++.++|+||-.+.
T Consensus 15 ~~l~~~l~~~~~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGs 94 (376)
T cd08193 15 ARLGELLAALGAKRVLVVTDPGILKAGLIDPLLASLEAAGIEVTVFDDVEADPPEAVVEAAVEAARAAGADGVIGFGGGS 94 (376)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 456677888898999888755444445678899999999987754444555556788999999999999999987754
Q ss_pred hhhHHHHHHHH
Q 003275 139 PDTGLTIFSVA 149 (834)
Q Consensus 139 ~~~~~~i~~~a 149 (834)
.-|+.+++...
T Consensus 95 ~iD~aK~ia~~ 105 (376)
T cd08193 95 SMDVAKLVAVL 105 (376)
T ss_pred HHHHHHHHHHH
Confidence 44666555443
No 310
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=79.42 E-value=58 Score=33.65 Aligned_cols=123 Identities=7% Similarity=0.067 Sum_probs=64.2
Q ss_pred ccCCCChhhhhcCCCCeeEeeC--chhhHHH-Hhhh---------cc-----------cccceEecCCHHHHHHHHhcCC
Q 003275 588 TSQIEGIDSLISSTEPIGVQDG--SFAWNYL-VDEL---------KI-----------AESRLVKLKNMEEYSIALARGP 644 (834)
Q Consensus 588 ~~~i~s~~dL~~~~~~v~~~~~--s~~~~~l-~~~~---------~~-----------~~~~~~~~~~~~~~~~~l~~~~ 644 (834)
...++|++||. .|.+|++... ...+.++ .+.. +. ..-++++. ...+...++.+
T Consensus 119 s~~iksl~DL~-~Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve~-~~~q~~~al~d-- 194 (272)
T PRK09861 119 SKKIKTVAQIK-EGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMEL-EGAQLPRVLDD-- 194 (272)
T ss_pred ccCCCCHHHcC-CCCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEc-CHHHhHhhccC--
Confidence 46899999996 5889999873 3222222 1111 11 11233333 45667777877
Q ss_pred CCCceEEEEechhhHHHHhhcCCccEEEeCCcccccceEEEEcCCCcchHHHHHHHHhhhccccHHHHHHhh
Q 003275 645 KGGGVAAIVDELPYIELFMSKTNCEFRTVGQEFTKSGWGFAFQRDSPLAIDLSTAILQLSENGDLQKIHNKW 716 (834)
Q Consensus 645 ~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~k~spl~~~~~~~i~~l~e~G~~~~i~~kw 716 (834)
|++|+++...++..---.+...+-.........+.-.++.+.+..=.+.+...+..++....-+.|.++|
T Consensus 195 --g~vD~a~i~~~~~~~ag~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 264 (272)
T PRK09861 195 --PKVDVAIISTTYIQQTGLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAETIF 264 (272)
T ss_pred --cccCEEEEchhHHHHcCCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 8899888887766431111001111111111111123455544334556666666666665555666654
No 311
>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes
Probab=79.40 E-value=60 Score=31.06 Aligned_cols=70 Identities=17% Similarity=0.190 Sum_probs=48.0
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
++-.+++..+.+..+ .+.++... ++..+++.+|.+|++|++++...... ..+ .+.|+....+++++++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~v~~~ 81 (203)
T cd08445 14 GLLPELIRRFRQAAP-DVEIELIE-------MTTVQQIEALKEGRIDVGFGRLRIED---PAI-RRIVLREEPLVVALPA 81 (203)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEe-------CChHHHHHHHHcCCCcEEEecCCCCC---CCc-eeEEEEeccEEEEeeC
Confidence 566788888888775 34455553 45789999999999999986332211 222 2456777888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 82 ~h 83 (203)
T cd08445 82 GH 83 (203)
T ss_pred CC
Confidence 55
No 312
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=79.30 E-value=63 Score=33.78 Aligned_cols=85 Identities=14% Similarity=0.178 Sum_probs=50.9
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
+.||||++.. ...++-.+++..+.+..+ ++.+.... ++.+.+..+|.+|++|+++...
T Consensus 93 g~l~i~~~~~--------------~~~~~l~~~l~~f~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~ 150 (296)
T PRK11062 93 LLFDVGVADA--------------LSKRLVSRVLLTAVPEDE-SIHLRCFE-------STHEMLLEQLSQHKLDMILSDC 150 (296)
T ss_pred eEEEEEecch--------------hhHhhHHHHHHHHHhcCC-ceEEEEEe-------CCHHHHHHHHHcCCCCEEEecC
Confidence 4789998321 113566788888877654 34455543 4578999999999999988532
Q ss_pred eeecCceeeEEecceeeeceEEEEEecC
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQ 481 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~ 481 (834)
.........+ ...|+....++++++.+
T Consensus 151 ~~~~~~~~~l-~~~~l~~~~~~~~~~~~ 177 (296)
T PRK11062 151 PVDSTQQEGL-FSKKLGECGVSFFCTNP 177 (296)
T ss_pred CCccccccch-hhhhhhccCcceEecCC
Confidence 2111111122 23466666666665543
No 313
>cd08551 Fe-ADH iron-containing alcohol dehydrogenases (Fe-ADH)-like. Large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. They contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol dehydrogenases; insect-type, or short-chain alcohol dehydrogenases; iron-containing alcohol dehydrogenases, and others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases, but lacks sequence homology, and differs in strand arrangement. ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)+ to NAD(P)H.
Probab=79.16 E-value=9.8 Score=41.50 Aligned_cols=90 Identities=7% Similarity=0.030 Sum_probs=65.6
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.++++.++.+++.+|+....+.....+.+.+.+++.|+++.....+..+.+.+++...+..++..++|+||-.+.
T Consensus 12 ~~l~~~l~~~~~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IiaiGGGs 91 (370)
T cd08551 12 EKLGEEIKNLGGRKALIVTDPGLVKTGVLDKVIDSLKEAGIEVVIFDGVEPNPTLSNVDAAVAAYREEGCDGVIAVGGGS 91 (370)
T ss_pred HHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 556777888898999888855444346678899999998887764444555556688999999999899999986644
Q ss_pred hhhHHHHHHHHH
Q 003275 139 PDTGLTIFSVAK 150 (834)
Q Consensus 139 ~~~~~~i~~~a~ 150 (834)
.-++.+++....
T Consensus 92 ~~D~AK~va~~~ 103 (370)
T cd08551 92 VLDTAKAIALLA 103 (370)
T ss_pred HHHHHHHHHHHH
Confidence 456666654433
No 314
>cd08189 Fe-ADH5 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown.
Probab=78.95 E-value=16 Score=39.81 Aligned_cols=90 Identities=7% Similarity=-0.025 Sum_probs=65.2
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe--C
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV--N 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~--~ 138 (834)
..+.+.++.+|-+++.+|+..........+.+.+.+++.|+.+.....+..+.+.+.+...+..+++.++|+||-.+ +
T Consensus 15 ~~l~~~l~~~g~~~~lvvt~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGS 94 (374)
T cd08189 15 AQLPAAISQLGVKKVLIVTDKGLVKLGLLDKVLEALEGAGIEYAVYDGVPPDPTIENVEAGLALYRENGCDAILAVGGGS 94 (374)
T ss_pred HHHHHHHHhcCCCeEEEEeCcchhhcccHHHHHHHHHhcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 45667788888889888875544444467889999999998776544555555668889999999999999998664 4
Q ss_pred hhhHHHHHHHHH
Q 003275 139 PDTGLTIFSVAK 150 (834)
Q Consensus 139 ~~~~~~i~~~a~ 150 (834)
.-|+.+++....
T Consensus 95 ~~D~aK~ia~~~ 106 (374)
T cd08189 95 VIDCAKAIAARA 106 (374)
T ss_pred HHHHHHHHHHHH
Confidence 456666554443
No 315
>cd08194 Fe-ADH6 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions.
Probab=77.73 E-value=11 Score=41.15 Aligned_cols=87 Identities=9% Similarity=0.014 Sum_probs=64.2
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.++++.++.+++.+|+....+..+..+.+.+.|++.|+++.....+..+.+.+++...+..++..++|+||-.+.
T Consensus 12 ~~l~~~~~~~~~~r~livt~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 91 (375)
T cd08194 12 DETGAVLADLGGKRPLIVTDKVMVKLGLVDKLTDSLKKEGIESAIFDDVVSEPTDESVEEGVKLAKEGGCDVIIALGGGS 91 (375)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhcchHHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 445667777788999888855555444678899999999988765555665666788999999999999999987654
Q ss_pred hhhHHHHHH
Q 003275 139 PDTGLTIFS 147 (834)
Q Consensus 139 ~~~~~~i~~ 147 (834)
.-|+.+++.
T Consensus 92 ~~D~AKaia 100 (375)
T cd08194 92 PIDTAKAIA 100 (375)
T ss_pred HHHHHHHHH
Confidence 445555554
No 316
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=77.67 E-value=62 Score=33.11 Aligned_cols=69 Identities=10% Similarity=0.070 Sum_probs=45.6
Q ss_pred HHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCc-ccEEeeeeeeecCc---ee--eEEecceeeeceEEEEE
Q 003275 405 DVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNK-FDAAVGDITIVTNR---TK--LVDFTQPYMESGLVVVA 478 (834)
Q Consensus 405 dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~-~D~~~~~~~i~~~r---~~--~vdfs~p~~~~~~~~vv 478 (834)
++...+.+..+.++.+++- .-..+..++.+|. +|+.+..-...... .. .-+...+|....+++++
T Consensus 46 ~i~~~F~~~~~~~V~~~f~---------gS~~l~~qIe~Ga~~D~fiSa~~~~~~~l~~~g~~~~~~~~~fa~n~lvl~~ 116 (258)
T COG0725 46 EIAKQFEKETGVKVEVEFG---------GSGALARQIEQGAPADLFISADDAYMDKLEDKGLIYADSRIVFAGNRLVLAV 116 (258)
T ss_pred HHHHHHHHHHCCeEEEEec---------chHHHHHHHHcCCCcCEEEECCHHHHHHHHhcCCccCCceEEeeCCeEEEEE
Confidence 6777777777777666653 3567888888876 88876643322211 11 23467888888999999
Q ss_pred ecCC
Q 003275 479 PVQK 482 (834)
Q Consensus 479 ~~~~ 482 (834)
++..
T Consensus 117 ~~~~ 120 (258)
T COG0725 117 PKGS 120 (258)
T ss_pred eCCC
Confidence 8776
No 317
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=77.39 E-value=66 Score=30.42 Aligned_cols=72 Identities=18% Similarity=0.109 Sum_probs=48.2
Q ss_pred eeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEe
Q 003275 400 KGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAP 479 (834)
Q Consensus 400 ~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~ 479 (834)
..+-.+++..+.+..+ .+++++.. ++...++.++.+|++|+++....... ...+. +.++....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~--~~~l~-~~~l~~~~~~~~~~ 80 (199)
T cd08430 12 YSFLPPILERFRAQHP-QVEIKLHT-------GDPADAIDKVLNGEADIAIAARPDKL--PARLA-FLPLATSPLVFIAP 80 (199)
T ss_pred eeeccHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHCCCCCEEEEecCCCC--CcccE-EEeeccceEEEEEe
Confidence 3556788999998885 34566654 56788999999999999986422111 11222 45666777777777
Q ss_pred cCC
Q 003275 480 VQK 482 (834)
Q Consensus 480 ~~~ 482 (834)
...
T Consensus 81 ~~~ 83 (199)
T cd08430 81 NIA 83 (199)
T ss_pred CCc
Confidence 654
No 318
>TIGR02638 lactal_redase lactaldehyde reductase. This clade of genes encoding iron-containing alcohol dehydrogenase (pfam00465) proteins is generally found in apparent operons for the catabolism of rhamnose or fucose. Catabolism of both of these monosaccharides results in lactaldehyde which is reduced by this enzyme to 1,2 propanediol. This protein is alternatively known by the name 1,2 propanediol oxidoreductase. This enzyme is active under anaerobic conditions in E. coli while being inactivated by reactive oxygen species under aerobic conditions. Under aerobic conditions the lactaldehyde product of rhamnose and fucose catabolism is believed to be oxidized to lactate by a separate enzyme, lactaldehyde dehydrogenase.
Probab=76.47 E-value=12 Score=41.06 Aligned_cols=88 Identities=9% Similarity=0.107 Sum_probs=62.8
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.+.+..+|.+++.+|+.....-.+..+.+.+.+++.|+.+.....+.++.+.+.+......+++.++|+||-.+.
T Consensus 18 ~~l~~~l~~~g~~r~lvvt~~~~~~~g~~~~v~~~L~~~~i~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiaiGGGS 97 (379)
T TIGR02638 18 EDIVDEVKRRGFKKALVVTDKDLIKFGVADKVTDLLDEAGIAYELFDEVKPNPTITVVKAGVAAFKASGADYLIAIGGGS 97 (379)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhccchHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCChH
Confidence 456677888898998888754433334678899999999987654444554556678888899999999999997654
Q ss_pred hhhHHHHHHH
Q 003275 139 PDTGLTIFSV 148 (834)
Q Consensus 139 ~~~~~~i~~~ 148 (834)
.-|+.+.+..
T Consensus 98 viD~aKaia~ 107 (379)
T TIGR02638 98 PIDTAKAIGI 107 (379)
T ss_pred HHHHHHHHHH
Confidence 3455554433
No 319
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=75.94 E-value=6.8 Score=40.01 Aligned_cols=78 Identities=17% Similarity=0.144 Sum_probs=59.7
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEE-eChhhHHHHHHHHHh
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVH-VNPDTGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~-~~~~~~~~i~~~a~~ 151 (834)
|++|.. ++.|.......+.+++++.|..+... .+...+.......++++.+.++|.|++. ..+.....+++++.+
T Consensus 1 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~--~~~~~d~~~q~~~i~~~i~~~~d~Iiv~~~~~~~~~~~l~~~~~ 78 (257)
T PF13407_consen 1 IGVIVPSMDNPFWQQVIKGAKAAAKELGYEVEIV--FDAQNDPEEQIEQIEQAISQGVDGIIVSPVDPDSLAPFLEKAKA 78 (257)
T ss_dssp EEEEESSSSSHHHHHHHHHHHHHHHHHTCEEEEE--EESTTTHHHHHHHHHHHHHTTESEEEEESSSTTTTHHHHHHHHH
T ss_pred cEEEeCCCCCHHHHHHHHHHHHHHHHcCCEEEEe--CCCCCCHHHHHHHHHHHHHhcCCEEEecCCCHHHHHHHHHHHhh
Confidence 455553 45688888999999999999998775 2333345666778888888899999887 456677889999999
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.|+
T Consensus 79 ~gI 81 (257)
T PF13407_consen 79 AGI 81 (257)
T ss_dssp TTS
T ss_pred cCc
Confidence 886
No 320
>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein. This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of this gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source.
Probab=75.86 E-value=1.1e+02 Score=32.05 Aligned_cols=137 Identities=7% Similarity=-0.047 Sum_probs=68.6
Q ss_pred CCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChH-HHHHHHHHHH-HHc-CCeEEEEEEEcCCc--c
Q 003275 11 PQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDY-YQMHAVADLV-EYY-GWREVIAIFVDDDY--G 85 (834)
Q Consensus 11 p~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~-~q~~aia~ll-~~~-~W~~v~iI~~d~~~--g 85 (834)
|..+.........+...+||+|.+....+. . +........|. ..+...++.+ ++. +-++|++|..+... .
T Consensus 64 ~~~~~~~~~~l~~~~~~giPvV~~~~~~~~--~---~~~~~v~~~Dn~~~g~~aa~~l~~~l~~~~~I~~i~g~~~~~~~ 138 (302)
T TIGR02637 64 ANDPDALVPALKKAMKRGIKVVTWDSGVAP--E---GRNLFLNQASADLIGRTQVQLAAEQIGNGGEIAILSAASTATNQ 138 (302)
T ss_pred CCChHHHHHHHHHHHHCCCEEEEeCCCCCC--C---ceeEEEecCCHHHHHHHHHHHHHHHcCCCcEEEEEECCCCCccH
Confidence 443333334445567789999987543221 1 12233333333 3344445544 332 22789888754322 2
Q ss_pred cchHHHHHHHHhcCC---cEEEeeecCCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHhCCCC
Q 003275 86 RNGISVLGDALSKKR---AKISYKAPFSPGASRSAINSLLVGANLME--SRVFVVHVNPDTGLTIFSVAKSLGMT 155 (834)
Q Consensus 86 ~~~~~~l~~~l~~~g---~~I~~~~~~~~~~~~~~~~~~l~~l~~~~--~~vivl~~~~~~~~~i~~~a~~~g~~ 155 (834)
....+.+.+.++++| .++... .....+.++-...+.++.+.. +++|+. .....+..+++++++.|..
T Consensus 139 ~~r~~g~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~~ai~~-~~d~~a~ga~~al~~~g~~ 210 (302)
T TIGR02637 139 NAWIEIMKKELKDPKYPKVKLVAT--VYGDDDAQKSYQEAQGLLKSYPNLKGIIA-PTTVGIKAAAQAVSDAKLI 210 (302)
T ss_pred HHHHHHHHHHHhhccCCCCEEEee--ecCCchHHHHHHHHHHHHHhCCCccEEEe-CCCchHHHHHHHHHhcCCC
Confidence 234577777777653 344322 111112233334444544333 445544 3455667788888888864
No 321
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=74.57 E-value=1e+02 Score=32.86 Aligned_cols=137 Identities=9% Similarity=-0.068 Sum_probs=78.0
Q ss_pred HHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcC---CcccchHHHHHHH
Q 003275 19 VISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDD---DYGRNGISVLGDA 95 (834)
Q Consensus 19 ~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~---~~g~~~~~~l~~~ 95 (834)
.....+...++|+|...... .... .......++...+..+++.+...|-++++++.... ..+....+.+.++
T Consensus 97 ~~l~~~~~~~iPvV~id~~~---~~~~--~~~~V~~D~~~~g~~a~~~L~~~g~~~i~~i~~g~~~~~~~~~R~~gf~~~ 171 (330)
T PRK10355 97 NVIKEAKQEGIKVLAYDRMI---NNAD--IDFYISFDNEKVGELQAKALVDKVPQGNYFLMGGSPVDNNAKLFRAGQMKV 171 (330)
T ss_pred HHHHHHHHCCCeEEEECCCC---CCCC--ccEEEecCHHHHHHHHHHHHHHhcCCCCEEEEeCCCCCccHHHHHHHHHHH
Confidence 33455677789999874422 1111 22346778888888889998777778876654322 2334457778888
Q ss_pred HhcC---C-cEEEeeecCCCCCChHHHHHHHHHhh-c--CCceEEEEEeChhhHHHHHHHHHhCCCCCCCeEEEEe
Q 003275 96 LSKK---R-AKISYKAPFSPGASRSAINSLLVGAN-L--MESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYVWIAT 164 (834)
Q Consensus 96 l~~~---g-~~I~~~~~~~~~~~~~~~~~~l~~l~-~--~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~vwi~~ 164 (834)
++++ | +.+....... ..+..+....++++. + ..+++| ++.+...+..+++.+++.|+. +-+.|.+
T Consensus 172 l~~~~~~~~i~~~~~~~~~-~~~~~~~~~~~~~lL~~~~~~~~aI-~~~nD~~A~g~l~al~~~g~~--~di~IiG 243 (330)
T PRK10355 172 LKPYIDSGKIKVVGDQWVD-GWLPENALKIMENALTANNNKIDAV-VASNDATAGGAIQALSAQGLS--GKVAISG 243 (330)
T ss_pred HhhhccCCCeEEecccCCC-CCCHHHHHHHHHHHHHhCCCCccEE-EECCCchHHHHHHHHHHCCCC--CCceEEc
Confidence 8764 4 4432221111 112223334444443 2 235654 445566777899999999975 3344443
No 322
>cd08188 Fe-ADH4 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown.
Probab=74.47 E-value=16 Score=40.05 Aligned_cols=88 Identities=8% Similarity=-0.028 Sum_probs=62.5
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.+++..+|.+++.+|+.....-....+.+.+.+++.|+.+.....+..+.+..++...+..++..++|+||-.+.
T Consensus 17 ~~l~~~l~~~g~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs 96 (377)
T cd08188 17 KLAGRYARRLGAKKVLLVSDPGVIKAGWVDRVIESLEEAGLEYVVFSDVSPNPRDEEVMAGAELYLENGCDVIIAVGGGS 96 (377)
T ss_pred HHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 456777888898999888754433334678899999988887654444544556678888899999999999987654
Q ss_pred hhhHHHHHHH
Q 003275 139 PDTGLTIFSV 148 (834)
Q Consensus 139 ~~~~~~i~~~ 148 (834)
.-|+.+.+..
T Consensus 97 viD~AK~ia~ 106 (377)
T cd08188 97 PIDCAKGIGI 106 (377)
T ss_pred HHHHHHHHHH
Confidence 3455554433
No 323
>cd08185 Fe-ADH1 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases-like (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase fold and is a member of the iron-containing alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown. They are present in bacteria and archaea.
Probab=74.03 E-value=16 Score=40.12 Aligned_cols=88 Identities=6% Similarity=-0.013 Sum_probs=63.4
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCC-cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDD-YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV-- 137 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~-~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~-- 137 (834)
..+.++++.+| +++.+|+.... ......+.+.+.+++.|+++.....+.++.+.+++......+++.++|+||-.+
T Consensus 15 ~~l~~~~~~~g-~r~livt~~~~~~~~g~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiavGGG 93 (380)
T cd08185 15 NELGEEALKPG-KKALIVTGNGSSKKTGYLDRVIELLKQAGVEVVVFDKVEPNPTTTTVMEGAALAREEGCDFVVGLGGG 93 (380)
T ss_pred HHHHHHHHhcC-CeEEEEeCCCchhhccHHHHHHHHHHHcCCeEEEeCCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCc
Confidence 44666777788 89888885443 245677889999999998876444555556668888888999999999999654
Q ss_pred ChhhHHHHHHHH
Q 003275 138 NPDTGLTIFSVA 149 (834)
Q Consensus 138 ~~~~~~~i~~~a 149 (834)
+.-|+.+.+...
T Consensus 94 S~iD~aK~ia~~ 105 (380)
T cd08185 94 SSMDTAKAIAFM 105 (380)
T ss_pred cHHHHHHHHHHH
Confidence 344666555443
No 324
>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2.7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....
Probab=72.82 E-value=52 Score=31.57 Aligned_cols=129 Identities=12% Similarity=0.155 Sum_probs=68.0
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCC--ccE-EecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELN--VPL-LSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAI 78 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~--vP~-Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI 78 (834)
.++++++||.+|+-...+..+++... +.. ++++...|.-.+ .+-.|.|-+ .. .+-++++.-..=...-
T Consensus 2 ~r~ivl~Gpsg~GK~~l~~~L~~~~~~~~~~~v~~TTR~~r~~E~~g~~y~fvs----~~---~f~~~~~~~~fie~~~- 73 (183)
T PF00625_consen 2 RRPIVLVGPSGSGKSTLAKRLIQEFPDKFGRVVSHTTRPPRPGEVDGVDYHFVS----KE---EFERMIKAGEFIEYGE- 73 (183)
T ss_dssp SSEEEEESSTTSSHHHHHHHHHHHSTTTEEEEEEEESS-GGTTS-TTTSEEE------HH---HHHHHHHTTHEEEEEE-
T ss_pred CCEEEEECCCCCCHHHHHHHHHHhcccccccceeecccCCcccccCCcceEEEe----ec---hhhhhhccccEEEEee-
Confidence 57899999999998888877877653 433 444444444433 334555542 11 1222332221111111
Q ss_pred EEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHh
Q 003275 79 FVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKS 151 (834)
Q Consensus 79 ~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~ 151 (834)
|.++.||.. .+.+...+++...+|... . ..-+.+|+....+.++++..+.....+-+.+++
T Consensus 74 ~~g~~YGt~-~~~i~~~~~~gk~~il~~---~--------~~g~~~L~~~~~~~~~IfI~~~s~~~l~~~l~~ 134 (183)
T PF00625_consen 74 YDGNYYGTS-KSAIDKVLEEGKHCILDV---D--------PEGVKQLKKAGFNPIVIFIKPPSPEVLKRRLRR 134 (183)
T ss_dssp ETTEEEEEE-HHHHHHHHHTTTEEEEEE---T--------HHHHHHHHHCTTTEEEEEEEESSHHHHHHHHHT
T ss_pred ecchhhhhc-cchhhHhhhcCCcEEEEc---c--------HHHHHHHHhcccCceEEEEEccchHHHHHHHhc
Confidence 445678854 577888888887776542 1 112344444455555555544444444444443
No 325
>KOG1419 consensus Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism]
Probab=72.77 E-value=6.2 Score=43.47 Aligned_cols=89 Identities=15% Similarity=0.227 Sum_probs=69.8
Q ss_pred hhhHHHHHHHHHHHHhhhheeecccCCCCCCCCCcchhhHHHHHHHHhhcc--CCCcccccchhhhHHHHHHHHHHhhhc
Q 003275 496 IPMWLVTGGFFLFVGAVVWILEHRFNNEFRGPPSQQLVTIFWFSFSTMFFS--HRENTVSSLGRVVLIVWLFVVLIINSS 573 (834)
Q Consensus 496 ~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~s~~~R~~~~~w~~~~lil~~~ 573 (834)
...|+.-++.+++.++++++.|.....+-.+.....+-.++||..-++.-- |...|..+.+|++..++-++++-+-+.
T Consensus 234 iTt~YIGFL~LIfsSflVYLaEKd~~~e~~n~~F~TyADALWWG~ITltTIGYGDk~P~TWlGr~laa~fsligiSFFAL 313 (654)
T KOG1419|consen 234 ITTWYIGFLVLIFSSFLVYLAEKDAQGEGTNDEFPTYADALWWGVITLTTIGYGDKTPQTWLGRLLAACFSLIGISFFAL 313 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccccccccccchhHHHHHHhhheeEEeeccCCcCcccchhHHHHHHHHHHHHHHHhc
Confidence 357899999999999999999988554444444567889999999988755 577999999999999988888776666
Q ss_pred cccceeeEEEE
Q 003275 574 YTASLTSILTV 584 (834)
Q Consensus 574 Yta~L~s~Lt~ 584 (834)
=.+.|-|-++.
T Consensus 314 PAGILGSGfAL 324 (654)
T KOG1419|consen 314 PAGILGSGFAL 324 (654)
T ss_pred ccccccchhhh
Confidence 66666655543
No 326
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=71.98 E-value=90 Score=29.44 Aligned_cols=70 Identities=13% Similarity=0.169 Sum_probs=48.2
Q ss_pred eeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecC
Q 003275 402 YCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQ 481 (834)
Q Consensus 402 ~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~ 481 (834)
+-.++++.+.+..+ .+.+++.. ++.+++...+.+|++|+++...... ....+ .+.++....++++++..
T Consensus 15 ~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~~~ 83 (199)
T cd08451 15 LVPGLIRRFREAYP-DVELTLEE-------ANTAELLEALREGRLDAAFVRPPVA--RSDGL-VLELLLEEPMLVALPAG 83 (199)
T ss_pred ccHHHHHHHHHHCC-CcEEEEec-------CChHHHHHHHHCCCccEEEEecCCC--CCCce-eEEEeecccEEEEecCC
Confidence 55778888888876 34466653 4578899999999999998643221 11122 35677788888888765
Q ss_pred C
Q 003275 482 K 482 (834)
Q Consensus 482 ~ 482 (834)
.
T Consensus 84 ~ 84 (199)
T cd08451 84 H 84 (199)
T ss_pred C
Confidence 4
No 327
>cd08181 PPD-like 1,3-propanediol dehydrogenase-like (PPD). 1,3-propanediol dehydrogenase-like (PPD). This family is a member of the iron-containing alcohol dehydrogenase superfamily, and exhibits a dehydroquinate synthase-like fold. Protein sequence similarity search and other biochemical evidences suggest that they are close to the iron-containing 1,3-propanediol dehydrogenase (EC 1.1.1.202). 1,3-propanediol dehydrogenase catalyzes the oxidation of propane-1,3-diol to 3-hydroxypropanal with the simultaneous reduction of NADP+ to NADPH. The protein structure of Thermotoga maritima TM0920 gene contains one NADP+ and one iron ion.
Probab=71.77 E-value=19 Score=38.95 Aligned_cols=86 Identities=7% Similarity=0.003 Sum_probs=61.1
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcc-cchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYG-RNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP 139 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g-~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~ 139 (834)
..+.++++.+| +++.+|+....+- .+..+.+.+.+++.|+++.....+.++.+.+++...++.+++.++|+||-.+.+
T Consensus 15 ~~l~~~~~~~g-~r~lvVt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 93 (357)
T cd08181 15 EKHGEELAALG-KRALIVTGKSSAKKNGSLDDVTKALEELGIEYEIFDEVEENPSLETIMEAVEIAKKFNADFVIGIGGG 93 (357)
T ss_pred HHHHHHHHHcC-CEEEEEeCCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 34566778888 8887777544423 335688999999999887654455555666889999999999999999987654
Q ss_pred --hhHHHHHH
Q 003275 140 --DTGLTIFS 147 (834)
Q Consensus 140 --~~~~~i~~ 147 (834)
-|+.+.+.
T Consensus 94 SviD~aK~ia 103 (357)
T cd08181 94 SPLDAAKAIA 103 (357)
T ss_pred hHHHHHHHHH
Confidence 35555443
No 328
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=71.73 E-value=1.2e+02 Score=31.71 Aligned_cols=82 Identities=12% Similarity=0.055 Sum_probs=52.1
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
++|+||++.. . ...+...++..+.+.. .+++++.. +.-+.++.++.+|++|+++...
T Consensus 90 g~l~I~~~~~--~------------~~~~l~~~l~~f~~~~--~i~i~l~~-------~~~~~~~~~l~~~~~d~~i~~~ 146 (294)
T PRK03635 90 LTLSIAVNAD--S------------LATWFLPALAPVLARS--GVLLDLVV-------EDQDHTAELLRRGEVVGAVTTE 146 (294)
T ss_pred eEEEEeecch--h------------HHHHHHHHHHHHHhCC--CcEEEEEe-------cCcHHHHHHHhCCCceEEEecc
Confidence 5799999321 1 1123345677777663 45566654 4456889999999999998632
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCC
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
.. .... -.+.|+....++++++...
T Consensus 147 ~~---~~~~-l~~~~l~~~~~~lv~~~~~ 171 (294)
T PRK03635 147 PQ---PVQG-CRVDPLGAMRYLAVASPAF 171 (294)
T ss_pred CC---CCCC-ceeeecccceEEEEEcchH
Confidence 21 1122 2567888888888887653
No 329
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport
Probab=71.71 E-value=93 Score=29.50 Aligned_cols=73 Identities=11% Similarity=0.074 Sum_probs=47.7
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. ++...+..+|.+|++|+++............+ -+.|.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~~~ 83 (200)
T cd08453 13 SVLPELVRRFREAYP-DVELQLRE-------ATSDVQLEALLAGEIDAGIVIPPPGASAPPAL-AYRPLLSEPLVLAVPA 83 (200)
T ss_pred HHHHHHHHHHHHhCC-CceEEEEe-------CCHHHHHHHHHcCCCCEEEEecCcccCCCcce-eEEEeeeCceEEEEEC
Confidence 455778888887764 34566654 45678999999999999886332111011122 3567777888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 84 ~h 85 (200)
T cd08453 84 AW 85 (200)
T ss_pred CC
Confidence 65
No 330
>PF13685 Fe-ADH_2: Iron-containing alcohol dehydrogenase; PDB: 3CE9_C.
Probab=71.50 E-value=23 Score=35.92 Aligned_cols=98 Identities=11% Similarity=0.208 Sum_probs=58.0
Q ss_pred HHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChh-
Q 003275 62 AVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPD- 140 (834)
Q Consensus 62 aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~- 140 (834)
.+.++++.++.+++.+|...+-| ....+.+.+.+++.|+++..........+..++.....+++..++++||-.+.+.
T Consensus 9 ~l~~~l~~~~~~~~lvv~d~~t~-~~~g~~v~~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ii~vGgG~i 87 (250)
T PF13685_consen 9 KLPEILSELGLKKVLVVTDENTY-KAAGEKVEESLKSAGIEVAVIEEFVGDADEDEVEKLVEALRPKDADLIIGVGGGTI 87 (250)
T ss_dssp GHHHHHGGGT-SEEEEEEETTHH-HHHHHHHHHHHHTTT-EEEEEE-EE---BHHHHHHHHTTS--TT--EEEEEESHHH
T ss_pred HHHHHHHhcCCCcEEEEEcCCHH-HHHHHHHHHHHHHcCCeEEEEecCCCCCCHHHHHHHHHHhcccCCCEEEEeCCcHH
Confidence 35677888888999888866544 3345788889999999887443233334556677777777777889888887764
Q ss_pred -hHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 141 -TGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 141 -~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
|..+. .|.+.| ..|+-+.|.
T Consensus 88 ~D~~K~--~A~~~~---~p~isVPTa 108 (250)
T PF13685_consen 88 IDIAKY--AAFELG---IPFISVPTA 108 (250)
T ss_dssp HHHHHH--HHHHHT-----EEEEES-
T ss_pred HHHHHH--HHHhcC---CCEEEeccc
Confidence 33433 344445 456777764
No 331
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=70.85 E-value=1.3e+02 Score=30.67 Aligned_cols=71 Identities=20% Similarity=0.120 Sum_probs=46.4
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+..+++..+.+..+ .+.+.+.. ++..+++.+|.+|++|+++...... ....+. ..+.....++++++.
T Consensus 80 ~~~~~~l~~~~~~~p-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~~~--~~~~~~-~~~l~~~~~~~v~~~ 148 (269)
T PRK11716 80 SHLPPILDRFRAEHP-LVEIKLTT-------GDAADAVEKVQSGEADLAIAAKPET--LPASVA-FSPIDEIPLVLIAPA 148 (269)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEE-------CCHHHHHHHHHCCCccEEEEecCCC--CCcceE-EEEcccceEEEEEcC
Confidence 355788888888775 34466654 4567899999999999998643211 111122 356667777777765
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 149 ~~ 150 (269)
T PRK11716 149 LP 150 (269)
T ss_pred Cc
Confidence 53
No 332
>KOG3857 consensus Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=70.54 E-value=31 Score=35.92 Aligned_cols=96 Identities=13% Similarity=0.043 Sum_probs=73.6
Q ss_pred CCCCceEEccCChHHHHHH----HHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHH
Q 003275 44 LQYPYFLRTTQSDYYQMHA----VADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAIN 119 (834)
Q Consensus 44 ~~~p~~~r~~ps~~~q~~a----ia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~ 119 (834)
+..+|-|-+.||....+.+ +++-++..|.|++.+|.+-+.--....+...+.|+++|+.+.......++.+..++.
T Consensus 38 k~~~~af~m~~s~~rfG~gv~~Evg~dikn~gaKk~llvTDkni~~~~~~~~a~~~L~~~~I~~~vyD~v~~ePtv~s~~ 117 (465)
T KOG3857|consen 38 KMMSVAFFMIPSTSRFGKGVLAEVGDDIKNLGAKKTLLVTDKNIAKLGLVKVAQDSLEENGINVEVYDKVQPEPTVGSVT 117 (465)
T ss_pred ccceeeEEeccchhhhcchhHHHHHHHHHhcCccceEEeeCCChhhcccHHHHHHHHHHcCCceEEecCccCCCchhhHH
Confidence 3346666677776655443 344578899999998886666666678889999999999987766666666778899
Q ss_pred HHHHHhhcCCceEEEEEeCh
Q 003275 120 SLLVGANLMESRVFVVHVNP 139 (834)
Q Consensus 120 ~~l~~l~~~~~~vivl~~~~ 139 (834)
..+.-+|..+.|.+|-.+.+
T Consensus 118 ~alefak~~~fDs~vaiGGG 137 (465)
T KOG3857|consen 118 AALEFAKKKNFDSFVAIGGG 137 (465)
T ss_pred HHHHHHHhcccceEEEEcCc
Confidence 99999999999988877654
No 333
>cd08170 GlyDH Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway . In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=70.40 E-value=15 Score=39.71 Aligned_cols=84 Identities=11% Similarity=0.056 Sum_probs=60.5
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP- 139 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~- 139 (834)
..+.++++.++ +++.+|+....+. ...+.+.+.+++.|+.+.+. .+..+.+.+++...++.+++.++|+||-.+.+
T Consensus 12 ~~l~~~~~~~~-~r~livt~~~~~~-~~~~~v~~~L~~~~i~~~~~-~~~~~p~~~~v~~~~~~~~~~~~D~IIavGGGS 88 (351)
T cd08170 12 DELGEYLARLG-KRALIIADEFVLD-LVGAKIEESLAAAGIDARFE-VFGGECTRAEIERLAEIARDNGADVVIGIGGGK 88 (351)
T ss_pred HHHHHHHHHhC-CeEEEEECHHHHH-HHHHHHHHHHHhCCCeEEEE-EeCCcCCHHHHHHHHHHHhhcCCCEEEEecCch
Confidence 44666777776 8888888444443 67888999999999887643 35545566788899999999999999877543
Q ss_pred -hhHHHHHH
Q 003275 140 -DTGLTIFS 147 (834)
Q Consensus 140 -~~~~~i~~ 147 (834)
-|+.+++.
T Consensus 89 ~iD~aK~ia 97 (351)
T cd08170 89 TLDTAKAVA 97 (351)
T ss_pred hhHHHHHHH
Confidence 45555543
No 334
>cd08176 LPO Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. Lactadehyde:propanediol oxidoreductase (LPO) is a member of the group III iron-activated dehydrogenases which catalyze the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. L-Fucose and L-rhamnose is used by Escherichia coli through an inducible pathway mediated by the fucose regulon comprising four linked oeprons fucO, fucA, fucPIK, and fucR. The fucA-encoded aldolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Under anaerobic conditions, with NADH as a cofactor, lactaldehyde is converted by a fucO-encoded Lactadehyde:propanediol oxidoreductase (LPO) to L-1,2-propanediol, which is excreted as a fermentation product. In mutant strains, E. coli adapted to grow on L-1,2-propanediol, FucO catalyzes the oxidation of the polyol to
Probab=70.33 E-value=18 Score=39.49 Aligned_cols=87 Identities=8% Similarity=0.088 Sum_probs=61.8
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.+.++.+|-+++.+|+....+-....+.+.+.+++.|+.+.....+..+.+.+.+...+..+++.++|+||-.+.
T Consensus 17 ~~l~~~l~~~g~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGGS 96 (377)
T cd08176 17 KEIGDELKNLGFKKALIVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVKPNPTITNVKDGLAVFKKEGCDFIISIGGGS 96 (377)
T ss_pred HHHHHHHHHhCCCeEEEECCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCcH
Confidence 456677888888888777744333335678899999998987655444554556678899999999999999996654
Q ss_pred hhhHHHHHH
Q 003275 139 PDTGLTIFS 147 (834)
Q Consensus 139 ~~~~~~i~~ 147 (834)
.-|+.+.+.
T Consensus 97 ~iD~aK~ia 105 (377)
T cd08176 97 PHDCAKAIG 105 (377)
T ss_pred HHHHHHHHH
Confidence 345555543
No 335
>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.
Probab=70.05 E-value=71 Score=30.57 Aligned_cols=87 Identities=9% Similarity=-0.068 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcC--CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEE
Q 003275 57 YYQMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKK--RAKISYKAPFSPGASRSAINSLLVGANLMESRVFV 134 (834)
Q Consensus 57 ~~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~--g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~viv 134 (834)
...+..+.+.....+ .++.++.... +.++.+.+.+++. |++|+... . ..++.+-...+.+|.+++||+++
T Consensus 34 ~dl~~~l~~~~~~~~-~~vfllG~~~----~v~~~~~~~l~~~yP~l~i~g~~--g-~f~~~~~~~i~~~I~~s~~dil~ 105 (177)
T TIGR00696 34 PDLMEELCQRAGKEK-LPIFLYGGKP----DVLQQLKVKLIKEYPKLKIVGAF--G-PLEPEERKAALAKIARSGAGIVF 105 (177)
T ss_pred HHHHHHHHHHHHHcC-CeEEEECCCH----HHHHHHHHHHHHHCCCCEEEEEC--C-CCChHHHHHHHHHHHHcCCCEEE
Confidence 345566666666677 4666776544 3566666666665 77887752 1 12345557789999999999999
Q ss_pred EEeChhhHHHHHHHHHh
Q 003275 135 VHVNPDTGLTIFSVAKS 151 (834)
Q Consensus 135 l~~~~~~~~~i~~~a~~ 151 (834)
+.+..+.-..++.+.+.
T Consensus 106 VglG~PkQE~~~~~~~~ 122 (177)
T TIGR00696 106 VGLGCPKQEIWMRNHRH 122 (177)
T ss_pred EEcCCcHhHHHHHHhHH
Confidence 99888777777765543
No 336
>cd08191 HHD 6-hydroxyhexanoate dehydrogenase (HHD) catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. 6-hydroxyhexanoate dehydrogenase (HHD). The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. Some bacteria can grow on cyclic ketones, cyclohexylamine, and alcohols as sole carbon source. Cyclohexylamine is an insecticide and antiseptic in various industries and is considered a possible environmental pollutant. The degradation of these chemical compounds are through the cyclohexanol and cyclohexanone biological oxidation pathway. The intermediates of this pathway include cyclohexanol, cyclohexanone, e-caprolactone, 6-hydroxyhexanoate, 6-oxohexanoate and adipate. The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate.
Probab=69.45 E-value=24 Score=38.68 Aligned_cols=89 Identities=13% Similarity=0.051 Sum_probs=60.2
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.++++.+| +++.+|+....+.....+.+.+.+++.|+++.....+.+..+..++...+...++.++|+||-.+.
T Consensus 12 ~~l~~~~~~~g-~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~~~~~~v~~~~~~~~~~~~D~IIaiGGGS 90 (386)
T cd08191 12 RQLPRLAARLG-SRALIVTDERMAGTPVFAELVQALAAAGVEVEVFDGVLPDLPRSELCDAASAAARAGPDVIIGLGGGS 90 (386)
T ss_pred HHHHHHHHHcC-CeEEEEECcchhhcchHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 44667788888 888878743333346788899999999987654434433334566777788888889999987654
Q ss_pred hhhHHHHHHHHH
Q 003275 139 PDTGLTIFSVAK 150 (834)
Q Consensus 139 ~~~~~~i~~~a~ 150 (834)
.-|+.+++....
T Consensus 91 ~iD~aK~ia~~~ 102 (386)
T cd08191 91 CIDLAKIAGLLL 102 (386)
T ss_pred HHHHHHHHHHHH
Confidence 446666554433
No 337
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=69.00 E-value=1e+02 Score=28.95 Aligned_cols=70 Identities=16% Similarity=0.148 Sum_probs=48.0
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. ++..+++..|.+|++|+++...... ...+ .+.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~ 80 (196)
T cd08450 13 QWLPEVLPILREEHP-DLDVELSS-------LFSPQLAEALMRGKLDVAFMRPEIQ---SDGI-DYQLLLKEPLIVVLPA 80 (196)
T ss_pred hhHHHHHHHHHhhCC-CcEEEEEe-------cChHHHHHHHhcCCccEEEEeCCCC---CCCc-EEEEEEccceEEEecC
Confidence 455788888888776 34566654 4567899999999999998643221 1222 2466777788888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~~ 82 (196)
T cd08450 81 DH 82 (196)
T ss_pred CC
Confidence 65
No 338
>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 3LFT_A 3LKV_A.
Probab=68.38 E-value=62 Score=33.91 Aligned_cols=118 Identities=13% Similarity=0.187 Sum_probs=66.0
Q ss_pred hhhHHHHHHhhccCCccEEecccCCCCCCC----CCCC--ceEEccCChHHHHHHHHHHHHHc--CCeEEEEEEEcCCc-
Q 003275 14 SGIAHVISHVVNELNVPLLSFGATDPTLTS----LQYP--YFLRTTQSDYYQMHAVADLVEYY--GWREVIAIFVDDDY- 84 (834)
Q Consensus 14 S~~~~~~~~~~~~~~vP~Is~~at~~~ls~----~~~p--~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~~d~~~- 84 (834)
+..+..+....... +|+|..+.++|.... ...| ++.-+. +..-...-.++++.+ +-++++++|.++.-
T Consensus 68 t~aa~~~~~~~~~~-iPVVf~~V~dp~~~~l~~~~~~~~~nvTGv~--~~~~~~~~l~l~~~l~P~~k~igvl~~~~~~~ 144 (294)
T PF04392_consen 68 TPAAQALAKHLKDD-IPVVFCGVSDPVGAGLVDSLDRPGKNVTGVS--ERPPIEKQLELIKKLFPDAKRIGVLYDPSEPN 144 (294)
T ss_dssp HHHHHHHHHH-SS--S-EEEECES-TTTTTS-S-SSS--SSEEEEE--E---HHHHHHHHHHHSTT--EEEEEEETT-HH
T ss_pred cHHHHHHHHhcCCC-cEEEEEeccChhhhhccccccCCCCCEEEEE--CCcCHHHHHHHHHHhCCCCCEEEEEecCCCcc
Confidence 34455555544433 999987777776432 2222 443333 333445555666554 46999999976643
Q ss_pred ccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003275 85 GRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP 139 (834)
Q Consensus 85 g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~ 139 (834)
+....+.+.+++++.|+++... .++ +..++...+.++.. +.+++++..+.
T Consensus 145 ~~~~~~~~~~~a~~~g~~l~~~-~v~---~~~~~~~~~~~l~~-~~da~~~~~~~ 194 (294)
T PF04392_consen 145 SVAQIEQLRKAAKKLGIELVEI-PVP---SSEDLEQALEALAE-KVDALYLLPDN 194 (294)
T ss_dssp HHHHHHHHHHHHHHTT-EEEEE-EES---SGGGHHHHHHHHCT-T-SEEEE-S-H
T ss_pred HHHHHHHHHHHHHHcCCEEEEE-ecC---cHhHHHHHHHHhhc-cCCEEEEECCc
Confidence 4566888899999999987643 333 34678888888854 56888776543
No 339
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=68.20 E-value=14 Score=34.72 Aligned_cols=102 Identities=16% Similarity=0.201 Sum_probs=58.7
Q ss_pred CCCChhhhhcCCCCeeEeeCchhhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCcc
Q 003275 590 QIEGIDSLISSTEPIGVQDGSFAWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCE 669 (834)
Q Consensus 590 ~i~s~~dL~~~~~~v~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~ 669 (834)
.+++++||.+ +.+|+...-.....||.+ .+.+ .+++.....-|..-.+ |-.|++++-......+.++ +
T Consensus 57 ~~~~~~~l~~-~~rIATkyp~l~~~yf~~-~g~~-~~ii~l~GsvE~ap~~------glAD~IvDiv~TG~TLr~N---g 124 (163)
T PF01634_consen 57 PYKSVEDLKA-GLRIATKYPNLTRRYFAE-KGIN-VEIIKLSGSVELAPPL------GLADAIVDIVETGTTLRAN---G 124 (163)
T ss_dssp CGCCGGGGSS-TEEEEES-HHHHHHHHHH-CT-E-EEEEE-SS-TTHHHHT------TSSSEEEEEESSSHHHHHT---T
T ss_pred CCCCHHHhcc-CCEEEECCHHHHHHHHHH-cCCc-EEEEEccCCccccCCC------CCCCEEEEeccCcHHHHHC---C
Confidence 4677788863 667888777778888854 4444 5566655555544333 6789999877665555444 5
Q ss_pred EEEeCCcccccceEEEEcCCCc--chHHHHHHHHhhh
Q 003275 670 FRTVGQEFTKSGWGFAFQRDSP--LAIDLSTAILQLS 704 (834)
Q Consensus 670 l~~v~~~~~~~~~~~~~~k~sp--l~~~~~~~i~~l~ 704 (834)
|..++..+.+... +...+.+- -.+.++..+.+|.
T Consensus 125 L~~i~~i~~s~a~-LI~n~~~~~~k~~~i~~l~~~l~ 160 (163)
T PF01634_consen 125 LKEIETILESSAR-LIANKASLKEKEEKIDELVTRLR 160 (163)
T ss_dssp EEEEEEEEEEEEE-EEEEHHHHHHCHHHHHHHHHHHH
T ss_pred CEEeEEEEEEEEE-EEEcCccchhhHHHHHHHHHHHH
Confidence 7777555554443 44444432 2334555555543
No 340
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=67.29 E-value=24 Score=35.13 Aligned_cols=103 Identities=17% Similarity=0.190 Sum_probs=48.9
Q ss_pred CCCeeEeeCchhhHHHHhhhccccc--ceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEe--CC-
Q 003275 601 TEPIGVQDGSFAWNYLVDELKIAES--RLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTV--GQ- 675 (834)
Q Consensus 601 ~~~v~~~~~s~~~~~l~~~~~~~~~--~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v--~~- 675 (834)
|.+||+-..|.-+..+.+.. +... .+++. +..++++.+.+ |.+||.+.....+. .. ..++..+ ..
T Consensus 114 GmRVGiD~~S~Dq~~LT~~~-~~gk~Ve~Vei-~Y~q~~~~l~~----g~IDA~IWN~d~i~--~~--~~~l~~~~l~~~ 183 (232)
T PF14503_consen 114 GMRVGIDPSSIDQKILTEAE-FEGKNVEFVEI-PYNQLLELLRS----GEIDAAIWNYDEIE--DK--NFGLKYVPLKDD 183 (232)
T ss_dssp --EEEE-TT-HHHHHHHHHH-HTTS--EEEE---HHHHHHHHHH----TS--EEEEE--HHC--CH--HCTEEEEE--SS
T ss_pred eeEeecCCCCccHHHHHHHH-hCCCceEEEEe-cHHHHHHHHHC----CCccEEEECCcccc--cc--cCCeeEEeCCch
Confidence 78899999887777775432 2222 34444 67899999999 99999999866211 11 1233332 22
Q ss_pred -ccc-ccceEEEEcCCCc-chHHHHHHHHhhhccccHHHHHHhhc
Q 003275 676 -EFT-KSGWGFAFQRDSP-LAIDLSTAILQLSENGDLQKIHNKWL 717 (834)
Q Consensus 676 -~~~-~~~~~~~~~k~sp-l~~~~~~~i~~l~e~G~~~~i~~kw~ 717 (834)
... ...-.+..+++.+ +...+++.| ....+-+++++-.
T Consensus 184 ~~~~~~seAVivi~~~~~~i~~ll~~~i----d~~~vl~iQ~~V~ 224 (232)
T PF14503_consen 184 PMSKDASEAVIVIRKDNEPIKALLRKLI----DVEKVLEIQKKVL 224 (232)
T ss_dssp CHHHHTT-EEEEEETT-HHHHHHHHHH------HHHHHHHHHHHH
T ss_pred HHHHhcCeeEEEEeCCCHHHHHHHHHhc----CHHHHHHHHHHHH
Confidence 111 2234567788775 444443333 3334445555443
No 341
>PLN02245 ATP phosphoribosyl transferase
Probab=66.82 E-value=45 Score=36.11 Aligned_cols=104 Identities=12% Similarity=0.038 Sum_probs=60.6
Q ss_pred CCCChhhhhc-------CCCCeeEeeCchhhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHH
Q 003275 590 QIEGIDSLIS-------STEPIGVQDGSFAWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELF 662 (834)
Q Consensus 590 ~i~s~~dL~~-------~~~~v~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~ 662 (834)
.+++++||.. ..++|+...-.....||. +.++...+++.....-|. +-.. |-.|++++-......+
T Consensus 178 ~~~s~~dL~g~~~~~~~~~~RIATkYp~ltr~ff~-~~Gv~~v~Iv~l~GAvE~--AP~l----GlADaIvDIVsTGtTL 250 (403)
T PLN02245 178 NINSLKELAQMPQWTEERPLRVVTGFTYLGPKFMK-DNGFKHVTFSTADGALEA--APAM----GIADAILDLVSSGTTL 250 (403)
T ss_pred ccCCHHHhcccccccccCceEEEeCCHHHHHHHHH-HcCCCeEEEEECcCceec--cccc----CchhhhcchhccHHHH
Confidence 5778888862 015677777777888885 456644566666555554 2222 6778888766665555
Q ss_pred hhcCCccEEEeC-CcccccceEEEEcCCCc-----chHHHHHHHHhh
Q 003275 663 MSKTNCEFRTVG-QEFTKSGWGFAFQRDSP-----LAIDLSTAILQL 703 (834)
Q Consensus 663 ~~~~~~~l~~v~-~~~~~~~~~~~~~k~sp-----l~~~~~~~i~~l 703 (834)
.++ +|.+++ +.+....-.+...+++. -++.++..+.+|
T Consensus 251 raN---gLk~i~~~~Il~S~A~LIan~~sl~~~~~~~~~i~~ll~rl 294 (403)
T PLN02245 251 REN---NLKEIEGGVVLESQAVLVASRRALLERKGALEVVHEILERL 294 (403)
T ss_pred HHC---CCEEccCceEEEEEEEEEEecchhhcchhHHHHHHHHHHHH
Confidence 444 678885 33334444455556543 223455555544
No 342
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=66.57 E-value=1.2e+02 Score=28.82 Aligned_cols=70 Identities=10% Similarity=0.066 Sum_probs=45.2
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.++.+ .+++++.. ++-++++.+|.+|++|+++....... ..+ .+.++....++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~~~---~~l-~~~~l~~~~~~~~~~~ 81 (198)
T cd08485 14 HTLPLLLRQLLSVAP-SATVSLTQ-------MSKNRQIEALDAGTIDIGFGRFYPYQ---EGV-VVRNVTNERLFLGAQK 81 (198)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEE-------CCHHHHHHHHHcCCccEEEecCCCCC---CCe-EEEEeeccceEEEeCC
Confidence 445678888877664 45566653 45678999999999999986432211 222 2456667777776655
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 82 ~~ 83 (198)
T cd08485 82 SR 83 (198)
T ss_pred CC
Confidence 44
No 343
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=66.55 E-value=1.6e+02 Score=30.27 Aligned_cols=84 Identities=8% Similarity=-0.043 Sum_probs=57.0
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
++.++||+... ....+-.+++..+.+..+ .+.+.+.. +...++++.|.+|++|+++..
T Consensus 88 ~~~l~Ig~~~~--------------~~~~~l~~~l~~f~~~~P-~v~v~~~~-------~~~~~~~~~l~~g~~Dl~i~~ 145 (275)
T PRK03601 88 HNELSIGASAS--------------LWECMLTPWLGRLYQNQE-ALQFEARI-------AQRQSLVKQLHERQLDLLITT 145 (275)
T ss_pred CceEEEeccHH--------------HHHHHHHHHHHHHHHhCC-CcEEEEEE-------CChHHHHHHHHcCCCCEEEEc
Confidence 35789998321 113556788888887665 34566554 557889999999999999974
Q ss_pred eeeecCceeeEEecceeeeceEEEEEecCC
Q 003275 453 ITIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 453 ~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
..... ..+ ...|+....+++++++..
T Consensus 146 ~~~~~---~~l-~~~~l~~~~~~~v~~~~~ 171 (275)
T PRK03601 146 EAPKM---DEF-SSQLLGHFTLALYTSAPS 171 (275)
T ss_pred CCCcc---CCc-cEEEecceeEEEEecCch
Confidence 43322 123 356888888999887655
No 344
>cd08187 BDH Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. The butanol dehydrogenase (BDH) is involved in the final step of the butanol formation pathway in anaerobic micro-organism. Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. Activity in the reverse direction was 50-fold lower than that in the forward direction. The NADH-BDH had higher activity with longer chained aldehydes and was inhibited by metabolites containing an adenine moiety. This protein family belongs to the so-called iron-containing alcohol dehydrogenase superfamily. Since members of this superfamily use different divalent ions, preferentially iron or zinc, it has been suggested to be renamed to family III metal-dependent polyol dehydrogenases.
Probab=66.23 E-value=26 Score=38.43 Aligned_cols=87 Identities=6% Similarity=0.051 Sum_probs=60.7
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCc-ccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDY-GRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~-g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~- 138 (834)
..+.++++.++ +++.+|.....+ .....+.+.+.+++.|+++.....+..+.+.+++...+..++..++|+||-.+.
T Consensus 18 ~~l~~~~~~~~-~r~livt~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 96 (382)
T cd08187 18 SELGKELKKYG-KKVLLVYGGGSIKKNGLYDRVIASLKEAGIEVVELGGVEPNPRLETVREGIELCKEEKVDFILAVGGG 96 (382)
T ss_pred HHHHHHHHHhC-CEEEEEeCCcHHHhcCcHHHHHHHHHHcCCeEEEECCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCh
Confidence 45667777775 888777654333 234578899999999988765445555556678888999999999999986654
Q ss_pred -hhhHHHHHHH
Q 003275 139 -PDTGLTIFSV 148 (834)
Q Consensus 139 -~~~~~~i~~~ 148 (834)
.-|+.+++..
T Consensus 97 S~iD~aK~ia~ 107 (382)
T cd08187 97 SVIDSAKAIAA 107 (382)
T ss_pred HHHHHHHHHHh
Confidence 3455555433
No 345
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=66.16 E-value=1.2e+02 Score=28.61 Aligned_cols=70 Identities=10% Similarity=0.116 Sum_probs=47.9
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
++-.+++..+.++.+ .+++++.. +.+..+.++|.+|++|+++...... ...+ -+.++....++++++.
T Consensus 14 ~~l~~~i~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~ 81 (198)
T cd08446 14 DTVPRLLRAFLTARP-DVTVSLHN-------MTKDEQIEALRAGRIHIGFGRFYPV---EPDI-AVENVAQERLYLAVPK 81 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEee-------CCHHHHHHHHHCCCccEEEEecCCC---CCCc-eeEEeeeccEEEEEeC
Confidence 355778888888776 45566654 5678899999999999998633221 1112 2556777888888876
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 82 ~~ 83 (198)
T cd08446 82 SH 83 (198)
T ss_pred CC
Confidence 65
No 346
>cd08182 HEPD Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP). Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP) with either NADH or NADPH as a cofactor. NADH is the preferred cofactor. PnAA is a biosynthetic intermediate for several phosphonates such as the antibiotic fosfomycin, phosphinothricin tripeptide (PTT), and 2-aminoethylphosphonate (AEP). This enzyme is named PhpC in PTT biosynthesis pathway in Streptomyces hygroscopicus and S. viridochromogenes. Members of this family are only found in bacteria.
Probab=66.15 E-value=28 Score=37.89 Aligned_cols=86 Identities=9% Similarity=-0.013 Sum_probs=61.0
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.+++..+|.+++.+|+....+ ..+.+.+.+++.|+.+.....+..+.+.+.+...+..+++.++|+||-.+.
T Consensus 12 ~~l~~~~~~~g~~~~livtd~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIavGGGs 88 (367)
T cd08182 12 AKLPSLLKGLGGKRVLLVTGPRSA---IASGLTDILKPLGTLVVVFDDVQPNPDLEDLAAGIRLLREFGPDAVLAVGGGS 88 (367)
T ss_pred HHHHHHHHhcCCCeEEEEeCchHH---HHHHHHHHHHHcCCeEEEEcCcCCCcCHHHHHHHHHHHHhcCcCEEEEeCCcH
Confidence 446677888888999888754443 456678888888877654444555556678888888998899999986654
Q ss_pred hhhHHHHHHHH
Q 003275 139 PDTGLTIFSVA 149 (834)
Q Consensus 139 ~~~~~~i~~~a 149 (834)
.-|+.+++...
T Consensus 89 ~~D~aK~ia~~ 99 (367)
T cd08182 89 VLDTAKALAAL 99 (367)
T ss_pred HHHHHHHHHHH
Confidence 45666665544
No 347
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=66.10 E-value=1.2e+02 Score=28.57 Aligned_cols=71 Identities=13% Similarity=0.055 Sum_probs=46.9
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. .+.+.++.+|.+|++|+++....... ...+ .+.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~~--~~~~-~~~~l~~~~~~~v~~~ 81 (195)
T cd08431 13 QPLYPLIAEFYQLNK-ATRIRLSE-------EVLGGTWDALASGRADLVIGATGELP--PGGV-KTRPLGEVEFVFAVAP 81 (195)
T ss_pred HHHHHHHHHHHHHCC-CCceEEEE-------eccchHHHHHhCCCCCEEEEecCCCC--CCce-EEEecccceEEEEEcC
Confidence 556788899988875 34566653 44678899999999999986321111 1122 3566667777777776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 82 ~h 83 (195)
T cd08431 82 NH 83 (195)
T ss_pred CC
Confidence 54
No 348
>cd07766 DHQ_Fe-ADH Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH). Dehydroquinate synthase-like. This superfamily divides into two subgroups: the dehydroquinate synthase-like, and a large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. Dehydroquinate synthase-like group includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. The alcohol dehydrogenases in this superfamily contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alc
Probab=65.60 E-value=76 Score=33.93 Aligned_cols=100 Identities=9% Similarity=0.070 Sum_probs=65.6
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.+.++.+|.+++.+|+....+- ...+.+.+.+++. +++........+.+.+++...+..+++.++|+||-.+.
T Consensus 12 ~~l~~~~~~~g~~~~liv~~~~~~~-~~~~~v~~~l~~~-~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs 89 (332)
T cd07766 12 EKIGEEIKRGGFDRALVVSDEGVVK-GVGEKVADSLKKL-IAVHIFDGVGPNPTFEEVKEAVERARAAEVDAVIAVGGGS 89 (332)
T ss_pred HHHHHHHHhcCCCeEEEEeCCchhh-hHHHHHHHHHHhc-CcEEEeCCcCCCcCHHHHHHHHHHHHhcCcCEEEEeCCch
Confidence 3456677788889998888544333 6678888888876 65543333433346678889999998889999986654
Q ss_pred hhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 139 PDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 139 ~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
.-|+.+++......| ..++-|.|.
T Consensus 90 ~~D~aK~ia~~~~~~---~p~i~iPTt 113 (332)
T cd07766 90 TLDTAKAVAALLNRG---LPIIIVPTT 113 (332)
T ss_pred HHHHHHHHHHHhcCC---CCEEEEeCC
Confidence 446666654443323 345556554
No 349
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=64.47 E-value=27 Score=35.77 Aligned_cols=77 Identities=6% Similarity=0.055 Sum_probs=53.5
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhhHHHHHHHHHh
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-PDTGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-~~~~~~i~~~a~~ 151 (834)
|++|.. ++.|.......+.+++++.|.++..... ..+.......++.+...+.|.||+... ......+++.+++
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~l~~~~~~~vdgii~~~~~~~~~~~~i~~~~~ 78 (273)
T cd06305 2 IAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYDA---GGDDAKQADQIDQAIAQKVDAIIIQHGRAEVLKPWVKRALD 78 (273)
T ss_pred eEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEecCChhhhHHHHHHHHH
Confidence 566665 5677778899999999999999876321 223344456677776778999988643 3344566778887
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.|+
T Consensus 79 ~~i 81 (273)
T cd06305 79 AGI 81 (273)
T ss_pred cCC
Confidence 775
No 350
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=64.41 E-value=4.7 Score=49.25 Aligned_cols=55 Identities=13% Similarity=0.306 Sum_probs=47.3
Q ss_pred cchhhHHHHHHHHhhccC--CCcccccchhhhHHHHHHHHHHhhhccccceeeEEEE
Q 003275 530 QQLVTIFWFSFSTMFFSH--RENTVSSLGRVVLIVWLFVVLIINSSYTASLTSILTV 584 (834)
Q Consensus 530 ~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s~Lt~ 584 (834)
.+...++||++.++...| .-.|.+...|++.++|+++++++.++..+++++++..
T Consensus 249 ~~Yi~slYwai~TmtTVGYGDi~p~t~~E~i~~i~~ml~g~~~~a~~ig~i~~li~~ 305 (823)
T PLN03192 249 IRYISAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE 305 (823)
T ss_pred HHHHHHHHHHHHHHhhccCCCcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346668999999998665 5589999999999999999999999999999987654
No 351
>cd08186 Fe-ADH8 Iron-containing alcohol dehydrogenase. Type III Iron-containing alcohol dehydrogenases (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. The ADH of hyperthermophilic archaeon Thermococcus hydrothermalis oxidizes a series of primary aliphatic and aromatic alcohols preferentially from C2 to C8 but is also active towards methanol and glycerol and stereospecific for monoterpenes. It was suggested that the type III ADHs in microorganisms are involved in acetaldehyde detoxication rather than in alcohol turnover.
Probab=63.94 E-value=32 Score=37.69 Aligned_cols=89 Identities=8% Similarity=0.135 Sum_probs=61.7
Q ss_pred HHHHHHHHHc---CCeEEEEEEEcCCcc-cchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEE
Q 003275 61 HAVADLVEYY---GWREVIAIFVDDDYG-RNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVH 136 (834)
Q Consensus 61 ~aia~ll~~~---~W~~v~iI~~d~~~g-~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~ 136 (834)
..+.++++.+ |.+++.+|+....+. .+..+.+.+.+++.|+++.....+.++.+.+++...+..+++.++|+||-.
T Consensus 12 ~~l~~~l~~~~~~g~kr~livtd~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIai 91 (383)
T cd08186 12 EKIGEILKDLKSKGISKVLLVTGKSAYKKSGAWDKVEPALDEHGIEYVLYNKVTPNPTVDQVDEAAKLGREFGAQAVIAI 91 (383)
T ss_pred HHHHHHHHHhcccCCCEEEEEcCccHHhhcChHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence 4455667666 778888887544333 344688999999999876544445555566888999999999999999866
Q ss_pred e--ChhhHHHHHHHH
Q 003275 137 V--NPDTGLTIFSVA 149 (834)
Q Consensus 137 ~--~~~~~~~i~~~a 149 (834)
+ +.-|+.+++...
T Consensus 92 GGGS~iD~aK~ia~~ 106 (383)
T cd08186 92 GGGSPIDSAKSAAIL 106 (383)
T ss_pred CCccHHHHHHHHHHH
Confidence 4 344666655443
No 352
>cd08171 GlyDH-like2 Glycerol dehydrogenase-like. Glycerol dehydrogenases-like. The proteins in this family have not been characterized, but they show sequence homology with glycerol dehydrogenase. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=63.90 E-value=27 Score=37.59 Aligned_cols=86 Identities=12% Similarity=0.161 Sum_probs=59.2
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
.-+.+.++.++ +++.+|+....+ ....+.+.+.+++.|+.+.....+..+.+.+++.......++.++|+||-.+.
T Consensus 12 ~~l~~~~~~~~-~r~liv~d~~~~-~~~~~~v~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~iiavGGGs 89 (345)
T cd08171 12 KKIPEVCEKYG-KKVVVIGGKTAL-AAAKDKIKAALEQSGIEITDFIWYGGESTYENVERLKKNPAVQEADMIFAVGGGK 89 (345)
T ss_pred HHHHHHHHhcC-CEEEEEeCHHHH-HHHHHHHHHHHHHCCCeEEEEEecCCCCCHHHHHHHHHHHhhcCCCEEEEeCCcH
Confidence 44566677777 888777754433 34577888889888887654444544556677888888888889999987654
Q ss_pred hhhHHHHHHH
Q 003275 139 PDTGLTIFSV 148 (834)
Q Consensus 139 ~~~~~~i~~~ 148 (834)
.-|+.+++..
T Consensus 90 ~~D~aK~ia~ 99 (345)
T cd08171 90 AIDTVKVLAD 99 (345)
T ss_pred HHHHHHHHHH
Confidence 4466665543
No 353
>PF07302 AroM: AroM protein; InterPro: IPR010843 This family consists of several bacterial and archaeal AroM proteins. In Escherichia coli the aroM gene is cotranscribed with aroL []. The function of this family is unknown.
Probab=63.89 E-value=50 Score=32.64 Aligned_cols=115 Identities=16% Similarity=0.095 Sum_probs=71.1
Q ss_pred hccCCccEEecccCC--CCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCc
Q 003275 24 VNELNVPLLSFGATD--PTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRA 101 (834)
Q Consensus 24 ~~~~~vP~Is~~at~--~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~ 101 (834)
++..++..|-.-||. |.+.... + ++ -++......++.++.. .++++|....+ -.+...+.++..+.
T Consensus 83 le~~G~d~illlCTG~F~~l~~~~-~-ll---eP~ril~~lV~al~~~---~~vGVivP~~e----Q~~~~~~kW~~l~~ 150 (221)
T PF07302_consen 83 LEAQGYDVILLLCTGEFPGLTARN-P-LL---EPDRILPPLVAALVGG---HQVGVIVPLPE----QIAQQAEKWQPLGN 150 (221)
T ss_pred HHHCCCCEEEEeccCCCCCCCCCc-c-ee---ehHHhHHHHHHHhcCC---CeEEEEecCHH----HHHHHHHHHHhcCC
Confidence 334445555444443 3444322 2 22 2243334444444433 79999997654 34444455566666
Q ss_pred EEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe--ChhhHHHHHHHHH
Q 003275 102 KISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV--NPDTGLTIFSVAK 150 (834)
Q Consensus 102 ~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~--~~~~~~~i~~~a~ 150 (834)
.+.+...-|...+..++...-+++++.++|+||++| +....+.+++++.
T Consensus 151 ~~~~a~asPy~~~~~~l~~Aa~~L~~~gadlIvLDCmGYt~~~r~~~~~~~ 201 (221)
T PF07302_consen 151 PVVVAAASPYEGDEEELAAAARELAEQGADLIVLDCMGYTQEMRDIVQRAL 201 (221)
T ss_pred CeEEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEECCCCCHHHHHHHHHHh
Confidence 666666666545678999999999999999999996 5667777776544
No 354
>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=63.84 E-value=76 Score=32.10 Aligned_cols=122 Identities=8% Similarity=0.032 Sum_probs=76.4
Q ss_pred HHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHH--cCCeEEEEEEEcC-CcccchHHHHHHHH
Q 003275 20 ISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEY--YGWREVIAIFVDD-DYGRNGISVLGDAL 96 (834)
Q Consensus 20 ~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~--~~W~~v~iI~~d~-~~g~~~~~~l~~~l 96 (834)
........++|++...-..+. ...+++ ...++..-+..+++.+.. .|-+++++|.... ..+....+.+.+++
T Consensus 68 ~~~~~~~~~~PvV~i~~~~~~--~~~~~~---V~~D~~~~~~~a~~~L~~~~~G~~~Ia~i~~~~~~~~~~R~~gf~~~l 142 (247)
T cd06276 68 YFLLKKIPKEKLLILDHSIPE--GGEYSS---VAQDFEKAIYNALQEGLEKLKKYKKLILVFPNKTAIPKEIKRGFERFC 142 (247)
T ss_pred HHHHhccCCCCEEEEcCcCCC--CCCCCe---EEEccHHHHHHHHHHHHHHhcCCCEEEEEecCccHhHHHHHHHHHHHH
Confidence 334555578899886543221 112232 445666667777788777 8999999997543 34556688999999
Q ss_pred hcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCCCCCCeE
Q 003275 97 SKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGMTAGSYV 160 (834)
Q Consensus 97 ~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~~~~~~v 160 (834)
++.|+.... .. ... . . .+ .++++ |++.+...+..+++.+++.|+..+.-+
T Consensus 143 ~~~g~~~~~---~~-~~~-~---~---~~--~~~~a-i~~~~d~~A~g~~~~l~~~g~~iP~di 192 (247)
T cd06276 143 KDYNIETEI---IN-DYE-N---R---EI--EKGDL-YIILSDTDLVFLIKKARESGLLLGKDI 192 (247)
T ss_pred HHcCCCccc---cc-ccc-h---h---hc--cCCcE-EEEeCHHHHHHHHHHHHHcCCcCCcee
Confidence 999976431 11 000 0 0 01 12354 566677888899999999998655433
No 355
>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=63.81 E-value=24 Score=35.69 Aligned_cols=77 Identities=12% Similarity=0.057 Sum_probs=52.6
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
++++... +.++......+.+++++.|+.+.....- .+.+.....++++.+.+++.+|+..........+..+.+.
T Consensus 2 ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~~~---~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~l~~~ 78 (264)
T cd01537 2 IGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLANSQ---NDAEKQLSALENLIARGVDGIIIAPSDLTAPTIVKLARKA 78 (264)
T ss_pred eEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEecCCCcchhHHHHhhhc
Confidence 5677754 6688888999999999999887654322 2334566777777777899888876543333356666665
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
+.
T Consensus 79 ~i 80 (264)
T cd01537 79 GI 80 (264)
T ss_pred CC
Confidence 54
No 356
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=63.06 E-value=72 Score=31.78 Aligned_cols=92 Identities=15% Similarity=0.151 Sum_probs=52.3
Q ss_pred CCCChhhhhc--------CC--CCeeEeeCchhhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhH
Q 003275 590 QIEGIDSLIS--------ST--EPIGVQDGSFAWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYI 659 (834)
Q Consensus 590 ~i~s~~dL~~--------~~--~~v~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~ 659 (834)
.+++++||.. .+ .+|+...-.....||. ..+.+..+++.....-|..- .. |-.|++++-....
T Consensus 110 ~~~~~~dl~~~~~~~~~~~g~~~RIATkYp~it~~yf~-~~Gv~~~~Iv~l~GsvElaP--~~----GlAD~IvDivsTG 182 (228)
T PRK13583 110 DVDTMADLDDVAADFRARHGRRLRIATKYWRLTQQFLS-QKGVQDYRIVESLGATEGAP--AN----GSAEIIVDITSTG 182 (228)
T ss_pred ccCCHHHhhhhhhhhhhccCCceEEEeCCHHHHHHHHH-HcCCceeEEEECCCceeccc--cc----Ccchhhhhhhchh
Confidence 4566676641 12 4677777777788885 44554335666554444422 22 6777887766665
Q ss_pred HHHhhcCCccEEEeC-CcccccceEEEEcCCCc
Q 003275 660 ELFMSKTNCEFRTVG-QEFTKSGWGFAFQRDSP 691 (834)
Q Consensus 660 ~~~~~~~~~~l~~v~-~~~~~~~~~~~~~k~sp 691 (834)
....++ +|.+++ +.+..+.-.+...+.|.
T Consensus 183 ~TLr~N---gL~~i~~~~Il~SsA~LI~n~~s~ 212 (228)
T PRK13583 183 ETLRAN---HLKILSDGVILRSQACLVRARKAD 212 (228)
T ss_pred HHHHHC---CCEEecCceEEEEEEEEEEecccc
Confidence 554444 677886 23334444455566653
No 357
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=62.22 E-value=28 Score=35.75 Aligned_cols=78 Identities=8% Similarity=0.049 Sum_probs=54.7
Q ss_pred EEEEEEEc--CCcccchHHHHHHHHhc-CCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHH
Q 003275 74 EVIAIFVD--DDYGRNGISVLGDALSK-KRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSVA 149 (834)
Q Consensus 74 ~v~iI~~d--~~~g~~~~~~l~~~l~~-~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a 149 (834)
+|++|..+ +.|.......+.+++++ .|.++..... ..+.......++++.+.+.|.+++.... .....++..+
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~l 77 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGVELQFEDA---KNDVATQLSQVENFIAQGVDAIIVVPVDTAATAPIVKAA 77 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHHcCCcEEEEeCC---CCCHHHHHHHHHHHHHcCCCEEEEecCchhhhHHHHHHH
Confidence 36677754 67888888999999999 8998876432 1233556677888888889988886543 3345667777
Q ss_pred HhCCC
Q 003275 150 KSLGM 154 (834)
Q Consensus 150 ~~~g~ 154 (834)
.+.|.
T Consensus 78 ~~~~i 82 (272)
T cd06301 78 NAAGI 82 (272)
T ss_pred HHCCC
Confidence 77664
No 358
>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=62.10 E-value=31 Score=34.91 Aligned_cols=76 Identities=8% Similarity=-0.025 Sum_probs=54.2
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|+++..+ +.|.......+.+++++.|+.+..... ..+.......++++.+.+++.|++......... ++.+.+.
T Consensus 2 i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~~~~~~~d~iii~~~~~~~~~-~~~~~~~ 77 (264)
T cd06267 2 IGVIVPDISNPFFAELLRGIEEAAREAGYSVLLCNS---DEDPEKEREALELLLSRRVDGIILAPSRLDDEL-LEELAAL 77 (264)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHcCCEEEEEcC---CCCHHHHHHHHHHHHHcCcCEEEEecCCcchHH-HHHHHHc
Confidence 4566644 778888899999999999988765322 223345567777888888999988766555555 6677777
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|.
T Consensus 78 ~i 79 (264)
T cd06267 78 GI 79 (264)
T ss_pred CC
Confidence 75
No 359
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris
Probab=62.00 E-value=1.1e+02 Score=28.73 Aligned_cols=66 Identities=14% Similarity=0.014 Sum_probs=40.1
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+...++..+.+..+ .+.++... + + .+.++.+|++|+++...... ...+ .+.++....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~-------~--~-~~~~l~~g~~D~~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~ 77 (194)
T cd08432 13 RWLIPRLARFQARHP-DIDLRLST-------S--D-RLVDFAREGIDLAIRYGDGD---WPGL-EAERLMDEELVPVCSP 77 (194)
T ss_pred HHHHHHhHHHHHHCC-CeEEEEEe-------c--C-CccccccccccEEEEecCCC---CCCc-ceEEccCCcEEEecCH
Confidence 344567777777765 45566553 1 1 45678899999988632211 1122 3566777777777765
Q ss_pred C
Q 003275 481 Q 481 (834)
Q Consensus 481 ~ 481 (834)
.
T Consensus 78 ~ 78 (194)
T cd08432 78 A 78 (194)
T ss_pred H
Confidence 4
No 360
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=61.95 E-value=83 Score=37.17 Aligned_cols=67 Identities=15% Similarity=0.098 Sum_probs=45.7
Q ss_pred cCCeEEEEEEEcCC---------ccc---chHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe
Q 003275 70 YGWREVIAIFVDDD---------YGR---NGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV 137 (834)
Q Consensus 70 ~~W~~v~iI~~d~~---------~g~---~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~ 137 (834)
|..-+|++|..-|+ -|+ .....+...+++.|.++.....++. +...+...+.++.+ ++|+||..+
T Consensus 184 ~~~prv~vi~tG~El~~~~~~~~~g~i~dsn~~~l~~~l~~~g~~~~~~~~v~D--d~~~i~~~l~~~~~-~~D~iIttG 260 (633)
T PRK14498 184 YKKPRVGIISTGDELVEPGEPLKPGKIYDVNSYTLAAAVEEAGGEPVRYGIVPD--DEEELEAALRKALK-ECDLVLLSG 260 (633)
T ss_pred ecCcEEEEEecCccccCCCCCCCCCEEEEChHHHHHHHHHHCCCEEEEEEEeCC--CHHHHHHHHHHHHh-cCCEEEECC
Confidence 45567787765443 122 3466788889999999887766763 34677777777654 789998876
Q ss_pred Ch
Q 003275 138 NP 139 (834)
Q Consensus 138 ~~ 139 (834)
..
T Consensus 261 G~ 262 (633)
T PRK14498 261 GT 262 (633)
T ss_pred CC
Confidence 43
No 361
>cd06353 PBP1_BmpA_Med_like Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type I periplasmic sugar-binding protein-like fold.
Probab=61.25 E-value=58 Score=33.37 Aligned_cols=85 Identities=11% Similarity=0.011 Sum_probs=55.9
Q ss_pred EEEEEEE----cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003275 74 EVIAIFV----DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVA 149 (834)
Q Consensus 74 ~v~iI~~----d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a 149 (834)
+|+++++ |..|.....+.+.+..++.|+++.+.+..+ +..++.+.++++.+.++++||.++. .....+.+.|
T Consensus 1 kva~l~~g~~~D~~~n~~~~~G~~~~~~~~gv~~~~~e~~~---~~~~~~~~i~~~~~~g~dlIi~~g~-~~~~~~~~vA 76 (258)
T cd06353 1 KVAFVYVGPIGDQGWNYAHDEGRKAAEKALGVEVTYVENVP---EGADAERVLRELAAQGYDLIFGTSF-GFMDAALKVA 76 (258)
T ss_pred CEEEEEeCCCCccchhHHHHHHHHHHHHhcCCeEEEEecCC---chHhHHHHHHHHHHcCCCEEEECch-hhhHHHHHHH
Confidence 3677775 334555557788888788899988877664 3468889999998889999988443 2333344445
Q ss_pred HhCCCCCCCeEEEEeCC
Q 003275 150 KSLGMTAGSYVWIATDW 166 (834)
Q Consensus 150 ~~~g~~~~~~vwi~~~~ 166 (834)
.+- +.-.|+..+.
T Consensus 77 ~~~----p~~~F~~~d~ 89 (258)
T cd06353 77 KEY----PDVKFEHCSG 89 (258)
T ss_pred HHC----CCCEEEECCC
Confidence 542 3445666543
No 362
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=60.96 E-value=83 Score=31.87 Aligned_cols=89 Identities=8% Similarity=-0.020 Sum_probs=57.5
Q ss_pred hHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEE
Q 003275 56 DYYQMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGANLMESRVFV 134 (834)
Q Consensus 56 ~~~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~viv 134 (834)
....+..+.+.....| .+|.++..+.+ .++.+.+.+++. |+.|+....=. .+.++....+.+|.+++||+++
T Consensus 90 G~dl~~~ll~~~~~~~-~~v~llG~~~~----v~~~a~~~l~~~y~l~i~g~~~Gy--f~~~e~~~i~~~I~~s~~dil~ 162 (243)
T PRK03692 90 GADLWEALMARAGKEG-TPVFLVGGKPE----VLAQTEAKLRTQWNVNIVGSQDGY--FTPEQRQALFERIHASGAKIVT 162 (243)
T ss_pred hHHHHHHHHHHHHhcC-CeEEEECCCHH----HHHHHHHHHHHHhCCEEEEEeCCC--CCHHHHHHHHHHHHhcCCCEEE
Confidence 3344556666666667 56677775543 455555555433 77776543211 2345667789999999999999
Q ss_pred EEeChhhHHHHHHHHHh
Q 003275 135 VHVNPDTGLTIFSVAKS 151 (834)
Q Consensus 135 l~~~~~~~~~i~~~a~~ 151 (834)
+.+..+.-..++...++
T Consensus 163 VglG~PkQE~~~~~~~~ 179 (243)
T PRK03692 163 VAMGSPKQEIFMRDCRL 179 (243)
T ss_pred EECCCcHHHHHHHHHHH
Confidence 99887777777665544
No 363
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=60.87 E-value=65 Score=34.41 Aligned_cols=63 Identities=17% Similarity=0.192 Sum_probs=43.0
Q ss_pred CCCCCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCc-CEEEEecCCCCCCCChHHHHHHHHhCcccE
Q 003275 370 PNNGMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPV-PHNYIMYGNGKRNPIYNDIVQQVALNKFDA 448 (834)
Q Consensus 370 ~~~g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~-~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~ 448 (834)
|.+|++++++.. +|.. .-+.-.|++.+.+.+|+++ +++.. +-.-+...|.+|.+|+
T Consensus 25 ~~~~~~V~~~~~---~W~~-----------~~~~t~v~~~iLe~~GY~V~e~~~~---------~~~~~~~ala~GdiDv 81 (331)
T PRK11119 25 PGKGITVQPAQS---TIAE-----------ETFQTLLVSRALEKLGYDVNKPKEV---------DYNVFYTSIANGDATF 81 (331)
T ss_pred CCCCeEEEEeec---CccH-----------HHHHHHHHHHHHHHcCCceeeeccc---------CcHHHHHHHHcCCCeE
Confidence 456889999983 3321 1234577888888889885 44432 2367889999999999
Q ss_pred Eeeeeee
Q 003275 449 AVGDITI 455 (834)
Q Consensus 449 ~~~~~~i 455 (834)
.......
T Consensus 82 ~~~~W~P 88 (331)
T PRK11119 82 TAVNWFP 88 (331)
T ss_pred ehhhccc
Confidence 8765543
No 364
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=60.54 E-value=30 Score=37.60 Aligned_cols=97 Identities=13% Similarity=0.070 Sum_probs=65.3
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.+.++.+| +++.+|+....+ ....+.+.+.+++.|+++.+. .++.+.+.+.+...++.+++.++|+||-.+.
T Consensus 19 ~~l~~~l~~~g-~~~livtd~~~~-~~~~~~v~~~l~~~~~~~~~~-~~~~ep~~~~v~~~~~~~~~~~~d~IIavGGGs 95 (366)
T PRK09423 19 ARLGEYLKPLG-KRALVIADEFVL-GIVGDRVEASLKEAGLTVVFE-VFNGECSDNEIDRLVAIAEENGCDVVIGIGGGK 95 (366)
T ss_pred HHHHHHHHHcC-CEEEEEEChhHH-HHHHHHHHHHHHhCCCeEEEE-EeCCCCCHHHHHHHHHHHHhcCCCEEEEecChH
Confidence 44667778888 888888744443 346788888899888877543 3444556678888888888889999987654
Q ss_pred hhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 139 PDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 139 ~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
.-|+.+++... .+ ..++-|.|.
T Consensus 96 v~D~aK~iA~~--~~---~p~i~IPTt 117 (366)
T PRK09423 96 TLDTAKAVADY--LG---VPVVIVPTI 117 (366)
T ss_pred HHHHHHHHHHH--cC---CCEEEeCCc
Confidence 34555555422 23 345555553
No 365
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=59.31 E-value=1.6e+02 Score=27.81 Aligned_cols=70 Identities=13% Similarity=0.095 Sum_probs=46.8
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .++++... ++..++..+|.+|++|+++.... .....+. +.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~lv~~~ 80 (197)
T cd08452 13 EFLPPIVREYRKKFP-SVKVELRE-------LSSPDQVEELLKGRIDIGFLHPP---IQHTALH-IETVQSSPCVLALPK 80 (197)
T ss_pred hHHHHHHHHHHHHCC-CcEEEEEe-------cChHHHHHHHHCCCccEEEeeCC---CCCCCee-EEEeeeccEEEEEeC
Confidence 344678888888765 34566653 55788999999999999986321 1122232 456777777887776
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 81 ~h 82 (197)
T cd08452 81 QH 82 (197)
T ss_pred CC
Confidence 54
No 366
>cd08428 PBP2_IciA_ArgP The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold. The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-
Probab=59.31 E-value=1.6e+02 Score=27.72 Aligned_cols=66 Identities=5% Similarity=-0.025 Sum_probs=41.6
Q ss_pred eHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecC
Q 003275 403 CIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQ 481 (834)
Q Consensus 403 ~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~ 481 (834)
...++..+.++. .+++++.. ++.+.+.+++.+|++|+++..-. .....+ .+.++.....+++++..
T Consensus 15 l~~~l~~f~~~~--~v~l~l~~-------~~~~~~~~~l~~~~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~~~~~~ 80 (195)
T cd08428 15 FLPALAPVLKRE--RILLDLIV-------DDEDRTHDLLRDGEVVGCISTQA---QPMQGC-RSDYLGSMDYLLVASPD 80 (195)
T ss_pred hHHHHHHHHhCc--CeEEEEEe-------CCchhHHHHHHcCcceEEEEecC---CCCCCc-eeEEeeeeeEEEEECCc
Confidence 345677777763 55566654 45678999999999998774321 111122 35566677777776544
No 367
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=58.98 E-value=81 Score=32.31 Aligned_cols=71 Identities=17% Similarity=0.136 Sum_probs=42.0
Q ss_pred eHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCc-ccEEeeeeeeecCce---eeE-Eec-ceeeeceEEE
Q 003275 403 CIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNK-FDAAVGDITIVTNRT---KLV-DFT-QPYMESGLVV 476 (834)
Q Consensus 403 ~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~-~D~~~~~~~i~~~r~---~~v-dfs-~p~~~~~~~~ 476 (834)
.-++.+.+.++.|.++.+.+- + -..+..++..|. +|+.+++-....++. ..+ ..+ .+|....+++
T Consensus 41 ~~~l~~~Fe~~~g~~v~~~~~--------~-Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~~~a~n~lvl 111 (257)
T PRK10677 41 LQDIAAQYKKEKGVDVVSSFA--------S-SSTLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATRYTLLGNSLVV 111 (257)
T ss_pred HHHHHHHHHhhhCCeEEEEec--------c-cHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcchheeecCEEEE
Confidence 345666666666766444442 2 236778888877 999887542222221 122 121 3677888888
Q ss_pred EEecCC
Q 003275 477 VAPVQK 482 (834)
Q Consensus 477 vv~~~~ 482 (834)
++++..
T Consensus 112 ~~~~~~ 117 (257)
T PRK10677 112 VAPKAS 117 (257)
T ss_pred EEECCC
Confidence 888765
No 368
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=58.75 E-value=2.3e+02 Score=29.39 Aligned_cols=70 Identities=16% Similarity=0.151 Sum_probs=49.8
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+..+++..+.+..+ .+.+.+.. .+.++++..|.+|++|+++..... ....+. +.|+....+++++++
T Consensus 103 ~~l~~~~~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~ 170 (296)
T PRK09906 103 NLLPKVLPMFRLRHP-DTLIELVS-------LITTQQEEKLRRGELDVGFMRHPV---YSDEID-YLELLDEPLVVVLPV 170 (296)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEe-------CCcHHHHHHHHcCCeeEEEecCCC---CCCCce-EEEEecccEEEEecC
Confidence 445678888888775 45566553 456889999999999999874433 222333 468888899999887
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 171 ~~ 172 (296)
T PRK09906 171 DH 172 (296)
T ss_pred CC
Confidence 65
No 369
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=58.52 E-value=35 Score=35.03 Aligned_cols=79 Identities=6% Similarity=-0.004 Sum_probs=52.6
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|+.+ +.|....+..+.+++++.|..+.....-. ..+..+....++.+...++|.|++.....+....+..+.+.
T Consensus 2 Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~-~~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~~ 80 (268)
T cd06306 2 LCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGG-YPNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVAA 80 (268)
T ss_pred eEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecCCC-CCCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHHC
Confidence 5677754 66777888999999999999887642211 11224455677777788999998875433332245667776
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|+
T Consensus 81 gi 82 (268)
T cd06306 81 SI 82 (268)
T ss_pred CC
Confidence 65
No 370
>cd08183 Fe-ADH2 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. They are mainly found in bacteria.
Probab=57.39 E-value=48 Score=36.21 Aligned_cols=83 Identities=12% Similarity=0.081 Sum_probs=58.4
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.++++.++ +++.+|+..... ..+.+.+.+++.|+.+.... +..+.+.+++...+..++..++|+||-.+.
T Consensus 12 ~~l~~~l~~~~-~r~livtd~~~~---~~~~v~~~L~~~g~~~~~~~-~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 86 (374)
T cd08183 12 KELPALAAELG-RRVLLVTGASSL---RAAWLIEALRAAGIEVTHVV-VAGEPSVELVDAAVAEARNAGCDVVIAIGGGS 86 (374)
T ss_pred HHHHHHHHHcC-CcEEEEECCchH---HHHHHHHHHHHcCCeEEEec-CCCCcCHHHHHHHHHHHHhcCCCEEEEecCch
Confidence 34666777775 888878744333 67788889999998765433 334556678888999999999999987754
Q ss_pred hhhHHHHHHH
Q 003275 139 PDTGLTIFSV 148 (834)
Q Consensus 139 ~~~~~~i~~~ 148 (834)
.-|+.+++..
T Consensus 87 ~~D~aK~ia~ 96 (374)
T cd08183 87 VIDAGKAIAA 96 (374)
T ss_pred HHHHHHHHHH
Confidence 4466665544
No 371
>PRK10537 voltage-gated potassium channel; Provisional
Probab=57.31 E-value=8.8 Score=41.98 Aligned_cols=54 Identities=24% Similarity=0.324 Sum_probs=41.6
Q ss_pred CCCcchhhHHHHHHHHhhccC--CCcccccchhhhHHHHHHHHHHhhhccccceee
Q 003275 527 PPSQQLVTIFWFSFSTMFFSH--RENTVSSLGRVVLIVWLFVVLIINSSYTASLTS 580 (834)
Q Consensus 527 ~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~~~~~w~~~~lil~~~Yta~L~s 580 (834)
+...++..++||++.++...+ ...|.+..+|++.+++.++++.+..+..+.++.
T Consensus 164 ~~~~s~~dA~y~svvt~tTvGyGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~~ 219 (393)
T PRK10537 164 PPIESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIFG 219 (393)
T ss_pred cCCCCHHHHHHhhheeeecccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445689999999999887654 557899999999999999887766554444443
No 372
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=57.23 E-value=44 Score=34.02 Aligned_cols=77 Identities=9% Similarity=0.050 Sum_probs=51.7
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|.. .+.|.......+.+++++.|.++... ....+.......++++.+.++|.+++..........++.+.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~---~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (268)
T cd06289 2 IGLVINDLTNPFFAELAAGLEEVLEEAGYTVFLA---NSGEDVERQEQLLSTMLEHGVAGIILCPAAGTSPDLLKRLAES 78 (268)
T ss_pred EEEEecCCCcchHHHHHHHHHHHHHHcCCeEEEe---cCCCChHHHHHHHHHHHHcCCCEEEEeCCCCccHHHHHHHHhc
Confidence 455654 35677778899999999999887543 2112234456677888888899888875443334467777776
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|.
T Consensus 79 ~i 80 (268)
T cd06289 79 GI 80 (268)
T ss_pred CC
Confidence 64
No 373
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=56.80 E-value=1.3e+02 Score=26.09 Aligned_cols=83 Identities=10% Similarity=0.089 Sum_probs=43.6
Q ss_pred HHHcCCeEEEEEEEcCC-cccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHH
Q 003275 67 VEYYGWREVIAIFVDDD-YGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTI 145 (834)
Q Consensus 67 l~~~~W~~v~iI~~d~~-~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i 145 (834)
+...|.+.|+-+-.|.+ -+....+.+.+++++.|+...+.-......+..++....+.+......|.+.|.++..+..+
T Consensus 23 la~~GfktVInlRpd~E~~~qp~~~~~~~~a~~~Gl~y~~iPv~~~~~~~~~v~~f~~~l~~~~~Pvl~hC~sG~Ra~~l 102 (110)
T PF04273_consen 23 LAAQGFKTVINLRPDGEEPGQPSSAEEAAAAEALGLQYVHIPVDGGAITEEDVEAFADALESLPKPVLAHCRSGTRASAL 102 (110)
T ss_dssp HHHCT--EEEE-S-TTSTTT-T-HHCHHHHHHHCT-EEEE----TTT--HHHHHHHHHHHHTTTTSEEEE-SCSHHHHHH
T ss_pred HHHCCCcEEEECCCCCCCCCCCCHHHHHHHHHHcCCeEEEeecCCCCCCHHHHHHHHHHHHhCCCCEEEECCCChhHHHH
Confidence 34588899887777754 45556677889999999987653333333455677666666665544444444456655555
Q ss_pred HHHH
Q 003275 146 FSVA 149 (834)
Q Consensus 146 ~~~a 149 (834)
...+
T Consensus 103 ~~l~ 106 (110)
T PF04273_consen 103 WALA 106 (110)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 4433
No 374
>TIGR00035 asp_race aspartate racemase.
Probab=56.72 E-value=21 Score=35.91 Aligned_cols=40 Identities=15% Similarity=0.071 Sum_probs=21.3
Q ss_pred HHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEE
Q 003275 62 AVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKIS 104 (834)
Q Consensus 62 aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~ 104 (834)
+.++-++..|.++|+++....- -....+.+.+++.|+++.
T Consensus 107 ~~~~~~~~~~~~~VgvLaT~~T---~~s~~y~~~l~~~g~~v~ 146 (229)
T TIGR00035 107 ETAEAVKEDGVKKAGLLGTKGT---MKDGVYEREMKKHGIEIV 146 (229)
T ss_pred HHHHHHHHcCCCEEEEEecHHH---HHhHHHHHHHHHCCCEEE
Confidence 3334445556777777764422 122345666666676554
No 375
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=56.62 E-value=48 Score=33.71 Aligned_cols=77 Identities=3% Similarity=-0.064 Sum_probs=52.0
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|+++.. ++.|.......+.+++++.|..+..... ..+.......++++...+.|.||+.........+++.+.+.
T Consensus 2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (266)
T cd06282 2 VGVVLPSLANPVFAECVQGIQEEARAAGYSLLLATT---DYDAEREADAVETLLRQRVDGLILTVADAATSPALDLLDAE 78 (266)
T ss_pred eEEEeCCCCcchHHHHHHHHHHHHHHCCCEEEEeeC---CCCHHHHHHHHHHHHhcCCCEEEEecCCCCchHHHHHHhhC
Confidence 455654 3567778889999999999998876432 12334556677777778899988864322333467777777
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|.
T Consensus 79 ~i 80 (266)
T cd06282 79 RV 80 (266)
T ss_pred CC
Confidence 74
No 376
>cd06353 PBP1_BmpA_Med_like Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type I periplasmic sugar-binding protein-like fold.
Probab=56.44 E-value=81 Score=32.29 Aligned_cols=143 Identities=14% Similarity=0.079 Sum_probs=72.1
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccC-CccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEE
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNEL-NVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFV 80 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~-~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~ 80 (834)
+++...||+. +.....++..++.++ ++.++...+..+. +.-..+.|+... ..+.+-.+|.++..- .+|++|..
T Consensus 55 ~~g~dlIi~~-g~~~~~~~~~vA~~~p~~~F~~~d~~~~~--~Nv~~~~~~~~e-~~ylaG~~Aa~~t~t--~kVG~I~g 128 (258)
T cd06353 55 AQGYDLIFGT-SFGFMDAALKVAKEYPDVKFEHCSGYKTA--PNVGSYFARIYE-GRYLAGVVAGKMTKT--NKVGYVAA 128 (258)
T ss_pred HcCCCEEEEC-chhhhHHHHHHHHHCCCCEEEECCCCCCC--CCeeeEechhhH-HHHHHHHHHHHhhcC--CcEEEEcC
Confidence 3567788883 455556666666655 3444433221110 111122233321 223444455555433 57888875
Q ss_pred cC-CcccchHHHHHHHHhcCCcEEEeeecCCCCC-ChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCC
Q 003275 81 DD-DYGRNGISVLGDALSKKRAKISYKAPFSPGA-SRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLG 153 (834)
Q Consensus 81 d~-~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~-~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g 153 (834)
.+ +........|.+-++..+..+.....+.-.. +...-......+.+.++|+|+-.+ ....++++|++.|
T Consensus 129 ~~~~~~~~~~~gF~~G~~~~~p~~~v~~~~~g~~~D~~~a~~~a~~l~~~G~DvI~~~~---~~~g~~~aa~~~g 200 (258)
T cd06353 129 FPIPEVVRGINAFALGARSVNPDATVKVIWTGSWFDPAKEKEAALALIDQGADVIYQHT---DSPGVIQAAEEKG 200 (258)
T ss_pred cccHHHHHHHHHHHHHHHHHCCCcEEEEEEecCCCCcHHHHHHHHHHHHCCCcEEEecC---CChHHHHHHHHhC
Confidence 43 2223445566665554433332222222111 222334555666678999887776 3456888888876
No 377
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=55.64 E-value=44 Score=32.03 Aligned_cols=76 Identities=20% Similarity=0.230 Sum_probs=49.0
Q ss_pred CCCChhhhhcCCCCeeEeeCchhhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCcc
Q 003275 590 QIEGIDSLISSTEPIGVQDGSFAWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCE 669 (834)
Q Consensus 590 ~i~s~~dL~~~~~~v~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~ 669 (834)
++++.+||. +.+|+...-.....||. ..+.+ ..+++....-|..- .. |-.|++++-......+.++ +
T Consensus 100 ~~~~~~~l~--~~rIATkyp~i~~~~f~-~~Gi~-v~ii~l~GsvE~aP--~~----GlaD~IvDiv~TG~TL~~N---g 166 (182)
T TIGR00070 100 DISSVEDLK--GKRIATKYPNLARRYFE-KKGID-VEIIKLNGSVELAP--LL----GLADAIVDIVSTGTTLREN---G 166 (182)
T ss_pred CCCChHHhC--CCEEEECCHHHHHHHHH-HcCCe-EEEEECcceeeccc--CC----CceeEEEEEeCCHHHHHHC---C
Confidence 467778885 78899887778888885 45554 55666554444321 12 7889998876666665444 4
Q ss_pred EEEeCCccc
Q 003275 670 FRTVGQEFT 678 (834)
Q Consensus 670 l~~v~~~~~ 678 (834)
|.++.+.+.
T Consensus 167 L~~ie~i~~ 175 (182)
T TIGR00070 167 LRIIEVILE 175 (182)
T ss_pred CEEeeEEEe
Confidence 555544443
No 378
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=55.20 E-value=56 Score=33.91 Aligned_cols=77 Identities=10% Similarity=0.001 Sum_probs=54.5
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhhHHHHHHHHHh
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-PDTGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-~~~~~~i~~~a~~ 151 (834)
|++|..+ +.|.....+.+.+++++.|..+.....- .+.......++.+.+.++|.|++... .......++++.+
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~---~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l~~ 78 (288)
T cd01538 2 IGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQNAN---GDPAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAAD 78 (288)
T ss_pred eEEEEeCCCcHHHHHHHHHHHHHHHHcCCEEEEECCC---CCHHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHHHH
Confidence 5667654 5677788899999999999998764332 23345567777788888998888753 3344667777777
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.|.
T Consensus 79 ~~i 81 (288)
T cd01538 79 AGI 81 (288)
T ss_pred CCC
Confidence 664
No 379
>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=54.92 E-value=61 Score=33.06 Aligned_cols=75 Identities=12% Similarity=-0.029 Sum_probs=49.3
Q ss_pred EEEEEEc-----CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003275 75 VIAIFVD-----DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVA 149 (834)
Q Consensus 75 v~iI~~d-----~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a 149 (834)
|+++..+ +.|.....+.+.+++++.|..+..... . ....+....+..+...++|.|++.....+ ..++.+
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~-~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~--~~~~~l 76 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKFV-S--DEDEEEFELPSFLEDGKVDGIILLGGIST--EYIKEI 76 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEeC-C--CChHHHHHHHHHHHHCCCCEEEEeCCCCh--HHHHHH
Confidence 5666655 678888899999999999988765432 2 12233445556666778999988764333 236666
Q ss_pred HhCCC
Q 003275 150 KSLGM 154 (834)
Q Consensus 150 ~~~g~ 154 (834)
.+.|.
T Consensus 77 ~~~~i 81 (268)
T cd06277 77 KELGI 81 (268)
T ss_pred hhcCC
Confidence 66664
No 380
>PF14981 FAM165: FAM165 family
Probab=54.85 E-value=28 Score=24.26 Aligned_cols=33 Identities=18% Similarity=0.093 Sum_probs=28.2
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 003275 738 LKSFWGLFLICGIACFLALIFFFCRVCGQFRRF 770 (834)
Q Consensus 738 l~~~~g~f~il~~g~~lal~vf~~e~~~~~~~~ 770 (834)
++++--++||++.-.++-|+.|..--+|++++.
T Consensus 3 L~~vPlLlYILaaKtlilClaFAgvK~yQ~krl 35 (51)
T PF14981_consen 3 LDNVPLLLYILAAKTLILCLAFAGVKMYQRKRL 35 (51)
T ss_pred hhhchHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 567778899999999999999999888888765
No 381
>PRK09756 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=54.69 E-value=69 Score=29.97 Aligned_cols=80 Identities=9% Similarity=0.024 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHh-cCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe
Q 003275 59 QMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALS-KKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV 137 (834)
Q Consensus 59 q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~-~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~ 137 (834)
.++.+..++++++-+++. |..|........+.+.+.+. -.|+++... +.++....+.+ +..+-+++++.-
T Consensus 17 HGQV~~~W~~~~~~~~Ii-VvdD~vA~D~~~k~~lkma~~P~gvk~~i~-------sv~~a~~~l~~-~~~~~~vlvl~~ 87 (158)
T PRK09756 17 HGQVGVTWTSTIGANLLV-VVDDVVANDDIQQKLMGITAETYGFGIRFF-------TIEKTINVIGK-AAPHQKIFLICR 87 (158)
T ss_pred hHHHHHhhhcccCCCEEE-EEcchhcCCHHHHHHHHhcCCCCCCEEEEE-------EHHHHHHHHHh-ccCCceEEEEEC
Confidence 356677899999999985 44455555566666666655 577776641 33555666666 556678999999
Q ss_pred ChhhHHHHHH
Q 003275 138 NPDTGLTIFS 147 (834)
Q Consensus 138 ~~~~~~~i~~ 147 (834)
++.++..+++
T Consensus 88 ~~~da~~l~~ 97 (158)
T PRK09756 88 TPQTVRKLVE 97 (158)
T ss_pred CHHHHHHHHH
Confidence 9999998876
No 382
>TIGR00854 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters.
Probab=54.31 E-value=62 Score=30.01 Aligned_cols=80 Identities=15% Similarity=0.180 Sum_probs=57.3
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003275 60 MHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP 139 (834)
Q Consensus 60 ~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~ 139 (834)
++.+..++++++-+.+. |..|..-.....+.+.+.+.-.|+++... +.++....+.+-+..+.+++++.-++
T Consensus 14 GQV~~~W~~~~~~~~Ii-VvdD~~A~D~~~k~~lkma~P~gvk~~i~-------sve~a~~~l~~~~~~~~~v~vl~k~~ 85 (151)
T TIGR00854 14 GQVGTTWTKVAGANRII-VVNDDVANDEVRQTLMGIVAPTGFKVRFV-------SLEKTINVIHKPAYHDQTIFLLFRNP 85 (151)
T ss_pred hHhhhhhhcccCCCEEE-EEcccccCCHHHHHHHHhhCCCCCEEEEE-------EHHHHHHHHhCcCCCCceEEEEECCH
Confidence 56677889999999875 44455555567777777777778877642 23455555655455667899999999
Q ss_pred hhHHHHHH
Q 003275 140 DTGLTIFS 147 (834)
Q Consensus 140 ~~~~~i~~ 147 (834)
.++..+++
T Consensus 86 ~da~~l~~ 93 (151)
T TIGR00854 86 QDVLTLVE 93 (151)
T ss_pred HHHHHHHH
Confidence 99998875
No 383
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=54.25 E-value=22 Score=31.40 Aligned_cols=30 Identities=17% Similarity=0.073 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 003275 742 WGLFLICGIACFLALIFFFCRVCGQFRRFG 771 (834)
Q Consensus 742 ~g~f~il~~g~~lal~vf~~e~~~~~~~~~ 771 (834)
.-..+|+|+.+++.++++++-++.+|++++
T Consensus 65 ~i~~Ii~gv~aGvIg~Illi~y~irR~~Kk 94 (122)
T PF01102_consen 65 AIIGIIFGVMAGVIGIILLISYCIRRLRKK 94 (122)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHHS--
T ss_pred ceeehhHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 345666666666666666555555544444
No 384
>cd08550 GlyDH-like Glycerol_dehydrogenase-like. Families of proteins related to glycerol dehydrogenases. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site. Some subfamilies have not been characterized till now.
Probab=54.16 E-value=48 Score=35.81 Aligned_cols=84 Identities=15% Similarity=0.157 Sum_probs=55.9
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.++++.+| +++.+|+....+ ....+.+.+.+++.|+.+.... +..+.+.+.+...+..+++.++|+||-.+.
T Consensus 12 ~~l~~~~~~~g-~~~liv~~~~~~-~~~~~~v~~~l~~~~i~~~~~~-~~~~p~~~~v~~~~~~~~~~~~d~IIavGGGs 88 (349)
T cd08550 12 KEIAAILSTFG-SKVAVVGGKTVL-KKSRPRFEAALAKSIIVVDVIV-FGGECSTEEVVKALCGAEEQEADVIIGVGGGK 88 (349)
T ss_pred HHHHHHHHHcC-CeEEEEEChHHH-HHHHHHHHHHHHhcCCeeEEEE-cCCCCCHHHHHHHHHHHHhcCCCEEEEecCcH
Confidence 44667778888 888777643333 2456788888988887654332 333335577888888888889999886654
Q ss_pred hhhHHHHHH
Q 003275 139 PDTGLTIFS 147 (834)
Q Consensus 139 ~~~~~~i~~ 147 (834)
.-|+.+++.
T Consensus 89 ~~D~aK~ia 97 (349)
T cd08550 89 TLDTAKAVA 97 (349)
T ss_pred HHHHHHHHH
Confidence 345555553
No 385
>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=54.03 E-value=37 Score=35.13 Aligned_cols=79 Identities=11% Similarity=0.077 Sum_probs=50.8
Q ss_pred EEEEEEc---CCcccchHHHHHHHHhcCCcEEEeeecCCCC-CChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHH
Q 003275 75 VIAIFVD---DDYGRNGISVLGDALSKKRAKISYKAPFSPG-ASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAK 150 (834)
Q Consensus 75 v~iI~~d---~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~-~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~ 150 (834)
|++|..+ ++|....++.+.+++++.|..+......+.. .+.......++.+...+.|.||+..........++.+.
T Consensus 2 Igvi~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIv~~~~~~~~~~~~~l~ 81 (280)
T cd06303 2 IAVIYPGQQISDYWVRNIASFTARLEELNIPYELTQFSSRPGIDHRLQSQQLNEALQSKPDYLIFTLDSLRHRKLIERVL 81 (280)
T ss_pred eeEEecCccHHHHHHHHHHHHHHHHHHcCCcEEEEEeccCcccCHHHHHHHHHHHHHcCCCEEEEcCCchhhHHHHHHHH
Confidence 6777764 4677788899999999999877654222211 12234456677888889999988654333344556666
Q ss_pred hCC
Q 003275 151 SLG 153 (834)
Q Consensus 151 ~~g 153 (834)
+.+
T Consensus 82 ~~~ 84 (280)
T cd06303 82 ASG 84 (280)
T ss_pred hCC
Confidence 555
No 386
>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=53.96 E-value=52 Score=33.53 Aligned_cols=77 Identities=9% Similarity=0.014 Sum_probs=52.3
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhhHHHHHHHHHh
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-PDTGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-~~~~~~i~~~a~~ 151 (834)
|+++..| +.|.....+.+.+++++.|..+..... ..+.......+.++...++|.+++... .......++++.+
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~~---~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSIA---NQDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKK 78 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEecC---CCCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHHHH
Confidence 4556654 567778899999999999988865321 123344566777777788999888654 3333556677777
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.|+
T Consensus 79 ~~i 81 (267)
T cd06322 79 AGI 81 (267)
T ss_pred CCC
Confidence 664
No 387
>cd00001 PTS_IIB_man PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate.
Probab=53.85 E-value=63 Score=29.99 Aligned_cols=81 Identities=12% Similarity=0.092 Sum_probs=57.8
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003275 60 MHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP 139 (834)
Q Consensus 60 ~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~ 139 (834)
++.+..++++++-+++. |..|..-.....+.+...+.-.|+++... +.++....+.+-+..+.+++++.-++
T Consensus 13 GQV~~~W~~~~~~~~Iv-VvdD~~A~D~~~k~~l~ma~P~gvk~~i~-------sve~a~~~l~~~~~~~~~v~il~k~~ 84 (151)
T cd00001 13 GQVATTWTKELNANRII-VVNDEVANDELRKTLLKLAAPPGVKLRIF-------TVEKAIEAINSPKYDKQRVFLLFKNP 84 (151)
T ss_pred hHhhhhhhcccCCCEEE-EEcccccCCHHHHHHHHhhCCCCCeEEEE-------EHHHHHHHHhCcCCCCceEEEEECCH
Confidence 56778889999999885 44455555566777777777678876642 23455556665455667899999999
Q ss_pred hhHHHHHHH
Q 003275 140 DTGLTIFSV 148 (834)
Q Consensus 140 ~~~~~i~~~ 148 (834)
.++..+++.
T Consensus 85 ~~~~~l~~~ 93 (151)
T cd00001 85 QDVLRLVEG 93 (151)
T ss_pred HHHHHHHHc
Confidence 999988753
No 388
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=53.76 E-value=78 Score=29.72 Aligned_cols=66 Identities=14% Similarity=0.100 Sum_probs=38.4
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
++-.+++..+.+..+ .+.++... .+.+. ++.+|++|+++..... ....+. +.++....++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~-~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 78 (197)
T cd08422 14 LHLAPLLAEFLARYP-DVRLELVL---------SDRLV-DLVEEGFDLAIRIGEL---PDSSLV-ARRLGPVRRVLVASP 78 (197)
T ss_pred HHHHHHHHHHHHhCC-ceEEEEec---------Ccccc-chhhcCccEEEEeCCC---CCcchh-hhhhhccCcEEEECH
Confidence 555788888888775 44455542 12333 4567889999863221 122222 456666777777764
Q ss_pred C
Q 003275 481 Q 481 (834)
Q Consensus 481 ~ 481 (834)
.
T Consensus 79 ~ 79 (197)
T cd08422 79 A 79 (197)
T ss_pred H
Confidence 3
No 389
>PF03830 PTSIIB_sorb: PTS system sorbose subfamily IIB component; InterPro: IPR004720 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This entry is specific for the IIB components of this family of PTS transporters [].; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 3LFJ_B 1BLE_A 3P3V_B 1NRZ_C 3EYE_A 1VSQ_C 2JZH_A 2JZN_C 2JZO_D.
Probab=52.84 E-value=25 Score=32.57 Aligned_cols=81 Identities=14% Similarity=0.125 Sum_probs=60.7
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003275 60 MHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP 139 (834)
Q Consensus 60 ~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~ 139 (834)
++.+..++++++-+.+. |..|........+.+.+.+.-.|+++... +.++....+.+-...+.+++++.-++
T Consensus 14 GQV~~~W~~~~~~~~Ii-VvdD~~A~D~~~k~~l~ma~P~gvk~~i~-------sv~~a~~~l~~~~~~~~~v~ii~k~~ 85 (151)
T PF03830_consen 14 GQVATAWVKKLNANRII-VVDDEVANDPFQKMILKMAAPAGVKLSIF-------SVEEAIEKLKKPEYSKKRVLIIVKSP 85 (151)
T ss_dssp TTHHHHHHHHHTTSEEE-EE-HHHHHSHHHHHHHHHTSHTTSEEEEE--------HHHHHHHHCGGGGTTEEEEEEESSH
T ss_pred eeeeEEEhhhcccCEEE-EECHHHhcCHHHHHHHHHhhcCCCceEEE-------EHHHHHHHHHhcccCCceEEEEECCH
Confidence 45677899999999985 55566666677888887777788887652 34566667777666778999999999
Q ss_pred hhHHHHHHH
Q 003275 140 DTGLTIFSV 148 (834)
Q Consensus 140 ~~~~~i~~~ 148 (834)
.++..+++.
T Consensus 86 ~d~~~l~~~ 94 (151)
T PF03830_consen 86 EDALRLVEA 94 (151)
T ss_dssp HHHHHHHHT
T ss_pred HHHHHHHhc
Confidence 999988764
No 390
>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=52.61 E-value=49 Score=33.14 Aligned_cols=77 Identities=8% Similarity=0.068 Sum_probs=53.3
Q ss_pred EEEEEEc---CCcccchHHHHHHHHhc--CCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003275 75 VIAIFVD---DDYGRNGISVLGDALSK--KRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVA 149 (834)
Q Consensus 75 v~iI~~d---~~~g~~~~~~l~~~l~~--~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a 149 (834)
|++|..+ +.|+....+.+.+++++ .++++..... ..+..+....+.++...+++.+++.........+...+
T Consensus 2 Ig~i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~~ 78 (269)
T cd01391 2 IGVLLPLSGSAPFGAQLLAGIELAAEEIGRGLEVILADS---QSDPERALEALRDLIQQGVDGIIGPPSSSSALAVVELA 78 (269)
T ss_pred ceEEeecCCCcHHHHHHHHHHHHHHHHhCCceEEEEecC---CCCHHHHHHHHHHHHHcCCCEEEecCCCHHHHHHHHHH
Confidence 5667653 46778888999999999 7777665322 22334667777788777899998877665555467777
Q ss_pred HhCCC
Q 003275 150 KSLGM 154 (834)
Q Consensus 150 ~~~g~ 154 (834)
.+.+.
T Consensus 79 ~~~~i 83 (269)
T cd01391 79 AAAGI 83 (269)
T ss_pred HHcCC
Confidence 76664
No 391
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=52.38 E-value=69 Score=34.37 Aligned_cols=82 Identities=15% Similarity=0.062 Sum_probs=58.1
Q ss_pred CCeEEEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhhHHHHHH
Q 003275 71 GWREVIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-PDTGLTIFS 147 (834)
Q Consensus 71 ~W~~v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-~~~~~~i~~ 147 (834)
.-.++++|.. +++|.....+.+.+++++.|+++.... +...+...-...++.+.+.+++.|++... +......++
T Consensus 22 ~~~~i~~v~k~~~~pf~~~~~~Gi~~aa~~~G~~v~~~~--~~~~d~~~q~~~i~~li~~~vdgIiv~~~d~~al~~~l~ 99 (336)
T PRK15408 22 AAERIAFIPKLVGVGFFTSGGNGAKEAGKELGVDVTYDG--PTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALK 99 (336)
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHHHHHHhCCEEEEEC--CCCCCHHHHHHHHHHHHHcCCCEEEEecCCHHHHHHHHH
Confidence 4467888874 567888888999999999999987532 22222233346677777888999988653 444467888
Q ss_pred HHHhCCC
Q 003275 148 VAKSLGM 154 (834)
Q Consensus 148 ~a~~~g~ 154 (834)
+|.+.|.
T Consensus 100 ~a~~~gI 106 (336)
T PRK15408 100 RAMQRGV 106 (336)
T ss_pred HHHHCCC
Confidence 8888875
No 392
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=52.38 E-value=2.8e+02 Score=28.57 Aligned_cols=85 Identities=12% Similarity=0.063 Sum_probs=53.9
Q ss_pred CceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeee
Q 003275 374 MPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDI 453 (834)
Q Consensus 374 ~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~ 453 (834)
+.++||+.... ...+..++++.+.+..+ .+.+.+.. .+-++++.+|.+|++|+++...
T Consensus 97 ~~l~I~~~~~~--------------~~~~l~~~l~~f~~~~p-~i~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~ 154 (294)
T PRK09986 97 GRIEIGIVGTA--------------LWGRLRPAMRHFLKENP-NVEWLLRE-------LSPSMQMAALERRELDAGIWRM 154 (294)
T ss_pred ceEEEEEehHH--------------hHHHHHHHHHHHHHhCC-CeEEEEEe-------CCHHHHHHHHHcCCCCEEEecC
Confidence 57999983221 12344677788877766 34455543 3457889999999999988522
Q ss_pred eeecCceeeEEecceeeeceEEEEEecCC
Q 003275 454 TIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 454 ~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
. .......+. +.|+....+++++++..
T Consensus 155 ~-~~~~~~~l~-~~~l~~~~~~~v~~~~~ 181 (294)
T PRK09986 155 A-DLEPNPGFT-SRRLHESAFAVAVPEEH 181 (294)
T ss_pred C-ccCCCCCeE-EEEeecccEEEEEcCCC
Confidence 1 011122343 36777788888888766
No 393
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=51.96 E-value=58 Score=32.99 Aligned_cols=77 Identities=5% Similarity=-0.092 Sum_probs=51.5
Q ss_pred EEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHH
Q 003275 74 EVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSVAK 150 (834)
Q Consensus 74 ~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a~ 150 (834)
+|++|..+ +.|.....+.+.+++++.|+.+.....- .+.......++++...+.+.|++.... ......+..+.
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~---~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~~~~~~l~ 77 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDAQ---NDVSKQIQQIEDLIAQGVDGIIISPVDSAALTPALKKAN 77 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECCC---CCHHHHHHHHHHHHHcCCCEEEEeCCCchhHHHHHHHHH
Confidence 36777754 5688888999999999999887653222 133445567777777789988876543 33334566666
Q ss_pred hCC
Q 003275 151 SLG 153 (834)
Q Consensus 151 ~~g 153 (834)
+.+
T Consensus 78 ~~~ 80 (267)
T cd01536 78 AAG 80 (267)
T ss_pred HCC
Confidence 555
No 394
>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=51.84 E-value=53 Score=33.60 Aligned_cols=80 Identities=14% Similarity=0.125 Sum_probs=52.1
Q ss_pred EEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHHH
Q 003275 74 EVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDT-GLTIFSVAK 150 (834)
Q Consensus 74 ~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~-~~~i~~~a~ 150 (834)
+|++|..+ +.|.......+.++++++|.++.....-. ..+.......+.++...+.|.+|+...... ....++.+.
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgvii~~~~~~~~~~~l~~~~ 79 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQGPAS-ETDVAGQVNLLENAIARGPDAILLAPTDAKALVPPLKEAK 79 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHHcCCEEEEecCcc-CCCHHHHHHHHHHHHHhCCCEEEEcCCChhhhHHHHHHHH
Confidence 46777654 56777888999999999999887643211 113344556677777778898887543322 245666666
Q ss_pred hCCC
Q 003275 151 SLGM 154 (834)
Q Consensus 151 ~~g~ 154 (834)
+.|.
T Consensus 80 ~~~i 83 (273)
T cd06310 80 DAGI 83 (273)
T ss_pred HCCC
Confidence 6553
No 395
>PRK11425 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=51.03 E-value=78 Score=29.57 Aligned_cols=80 Identities=11% Similarity=0.086 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003275 59 QMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN 138 (834)
Q Consensus 59 q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~ 138 (834)
.++.+..++++++-+.+. |..|..-.....+.+...+.-.|+++... +.++....+++ ...+-+++++.-+
T Consensus 15 HGQV~~~W~~~~~~~~Iv-VvdD~~A~D~~~k~~l~ma~P~gvk~~i~-------sv~~a~~~l~~-~~~~~~v~il~k~ 85 (157)
T PRK11425 15 HGQVGVQWVGFAGANLVL-VANDEVAEDPVQQNLMEMVLAEGIAVRFW-------TLQKVIDNIHR-AADRQKILLVCKT 85 (157)
T ss_pred hHHhhhhhhcccCCCEEE-EEcchhcCCHHHHHHHHhhCCCCCeEEEE-------EHHHHHHHHhc-cCCCceEEEEECC
Confidence 356778889999998874 44455555566777777777678776542 33566666766 5566689999999
Q ss_pred hhhHHHHHH
Q 003275 139 PDTGLTIFS 147 (834)
Q Consensus 139 ~~~~~~i~~ 147 (834)
+.++..+++
T Consensus 86 ~~d~~~l~~ 94 (157)
T PRK11425 86 PADFLTLVK 94 (157)
T ss_pred HHHHHHHHH
Confidence 999998865
No 396
>cd06318 PBP1_ABC_sugar_binding_like_9 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=50.94 E-value=56 Score=33.66 Aligned_cols=77 Identities=5% Similarity=-0.078 Sum_probs=52.2
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHh
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a~~ 151 (834)
|+++.. .+.|.......+.+++++.|..+..... ..+.......+..+...++|.|++.... +.....++.+.+
T Consensus 2 igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~~---~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~ 78 (282)
T cd06318 2 IGFSQYTLNSPFFAALTEAAKAHAKALGYELISTDA---QGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKA 78 (282)
T ss_pred eeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEcC---CCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHH
Confidence 555554 3567778889999999999998865322 1233444567888888899999886433 333456677777
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.|.
T Consensus 79 ~~i 81 (282)
T cd06318 79 AGV 81 (282)
T ss_pred CCC
Confidence 664
No 397
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=50.67 E-value=57 Score=33.40 Aligned_cols=79 Identities=15% Similarity=0.121 Sum_probs=53.4
Q ss_pred EEEEEEEc---CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHH
Q 003275 74 EVIAIFVD---DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSVA 149 (834)
Q Consensus 74 ~v~iI~~d---~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a 149 (834)
+|++|..+ +.|.....+.+.+++++.|..+.....- ..+.......++++...++|.+|+.... ......++.+
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~~~--~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~l~~~ 78 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRGPE--TFDVADMARLIEAAIAAKPDGIVVTIPDPDALDPAIKRA 78 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEECCC--CCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHHHH
Confidence 35666643 5688888999999999999988654221 1133455677778878889988886533 2234566777
Q ss_pred HhCCC
Q 003275 150 KSLGM 154 (834)
Q Consensus 150 ~~~g~ 154 (834)
.+.|.
T Consensus 79 ~~~~i 83 (271)
T cd06312 79 VAAGI 83 (271)
T ss_pred HHCCC
Confidence 77664
No 398
>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=50.44 E-value=74 Score=32.29 Aligned_cols=76 Identities=12% Similarity=0.018 Sum_probs=52.6
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|.. +++|-......+.+++++.|..+..... ..+.......++.+...+.|.|++....... ..++++.+.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~-~~~~~l~~~ 77 (265)
T cd06299 2 IGVIVPDIRNPYFASLATAIQDAASAAGYSTIIGNS---DENPETENRYLDNLLSQRVDGIIVVPHEQSA-EQLEDLLKR 77 (265)
T ss_pred EEEEecCCCCccHHHHHHHHHHHHHHcCCEEEEEeC---CCCHHHHHHHHHHHHhcCCCEEEEcCCCCCh-HHHHHHHhC
Confidence 566665 4667778889999999999998875432 1233455677888888889988887543333 346777776
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|.
T Consensus 78 ~i 79 (265)
T cd06299 78 GI 79 (265)
T ss_pred CC
Confidence 64
No 399
>cd08178 AAD_C C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD). Alcohol dehydrogenase domain located on the C-terminal of a bifunctional two-domain protein. The N-terminal of the protein contains an acetaldehyde-CoA dehydrogenase domain. This protein is involved in pyruvate metabolism. Pyruvate is converted to acetyl-CoA and formate by pyruvate formate-lysase (PFL). Under anaerobic condition, acetyl-CoA is reduced to acetaldehyde and ethanol by this two-domain protein. Acetyl-CoA is first converted into an enzyme-bound thiohemiacetal by the N-terminal acetaldehyde dehydrogenase domain. The enzyme-bound thiohemiacetal is subsequently reduced by the C-terminal NAD+-dependent alcohol dehydrogenase domain. In E. coli, this protein is called AdhE and was shown pyruvate formate-lysase (PFL) deactivase activity, which is involved in the inactivation of PFL, a key enzyme in anaerobic metabolism. In Escherichi
Probab=50.42 E-value=61 Score=35.74 Aligned_cols=79 Identities=11% Similarity=0.061 Sum_probs=56.6
Q ss_pred cCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe--ChhhHHHHHH
Q 003275 70 YGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV--NPDTGLTIFS 147 (834)
Q Consensus 70 ~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~--~~~~~~~i~~ 147 (834)
.+.+++.+|+..........+.+.+.|++.|+++.....+.++.+.+.+...+..+++.++|+||-.+ +.-|+.+++.
T Consensus 19 ~~~~k~liVtd~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS~iD~AK~iA 98 (398)
T cd08178 19 KGKKRAFIVTDRFMVKLGYVDKVIDVLKRRGVETEVFSDVEPDPSLETVRKGLELMNSFKPDTIIALGGGSPMDAAKIMW 98 (398)
T ss_pred cCCCeEEEEcChhHHhCccHHHHHHHHHHCCCeEEEecCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHHHHHH
Confidence 45688887774443444478889999999998876544555555667888999999999999999664 4456666654
Q ss_pred H
Q 003275 148 V 148 (834)
Q Consensus 148 ~ 148 (834)
.
T Consensus 99 ~ 99 (398)
T cd08178 99 L 99 (398)
T ss_pred H
Confidence 3
No 400
>PRK14737 gmk guanylate kinase; Provisional
Probab=49.79 E-value=2e+02 Score=27.64 Aligned_cols=128 Identities=15% Similarity=0.175 Sum_probs=67.7
Q ss_pred CCcEEEECCCChhhHHHHHHhhccC-Ccc-EEecccCCCCCCC-CCCCceEEccCChHHHHHHHHHHHHH---cCCeEEE
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNEL-NVP-LLSFGATDPTLTS-LQYPYFLRTTQSDYYQMHAVADLVEY---YGWREVI 76 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~-~vP-~Is~~at~~~ls~-~~~p~~~r~~ps~~~q~~aia~ll~~---~~W~~v~ 76 (834)
..+++|+||.+|+=...+..+.+.. ++. .+++++..|.-.+ .+-.|+|-+. .+. .+.+.. ..|..
T Consensus 4 ~~~ivl~GpsG~GK~tl~~~l~~~~~~~~~~v~~TTR~~r~gE~~G~dY~fvs~----~~F---~~~i~~~~f~e~~~-- 74 (186)
T PRK14737 4 PKLFIISSVAGGGKSTIIQALLEEHPDFLFSISCTTRAPRPGDEEGKTYFFLTI----EEF---KKGIADGEFLEWAE-- 74 (186)
T ss_pred CeEEEEECCCCCCHHHHHHHHHhcCCccccccCccCCCCCCCCCCCceeEeCCH----HHH---HHHHHcCCeEEEEE--
Confidence 4689999999999888888887764 221 1244333443333 3445666532 222 223322 23333
Q ss_pred EEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCce-EEEEEeChhhHHHHHHHHHhCC
Q 003275 77 AIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESR-VFVVHVNPDTGLTIFSVAKSLG 153 (834)
Q Consensus 77 iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~-vivl~~~~~~~~~i~~~a~~~g 153 (834)
|.++-||. ..+.+...+++..++|... . ... +..++..-++ +++++..++....+.+...+.|
T Consensus 75 --~~g~~YGt-~~~~i~~~~~~g~~~i~d~---~----~~g----~~~l~~~~~~~~~~Ifi~pps~e~l~~RL~~R~ 138 (186)
T PRK14737 75 --VHDNYYGT-PKAFIEDAFKEGRSAIMDI---D----VQG----AKIIKEKFPERIVTIFIEPPSEEEWEERLIHRG 138 (186)
T ss_pred --ECCeeecC-cHHHHHHHHHcCCeEEEEc---C----HHH----HHHHHHhCCCCeEEEEEECCCHHHHHHHHHhcC
Confidence 33667885 4555777777777776532 1 122 2333333343 3555555544444555555444
No 401
>PRK00945 acetyl-CoA decarbonylase/synthase complex subunit epsilon; Provisional
Probab=49.18 E-value=83 Score=29.82 Aligned_cols=113 Identities=18% Similarity=0.266 Sum_probs=62.5
Q ss_pred CCcEEEECCCChh---hHHHHHHhhccCCccEEecccCCCCCCCCC-CCceEEccCChHHHHHHHHHHHHHcCCeEE---
Q 003275 3 NEVVAAIGPQSSG---IAHVISHVVNELNVPLLSFGATDPTLTSLQ-YPYFLRTTQSDYYQMHAVADLVEYYGWREV--- 75 (834)
Q Consensus 3 ~~V~aiiGp~~S~---~~~~~~~~~~~~~vP~Is~~at~~~ls~~~-~p~~~r~~ps~~~q~~aia~ll~~~~W~~v--- 75 (834)
++.+.++|..... ....+.+++++.++|+++...+...|..+. .|. ..-...+..++..-+|.-+
T Consensus 35 KrPlIivG~ga~~~~ea~e~l~elaEkl~iPVvtT~~~~~~~~~kgv~~~--------~~~lg~lg~~~~~p~~e~~~g~ 106 (171)
T PRK00945 35 KRPLLVVGSLLLDDEELLDRAVKIAKKANIPVAATGGSYKGLIDKGVDAK--------YINLHELTNYLKDPNWKGLDGN 106 (171)
T ss_pred CCcEEEECcCccccchHHHHHHHHHHHHCCCEEEccccccccccCCccCC--------cccHHHHHhhccCchhhhhcCC
Confidence 4678899987754 667789999999999997554444454422 121 2222344555544444443
Q ss_pred ------EEEEEcCCcccchHHHHHHHHhcCCcE-EEeeecCCCC-------CChHHHHHHHHHhh
Q 003275 76 ------IAIFVDDDYGRNGISVLGDALSKKRAK-ISYKAPFSPG-------ASRSAINSLLVGAN 126 (834)
Q Consensus 76 ------~iI~~d~~~g~~~~~~l~~~l~~~g~~-I~~~~~~~~~-------~~~~~~~~~l~~l~ 126 (834)
.++..+..|....+..|+.-.. ++ |.....+.++ .++++....|++|-
T Consensus 107 ~~~DlvlfvG~~~~~~~~~l~~lk~f~~---~~~~~~~~~y~~~a~~s~~~~~~~~~~~~l~~li 168 (171)
T PRK00945 107 GNYDLVIFIGVTYYYASQGLSALKHFSP---LKTITIDRYYHPNADMSFPNLSKEEYLEYLDELI 168 (171)
T ss_pred CCcCEEEEecCCchhHHHHHHHHhhcCC---ceEEEecCCcCCCCceecCCCCHHHHHHHHHHHH
Confidence 3444556665555555553332 22 2222333332 24566667776653
No 402
>PRK07377 hypothetical protein; Provisional
Probab=48.61 E-value=43 Score=31.60 Aligned_cols=62 Identities=15% Similarity=0.203 Sum_probs=45.0
Q ss_pred CCceEEEecCccccccceeccCCCCceeeeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEee
Q 003275 373 GMPLRIAVPNRVSYNEFVAKDKSPPGVKGYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVG 451 (834)
Q Consensus 373 g~~lrv~~~~~~~~~p~~~~~~~~~~~~G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~ 451 (834)
...+|+|+... .++ .+...+-.++.++.+.++++.+ .++++| .+-..+.+.+.+|++|++.+
T Consensus 74 s~~~Rlgv~~~--------~~~-~~~~~~~l~~~l~~~~~~y~~r--lElv~y------~~~~~l~~aL~~~eVh~~c~ 135 (184)
T PRK07377 74 SLVMRLGVLEI--------ETE-TSSVFDQLIDQLRTILDKYHLR--LELVVY------PDLQALEQALRDKEVHAICL 135 (184)
T ss_pred ccEEEEEEEec--------ccc-ccccHHHHHHHHHHHHHHhCce--eeEEec------CCHHHHHHHHhcCCccEEec
Confidence 35789998432 011 2334455678889999999988 666665 45889999999999998876
No 403
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=48.42 E-value=3.3e+02 Score=28.20 Aligned_cols=63 Identities=10% Similarity=0.034 Sum_probs=35.9
Q ss_pred HHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecC
Q 003275 404 IDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQ 481 (834)
Q Consensus 404 ~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~ 481 (834)
..++..+.+..+ ++.+++.. . .....+.+|++|+++..... ....+. +.|+....+++++++.
T Consensus 110 ~~~l~~f~~~~p-~i~i~l~~-------~---~~~~~l~~g~~Dl~i~~~~~---~~~~l~-~~~l~~~~~~~~~~~~ 172 (297)
T PRK11139 110 VPRLSSFNEAHP-DIDVRLKA-------V---DRLEDFLRDDVDVAIRYGRG---NWPGLR-VEKLLDEYLLPVCSPA 172 (297)
T ss_pred HHHHHHHHHHCC-CceEEEEe-------C---CChhhhccCCCCEEEEeCCC---CCCCce-EEEeccceeEEEeCHH
Confidence 455666666554 34455542 1 12467889999999864321 112222 5677777777766543
No 404
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=48.41 E-value=3.3e+02 Score=28.15 Aligned_cols=65 Identities=9% Similarity=-0.040 Sum_probs=41.3
Q ss_pred HHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecCC
Q 003275 405 DVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQK 482 (834)
Q Consensus 405 dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~~ 482 (834)
..+..+.+.- .+.++... ++.++++.+|.+|++|+++..... ....+. +.|+....++++++...
T Consensus 107 ~~l~~~~~~~--~i~i~~~~-------~~~~~~~~~L~~~~~d~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~~ 171 (294)
T PRK13348 107 PALAAVLAGE--RILLELIV-------DDQDHTFALLERGEVVGCVSTQPK---PMRGCL-AEPLGTMRYRCVASPAF 171 (294)
T ss_pred HHHHHHHhCC--CeEEEEEE-------cchHHHHHHHhcCCeEEEEecCCc---ccCCcc-cccccccceEEEEccch
Confidence 4455554443 34455543 457889999999999998753322 122343 57778888888876553
No 405
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=47.92 E-value=2.8e+02 Score=27.47 Aligned_cols=92 Identities=17% Similarity=0.127 Sum_probs=56.4
Q ss_pred CCCeeEeeCchhhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEechhhHHHHhhcCCccEEEeCCccccc
Q 003275 601 TEPIGVQDGSFAWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDELPYIELFMSKTNCEFRTVGQEFTKS 680 (834)
Q Consensus 601 ~~~v~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~~~~~~~~~~~~~~l~~v~~~~~~~ 680 (834)
+.+|+...-.....||.+ .+.+ .+++.....-|..- .-|-.|++++-........++ +|.++.+.+.+.
T Consensus 115 ~~rIATkYp~it~~yf~~-~gv~-~~iv~l~GsvE~aP------~~GlAD~IvDivsTG~TLr~N---gL~~ie~Il~s~ 183 (215)
T PRK01686 115 RLRVATKYPNIARRYFAE-KGEQ-VEIIKLYGSVELAP------LVGLADAIVDIVETGNTLRAN---GLVEVEEIMDIS 183 (215)
T ss_pred CCEEEeCCHHHHHHHHHH-cCCe-EEEEECcCceeecc------ccCCccEEEEeecChHHHHHC---cCEEeeEEEeeE
Confidence 567888777778888854 4664 66666655555422 227788998877766665555 566676555444
Q ss_pred ceEEEEcCCCc--chHHHHHHHHhhh
Q 003275 681 GWGFAFQRDSP--LAIDLSTAILQLS 704 (834)
Q Consensus 681 ~~~~~~~k~sp--l~~~~~~~i~~l~ 704 (834)
. .+...+.|. -.+.++..+.++.
T Consensus 184 A-~LI~n~~s~~~k~~~i~~l~~~l~ 208 (215)
T PRK01686 184 A-RLIVNRASLKLKREEIRPLIEKLR 208 (215)
T ss_pred E-EEEEecccchhhHHHHHHHHHHHH
Confidence 3 455566554 2345555555553
No 406
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=47.45 E-value=2.2e+02 Score=25.91 Aligned_cols=92 Identities=12% Similarity=-0.032 Sum_probs=55.9
Q ss_pred HHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecC----CCCCChHHH-HHHHHHhhcCCceEEEEE
Q 003275 62 AVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPF----SPGASRSAI-NSLLVGANLMESRVFVVH 136 (834)
Q Consensus 62 aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~----~~~~~~~~~-~~~l~~l~~~~~~vivl~ 136 (834)
.+.+.+...+-....-+|.+.... .....+.++++..|.++...... .....+..+ ...+..+...+.+.||+.
T Consensus 28 ~l~~~~~~~~~~~~~r~y~~~~~~-~~~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLv 106 (149)
T cd06167 28 KLLEFLRDGGEIVLARAYGNWTSP-ERQRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLV 106 (149)
T ss_pred HHHHHHHhCCeEEEEEEEEecCCc-hhHHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEE
Confidence 344444433223333444433211 46788999999999998765533 112222222 334444444578899999
Q ss_pred eChhhHHHHHHHHHhCCC
Q 003275 137 VNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 137 ~~~~~~~~i~~~a~~~g~ 154 (834)
+...+...+++.+++.|.
T Consensus 107 SgD~Df~~~i~~lr~~G~ 124 (149)
T cd06167 107 SGDSDFVPLVERLRELGK 124 (149)
T ss_pred ECCccHHHHHHHHHHcCC
Confidence 888899999999998864
No 407
>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=47.17 E-value=88 Score=31.91 Aligned_cols=76 Identities=8% Similarity=-0.000 Sum_probs=50.2
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|.. ++.|-......+.+++++.|..+.....- .+.......++.+...+.+.+++.........+++.+++.
T Consensus 2 Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~ 78 (269)
T cd06281 2 IGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIANSL---NDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALASL 78 (269)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEeCC---CChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHhC
Confidence 566664 45677778889999999999887654221 2234456677777777888888765433334566666665
Q ss_pred C
Q 003275 153 G 153 (834)
Q Consensus 153 g 153 (834)
+
T Consensus 79 ~ 79 (269)
T cd06281 79 D 79 (269)
T ss_pred C
Confidence 5
No 408
>PRK00002 aroB 3-dehydroquinate synthase; Reviewed
Probab=46.87 E-value=1.6e+02 Score=31.84 Aligned_cols=101 Identities=7% Similarity=-0.033 Sum_probs=63.0
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEee--ecCCCCCChHHHHHHHHHhhcCCc---eEEEE
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYK--APFSPGASRSAINSLLVGANLMES---RVFVV 135 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~--~~~~~~~~~~~~~~~l~~l~~~~~---~vivl 135 (834)
..+.+++..++++++.+|+.... .....+.+.+.+++.|+.+... .....+.+.+.+...++.+++.+. |+||-
T Consensus 20 ~~l~~~l~~~~~~~~livtd~~~-~~~~~~~v~~~L~~~gi~~~~~~~~~~e~~~~~~~v~~~~~~~~~~~~~r~d~IIa 98 (358)
T PRK00002 20 SELGELLAPLKGKKVAIVTDETV-APLYLEKLRASLEAAGFEVDVVVLPDGEQYKSLETLEKIYDALLEAGLDRSDTLIA 98 (358)
T ss_pred HHHHHHHHhcCCCeEEEEECCch-HHHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCCEEEE
Confidence 44666777778899988885444 3457788888898888765421 122223345677888888876654 88876
Q ss_pred EeC--hhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 136 HVN--PDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 136 ~~~--~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
.+. .-++..++......| ..++-|.|.
T Consensus 99 vGGGsv~D~aK~iA~~~~~g---ip~i~IPTT 127 (358)
T PRK00002 99 LGGGVIGDLAGFAAATYMRG---IRFIQVPTT 127 (358)
T ss_pred EcCcHHHHHHHHHHHHhcCC---CCEEEcCch
Confidence 654 446666654434333 345555554
No 409
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=46.59 E-value=3.5e+02 Score=27.92 Aligned_cols=65 Identities=9% Similarity=0.014 Sum_probs=41.3
Q ss_pred HHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecC
Q 003275 404 IDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQ 481 (834)
Q Consensus 404 ~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~ 481 (834)
..++..+.+.. .+.+.... ++-..+++.|.+|++|+++...... ...+. +.|+.+..++++++++
T Consensus 106 ~~~l~~~~~~~--~i~i~l~~-------~~~~~~~~~l~~g~~d~~i~~~~~~---~~~l~-~~~l~~~~~~~v~~~~ 170 (292)
T TIGR03298 106 LPALAPVLAQE--GVLLDLVV-------EDQDHTAELLRSGEVLGAVTTQAKP---VQGCR-VVPLGAMRYLAVASPA 170 (292)
T ss_pred HHHHHHHHhCC--CceEEEEe-------CcchhHHHHHhCCCceEEEecCCCC---CCCce-EEecCCceEEEEECch
Confidence 34566666653 34455543 3456789999999999998643222 12233 4677788888887654
No 410
>cd08175 G1PDH Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner. Glycerol-1-phosphate dehydrogenase (G1PDH) plays a role in the synthesis of phosphoglycerolipids in Gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires a Ni++ ion. In Bacillus subtilis, it has been described as AraM gene in L-arabinose (ara) operon. AraM protein forms homodimer. This family is bacteria specific.
Probab=46.17 E-value=79 Score=34.10 Aligned_cols=98 Identities=9% Similarity=0.162 Sum_probs=61.2
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCC--CChHHHHHHHHHhhcCCceEEEEEeC
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPG--ASRSAINSLLVGANLMESRVFVVHVN 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~--~~~~~~~~~l~~l~~~~~~vivl~~~ 138 (834)
..+.++++.++.+++.+|+....+ ....+.+.+.+++.|+.+......... .+.+.+...+..+++ ++|+||-.+.
T Consensus 12 ~~l~~~~~~~~~~~~livtd~~~~-~~~~~~v~~~l~~~~i~~~~~~~~~~~~~pt~~~v~~~~~~~~~-~~d~IIaIGG 89 (348)
T cd08175 12 ERLPEILKEFGYKKALIVADENTY-AAAGKKVEALLKRAGVVVLLIVLPAGDLIADEKAVGRVLKELER-DTDLIIAVGS 89 (348)
T ss_pred HHHHHHHHhcCCCcEEEEECCcHH-HHHHHHHHHHHHHCCCeeEEeecCCCcccCCHHHHHHHHHHhhc-cCCEEEEECC
Confidence 446677777888898888733332 223578888999888866433323222 455777788888877 8899886654
Q ss_pred --hhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 139 --PDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 139 --~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
.-|+.+++... . +..++-|.|.
T Consensus 90 Gs~~D~aK~vA~~--~---~~p~i~IPTT 113 (348)
T cd08175 90 GTINDITKYVSYK--T---GIPYISVPTA 113 (348)
T ss_pred cHHHHHHHHHHHh--c---CCCEEEecCc
Confidence 44666665422 2 2345555554
No 411
>PRK10200 putative racemase; Provisional
Probab=46.16 E-value=88 Score=31.42 Aligned_cols=71 Identities=8% Similarity=0.024 Sum_probs=36.6
Q ss_pred CcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCC
Q 003275 4 EVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDD 83 (834)
Q Consensus 4 ~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~ 83 (834)
|+.+|+=|..+..+. .-.+-+..++|+|+- .+++++.++..+-++|+++....
T Consensus 75 g~~~iviaCNTah~~-~~~l~~~~~iPii~i-------------------------i~~~~~~~~~~~~~~VglLaT~~- 127 (230)
T PRK10200 75 GAEGIVLCTNTMHKV-ADAIESRCSLPFLHI-------------------------ADATGRAITGAGMTRVALLGTRY- 127 (230)
T ss_pred CCCEEEECCchHHHH-HHHHHHhCCCCEeeh-------------------------HHHHHHHHHHcCCCeEEEeccHH-
Confidence 455555554444444 344555566776651 12333344445667788777543
Q ss_pred cccchHHHHHHHHhcC-CcEE
Q 003275 84 YGRNGISVLGDALSKK-RAKI 103 (834)
Q Consensus 84 ~g~~~~~~l~~~l~~~-g~~I 103 (834)
.-....+.+.+++. |+++
T Consensus 128 --Ti~s~~Y~~~l~~~~g~~~ 146 (230)
T PRK10200 128 --TMEQDFYRGRLTEQFSINC 146 (230)
T ss_pred --HHHHhHHHHHHHHhcCCeE
Confidence 22334455555544 6665
No 412
>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=46.12 E-value=29 Score=30.51 Aligned_cols=86 Identities=17% Similarity=0.121 Sum_probs=45.8
Q ss_pred eEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhh--cCCceEEEEEeChhhHHHHHHHHH
Q 003275 73 REVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGAN--LMESRVFVVHVNPDTGLTIFSVAK 150 (834)
Q Consensus 73 ~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~--~~~~~vivl~~~~~~~~~i~~~a~ 150 (834)
|+|++|...++-+. ....+...+.+.|.+|... .+..+.-+=......+. -...|++++...+.....+++++.
T Consensus 1 ksiAVvGaS~~~~~-~g~~v~~~l~~~G~~v~~V---np~~~~i~G~~~y~sl~e~p~~iDlavv~~~~~~~~~~v~~~~ 76 (116)
T PF13380_consen 1 KSIAVVGASDNPGK-FGYRVLRNLKAAGYEVYPV---NPKGGEILGIKCYPSLAEIPEPIDLAVVCVPPDKVPEIVDEAA 76 (116)
T ss_dssp -EEEEET--SSTTS-HHHHHHHHHHHTT-EEEEE---STTCSEETTEE-BSSGGGCSST-SEEEE-S-HHHHHHHHHHHH
T ss_pred CEEEEEcccCCCCC-hHHHHHHHHHhCCCEEEEE---CCCceEECcEEeeccccCCCCCCCEEEEEcCHHHHHHHHHHHH
Confidence 56777775443332 2333444555577676532 22211100011223333 357899999999999999999999
Q ss_pred hCCCCCCCeEEEEeC
Q 003275 151 SLGMTAGSYVWIATD 165 (834)
Q Consensus 151 ~~g~~~~~~vwi~~~ 165 (834)
++| .+.+|+.+.
T Consensus 77 ~~g---~~~v~~~~g 88 (116)
T PF13380_consen 77 ALG---VKAVWLQPG 88 (116)
T ss_dssp HHT----SEEEE-TT
T ss_pred HcC---CCEEEEEcc
Confidence 988 567999976
No 413
>cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322
Probab=45.49 E-value=18 Score=26.07 Aligned_cols=29 Identities=24% Similarity=0.485 Sum_probs=23.0
Q ss_pred hhhHHHHHHHHHHHHhhhheeecccCCCC
Q 003275 496 IPMWLVTGGFFLFVGAVVWILEHRFNNEF 524 (834)
Q Consensus 496 ~~vW~~i~~~~~~~~~v~~~~~~~~~~~~ 524 (834)
.++|.++..+++++++++|.+..+..+.+
T Consensus 11 a~~~~l~~~~~~Figiv~wa~~p~~k~~f 39 (48)
T cd01324 11 ADSWGLLYLALFFLGVVVWAFRPGRKKAF 39 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCcchhH
Confidence 36799999999999999999976654433
No 414
>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=45.40 E-value=88 Score=31.82 Aligned_cols=78 Identities=8% Similarity=-0.027 Sum_probs=50.2
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|..+ +.|.......+.+++++.|..+.....-. ..+......++.+...+.+.+++..........++.+.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 79 (270)
T cd01545 2 IGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCDS--GSPDLAERVRALLQRSRVDGVILTPPLSDNPELLDLLDEA 79 (270)
T ss_pred EEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCCC--CchHHHHHHHHHHHHCCCCEEEEeCCCCCccHHHHHHHhc
Confidence 4566643 67888889999999999998876542221 1122455666667777889887764322234556666666
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
+.
T Consensus 80 ~i 81 (270)
T cd01545 80 GV 81 (270)
T ss_pred CC
Confidence 64
No 415
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=45.00 E-value=85 Score=32.04 Aligned_cols=77 Identities=6% Similarity=-0.017 Sum_probs=51.9
Q ss_pred EEEEEE---cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHH
Q 003275 75 VIAIFV---DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSVAK 150 (834)
Q Consensus 75 v~iI~~---d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a~ 150 (834)
|++|.. ++.|+....+.+.+++++.|..+..... ..+.......++.+...++|.|++.... +.....++.+.
T Consensus 2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~l~~~~ 78 (275)
T cd06317 2 IGYTQNNVGSHSYQTTYNKAFQAAAEEDGVEVIVLDA---NGDVARQAAQVEDLIAQKVDGIILWPTDGQAYIPGLRKAK 78 (275)
T ss_pred eEEEecccCCCHHHHHHHHHHHHHHHhcCCEEEEEcC---CcCHHHHHHHHHHHHHcCCCEEEEecCCccccHHHHHHHH
Confidence 455653 4578888899999999999998775422 2233444566777777889988886543 33345667777
Q ss_pred hCCC
Q 003275 151 SLGM 154 (834)
Q Consensus 151 ~~g~ 154 (834)
+.|.
T Consensus 79 ~~~i 82 (275)
T cd06317 79 QAGI 82 (275)
T ss_pred HCCC
Confidence 7664
No 416
>TIGR00315 cdhB CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis.
Probab=44.89 E-value=1.1e+02 Score=28.63 Aligned_cols=115 Identities=13% Similarity=0.210 Sum_probs=62.1
Q ss_pred CCcEEEECCCCh--hhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEE-----
Q 003275 3 NEVVAAIGPQSS--GIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREV----- 75 (834)
Q Consensus 3 ~~V~aiiGp~~S--~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v----- 75 (834)
++.+.++|+... .....+..+++..++|+++.......+.+.. .+ ..| .-...+..++..-+|.-+
T Consensus 28 KRPvIivG~ga~~~~a~e~l~~laEklgiPVvtT~~~~~~~~~kg--v~--~~~---~~lg~~g~~~~~p~~e~~~g~g~ 100 (162)
T TIGR00315 28 KRPLLIVGPENLEDEEKELIVKFIEKFDLPVVATADTYRALIEAG--IE--SEE---MNLHEITQFLADPSWEGFDGEGN 100 (162)
T ss_pred CCcEEEECCCcCcccHHHHHHHHHHHHCCCEEEcCccccccccCC--ee--cCC---CCHHHHHHhccCchhhhccCCCC
Confidence 467889998764 7788889999999999997433222333322 11 111 112345555555455544
Q ss_pred ----EEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCC-------CChHHHHHHHHHhh
Q 003275 76 ----IAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPG-------ASRSAINSLLVGAN 126 (834)
Q Consensus 76 ----~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~-------~~~~~~~~~l~~l~ 126 (834)
.++..+..++...+..|+.-. +=-.|+....+.++ .+.+++...|+++.
T Consensus 101 ~DlvlfvG~~~y~~~~~ls~lk~f~--~~~~i~l~~~y~pnA~~Sf~n~~~~~~~~~l~~~~ 160 (162)
T TIGR00315 101 YDLVLFLGIIYYYLSQMLSSLKHFS--HIVTIAIDKYYQPNADYSFPNLSKDEYLDYLRKLL 160 (162)
T ss_pred cCEEEEeCCcchHHHHHHHHHHhhc--CcEEEEecCCCCCCCceeccccCHHHHHHHHHHHh
Confidence 334455555555566555433 21123333333333 23456666666653
No 417
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=44.68 E-value=1.2e+02 Score=32.42 Aligned_cols=79 Identities=11% Similarity=0.029 Sum_probs=53.8
Q ss_pred eEEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHH
Q 003275 73 REVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAK 150 (834)
Q Consensus 73 ~~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~ 150 (834)
+.++++..+ +.|.......+.+++++.|..+..... ..+.......++.+...+.|.|++..........+..+.
T Consensus 65 ~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l~ 141 (342)
T PRK10014 65 GVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQG---GKDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMAE 141 (342)
T ss_pred CEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEeC---CCCHHHHHHHHHHHHhCCCCEEEEeCCCCCcHHHHHHHh
Confidence 467888754 567778889999999999987654321 123345567778888888998888754333345666666
Q ss_pred hCCC
Q 003275 151 SLGM 154 (834)
Q Consensus 151 ~~g~ 154 (834)
+.|.
T Consensus 142 ~~~i 145 (342)
T PRK10014 142 EKGI 145 (342)
T ss_pred hcCC
Confidence 6553
No 418
>TIGR00249 sixA phosphohistidine phosphatase SixA.
Probab=44.47 E-value=1.3e+02 Score=27.82 Aligned_cols=98 Identities=9% Similarity=-0.012 Sum_probs=58.3
Q ss_pred ccCChHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCce
Q 003275 52 TTQSDYYQMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESR 131 (834)
Q Consensus 52 ~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~ 131 (834)
.++....|+..+++.+...+..--.++.+.-....+.++.+.+.+.. ...+.....+.+..+..++...+.++...+.+
T Consensus 23 Lt~~G~~qa~~~~~~l~~~~~~~d~i~sSp~~Ra~qTa~~l~~~~~~-~~~~~~~~~l~p~~~~~~~~~~l~~~~~~~~~ 101 (152)
T TIGR00249 23 LTTNGCDESRLVAQWLKGQGVEIERILVSPFVRAEQTAEIVGDCLNL-PSSAEVLEGLTPCGDIGLVSDYLEALTNEGVA 101 (152)
T ss_pred cCHHHHHHHHHHHHHHHhCCCCCCEEEECCcHHHHHHHHHHHHHcCC-CcceEEccCcCCCCCHHHHHHHHHHHHhcCCC
Confidence 34455678899999988765443344555555444555555544421 12333333444344455677777777654556
Q ss_pred EEEEEeChhhHHHHHHHHH
Q 003275 132 VFVVHVNPDTGLTIFSVAK 150 (834)
Q Consensus 132 vivl~~~~~~~~~i~~~a~ 150 (834)
.+++.+..+....++...-
T Consensus 102 ~vliVgH~P~i~~l~~~l~ 120 (152)
T TIGR00249 102 SVLLVSHLPLVGYLVAELC 120 (152)
T ss_pred EEEEEeCCCCHHHHHHHHh
Confidence 6777787777777777665
No 419
>TIGR03414 ABC_choline_bnd choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PubMed:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins.
Probab=44.41 E-value=2.2e+02 Score=29.72 Aligned_cols=40 Identities=10% Similarity=0.056 Sum_probs=30.3
Q ss_pred HHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeee
Q 003275 404 IDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGD 452 (834)
Q Consensus 404 ~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~ 452 (834)
-.|+..+.+.+|+++++. . .+-.-+...|.+|++|+.+..
T Consensus 24 ~~i~~~iLE~~Gy~Ve~~--~-------~~~~~~~~al~~GdiD~~~e~ 63 (290)
T TIGR03414 24 TALASVLLEGLGYQPKVT--L-------LSVPVTYAGLKDGDLDVFLGN 63 (290)
T ss_pred HHHHHHHHHHcCCcceeE--E-------ccHHHHHHHHHcCCceEeccc
Confidence 567777778889987664 2 335677889999999998764
No 420
>COG3340 PepE Peptidase E [Amino acid transport and metabolism]
Probab=43.59 E-value=2e+02 Score=28.20 Aligned_cols=85 Identities=15% Similarity=0.150 Sum_probs=51.4
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcc--cchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe
Q 003275 60 MHAVADLVEYYGWREVIAIFVDDDYG--RNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV 137 (834)
Q Consensus 60 ~~aia~ll~~~~W~~v~iI~~d~~~g--~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~ 137 (834)
-.-|++.++.+ -++|+.|=.-..-. ...++..++++++.|..|..-....+ +..++.+.|.+ +|+|+|.+
T Consensus 21 ~~~i~n~l~g~-~~~i~FIPtAs~~~~~~~Yv~k~~~~l~~lg~~v~~L~l~~~--~~~~Ie~~l~~-----~d~IyVgG 92 (224)
T COG3340 21 LPFIANFLQGK-RKTIAFIPTASVDSEDDFYVEKVRNALAKLGLEVSELHLSKP--PLAAIENKLMK-----ADIIYVGG 92 (224)
T ss_pred hHHHHHHhcCC-CceEEEEecCccccchHHHHHHHHHHHHHcCCeeeeeeccCC--CHHHHHHhhhh-----ccEEEECC
Confidence 34455555555 36888775322111 23789999999999999876444432 22444444433 57887754
Q ss_pred ChhhHHHHHHHHHhCCC
Q 003275 138 NPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 138 ~~~~~~~i~~~a~~~g~ 154 (834)
. .+..+++..++.|+
T Consensus 93 G--NTF~LL~~lke~gl 107 (224)
T COG3340 93 G--NTFNLLQELKETGL 107 (224)
T ss_pred c--hHHHHHHHHHHhCc
Confidence 4 45666777776665
No 421
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=43.12 E-value=1.3e+02 Score=31.74 Aligned_cols=80 Identities=8% Similarity=-0.031 Sum_probs=51.3
Q ss_pred CeEEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003275 72 WREVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVA 149 (834)
Q Consensus 72 W~~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a 149 (834)
-+.|+++..+ +.|.......+.+++++.|..+.....- .+...-...+..+...+.|.||+..........++.+
T Consensus 61 ~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~---~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 137 (328)
T PRK11303 61 TRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSD---DQPDNEMRCAEHLLQRQVDALIVSTSLPPEHPFYQRL 137 (328)
T ss_pred CceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEcCCCCCChHHHHHH
Confidence 4567877753 5677778889999999999988754221 1223334566777777889888864322223455566
Q ss_pred HhCCC
Q 003275 150 KSLGM 154 (834)
Q Consensus 150 ~~~g~ 154 (834)
.+.|.
T Consensus 138 ~~~~i 142 (328)
T PRK11303 138 QNDGL 142 (328)
T ss_pred HhcCC
Confidence 65553
No 422
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=42.90 E-value=1e+02 Score=33.02 Aligned_cols=81 Identities=6% Similarity=-0.062 Sum_probs=54.0
Q ss_pred CeEEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHH
Q 003275 72 WREVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSV 148 (834)
Q Consensus 72 W~~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~ 148 (834)
=+.|++|..+ +.|.....+.+.+++++.|..+.....-.. .+.......++.+...++|.|++.... ......+ +
T Consensus 46 t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~~-~~~~~q~~~i~~l~~~~vdgIIl~~~~~~~~~~~l-~ 123 (343)
T PRK10936 46 AWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGGY-YNLAKQQQQLEQCVAWGADAILLGAVTPDGLNPDL-E 123 (343)
T ss_pred CeEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCCC-CCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHH-H
Confidence 3788888855 567777888999999999998876533211 122344567777778889988886543 3333444 6
Q ss_pred HHhCCC
Q 003275 149 AKSLGM 154 (834)
Q Consensus 149 a~~~g~ 154 (834)
+.+.|.
T Consensus 124 ~~~~gi 129 (343)
T PRK10936 124 LQAANI 129 (343)
T ss_pred HHHCCC
Confidence 666664
No 423
>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=42.87 E-value=87 Score=32.06 Aligned_cols=79 Identities=10% Similarity=0.002 Sum_probs=50.7
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHh
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a~~ 151 (834)
+++|.. ++.|.....+.+.+++++.|..+.....-. ..+.......++++...+.+.+++.... ......++.+.+
T Consensus 2 igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~ 80 (275)
T cd06320 2 YGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAAPS-EGDQQGQLSIAENMINKGYKGLLFSPISDVNLVPAVERAKK 80 (275)
T ss_pred eeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEccCC-CCCHHHHHHHHHHHHHhCCCEEEECCCChHHhHHHHHHHHH
Confidence 556664 456777888999999999998876532221 1122344566777777788988776432 223445667776
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.|.
T Consensus 81 ~~i 83 (275)
T cd06320 81 KGI 83 (275)
T ss_pred CCC
Confidence 664
No 424
>KOG3713 consensus Voltage-gated K+ channel KCNB/KCNC [Inorganic ion transport and metabolism]
Probab=42.72 E-value=28 Score=38.26 Aligned_cols=62 Identities=16% Similarity=0.293 Sum_probs=45.9
Q ss_pred HHHHhhhheeecccCCCCCCCCCcchhhHHHHHHHHhhccC--CCcccccchhhhHHHHHHHHHHhhh
Q 003275 507 LFVGAVVWILEHRFNNEFRGPPSQQLVTIFWFSFSTMFFSH--RENTVSSLGRVVLIVWLFVVLIINS 572 (834)
Q Consensus 507 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~~~~~w~~~~lil~~ 572 (834)
++.+.+++++|+-.+ +++..++-.++|++..+|.-.| .-.|++.++|++...-.+.++++.+
T Consensus 357 ~iFStlvY~~Ek~~~----~~~FtSIPa~~WWaiVTMTTVGYGDm~P~T~~Gklvas~cil~GVLvlA 420 (477)
T KOG3713|consen 357 VIFSTLVYFAEKDEP----DTKFTSIPAGFWWAVVTMTTVGYGDMVPVTVLGKLVASLCILCGVLVLA 420 (477)
T ss_pred HHHHHHHHHhhhcCC----CCCCccccchhheeeEEEeeecccCccccccchHHHHHHHHHHhHHHhh
Confidence 344556677776533 3336678889999999997664 6689999999999988888776543
No 425
>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=42.53 E-value=83 Score=32.49 Aligned_cols=76 Identities=16% Similarity=0.117 Sum_probs=52.3
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHh
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a~~ 151 (834)
|++|..+ +.|.....+.+.+++++.|..+... ... +.......++++...++|.|++.... .....+++++.+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~---~~~-~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~~~~ 77 (289)
T cd01540 2 IGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKI---DVP-DGEKVLSAIDNLGAQGAKGFVICVPDVKLGPAIVAKAKA 77 (289)
T ss_pred eeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEc---cCC-CHHHHHHHHHHHHHcCCCEEEEccCchhhhHHHHHHHHh
Confidence 5666643 5677788899999999999887653 222 23444567777888889988886542 344566778887
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.|.
T Consensus 78 ~~i 80 (289)
T cd01540 78 YNM 80 (289)
T ss_pred CCC
Confidence 664
No 426
>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=42.38 E-value=1.3e+02 Score=30.80 Aligned_cols=78 Identities=9% Similarity=-0.001 Sum_probs=49.1
Q ss_pred CCeEEEEEEE---------cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhh
Q 003275 71 GWREVIAIFV---------DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDT 141 (834)
Q Consensus 71 ~W~~v~iI~~---------d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~ 141 (834)
..+.|++|.. ++.|.....+.+.+++++.|..+..... .. .+.....+.+.+.++|.|++......
T Consensus 2 ~s~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~~~v~~~---~~--~~~~~~~~~l~~~~~dgiii~~~~~~ 76 (275)
T cd06295 2 RTDTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYDLLLSFV---SS--PDRDWLARYLASGRADGVILIGQHDQ 76 (275)
T ss_pred CceEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCEEEEEeC---Cc--hhHHHHHHHHHhCCCCEEEEeCCCCC
Confidence 3567888885 3346667788899999999988765321 11 12334445565678998887653322
Q ss_pred HHHHHHHHHhCCC
Q 003275 142 GLTIFSVAKSLGM 154 (834)
Q Consensus 142 ~~~i~~~a~~~g~ 154 (834)
...++.+.+.|.
T Consensus 77 -~~~~~~~~~~~i 88 (275)
T cd06295 77 -DPLPERLAETGL 88 (275)
T ss_pred -hHHHHHHHhCCC
Confidence 244667776664
No 427
>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=42.29 E-value=1.2e+02 Score=30.77 Aligned_cols=76 Identities=8% Similarity=-0.062 Sum_probs=50.3
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|.. ++.|.......+.+++++.|..+.....- .+...-...++.+.+.++|.|++....... ..++++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~~~---~~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~~~~~~~~~ 77 (268)
T cd06270 2 IGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITAGH---HSAEKEREAIEFLLERRCDALILHSKALSD-DELIELAAQ 77 (268)
T ss_pred EEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEeCC---CchHHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhC
Confidence 455553 46788888999999999999988753321 122344567777778889988887543222 226666666
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|.
T Consensus 78 ~i 79 (268)
T cd06270 78 VP 79 (268)
T ss_pred CC
Confidence 63
No 428
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=42.27 E-value=2e+02 Score=25.34 Aligned_cols=62 Identities=15% Similarity=0.157 Sum_probs=38.3
Q ss_pred chHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh----hhHHHHHHHHHhCCC
Q 003275 87 NGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP----DTGLTIFSVAKSLGM 154 (834)
Q Consensus 87 ~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~----~~~~~i~~~a~~~g~ 154 (834)
-+..-+...++..|.+|.+--... .....+..+.+.++++|++++.. ..+..++++.++.+.
T Consensus 14 lG~~~~~~~l~~~G~~vi~lG~~v------p~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~ 79 (122)
T cd02071 14 RGAKVIARALRDAGFEVIYTGLRQ------TPEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELGA 79 (122)
T ss_pred HHHHHHHHHHHHCCCEEEECCCCC------CHHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhcCC
Confidence 345556667788888877643322 22345566666788888887643 445566666666654
No 429
>cd08197 DOIS 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-Deoxystreptamine (DOS)-containing aminoglycoside antibiotics includes neomycin, kanamycin, gentamicin, and ribostamycin. They are important antibacterial agents. DOIS is a homologue of the dehydroquinate synthase which catalyzes the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate (DHQ) in the shikimate pathway.
Probab=42.17 E-value=2.5e+02 Score=30.30 Aligned_cols=100 Identities=13% Similarity=-0.009 Sum_probs=63.4
Q ss_pred HHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeee--cCCCCCChHHHHHHHHHhhcCCce---EEEEE
Q 003275 62 AVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKA--PFSPGASRSAINSLLVGANLMESR---VFVVH 136 (834)
Q Consensus 62 aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~--~~~~~~~~~~~~~~l~~l~~~~~~---vivl~ 136 (834)
-+.+.+..++-+++.+|+....+ ....+.+.+.+++.|+.+.... ......+.+.+...+..+++.++| +||-.
T Consensus 13 ~l~~~l~~~g~~rvlvVtd~~v~-~~~~~~l~~~L~~~g~~~~~~~~~~~e~~k~~~~v~~~~~~~~~~~~dr~~~IIAv 91 (355)
T cd08197 13 SVLGYLPELNADKYLLVTDSNVE-DLYGHRLLEYLREAGAPVELLSVPSGEEHKTLSTLSDLVERALALGATRRSVIVAL 91 (355)
T ss_pred HHHHHHHhcCCCeEEEEECccHH-HHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEEE
Confidence 35566777777888888755443 3366788899998887653221 222223446788888888888887 77765
Q ss_pred eC--hhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 137 VN--PDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 137 ~~--~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
+. .-++..++......| ..++.|.|.
T Consensus 92 GGGsv~D~ak~~A~~~~rg---ip~I~IPTT 119 (355)
T cd08197 92 GGGVVGNIAGLLAALLFRG---IRLVHIPTT 119 (355)
T ss_pred CCcHHHHHHHHHHHHhccC---CCEEEecCc
Confidence 44 456666655433223 466777765
No 430
>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].
Probab=42.13 E-value=39 Score=32.76 Aligned_cols=36 Identities=14% Similarity=0.038 Sum_probs=23.5
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 003275 735 RLSLKSFWGLFLICGIACFLALIFFFCRVCGQFRRF 770 (834)
Q Consensus 735 ~l~l~~~~g~f~il~~g~~lal~vf~~e~~~~~~~~ 770 (834)
..+-+-+.-++-+++..+.+.|+||+.-+++++|+.
T Consensus 31 ~~~~d~~~I~iaiVAG~~tVILVI~i~v~vR~CRq~ 66 (221)
T PF08374_consen 31 SRSKDYVKIMIAIVAGIMTVILVIFIVVLVRYCRQS 66 (221)
T ss_pred cccccceeeeeeeecchhhhHHHHHHHHHHHHHhhc
Confidence 344445555666777777777888877777655533
No 431
>cd06315 PBP1_ABC_sugar_binding_like_6 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=41.43 E-value=1.3e+02 Score=31.06 Aligned_cols=79 Identities=11% Similarity=-0.004 Sum_probs=52.7
Q ss_pred eEEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHH
Q 003275 73 REVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDT-GLTIFSVA 149 (834)
Q Consensus 73 ~~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~-~~~i~~~a 149 (834)
|.|++|..+ +.|....+..+.+++++.|..+..... ..+.+.....++.+...+.|.||+...... ....++.+
T Consensus 1 ~~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiil~~~~~~~~~~~~~~~ 77 (280)
T cd06315 1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRILDG---RGSEAGQAAALNQAIALKPDGIVLGGVDAAELQAELELA 77 (280)
T ss_pred CeEEEEecccCCcHHHHHHHHHHHHHHHcCcEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHHHHHHH
Confidence 457777754 567777889999999999988765422 123344567788888889999988654322 23445566
Q ss_pred HhCCC
Q 003275 150 KSLGM 154 (834)
Q Consensus 150 ~~~g~ 154 (834)
.+.+.
T Consensus 78 ~~~~i 82 (280)
T cd06315 78 QKAGI 82 (280)
T ss_pred HHCCC
Confidence 66553
No 432
>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=41.43 E-value=1.2e+02 Score=30.94 Aligned_cols=76 Identities=8% Similarity=0.048 Sum_probs=50.1
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
++++.. ++.|.......+.+++++.|.++.....- .+.......++.+...+.|.+++....... ..++.+.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (270)
T cd06296 2 IGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSESG---RRTSPERQWVERLSARRTDGVILVTPELTS-AQRAALRRT 77 (270)
T ss_pred eEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecCC---CchHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHhcC
Confidence 455654 46788889999999999999987654222 122345566777777888988776443222 346666665
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
+.
T Consensus 78 ~i 79 (270)
T cd06296 78 GI 79 (270)
T ss_pred CC
Confidence 53
No 433
>PF02608 Bmp: Basic membrane protein; InterPro: IPR003760 This is a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. All of these proteins are outer membrane proteins and are thus antigenic in nature when possessed by the pathogenic members of the family []. The Bacillus subtilis degR, a positive regulator of the production of degradative enzymes, is also a member of this group [].; GO: 0005886 plasma membrane; PDB: 2HQB_A 3S99_A 2FQW_A 2FQY_A 2FQX_A.
Probab=41.21 E-value=1.4e+02 Score=31.39 Aligned_cols=88 Identities=14% Similarity=0.077 Sum_probs=58.5
Q ss_pred eEEEEEE----EcCCcccchHHHHHHHHhcC-CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHH
Q 003275 73 REVIAIF----VDDDYGRNGISVLGDALSKK-RAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFS 147 (834)
Q Consensus 73 ~~v~iI~----~d~~~g~~~~~~l~~~l~~~-g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~ 147 (834)
++++++. .|..|.+...+.+.+..++. |+++...+..+. +..++...++++.+.+.|+||.++.. ....+.+
T Consensus 2 ~~v~~~~~g~~~D~g~n~~~~~G~~~~~~~~~~i~~~~~e~~~~--~~~~~~~~~~~~~~~g~dlIi~~g~~-~~~~~~~ 78 (306)
T PF02608_consen 2 KKVALLDPGGINDKGFNQSAYEGLKRAEKELDGIEIIYVENVPE--TDADYEEAIRQLADQGYDLIIGHGFE-YSDALQE 78 (306)
T ss_dssp EEEEEESSS-CCCSSHHHHHHHHHHHHHHHCTTEEEEEEES-S---TCHHHHHHHHHHHHTT-SEEEEESGG-GHHHHHH
T ss_pred eEEEEEECCCCCCccHHHHHHHHHHHHHHHcCCceEEEEecCCc--cHHHHHHHHHHHHHcCCCEEEEccHH-HHHHHHH
Confidence 3455554 35567777788888888889 999988877763 34789999999999999999997653 2334444
Q ss_pred HHHhCCCCCCCeEEEEeCCC
Q 003275 148 VAKSLGMTAGSYVWIATDWL 167 (834)
Q Consensus 148 ~a~~~g~~~~~~vwi~~~~~ 167 (834)
.|.+- ++-.|+..++.
T Consensus 79 vA~~y----Pd~~F~~~d~~ 94 (306)
T PF02608_consen 79 VAKEY----PDTKFIIIDGY 94 (306)
T ss_dssp HHTC-----TTSEEEEESS-
T ss_pred HHHHC----CCCEEEEEecC
Confidence 44432 45566766644
No 434
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=41.17 E-value=1.2e+02 Score=32.37 Aligned_cols=80 Identities=10% Similarity=-0.025 Sum_probs=56.2
Q ss_pred CeEEEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHH
Q 003275 72 WREVIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDT-GLTIFSV 148 (834)
Q Consensus 72 W~~v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~-~~~i~~~ 148 (834)
-..|+++.. ++.|....++.+.+++++.|..+..... ..+.......++.+...++|.+++...... ....++.
T Consensus 25 ~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~~~---~~~~~~~~~~i~~l~~~~vDGiIi~~~~~~~~~~~l~~ 101 (330)
T PRK10355 25 EVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSA---NGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVIKE 101 (330)
T ss_pred CceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEeCCChhhHHHHHHH
Confidence 366777763 5778889999999999999998876422 223355667788888889999988754322 3455666
Q ss_pred HHhCCC
Q 003275 149 AKSLGM 154 (834)
Q Consensus 149 a~~~g~ 154 (834)
+.+.|.
T Consensus 102 ~~~~~i 107 (330)
T PRK10355 102 AKQEGI 107 (330)
T ss_pred HHHCCC
Confidence 666663
No 435
>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=40.54 E-value=99 Score=31.62 Aligned_cols=77 Identities=9% Similarity=-0.091 Sum_probs=50.5
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHHHh
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPD-TGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~-~~~~i~~~a~~ 151 (834)
|++|.. ++.|.......+.+++++.|.++... ....+...-...++++...++|.||+..... .....++.+.+
T Consensus 2 i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~---~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~l~~~~~ 78 (277)
T cd06319 2 IAYIVSDLRIPFWQIMGRGVKSKAKALGYDAVEL---SAENSAKKELENLRTAIDKGVSGIIISPTNSSAAVTLLKLAAQ 78 (277)
T ss_pred eEEEeCCCCchHHHHHHHHHHHHHHhcCCeEEEe---cCCCCHHHHHHHHHHHHhcCCCEEEEcCCchhhhHHHHHHHHH
Confidence 555654 46777788899999999999887642 2122333445667777778899888754332 23456677776
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.|.
T Consensus 79 ~~i 81 (277)
T cd06319 79 AKI 81 (277)
T ss_pred CCC
Confidence 663
No 436
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.52 E-value=3.4e+02 Score=28.65 Aligned_cols=124 Identities=18% Similarity=0.108 Sum_probs=78.3
Q ss_pred cccCCCChhhhhcCCC---C-eeEee---Cch---hhHHHHhhhcccccceEecCCHHHHHHHHhcCCCCCceEEEEech
Q 003275 587 LTSQIEGIDSLISSTE---P-IGVQD---GSF---AWNYLVDELKIAESRLVKLKNMEEYSIALARGPKGGGVAAIVDEL 656 (834)
Q Consensus 587 ~~~~i~s~~dL~~~~~---~-v~~~~---~s~---~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~a~~~~~ 656 (834)
...+.+|++||++.-+ . +-+.. |+. ....+.+..++ +.+.++|+...+.+.+|.. |++++..+..
T Consensus 130 ~~s~~~t~~dlv~~~k~~p~~v~~~~~g~Gs~dhl~~~~~~k~~Gi-~~~~Vpy~g~gea~taLlg----g~v~a~~~~~ 204 (319)
T COG3181 130 ADSPYKTLKDLVAYAKADPGSVIGGGSGLGSADHLAGALFAKAAGI-KITYVPYKGGGEALTALLG----GHVDAGSTNL 204 (319)
T ss_pred CCCCcccHHHHHHHHHhCCCeEEecCCCCCcHHHHHHHHHHHHhCC-ceeEEeecCccHHHHHHhc----CceeeeecCh
Confidence 3578999999885221 1 22221 111 11223344455 4788899999999999998 8999999886
Q ss_pred hhHHHHhhcCCcc-EEEeC------------------CcccccceEEEEcCCCc--chHHHHHHHHhhhccccHHHHHHh
Q 003275 657 PYIELFMSKTNCE-FRTVG------------------QEFTKSGWGFAFQRDSP--LAIDLSTAILQLSENGDLQKIHNK 715 (834)
Q Consensus 657 ~~~~~~~~~~~~~-l~~v~------------------~~~~~~~~~~~~~k~sp--l~~~~~~~i~~l~e~G~~~~i~~k 715 (834)
....-+.+...-+ +-+.. +.+.....++..|++-| ....++.++.++.++..+++..++
T Consensus 205 se~~~~vksG~lr~Lav~s~eRl~~~pdvPT~~E~G~~~~~~~wrgvfap~g~~~e~~~~~~~a~kk~l~s~e~~~~~~~ 284 (319)
T COG3181 205 SELLSQVKSGTLRLLAVFSEERLPGLPDVPTLKEQGYDVVMSIWRGVFAPAGTPDEIIAKLSAALKKALASPEWQKRLKE 284 (319)
T ss_pred hhhhhhhccCceEEEEeechhhcCCCCCCCChHhcCCceeeeeeeEEEeCCCCCHHHHHHHHHHHHHHhcCHHHHHHHHh
Confidence 6554443321111 11110 01123345788899987 999999999999999987655443
No 437
>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=40.49 E-value=1.1e+02 Score=31.29 Aligned_cols=80 Identities=4% Similarity=-0.040 Sum_probs=50.8
Q ss_pred EEEEEEE--cCCcccchHHHHHHHHhcC---CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHH
Q 003275 74 EVIAIFV--DDDYGRNGISVLGDALSKK---RAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFS 147 (834)
Q Consensus 74 ~v~iI~~--d~~~g~~~~~~l~~~l~~~---g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~ 147 (834)
+|+++.. ++.|-......+.+++++. |.++..... ....+.......++++...+.|.||+.... ......+.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i~-~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~l~ 79 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIVT-SADGDVAQQIADIRNLIAQGVDAIIINPASPTALNPVIE 79 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEEe-cCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHH
Confidence 3566653 3456677888999999988 874322211 212233556777888888899999887543 33344667
Q ss_pred HHHhCCC
Q 003275 148 VAKSLGM 154 (834)
Q Consensus 148 ~a~~~g~ 154 (834)
.+++.|.
T Consensus 80 ~~~~~~i 86 (272)
T cd06300 80 EACEAGI 86 (272)
T ss_pred HHHHCCC
Confidence 7777664
No 438
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR 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 wh
Probab=40.46 E-value=1.3e+02 Score=30.43 Aligned_cols=75 Identities=11% Similarity=-0.103 Sum_probs=49.6
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|..| +.|.....+.+.+++++.|.++..... ..+.......++++...++|.+|+...... ..++..+.+.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~~dgii~~~~~~~-~~~~~~~~~~ 77 (259)
T cd01542 2 IGVIVPRLDSFSTSRTVKGILAALYENGYQMLLMNT---NFSIEKEIEALELLARQKVDGIILLATTIT-DEHREAIKKL 77 (259)
T ss_pred eEEEecCCccchHHHHHHHHHHHHHHCCCEEEEEeC---CCCHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHHHHHHhcC
Confidence 4556643 456677889999999999998865322 223345566778888888999988754322 3455566655
Q ss_pred C
Q 003275 153 G 153 (834)
Q Consensus 153 g 153 (834)
|
T Consensus 78 ~ 78 (259)
T cd01542 78 N 78 (259)
T ss_pred C
Confidence 5
No 439
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=40.29 E-value=1.2e+02 Score=31.68 Aligned_cols=80 Identities=4% Similarity=-0.014 Sum_probs=53.4
Q ss_pred CeEEEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHH
Q 003275 72 WREVIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSV 148 (834)
Q Consensus 72 W~~v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~ 148 (834)
-+.+++|.. ++.|.......+.++++++|..+..... ..+.......++++...+++.+++.... ......++.
T Consensus 26 ~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~~~~~~~---~~d~~~~~~~~~~l~~~~~dgiii~~~~~~~~~~~l~~ 102 (295)
T PRK10653 26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDS---QNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKM 102 (295)
T ss_pred CCeEEEEecCCCChHHHHHHHHHHHHHHHcCCeEEEecC---CCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHH
Confidence 567787875 3567778889999999999998865322 1123444566777777788877776433 233456667
Q ss_pred HHhCCC
Q 003275 149 AKSLGM 154 (834)
Q Consensus 149 a~~~g~ 154 (834)
+++.|.
T Consensus 103 ~~~~~i 108 (295)
T PRK10653 103 ANQANI 108 (295)
T ss_pred HHHCCC
Confidence 776664
No 440
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=40.13 E-value=1.9e+02 Score=24.39 Aligned_cols=74 Identities=14% Similarity=0.165 Sum_probs=44.7
Q ss_pred EEEEcCCcccchHHHHHHHHhcCCc-EEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe--ChhhHHHHHHHHHhCC
Q 003275 77 AIFVDDDYGRNGISVLGDALSKKRA-KISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV--NPDTGLTIFSVAKSLG 153 (834)
Q Consensus 77 iI~~d~~~g~~~~~~l~~~l~~~g~-~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~--~~~~~~~i~~~a~~~g 153 (834)
+|.+|+. .....+...++..|. .+.. . .+....+..++...++++++.. ...++..++++.++.+
T Consensus 2 livd~~~---~~~~~l~~~l~~~~~~~v~~---~------~~~~~~~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~~~~ 69 (112)
T PF00072_consen 2 LIVDDDP---EIRELLEKLLERAGYEEVTT---A------SSGEEALELLKKHPPDLIIIDLELPDGDGLELLEQIRQIN 69 (112)
T ss_dssp EEEESSH---HHHHHHHHHHHHTTEEEEEE---E------SSHHHHHHHHHHSTESEEEEESSSSSSBHHHHHHHHHHHT
T ss_pred EEEECCH---HHHHHHHHHHHhCCCCEEEE---E------CCHHHHHHHhcccCceEEEEEeeecccccccccccccccc
Confidence 3444444 356667777777777 4432 1 2334555666667788988874 4457777888887766
Q ss_pred CCCCCeEEEEe
Q 003275 154 MTAGSYVWIAT 164 (834)
Q Consensus 154 ~~~~~~vwi~~ 164 (834)
....+.+.+
T Consensus 70 --~~~~ii~~t 78 (112)
T PF00072_consen 70 --PSIPIIVVT 78 (112)
T ss_dssp --TTSEEEEEE
T ss_pred --ccccEEEec
Confidence 233344444
No 441
>PF15179 Myc_target_1: Myc target protein 1
Probab=40.06 E-value=41 Score=31.51 Aligned_cols=38 Identities=11% Similarity=0.070 Sum_probs=29.9
Q ss_pred CCcccccchhHHHHH-HHHHHHHHHHHHHHHHHHHhhcc
Q 003275 733 GSRLSLKSFWGLFLI-CGIACFLALIFFFCRVCGQFRRF 770 (834)
Q Consensus 733 ~~~l~l~~~~g~f~i-l~~g~~lal~vf~~e~~~~~~~~ 770 (834)
.+.++.+++..+|.+ +++|++|+.+|+++-.+..|||.
T Consensus 13 ~~~f~~~~lIlaF~vSm~iGLviG~li~~LltwlSRRRA 51 (197)
T PF15179_consen 13 LENFDWEDLILAFCVSMAIGLVIGALIWALLTWLSRRRA 51 (197)
T ss_pred hhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 456777888888866 78899999999988877776665
No 442
>COG0134 TrpC Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism]
Probab=40.03 E-value=54 Score=33.14 Aligned_cols=88 Identities=15% Similarity=0.097 Sum_probs=67.4
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe---
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV--- 137 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~--- 137 (834)
..+++..+++|-.-+++++ |-.|..+..+.|+..-+...+.|.-+..+. + .-++...+..++|+|++..
T Consensus 69 ~~ia~~Ye~~GAa~iSVLT-d~~~F~Gs~e~L~~v~~~v~~PvL~KDFii---D----~yQI~~Ar~~GADavLLI~~~L 140 (254)
T COG0134 69 VEIAKAYEEGGAAAISVLT-DPKYFQGSFEDLRAVRAAVDLPVLRKDFII---D----PYQIYEARAAGADAVLLIVAAL 140 (254)
T ss_pred HHHHHHHHHhCCeEEEEec-CccccCCCHHHHHHHHHhcCCCeeeccCCC---C----HHHHHHHHHcCcccHHHHHHhc
Confidence 4477778889988888777 667888899999888888788776655553 1 2356777788999887653
Q ss_pred ChhhHHHHHHHHHhCCCCC
Q 003275 138 NPDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 138 ~~~~~~~i~~~a~~~g~~~ 156 (834)
+......+...|.++||..
T Consensus 141 ~~~~l~el~~~A~~LGm~~ 159 (254)
T COG0134 141 DDEQLEELVDRAHELGMEV 159 (254)
T ss_pred CHHHHHHHHHHHHHcCCee
Confidence 4566899999999999964
No 443
>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid [].; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.
Probab=39.68 E-value=21 Score=34.88 Aligned_cols=31 Identities=19% Similarity=0.461 Sum_probs=25.6
Q ss_pred CcEEEECCCChhhHHHHHHhhccCCccEEec
Q 003275 4 EVVAAIGPQSSGIAHVISHVVNELNVPLLSF 34 (834)
Q Consensus 4 ~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~ 34 (834)
+|.+|+||.+++=+.....++++.+.|+|+-
T Consensus 2 ~v~~i~GpT~tGKt~~ai~lA~~~g~pvI~~ 32 (233)
T PF01745_consen 2 KVYLIVGPTGTGKTALAIALAQKTGAPVISL 32 (233)
T ss_dssp EEEEEE-STTSSHHHHHHHHHHHH--EEEEE
T ss_pred cEEEEECCCCCChhHHHHHHHHHhCCCEEEe
Confidence 5889999999999999999999999999973
No 444
>PRK09189 uroporphyrinogen-III synthase; Validated
Probab=39.58 E-value=98 Score=31.21 Aligned_cols=89 Identities=10% Similarity=-0.011 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHHc--CCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEE
Q 003275 57 YYQMHAVADLVEYY--GWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFV 134 (834)
Q Consensus 57 ~~q~~aia~ll~~~--~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~viv 134 (834)
...++.+++++... .-++|.++. |....+.|.+.|++.|..|.....|.......+.......+++.+.++|+
T Consensus 101 ~~~~e~L~~~~~~~~~~~~~vL~~r-----g~~~r~~l~~~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~l~~~~~d~i~ 175 (240)
T PRK09189 101 GGDGVRLAETVAAALAPTARLLYLA-----GRPRAPVFEDRLAAAGIPFRVAECYDMLPVMYSPATLSAILGGAPFDAVL 175 (240)
T ss_pred CCCHHHHHHHHHHhcCCCCcEEEec-----cCcccchhHHHHHhCCCeeEEEEEEEeecCCCChHHHHHHHhcCCCCEEE
Confidence 34567788776442 335555554 33455778899999999876655443211111223344555555666655
Q ss_pred EEeChhhHHHHHHHHHh
Q 003275 135 VHVNPDTGLTIFSVAKS 151 (834)
Q Consensus 135 l~~~~~~~~~i~~~a~~ 151 (834)
+ .++..+..|++....
T Consensus 176 f-~S~~~~~~f~~~~~~ 191 (240)
T PRK09189 176 L-YSRVAARRFFALMRL 191 (240)
T ss_pred E-eCHHHHHHHHHHHhh
Confidence 4 556678888876643
No 445
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=39.53 E-value=3e+02 Score=25.55 Aligned_cols=64 Identities=16% Similarity=0.054 Sum_probs=36.0
Q ss_pred eHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEecC
Q 003275 403 CIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPVQ 481 (834)
Q Consensus 403 ~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~~ 481 (834)
-.+++..+.++.+ .+++++... +. ...+.+|++|+++..... ....+. +.++.+..++++++..
T Consensus 15 l~~~l~~f~~~~P-~i~i~i~~~-------~~---~~~l~~~~~Dl~l~~~~~---~~~~~~-~~~l~~~~~~~v~~~~ 78 (194)
T cd08481 15 LIPRLPDFLARHP-DITVNLVTR-------DE---PFDFSQGSFDAAIHFGDP---VWPGAE-SEYLMDEEVVPVCSPA 78 (194)
T ss_pred HHhhhhHHHHHCC-CceEEEEec-------cc---ccCcccCCCCEEEEcCCC---CCCCcc-ceecccCeeeecCCHH
Confidence 3466677777665 344555431 11 135888999999863221 112222 4566677777776543
No 446
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=39.48 E-value=1.1e+02 Score=32.09 Aligned_cols=78 Identities=12% Similarity=0.025 Sum_probs=52.5
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHh
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a~~ 151 (834)
|++|.. ++.|.......+.+++++.|..+.... +...+.......++.+...++|.||+.... +....+++++++
T Consensus 2 I~vi~~~~~~~f~~~i~~gi~~~a~~~g~~v~~~~--~~~~d~~~~~~~i~~~~~~~~DgiIi~~~~~~~~~~~~~~~~~ 79 (298)
T cd06302 2 IAFVPKVTGIPYFNRMEEGAKEAAKELGVDAIYVG--PTTADAAGQVQIIEDLIAQGVDAIAVVPNDPDALEPVLKKARE 79 (298)
T ss_pred EEEEEcCCCChHHHHHHHHHHHHHHHhCCeEEEEC--CCCCCHHHHHHHHHHHHhcCCCEEEEecCCHHHHHHHHHHHHH
Confidence 455553 456777888999999999999876421 111233455677777777889988886433 334567777777
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.|+
T Consensus 80 ~~i 82 (298)
T cd06302 80 AGI 82 (298)
T ss_pred CCC
Confidence 664
No 447
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=39.45 E-value=4.2e+02 Score=29.99 Aligned_cols=140 Identities=12% Similarity=0.118 Sum_probs=72.9
Q ss_pred EECCCChhhHHHHHHhhc-cCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCCcc-
Q 003275 8 AIGPQSSGIAHVISHVVN-ELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDDYG- 85 (834)
Q Consensus 8 iiGp~~S~~~~~~~~~~~-~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~~g- 85 (834)
|+||++.....++..+.. ...+=+|.++- .-++|- +.....+...+++....=+++.||| .+.||
T Consensus 198 i~~p~~~~v~~~l~~~~~l~l~~~~i~p~H----------G~i~r~--~~~~~l~~Y~~~~~~~~~~kv~IvY-~S~~Gn 264 (479)
T PRK05452 198 ILTPFSRLVTPKITEILGFNLPVDMIATSH----------GVVWRD--NPTQIVELYLKWAADYQEDRITIFY-DTMSNN 264 (479)
T ss_pred hhhhhHHHHHHHHHHHhhcCCCCCEEECCC----------CceEeC--CHHHHHHHHHHHhhccCcCcEEEEE-ECCccH
Confidence 567776665555555554 23344443321 123552 2333344445555543447888888 44555
Q ss_pred -cchHHHHHHHHhcC--CcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh------hhHHHHHHHHHhCCCCC
Q 003275 86 -RNGISVLGDALSKK--RAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP------DTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 86 -~~~~~~l~~~l~~~--g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~------~~~~~i~~~a~~~g~~~ 156 (834)
+..++.+.+.+++. |+.+.... +. +.+...++..+. .++.|++.++. +....++.......+.+
T Consensus 265 Te~mA~~ia~gl~~~g~gv~v~~~~-v~----~~~~~~i~~~~~--~ad~vilGspT~~~~~~p~~~~fl~~l~~~~l~g 337 (479)
T PRK05452 265 TRMMADAIAQGIAEVDPRVAVKIFN-VA----RSDKNEILTNVF--RSKGVLVGSSTMNNVMMPKIAGLLEEITGLRFRN 337 (479)
T ss_pred HHHHHHHHHHHHHhhCCCceEEEEE-CC----CCCHHHHHhHHh--hCCEEEEECCccCCcchHHHHHHHHHhhccCcCC
Confidence 45578888888876 55554322 22 123344444443 45777776543 24555666666555544
Q ss_pred CCeEEEEeCCC
Q 003275 157 GSYVWIATDWL 167 (834)
Q Consensus 157 ~~~vwi~~~~~ 167 (834)
+...-+.+-+|
T Consensus 338 K~~~vFGSygw 348 (479)
T PRK05452 338 KRASAFGSHGW 348 (479)
T ss_pred CEEEEEECCCc
Confidence 33334444333
No 448
>cd08177 MAR Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes. Maleylacetate reductases (MAR) play an important role in the degradation of aromatic compounds in aerobic microbes. In fungi and yeasts, the enzymes are involved in the catabolism of compounds such as phenol, tyrosine, benzoate, 4-hydroxybenzoate and resorcinol. In bacteria, the enzymes contribute to the degradation of resorcinol, 2,4-dihydroxybenzoate ([beta]-resorcylate) and 2,6-dihydroxybenzoate ([gamma]-resorcylate) via hydroxyquinol and maleylacetate. Maleylacetate reductases catalyze NADH- or NADPH-dependent reduction, at the carbon-carbon double bond, of maleylacetate or 2-chloromaleylacetate to 3-oxoadipate. In the case of 2-chloromaleylacetate, Maleylacetate reductases initially catalyses the NAD(P)H-dependent dechlorination to maleylacetate, which is then reduced to 3-oxoadipate. This enzyme is a homodimer. It is inhibited by thiol-blocking reagents such as p-
Probab=39.38 E-value=82 Score=33.79 Aligned_cols=97 Identities=11% Similarity=0.008 Sum_probs=62.7
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+.+.++.+|.+++.+|+....+-. ..+.+.+.+++.+..+ + ..+..+.+.+.+...+..+++.++|+||-.+.
T Consensus 12 ~~l~~~l~~~g~~~~livt~~~~~~~-~~~~v~~~l~~~~~~~-~-~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs 88 (337)
T cd08177 12 AALAAELERLGASRALVLTTPSLATK-LAERVASALGDRVAGT-F-DGAVMHTPVEVTEAAVAAAREAGADGIVAIGGGS 88 (337)
T ss_pred HHHHHHHHHcCCCeEEEEcChHHHHH-HHHHHHHHhccCCcEE-e-CCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCcH
Confidence 45677888999999888875444333 6667788887765433 2 23333445577888888888889999986654
Q ss_pred hhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 139 PDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 139 ~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
.-|+.+++.... ...++-|.|.
T Consensus 89 ~iD~aK~ia~~~-----~~p~i~IPTt 110 (337)
T cd08177 89 TIDLAKAIALRT-----GLPIIAIPTT 110 (337)
T ss_pred HHHHHHHHHHHh-----cCCEEEEcCC
Confidence 345555554322 2345556654
No 449
>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=39.01 E-value=1.4e+02 Score=30.30 Aligned_cols=76 Identities=11% Similarity=-0.008 Sum_probs=49.7
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|+++.. ++.|.......+.+++++.|..+... ....+.......++++.+.+.|.+++..... ....++.+++.
T Consensus 2 i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~---~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~-~~~~~~~l~~~ 77 (268)
T cd06273 2 IGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVA---SSGYDLDREYAQARKLLERGVDGLALIGLDH-SPALLDLLARR 77 (268)
T ss_pred eEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEe---cCCCCHHHHHHHHHHHHhcCCCEEEEeCCCC-CHHHHHHHHhC
Confidence 566664 46677788899999999999888752 2222334456677778777888888754322 23445566665
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|.
T Consensus 78 ~i 79 (268)
T cd06273 78 GV 79 (268)
T ss_pred CC
Confidence 53
No 450
>cd06315 PBP1_ABC_sugar_binding_like_6 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=38.99 E-value=4.4e+02 Score=26.93 Aligned_cols=132 Identities=11% Similarity=0.036 Sum_probs=67.1
Q ss_pred HhhccCCccEEecccCCCCCCCCCCC-ceEEccCChHHHHHHHHHHHHHc--CCeEEEEEEEcC-Cccc---chHHHHHH
Q 003275 22 HVVNELNVPLLSFGATDPTLTSLQYP-YFLRTTQSDYYQMHAVADLVEYY--GWREVIAIFVDD-DYGR---NGISVLGD 94 (834)
Q Consensus 22 ~~~~~~~vP~Is~~at~~~ls~~~~p-~~~r~~ps~~~q~~aia~ll~~~--~W~~v~iI~~d~-~~g~---~~~~~l~~ 94 (834)
..+...++|+|......+. .....+ .+-....++...+..+++.+... |-++++++.... .... ...+.+.+
T Consensus 75 ~~~~~~~iPvV~~d~~~~~-~~~~~~~~~~~v~~D~~~~~~~~~~~L~~~~~G~~~i~~i~~~~~~~~~~r~~~~~~~~~ 153 (280)
T cd06315 75 ELAQKAGIPVVGWHAGPEP-GPIEEPGIFYNVTTDPLAVAEVAALYAIANSGGKAGVVIFTDSRFSIAKAKANAMKEIIE 153 (280)
T ss_pred HHHHHCCCCEEEecCCCCC-CcccCCceeEEecCCHHHHHHHHHHHHHHHcCCCceEEEEeCCCCccHHHHHHHHHHHHH
Confidence 3455679999987542211 100001 13345666777778888877555 889998886332 1111 23344444
Q ss_pred HHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc---CCceEEEEEeChhhHHHHHHHHHhCCCCCC
Q 003275 95 ALSKKRAKISYKAPFSPGASRSAINSLLVGANL---MESRVFVVHVNPDTGLTIFSVAKSLGMTAG 157 (834)
Q Consensus 95 ~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~---~~~~vivl~~~~~~~~~i~~~a~~~g~~~~ 157 (834)
++++.++ ..................++++.+ ..+++| ++++...+..+++.+++.|+..+
T Consensus 154 a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai-~~~~D~~A~g~~~~l~~~g~~~p 216 (280)
T cd06315 154 ACKGCTV--LSIEDVPISRTATRMPALTARLLQRYGDKWTHS-LAINDLYFDYMAPPLASAGRKAD 216 (280)
T ss_pred hCCCCEE--EEecccCcchhhhhhHHHHHHHHHhcCccccee-cccchhhhHHhHHHHHHhcccCC
Confidence 4443343 111111111111111123334332 225654 44555677788899999998654
No 451
>PRK09701 D-allose transporter subunit; Provisional
Probab=38.67 E-value=1.4e+02 Score=31.46 Aligned_cols=85 Identities=7% Similarity=-0.028 Sum_probs=57.0
Q ss_pred HcCCeEEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHH
Q 003275 69 YYGWREVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPD-TGLTI 145 (834)
Q Consensus 69 ~~~W~~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~-~~~~i 145 (834)
.+.-..|++|..+ +.|.....+.+.+++++.|..+..... +...+.......++.+...++|.||+..... .....
T Consensus 21 ~~~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~v~~~~~-~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~~ 99 (311)
T PRK09701 21 AFAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFAS-PSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMP 99 (311)
T ss_pred hccCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCeEEEecC-CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHH
Confidence 4556789999854 668888899999999999988765321 1112224455667777778899998875432 23344
Q ss_pred HHHHHhCCC
Q 003275 146 FSVAKSLGM 154 (834)
Q Consensus 146 ~~~a~~~g~ 154 (834)
+.++.+.|+
T Consensus 100 l~~~~~~gi 108 (311)
T PRK09701 100 VARAWKKGI 108 (311)
T ss_pred HHHHHHCCC
Confidence 566666664
No 452
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=38.30 E-value=1.1e+02 Score=31.00 Aligned_cols=77 Identities=4% Similarity=-0.049 Sum_probs=50.8
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHh
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSVAKS 151 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a~~ 151 (834)
|++|.. ++.|.......+.+++++.|..+... ....+..+....+.++...+++.+++.... ......++.+.+
T Consensus 2 I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~---~~~~~~~~~~~~~~~~~~~~~dgii~~~~~~~~~~~~l~~l~~ 78 (268)
T cd06323 2 IGLSVSTLNNPFFVTLKDGAQKEAKELGYELTVL---DAQNDAAKQLNDIEDLITRGVDAIIINPTDSDAVVPAVKAANE 78 (268)
T ss_pred eeEecccccCHHHHHHHHHHHHHHHHcCceEEec---CCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHH
Confidence 455553 46678888999999999999888652 222233455677888877889988775432 223456666666
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.+.
T Consensus 79 ~~i 81 (268)
T cd06323 79 AGI 81 (268)
T ss_pred CCC
Confidence 553
No 453
>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=38.27 E-value=1.5e+02 Score=29.94 Aligned_cols=76 Identities=7% Similarity=-0.031 Sum_probs=50.8
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|..+ +.|.......+.+++++.|..+..... ..+.......++.+...++|.|++....... ..++++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (265)
T cd06285 2 IGVLVPRLTDTVMATMYEGIEEAAAERGYSTFVANT---GDNPDAQRRAIEMLLDRRVDGLILGDARSDD-HFLDELTRR 77 (265)
T ss_pred EEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHHHc
Confidence 5666654 667788889999999999998754221 2233455667778888889988886543332 346666666
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
+.
T Consensus 78 ~i 79 (265)
T cd06285 78 GV 79 (265)
T ss_pred CC
Confidence 63
No 454
>cd08180 PDD 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism. 1,3-propanediol dehydrogenase (PPD) plays a role in glycerol metabolism of some bacteria in anaerobic conditions. In this degradation pathway, glycerol is converted in a two-step process to 1,3-propanediol (1,3-PD) which is then excreted into the extracellular medium. The first reaction involves the transformation of glycerol into 3-hydroxypropionaldehyde (3-HPA) by a coenzyme B-12-dependent dehydratase. The second reaction involves the dismutation of the 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol by the NADH-linked 1,3-propanediol dehydrogenase (PPD). The enzyme require iron ion for its function. Because many genes in this pathway are present in the pdu (propanediol utilisation) operon, they are also named pdu genes. PPD is a member of the iron-containing alcohol dehydrogenase superfamily. The PPD structure has a dehydroquinat
Probab=38.25 E-value=77 Score=33.91 Aligned_cols=78 Identities=5% Similarity=-0.028 Sum_probs=51.2
Q ss_pred HHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--hhhHHHH
Q 003275 68 EYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN--PDTGLTI 145 (834)
Q Consensus 68 ~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~--~~~~~~i 145 (834)
..++.+++.+|+....+.....+.+.+.+++. +.+.....+..+.+.+.+...+..+++.++|+||-.+. .-|+.+.
T Consensus 18 ~~~~~~~~lvv~~~~~~~~g~~~~v~~~l~~~-~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IiaiGGGs~~D~aKa 96 (332)
T cd08180 18 KELKNKRVLIVTDPFMVKSGMLDKVTDHLDSS-IEVEIFSDVVPDPPIEVVAKGIKKFLDFKPDIVIALGGGSAIDAAKA 96 (332)
T ss_pred HHhCCCeEEEEeCchhhhCccHHHHHHHHHhc-CcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEECCchHHHHHHH
Confidence 44556888888754443334677888888876 55433333444445678888889999999999986644 3455554
Q ss_pred H
Q 003275 146 F 146 (834)
Q Consensus 146 ~ 146 (834)
+
T Consensus 97 ~ 97 (332)
T cd08180 97 I 97 (332)
T ss_pred H
Confidence 4
No 455
>cd08179 NADPH_BDH NADPH-dependent butanol dehydrogenase involved in the butanol and ethanol formation pathway in bacteria. NADPH-dependent butanol dehydrogenase (BDH) is involved in the butanol and ethanol formation pathway of some bacteria. The fermentation process is characterized by an acid producing growth phase, followed by a solvent producing phase. The latter phase is associated with the induction of solventogenic enzymes such as butanol dehydrogenase. The activity of the enzymes require NADPH as cofactor, as well as divalent ions zinc or iron. This family is a member of the iron-containing alcohol dehydrogenase superfamily. Protein structure has a dehydroquinate synthase-like fold.
Probab=38.19 E-value=75 Score=34.67 Aligned_cols=79 Identities=6% Similarity=-0.018 Sum_probs=54.3
Q ss_pred cCCeEEEEEEEcCCcc-cchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--hhhHHHHH
Q 003275 70 YGWREVIAIFVDDDYG-RNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN--PDTGLTIF 146 (834)
Q Consensus 70 ~~W~~v~iI~~d~~~g-~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~--~~~~~~i~ 146 (834)
++.+++.+|+....+- .+..+.+.+.+++.|+++.....+.++.+.+.+...+..+++.++|+||-.+. .-|+.+.+
T Consensus 21 ~~~~r~livt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGGSviD~AK~i 100 (375)
T cd08179 21 LKGKKAFIVTGGGSMKKFGFLDKVEAYLKEAGIEVEVFEGVEPDPSVETVLKGAEAMREFEPDWIIALGGGSPIDAAKAM 100 (375)
T ss_pred hcCCeEEEEeCchHHHhCChHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHHHHH
Confidence 3447887777443222 34567888999988987764444555556678899999999999999987754 34555555
Q ss_pred HH
Q 003275 147 SV 148 (834)
Q Consensus 147 ~~ 148 (834)
..
T Consensus 101 a~ 102 (375)
T cd08179 101 WI 102 (375)
T ss_pred HH
Confidence 43
No 456
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=38.15 E-value=74 Score=30.47 Aligned_cols=28 Identities=21% Similarity=0.557 Sum_probs=25.9
Q ss_pred EEEECCCChhhHHHHHHhhccCCccEEe
Q 003275 6 VAAIGPQSSGIAHVISHVVNELNVPLLS 33 (834)
Q Consensus 6 ~aiiGp~~S~~~~~~~~~~~~~~vP~Is 33 (834)
+.|+||.+|+=+-....+++.+++|+||
T Consensus 3 iiilG~pGaGK~T~A~~La~~~~i~hls 30 (178)
T COG0563 3 ILILGPPGAGKSTLAKKLAKKLGLPHLD 30 (178)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCcEEc
Confidence 6899999999998889999999999997
No 457
>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=37.86 E-value=1.4e+02 Score=30.22 Aligned_cols=75 Identities=9% Similarity=0.061 Sum_probs=49.4
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|.. ++.|.....+.+.+++++.|..+.....- .. .+....++++.+.++|.|++...... ...++.+.+.
T Consensus 2 I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~---~~-~~~~~~i~~~~~~~vdgiii~~~~~~-~~~~~~~~~~ 76 (266)
T cd06278 2 IGVVVADLDNPFYSELLEALSRALQARGYQPLLINTD---DD-EDLDAALRQLLQYRVDGVIVTSGTLS-SELAEECRRN 76 (266)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEEcCC---CC-HHHHHHHHHHHHcCCCEEEEecCCCC-HHHHHHHhhc
Confidence 455554 35677788899999999999987654221 12 25566777777788998887643322 2346667766
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|.
T Consensus 77 ~i 78 (266)
T cd06278 77 GI 78 (266)
T ss_pred CC
Confidence 64
No 458
>cd08549 G1PDH_related Glycerol-1-phosphate_dehydrogenase and related proteins. Bacterial and archeal glycerol-1-phosphate dehydrogenase-like oxidoreductases. The proteins have similarity with glycerol-1-phosphate dehydrogenase (G1PDH). G1PDH plays a role in the synthesis of phosphoglycerolipids in gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires Ni++ ion. It also contains archaeal Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) that plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids.
Probab=37.83 E-value=1.4e+02 Score=31.94 Aligned_cols=98 Identities=7% Similarity=0.089 Sum_probs=60.3
Q ss_pred HHHHHHHHHcCC-eEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeee-cCCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003275 61 HAVADLVEYYGW-REVIAIFVDDDYGRNGISVLGDALSKKRAKISYKA-PFSPGASRSAINSLLVGANLMESRVFVVHVN 138 (834)
Q Consensus 61 ~aia~ll~~~~W-~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~-~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~ 138 (834)
..+.++++.++. +++.+|+....+.. ..+.+.+.+++.|+++.... ....+.+.+.+...+..+++ ++|+||-.+.
T Consensus 12 ~~l~~~~~~~~~~~kvlivtd~~~~~~-~~~~i~~~L~~~~~~~~i~~~~~~~~p~~~~v~~~~~~~~~-~~d~IIaiGG 89 (332)
T cd08549 12 NDIGPIINKIGVNSKIMIVCGNNTYKV-AGKEIIERLESNNFTKEVLERDSLLIPDEYELGEVLIKLDK-DTEFLLGIGS 89 (332)
T ss_pred HHHHHHHHHcCCCCcEEEEECCcHHHH-HHHHHHHHHHHcCCeEEEEecCCCCCCCHHHHHHHHHHhhc-CCCEEEEECC
Confidence 345667777776 78877775444332 34788888988887554211 22223345777888888877 8898887654
Q ss_pred --hhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 139 --PDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 139 --~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
.-|+.+++. ...| ..++-|.|.
T Consensus 90 Gsv~D~aK~iA--~~~g---ip~I~VPTT 113 (332)
T cd08549 90 GTIIDLVKFVS--FKVG---KPFISVPTA 113 (332)
T ss_pred cHHHHHHHHHH--HHcC---CCEEEeCCC
Confidence 456666654 2223 355666654
No 459
>PRK10481 hypothetical protein; Provisional
Probab=37.70 E-value=3.1e+02 Score=27.33 Aligned_cols=75 Identities=11% Similarity=-0.041 Sum_probs=47.9
Q ss_pred HHHHHHc-CCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhH
Q 003275 64 ADLVEYY-GWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTG 142 (834)
Q Consensus 64 a~ll~~~-~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~ 142 (834)
..++... +-+++++|....+- .+.-...+.+.|..+.+...-|...+...+....++++..++|+||+.|..-..
T Consensus 120 ~~lv~Al~~g~riGVitP~~~q----i~~~~~kw~~~G~~v~~~~aspy~~~~~~l~~aa~~L~~~gaD~Ivl~C~G~~~ 195 (224)
T PRK10481 120 PPLVAAIVGGHQVGVIVPVEEQ----LAQQAQKWQVLQKPPVFALASPYHGSEEELIDAGKELLDQGADVIVLDCLGYHQ 195 (224)
T ss_pred HHHHHHhcCCCeEEEEEeCHHH----HHHHHHHHHhcCCceeEeecCCCCCCHHHHHHHHHHhhcCCCCEEEEeCCCcCH
Confidence 4444332 44899999975442 233333444447777665544433445578888888888999999999865443
No 460
>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B, proteobacterial. This model represents the MoaB protein molybdopterin biosynthesis regions in Proteobacteria. This crystallized but incompletely characterized protein is thought to be involved in, though not required for, early steps in molybdopterin biosynthesis. It may bind a molybdopterin precursor. A distinctive conserved motif PCN near the C-terminus helps distinguish this clade from other homologs, including sets of proteins designated MogA.
Probab=37.61 E-value=1.5e+02 Score=27.94 Aligned_cols=65 Identities=11% Similarity=0.056 Sum_probs=44.2
Q ss_pred CeEEEEEEEcCCccc---chHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc-CCceEEEEEeC
Q 003275 72 WREVIAIFVDDDYGR---NGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANL-MESRVFVVHVN 138 (834)
Q Consensus 72 W~~v~iI~~d~~~g~---~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~-~~~~vivl~~~ 138 (834)
..++++|...|.-+. .....+...+++.|.++.....++. +.+.+...+++..+ .+.|+|+..+.
T Consensus 4 ~~rv~vit~~d~~~~~~d~n~~~l~~~L~~~G~~v~~~~iv~D--d~~~i~~~l~~~~~~~~~DlVIttGG 72 (163)
T TIGR02667 4 PLRIAILTVSDTRTEEDDTSGQYLVERLTEAGHRLADRAIVKD--DIYQIRAQVSAWIADPDVQVILITGG 72 (163)
T ss_pred ccEEEEEEEeCcCCccCCCcHHHHHHHHHHCCCeEEEEEEcCC--CHHHHHHHHHHHHhcCCCCEEEECCC
Confidence 456777765443222 2355778888999999888777773 34678888877643 56898888753
No 461
>PF02602 HEM4: Uroporphyrinogen-III synthase HemD; InterPro: IPR003754 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents uroporphyrinogen III synthase (4.2.1.75 from EC) which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the inversion of the final pyrrole unit (ring D) of the linear tetrapyrrole molecule, linking it to the first pyrrole unit (ring A), thereby generating a large macrocyclic structure called uroporphyrinogen III []. The enzyme folds into two alpha/beta domains connected by a beta-ladder, the active site being located between the two domains []. Congenital erythropoietic porphyria (CEP) is an autosomal recessive inborn error of metabolism that results from the markedly deficient activity of uroporphyrinogen III synthase []. ; GO: 0004852 uroporphyrinogen-III synthase activity, 0033014 tetrapyrrole biosynthetic process; PDB: 1WD7_B 1WCX_A 1WCW_A 3D8R_A 3D8T_B 3D8S_A 3D8N_A 3RE1_A 3MW8_A 3P9Z_A ....
Probab=37.61 E-value=61 Score=32.38 Aligned_cols=92 Identities=15% Similarity=0.162 Sum_probs=59.4
Q ss_pred cCChHHHHHHHHHHHHH-cCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCce
Q 003275 53 TQSDYYQMHAVADLVEY-YGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESR 131 (834)
Q Consensus 53 ~ps~~~q~~aia~ll~~-~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~ 131 (834)
.|+....++.+++.+.. ..-+++.++. |......|.+.|++.|..|.....|.. ............+...+.+
T Consensus 97 ~~~~~~~s~~L~~~l~~~~~~~~vl~~~-----g~~~~~~l~~~L~~~g~~v~~~~vY~~-~~~~~~~~~~~~l~~~~~~ 170 (231)
T PF02602_consen 97 VPSSEGSSEGLAELLKEQLRGKRVLILR-----GEGGRPDLPEKLREAGIEVTEVIVYET-PPEELSPELKEALDRGEID 170 (231)
T ss_dssp E-TTSSSHHHHHGGHHHCCTTEEEEEEE-----SSSSCHHHHHHHHHTTEEEEEEECEEE-EEHHHHHHHHHHHHHTTTS
T ss_pred cCCCCCCHHHHHHHHHhhCCCCeEEEEc-----CCCccHHHHHHHHHCCCeEEEEEEeec-ccccchHHHHHHHHcCCCC
Confidence 45545556888887763 4447877665 334567788999999999877666654 2223334445555555565
Q ss_pred EEEEEeChhhHHHHHHHHHh
Q 003275 132 VFVVHVNPDTGLTIFSVAKS 151 (834)
Q Consensus 132 vivl~~~~~~~~~i~~~a~~ 151 (834)
+ |++.++..+..+++...+
T Consensus 171 ~-v~ftS~~~~~~~~~~~~~ 189 (231)
T PF02602_consen 171 A-VVFTSPSAVRAFLELLKK 189 (231)
T ss_dssp E-EEESSHHHHHHHHHHSSG
T ss_pred E-EEECCHHHHHHHHHHhHh
Confidence 5 566788888888877654
No 462
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member 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. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=37.52 E-value=1.3e+02 Score=31.40 Aligned_cols=77 Identities=14% Similarity=0.177 Sum_probs=51.7
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhc--CCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEe-ChhhHHHHHHHH
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSK--KRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHV-NPDTGLTIFSVA 149 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~--~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~-~~~~~~~i~~~a 149 (834)
|++|..+ +.|.......+.+++++ .|..+.... ...+.......+..+...+++.|++.. .+......++++
T Consensus 2 Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~~---~~~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~~ 78 (303)
T cd01539 2 IGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFYD---AKNNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINKA 78 (303)
T ss_pred eEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEec---CCCCHHHHHHHHHHHHHcCCCEEEEecCchhhHHHHHHHH
Confidence 5666643 55667778899999999 787766532 222334455677788888999888754 333346677787
Q ss_pred HhCCC
Q 003275 150 KSLGM 154 (834)
Q Consensus 150 ~~~g~ 154 (834)
.+.|.
T Consensus 79 ~~~gi 83 (303)
T cd01539 79 KQKNI 83 (303)
T ss_pred HHCCC
Confidence 77775
No 463
>cd08184 Fe-ADH3 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the iron-containing alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron or zinc ions. Members of this family are mainly found in bacteria.
Probab=37.33 E-value=1.5e+02 Score=31.82 Aligned_cols=84 Identities=12% Similarity=0.010 Sum_probs=53.9
Q ss_pred HHHHHHHHHcCC--eEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC---CceEEEE
Q 003275 61 HAVADLVEYYGW--REVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM---ESRVFVV 135 (834)
Q Consensus 61 ~aia~ll~~~~W--~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~---~~~vivl 135 (834)
..+.++++.+|. +.+.+++ |...- . +.+.+.+++.|+.+.....+..+.+.+++....+..++. ++|+||-
T Consensus 12 ~~l~~~~~~~g~~~~~~lvvt-d~~~~-~--~~v~~~L~~~g~~~~~f~~v~~nPt~~~v~~~~~~~~~~~~~~~D~IIa 87 (347)
T cd08184 12 DQLNDLLAPKRKNKDPAVFFV-DDVFQ-G--KDLISRLPVESEDMIIWVDATEEPKTDQIDALTAQVKSFDGKLPCAIVG 87 (347)
T ss_pred HHHHHHHHHcCCCCCeEEEEE-Ccchh-h--hHHHHHHHhcCCcEEEEcCCCCCcCHHHHHHHHHHHHhhCCCCCCEEEE
Confidence 446666777763 5566666 43221 1 567788888887654444565566667888888888876 8999986
Q ss_pred EeC--hhhHHHHHHH
Q 003275 136 HVN--PDTGLTIFSV 148 (834)
Q Consensus 136 ~~~--~~~~~~i~~~ 148 (834)
.+. .-|+.+.+..
T Consensus 88 iGGGS~iD~AKaia~ 102 (347)
T cd08184 88 IGGGSTLDVAKAVSN 102 (347)
T ss_pred eCCcHHHHHHHHHHH
Confidence 654 3455555443
No 464
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=37.29 E-value=1.4e+02 Score=31.50 Aligned_cols=80 Identities=6% Similarity=-0.034 Sum_probs=52.2
Q ss_pred CeEEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003275 72 WREVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVA 149 (834)
Q Consensus 72 W~~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a 149 (834)
-+.|+++..+ +.|.......+.+++++.|..+.....- .+.......+..+...+.|.+|+..........++.+
T Consensus 60 ~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~---~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 136 (327)
T TIGR02417 60 SRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACSD---DNPDQEKVVIENLLARQVDALIVASCMPPEDAYYQKL 136 (327)
T ss_pred CceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEeCCCCCChHHHHHH
Confidence 4578888753 5677788899999999999988654321 1223445667777778889888764332123445566
Q ss_pred HhCCC
Q 003275 150 KSLGM 154 (834)
Q Consensus 150 ~~~g~ 154 (834)
.+.+.
T Consensus 137 ~~~~i 141 (327)
T TIGR02417 137 QNEGL 141 (327)
T ss_pred HhcCC
Confidence 65553
No 465
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=36.98 E-value=1.2e+02 Score=32.07 Aligned_cols=78 Identities=21% Similarity=0.188 Sum_probs=43.4
Q ss_pred cCCCChhhhhcCCCCeeEee-CchhhH---HHHhhhcccccceEecC--CHHHHHHHHhcCCCCCceEEEEec----hhh
Q 003275 589 SQIEGIDSLISSTEPIGVQD-GSFAWN---YLVDELKIAESRLVKLK--NMEEYSIALARGPKGGGVAAIVDE----LPY 658 (834)
Q Consensus 589 ~~i~s~~dL~~~~~~v~~~~-~s~~~~---~l~~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~g~~~a~~~~----~~~ 658 (834)
..|+++.||. |++|.+.. ||-.+- .+.+..++......... ...+..+++.+ |.+||++.- .+.
T Consensus 127 ~~Ikti~DL~--GKrV~iG~~gSgt~~~a~~il~a~Gi~~~~~~~~~~~~~a~~~~~l~~----g~iDA~~~~~G~p~~a 200 (321)
T COG2358 127 AGIKTIADLK--GKRVAIGPPGSGTEATARQILEALGITYDDYELDLGLGDAESADALKN----GTIDAAFYVAGVPNPA 200 (321)
T ss_pred CCcceehhcC--CCEEeecCCCCccHHHHHHHHHHcCCCCcchhhhhhcCchhhHHHhhC----CcccEEEEecCCCCcc
Confidence 5799999997 99888753 332222 22234555433332111 22344677777 899988765 222
Q ss_pred HHHHhhcCCccEEEeC
Q 003275 659 IELFMSKTNCEFRTVG 674 (834)
Q Consensus 659 ~~~~~~~~~~~l~~v~ 674 (834)
+. .+.. -|++.+++
T Consensus 201 i~-el~~-~~~i~lv~ 214 (321)
T COG2358 201 IS-ELAT-TCDIVLVP 214 (321)
T ss_pred HH-HHHh-hCCeEEEe
Confidence 32 2233 46666664
No 466
>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=36.90 E-value=1.5e+02 Score=29.93 Aligned_cols=76 Identities=5% Similarity=-0.032 Sum_probs=49.6
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|.. ++.|.......+.+++++.|..+...... .+.......+..+...+.|.|++.....+... ++.+.+.
T Consensus 2 igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~-~~~~~~~ 77 (264)
T cd06274 2 IGLIIPDLENRSFARIAKRLEALARERGYQLLIACSD---DDPETERETVETLIARQVDALIVAGSLPPDDP-YYLCQKA 77 (264)
T ss_pred EEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEcCCCCchHH-HHHHHhc
Confidence 455553 35677778889999999999987664322 13344556778888889998888754322222 5566665
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|.
T Consensus 78 ~i 79 (264)
T cd06274 78 GL 79 (264)
T ss_pred CC
Confidence 63
No 467
>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=36.54 E-value=1.4e+02 Score=30.11 Aligned_cols=76 Identities=12% Similarity=0.062 Sum_probs=49.2
Q ss_pred EEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|..+ +.|.....+.+.+++++.|.++..... ..+.......++.+...++|.|++...... ...++.+.+.
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiii~~~~~~-~~~~~~~~~~ 77 (268)
T cd01575 2 VAVLVPSLSNSVFADVLQGISDVLEAAGYQLLLGNT---GYSPEREEELLRTLLSRRPAGLILTGLEHT-ERTRQLLRAA 77 (268)
T ss_pred EEEEeCCCcchhHHHHHHHHHHHHHHcCCEEEEecC---CCCchhHHHHHHHHHHcCCCEEEEeCCCCC-HHHHHHHHhc
Confidence 4566643 556677788999999999988765322 223345567788888888998888654322 3345555555
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|.
T Consensus 78 ~i 79 (268)
T cd01575 78 GI 79 (268)
T ss_pred CC
Confidence 53
No 468
>cd06321 PBP1_ABC_sugar_binding_like_11 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=36.53 E-value=1.3e+02 Score=30.52 Aligned_cols=77 Identities=8% Similarity=-0.054 Sum_probs=50.3
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhc--CCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHH
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSK--KRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNP-DTGLTIFSVA 149 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~--~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a 149 (834)
|++|.. ++.|.......+.+++++ .|.++..... ..+.......++.+...++|.|++.... ......++.+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~~~i~~~ 78 (271)
T cd06321 2 IGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVVSA---DYDLNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRA 78 (271)
T ss_pred eEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEccC---CCCHHHHHHHHHHHHHhCCCEEEEeCCChhHhHHHHHHH
Confidence 566664 467888889999999999 7776654321 1233445567777777889988886533 2235566777
Q ss_pred HhCCC
Q 003275 150 KSLGM 154 (834)
Q Consensus 150 ~~~g~ 154 (834)
.+.|.
T Consensus 79 ~~~~i 83 (271)
T cd06321 79 QAAGI 83 (271)
T ss_pred HHCCC
Confidence 76553
No 469
>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=36.37 E-value=1.4e+02 Score=30.23 Aligned_cols=76 Identities=8% Similarity=0.001 Sum_probs=44.3
Q ss_pred EEEEEEc------CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHH
Q 003275 75 VIAIFVD------DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSV 148 (834)
Q Consensus 75 v~iI~~d------~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~ 148 (834)
|++|..+ +.|.......+.+++++.|+.+.....-. .........+.+...+.|.|++....... ..++.
T Consensus 2 igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~vdgiii~~~~~~~-~~~~~ 77 (268)
T cd06271 2 IGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYDLVLLPVDP---DEDPLEVYRRLVESGLVDGVIISRTRPDD-PRVAL 77 (268)
T ss_pred eEEEeCCcccccCCccHHHHHHHHHHHHHHCCceEEEecCCC---cHHHHHHHHHHHHcCCCCEEEEecCCCCC-hHHHH
Confidence 4555544 67888888999999999998876643221 11222333333445568888876532222 23445
Q ss_pred HHhCCC
Q 003275 149 AKSLGM 154 (834)
Q Consensus 149 a~~~g~ 154 (834)
+.+.+.
T Consensus 78 ~~~~~i 83 (268)
T cd06271 78 LLERGF 83 (268)
T ss_pred HHhcCC
Confidence 555553
No 470
>cd06324 PBP1_ABC_sugar_binding_like_13 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 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=36.13 E-value=1.3e+02 Score=31.59 Aligned_cols=77 Identities=8% Similarity=0.057 Sum_probs=50.5
Q ss_pred EEEEEE---cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHH
Q 003275 75 VIAIFV---DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLM--ESRVFVVHVNPDTGLTIFSVA 149 (834)
Q Consensus 75 v~iI~~---d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~--~~~vivl~~~~~~~~~i~~~a 149 (834)
|++|.. ++.|.......+.+++++.|..+..... ..+.......++.+... ++|.|++.........+++.+
T Consensus 2 Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~~~---~~~~~~~~~~i~~~~~~~~~vdgiIi~~~~~~~~~~~~~~ 78 (305)
T cd06324 2 VVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVLYA---ERDRFLMLQQARTILQRPDKPDALIFTNEKSVAPELLRLA 78 (305)
T ss_pred eEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHHHhccCCCEEEEcCCccchHHHHHHH
Confidence 455553 4567777888999999999998765422 12333445667777777 899888864333345566777
Q ss_pred HhCCC
Q 003275 150 KSLGM 154 (834)
Q Consensus 150 ~~~g~ 154 (834)
.+.|.
T Consensus 79 ~~~gi 83 (305)
T cd06324 79 EGAGV 83 (305)
T ss_pred HhCCC
Confidence 77664
No 471
>PRK13957 indole-3-glycerol-phosphate synthase; Provisional
Probab=35.83 E-value=2.4e+02 Score=28.54 Aligned_cols=88 Identities=18% Similarity=0.187 Sum_probs=61.9
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
..+|......|-.-++++. |..|..+..+.+...-+...+.|..+..+- + ..++.+.+..++|+|++...
T Consensus 64 ~~~A~~y~~~GA~aISVlT-e~~~F~Gs~~~l~~v~~~v~~PvL~KDFIi---d----~~QI~ea~~~GADavLLI~~~L 135 (247)
T PRK13957 64 VQIAKTYETLGASAISVLT-DQSYFGGSLEDLKSVSSELKIPVLRKDFIL---D----EIQIREARAFGASAILLIVRIL 135 (247)
T ss_pred HHHHHHHHHCCCcEEEEEc-CCCcCCCCHHHHHHHHHhcCCCEEeccccC---C----HHHHHHHHHcCCCEEEeEHhhC
Confidence 4566667788888887776 555555777888777666666666554443 1 23556666789999988753
Q ss_pred -hhhHHHHHHHHHhCCCCC
Q 003275 139 -PDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 139 -~~~~~~i~~~a~~~g~~~ 156 (834)
......++..|.++||..
T Consensus 136 ~~~~l~~l~~~a~~lGle~ 154 (247)
T PRK13957 136 TPSQIKSFLKHASSLGMDV 154 (247)
T ss_pred CHHHHHHHHHHHHHcCCce
Confidence 457888999999999964
No 472
>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=35.41 E-value=1.7e+02 Score=29.46 Aligned_cols=76 Identities=7% Similarity=0.036 Sum_probs=49.3
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|.. ++.|.......+.+++++.|..+..... ..+.......++++...+.|.|++........ .++.+.+.
T Consensus 2 igvi~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~~dgiii~~~~~~~~-~l~~~~~~ 77 (267)
T cd06283 2 IGVIVADITNPFSSLVLKGIEDVCRAHGYQVLVCNS---DNDPEKEKEYLESLLAYQVDGLIVNPTGNNKE-LYQRLAKN 77 (267)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEcC---CCCHHHHHHHHHHHHHcCcCEEEEeCCCCChH-HHHHHhcC
Confidence 445553 4567778889999999999988764321 22334456677788888889888865433332 35666665
Q ss_pred CC
Q 003275 153 GM 154 (834)
Q Consensus 153 g~ 154 (834)
|.
T Consensus 78 ~i 79 (267)
T cd06283 78 GK 79 (267)
T ss_pred CC
Confidence 53
No 473
>cd08173 Gro1PDH Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate using either NADH or NADPH as a coenzyme. Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH, EC 1.1.1.261) plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids. It catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate using either NADH or NADPH as a coenzyme. The activity is zinc-dependent. One characteristic feature of archaea is that their cellular membrane has an ether linkage between the glycerol backbone and the hydrocarbon residues. The polar lipids of the members of Archaea consist of di- and tetraethers of glycerol with isoprenoid alcohols bound at the sn-2 and sn-3 positions of the glycerol moiety. The archaeal polar lipids have the enantiomeric configuration of a glycerophosph
Probab=34.86 E-value=1.4e+02 Score=32.02 Aligned_cols=95 Identities=7% Similarity=0.029 Sum_probs=60.5
Q ss_pred HHHHHHH-HcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003275 62 AVADLVE-YYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-- 138 (834)
Q Consensus 62 aia~ll~-~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-- 138 (834)
.+.++++ ..+.+++.+|+.... .....+.+.+.+++.| .+... +..+.+.+.+...+..+++.++|+||-.+.
T Consensus 14 ~l~~~l~~~~~~~~~liv~d~~~-~~~~~~~v~~~l~~~~-~~~~~--~~~~~~~~~v~~~~~~~~~~~~d~iIaiGGGs 89 (339)
T cd08173 14 KIPNVLRDLLLGGRVLVVTGPTT-KSIAGKKVEALLEDEG-EVDVV--IVEDATYEEVEKVESSARDIGADFVIGVGGGR 89 (339)
T ss_pred HHHHHHHHhCCCCeEEEEECCch-HHHHHHHHHHHHHhcC-CeEEE--EeCCCCHHHHHHHHHHhhhcCCCEEEEeCCch
Confidence 3556666 457789888874433 3356778888888887 44322 223446678888889998889999886654
Q ss_pred hhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 139 PDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 139 ~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
.-|+.+++. ...| ..++-|.|.
T Consensus 90 ~~D~aK~~a--~~~~---~p~i~iPTT 111 (339)
T cd08173 90 VIDVAKVAA--YKLG---IPFISVPTA 111 (339)
T ss_pred HHHHHHHHH--HhcC---CCEEEecCc
Confidence 445666554 2223 345555554
No 474
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=34.18 E-value=3.4e+02 Score=24.14 Aligned_cols=75 Identities=19% Similarity=0.123 Sum_probs=41.5
Q ss_pred ChHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEE
Q 003275 55 SDYYQMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFV 134 (834)
Q Consensus 55 s~~~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~viv 134 (834)
+-..|-..+-++....||.-+. +|.|...+.. + ......+...|..++....++||
T Consensus 15 s~~~Q~~~~~~~a~~~g~~i~~-~~~d~~~s~~----------------------~-~~~R~~~~~ll~~~~~~~~d~iv 70 (137)
T cd00338 15 SLERQREALREYAARNGLEVVG-EYEDAGSSAT----------------------S-LVDRPGLQRLLADVKAGKIDVVL 70 (137)
T ss_pred CHHHHHHHHHHHHHHCCCEEEE-EEEeCCCCcc----------------------c-ccCCHHHHHHHHHHHcCCCCEEE
Confidence 3446777788888777887554 5555432210 0 11235666666666665566666
Q ss_pred EEeC------hhhHHHHHHHHHhCC
Q 003275 135 VHVN------PDTGLTIFSVAKSLG 153 (834)
Q Consensus 135 l~~~------~~~~~~i~~~a~~~g 153 (834)
+.-. +.+...+++.+.+.|
T Consensus 71 v~~~~Rl~R~~~~~~~~~~~l~~~g 95 (137)
T cd00338 71 VEKLDRLSRNLVDLLELLELLEAHG 95 (137)
T ss_pred EEecchhhCCHHHHHHHHHHHHHCC
Confidence 5532 234455555555544
No 475
>cd06316 PBP1_ABC_sugar_binding_like_7 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=34.11 E-value=1.3e+02 Score=31.10 Aligned_cols=79 Identities=5% Similarity=0.056 Sum_probs=50.6
Q ss_pred EEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHHH
Q 003275 74 EVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPD-TGLTIFSVAK 150 (834)
Q Consensus 74 ~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~-~~~~i~~~a~ 150 (834)
+|++|..+ +.|.......+.+++++.|..+.... ....+.......+..+...++|.|++..... ....+++++.
T Consensus 1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~--~~~~~~~~~~~~l~~~~~~~~dgiii~~~~~~~~~~~i~~~~ 78 (294)
T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVATT--DAQFDPAKQVADIETTISQKPDIIISIPVDPVSTAAAYKKVA 78 (294)
T ss_pred CeEEEecCCCChHHHHHHHHHHHHHHHcCCEEEEec--CCCCCHHHHHHHHHHHHHhCCCEEEEcCCCchhhhHHHHHHH
Confidence 35666643 45666778889999999998876321 1122334445667777777899888764332 2356777888
Q ss_pred hCCC
Q 003275 151 SLGM 154 (834)
Q Consensus 151 ~~g~ 154 (834)
+.|.
T Consensus 79 ~~~i 82 (294)
T cd06316 79 EAGI 82 (294)
T ss_pred HcCC
Confidence 7764
No 476
>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein. This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of this gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source.
Probab=33.53 E-value=1.4e+02 Score=31.24 Aligned_cols=77 Identities=12% Similarity=0.119 Sum_probs=48.4
Q ss_pred EEEEE--cCCcccchHHHHHHHHhcCC-cEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhhHHHHHHHHHh
Q 003275 76 IAIFV--DDDYGRNGISVLGDALSKKR-AKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-PDTGLTIFSVAKS 151 (834)
Q Consensus 76 ~iI~~--d~~~g~~~~~~l~~~l~~~g-~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-~~~~~~i~~~a~~ 151 (834)
++|.. ++.|.......+.+++++.| ..+.+.. +...+.......++.+...++|.|++... .......++++++
T Consensus 2 gvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~i~~~--~~~~d~~~q~~~i~~l~~~~vdgiIi~~~~~~~~~~~l~~~~~ 79 (302)
T TIGR02637 2 GLVVKSLGNPFFEAANKGAEEAAKELGSVYIIYTG--PTGTTAEGQIEVVNSLIAQKVDAIAISANDPDALVPALKKAMK 79 (302)
T ss_pred EEEeccCCCHHHHHHHHHHHHHHHHhCCeeEEEEC--CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHH
Confidence 34443 35677777889999999998 4443321 11122344456778887788998888653 3334566777777
Q ss_pred CCC
Q 003275 152 LGM 154 (834)
Q Consensus 152 ~g~ 154 (834)
.|.
T Consensus 80 ~gi 82 (302)
T TIGR02637 80 RGI 82 (302)
T ss_pred CCC
Confidence 774
No 477
>PF04971 Lysis_S: Lysis protein S ; InterPro: IPR007054 The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane [].
Probab=33.37 E-value=48 Score=25.65 Aligned_cols=32 Identities=6% Similarity=-0.007 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccCCcc
Q 003275 743 GLFLICGIACFLALIFFFCRVCGQFRRFGSED 774 (834)
Q Consensus 743 g~f~il~~g~~lal~vf~~e~~~~~~~~~~~~ 774 (834)
+.++-+..|++++++.++.-+++++++.+|+.
T Consensus 33 W~aIGvi~gi~~~~lt~ltN~YFK~k~drr~~ 64 (68)
T PF04971_consen 33 WAAIGVIGGIFFGLLTYLTNLYFKIKEDRRKA 64 (68)
T ss_pred chhHHHHHHHHHHHHHHHhHhhhhhhHhhhHh
Confidence 44555667788889999999988888877765
No 478
>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=33.37 E-value=1.7e+02 Score=29.61 Aligned_cols=75 Identities=9% Similarity=-0.082 Sum_probs=48.4
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhC
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSL 152 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~ 152 (834)
|++|.. ++.|-....+.+.+++++.|..+..... ..+.......++++...++|.+++..... ...++..+.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~-~~~~~~~l~~~ 77 (268)
T cd06298 2 VGVIIPDITNSYFAELARGIDDIATMYKYNIILSNS---DNDKEKELKVLNNLLAKQVDGIIFMGGKI-SEEHREEFKRS 77 (268)
T ss_pred EEEEECCCcchHHHHHHHHHHHHHHHcCCeEEEEeC---CCCHHHHHHHHHHHHHhcCCEEEEeCCCC-cHHHHHHHhcC
Confidence 456664 3667778889999999999988765432 12334456677777778899888864321 12355555544
Q ss_pred C
Q 003275 153 G 153 (834)
Q Consensus 153 g 153 (834)
+
T Consensus 78 ~ 78 (268)
T cd06298 78 P 78 (268)
T ss_pred C
Confidence 4
No 479
>PLN02727 NAD kinase
Probab=33.36 E-value=3.1e+02 Score=33.33 Aligned_cols=108 Identities=8% Similarity=0.001 Sum_probs=65.8
Q ss_pred CCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeec-CCCCCChHH
Q 003275 39 PTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAP-FSPGASRSA 117 (834)
Q Consensus 39 ~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~-~~~~~~~~~ 117 (834)
+.+++..---++|..+....+.+.++ ..|-|.|+-+-.|++-+........++.++.|++..+.-. .....+.++
T Consensus 253 ~~~~~~~~~~~~rsgQpspe~la~LA----~~GfKTIINLRpd~E~~q~~~~ee~eAae~~GL~yVhIPVs~~~apt~Eq 328 (986)
T PLN02727 253 DIDSKESEAAFWRGGQVTEEGLKWLL----EKGFKTIVDLRAEIVKDNFYQAAVDDAISSGKIEVVKIPVEVRTAPSAEQ 328 (986)
T ss_pred ccccccceeeEEEeCCCCHHHHHHHH----HCCCeEEEECCCCCcCCCchhHHHHHHHHHcCCeEEEeecCCCCCCCHHH
Confidence 44444222356777776665544333 3699999888777664455567788999999999775422 122235677
Q ss_pred HHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHH
Q 003275 118 INSLLVGANLMESRVFVVHVNP-DTGLTIFSVAK 150 (834)
Q Consensus 118 ~~~~l~~l~~~~~~vivl~~~~-~~~~~i~~~a~ 150 (834)
+......+++.-+.=|++||-. .+-..++-+..
T Consensus 329 Ve~fa~~l~~slpkPVLvHCKSGarRAGamvA~y 362 (986)
T PLN02727 329 VEKFASLVSDSSKKPIYLHSKEGVWRTSAMVSRW 362 (986)
T ss_pred HHHHHHHHHhhcCCCEEEECCCCCchHHHHHHHH
Confidence 7777777745445667888753 33333443433
No 480
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=33.28 E-value=25 Score=28.02 Aligned_cols=18 Identities=6% Similarity=-0.005 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHHHhhccC
Q 003275 754 LALIFFFCRVCGQFRRFG 771 (834)
Q Consensus 754 lal~vf~~e~~~~~~~~~ 771 (834)
+.++|..++++.++++++
T Consensus 13 f~ifVap~wl~lHY~~k~ 30 (75)
T TIGR02976 13 FVIFVAPLWLILHYRSKR 30 (75)
T ss_pred HHHHHHHHHHHHHHHhhh
Confidence 344444555555555443
No 481
>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=33.20 E-value=1.8e+02 Score=29.41 Aligned_cols=69 Identities=7% Similarity=0.015 Sum_probs=41.2
Q ss_pred CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHhCCC
Q 003275 82 DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAKSLGM 154 (834)
Q Consensus 82 ~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~~~g~ 154 (834)
+.|.....+.+.+++++.|.++.....- + ...........+...++|.||+...... ...++.+.+.|.
T Consensus 16 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~--~-~~~~~~~~~~~~~~~~~dgiii~~~~~~-~~~~~~~~~~~i 84 (270)
T cd06294 16 NPFFIEVLRGISAVANENGYDISLATGK--N-EEELLEEVKKMIQQKRVDGFILLYSRED-DPIIDYLKEEKF 84 (270)
T ss_pred CCCHHHHHHHHHHHHHHCCCEEEEecCC--C-cHHHHHHHHHHHHHcCcCEEEEecCcCC-cHHHHHHHhcCC
Confidence 5577778889999999999887653211 1 2223333333344556888888653222 345666666664
No 482
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=33.19 E-value=4.1e+02 Score=24.81 Aligned_cols=66 Identities=11% Similarity=0.027 Sum_probs=37.7
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
++..+++..+.+..+ .+.+++.. .+.+...+ .+++|+++.... .....+ -+.++....++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~v~~~~---------~~~~~~~l-~~~~D~~i~~~~---~~~~~l-~~~~l~~~~~~~v~~~ 78 (202)
T cd08472 14 LLLIPALPDFLARYP-DIELDLGV---------SDRPVDLI-REGVDCVIRVGE---LADSSL-VARRLGELRMVTCASP 78 (202)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEE---------CCCcchhh-cccccEEEEcCC---CCCccE-EEEEccceeEEEEECH
Confidence 455788888888876 34455432 12344444 567999985321 111222 3456667777777764
Q ss_pred C
Q 003275 481 Q 481 (834)
Q Consensus 481 ~ 481 (834)
.
T Consensus 79 ~ 79 (202)
T cd08472 79 A 79 (202)
T ss_pred H
Confidence 3
No 483
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=33.15 E-value=1.3e+02 Score=26.30 Aligned_cols=72 Identities=17% Similarity=0.137 Sum_probs=0.0
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeec-CCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003275 60 MHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAP-FSPGASRSAINSLLVGANLMESRVFVVHVN 138 (834)
Q Consensus 60 ~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~-~~~~~~~~~~~~~l~~l~~~~~~vivl~~~ 138 (834)
...++.+++..|| +|.++-.+... +.+.+.+.+.+..++.-.. ..... ......++.+|+..+++.++.+.
T Consensus 17 l~~la~~l~~~G~-~v~~~d~~~~~-----~~l~~~~~~~~pd~V~iS~~~~~~~--~~~~~l~~~~k~~~p~~~iv~GG 88 (121)
T PF02310_consen 17 LLYLAAYLRKAGH-EVDILDANVPP-----EELVEALRAERPDVVGISVSMTPNL--PEAKRLARAIKERNPNIPIVVGG 88 (121)
T ss_dssp HHHHHHHHHHTTB-EEEEEESSB-H-----HHHHHHHHHTTCSEEEEEESSSTHH--HHHHHHHHHHHTTCTTSEEEEEE
T ss_pred HHHHHHHHHHCCC-eEEEECCCCCH-----HHHHHHHhcCCCcEEEEEccCcCcH--HHHHHHHHHHHhcCCCCEEEEEC
Q ss_pred h
Q 003275 139 P 139 (834)
Q Consensus 139 ~ 139 (834)
+
T Consensus 89 ~ 89 (121)
T PF02310_consen 89 P 89 (121)
T ss_dssp S
T ss_pred C
No 484
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari
Probab=32.71 E-value=1.3e+02 Score=28.10 Aligned_cols=68 Identities=7% Similarity=-0.048 Sum_probs=45.6
Q ss_pred eeeHHHHHHHHHhCCCCcCEEEEecCCCCCCCChHHHHHHHHhCcccEEeeeeeeecCceeeEEecceeeeceEEEEEec
Q 003275 401 GYCIDVFEAAVNLLPYPVPHNYIMYGNGKRNPIYNDIVQQVALNKFDAAVGDITIVTNRTKLVDFTQPYMESGLVVVAPV 480 (834)
Q Consensus 401 G~~~dll~~l~~~l~~~~~~~~~~~~~~~~n~s~~~~~~~l~~g~~D~~~~~~~i~~~r~~~vdfs~p~~~~~~~~vv~~ 480 (834)
.+-.+++..+.+..+ .+++++.. +....+.++|.+|++|+++.... . .. ..+.++....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~--~---~~-~~~~~l~~~~~~~v~~~ 78 (185)
T cd08439 13 TILPFLLNRFASVYP-RLAIEVVC-------KRTPRLMEMLERGEVDLALITHP--P---PG-ASATILRRSPTVWYCAA 78 (185)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEE-------CChHHHHHHHHCCCCcEEEEecc--C---CC-CCceEEEEecCEEEECC
Confidence 344677777777664 34466553 44678999999999999886321 1 11 12577778888888877
Q ss_pred CC
Q 003275 481 QK 482 (834)
Q Consensus 481 ~~ 482 (834)
..
T Consensus 79 ~~ 80 (185)
T cd08439 79 GY 80 (185)
T ss_pred CC
Confidence 65
No 485
>PF00218 IGPS: Indole-3-glycerol phosphate synthase; InterPro: IPR013798 Indole-3-glycerol phosphate synthase (4.1.1.48 from EC) (IGPS) catalyses the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyses N-(5'-phosphoribosyl)anthranilate isomerase (5.3.1.24 from EC) (PRAI) activity (see IPR001240 from INTERPRO), the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (2.4.2 from EC) (GATase) N-terminal domain (see IPR000991 from INTERPRO). A structure of the IGPS domain of the bifunctional enzyme from the mesophilic bacterium E. coli (eIGPS) has been compared with the monomeric indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus (sIGPS). Both are single-domain (beta/alpha)8 barrel proteins, with one (eIGPS) or two (sIGPS) additional helices inserted before the first beta strand []. ; GO: 0004425 indole-3-glycerol-phosphate synthase activity; PDB: 1VC4_A 1PII_A 1JCM_P 1I4N_B 1J5T_A 3TSM_B 4FB7_A 3QJA_A 1JUL_A 2C3Z_A ....
Probab=32.62 E-value=2e+02 Score=29.29 Aligned_cols=89 Identities=13% Similarity=0.090 Sum_probs=59.3
Q ss_pred HHHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-
Q 003275 60 MHAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN- 138 (834)
Q Consensus 60 ~~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~- 138 (834)
...++.-....|-.-+++++ |..|..+..+.|...-+..++.|..+..+- + .-++.+.+..++|.|++...
T Consensus 70 ~~~~a~~y~~~GA~aiSVlT-e~~~F~Gs~~dL~~v~~~~~~PvL~KDFIi---d----~~QI~eA~~~GADaVLLI~~~ 141 (254)
T PF00218_consen 70 PAEIAKAYEEAGAAAISVLT-EPKFFGGSLEDLRAVRKAVDLPVLRKDFII---D----PYQIYEARAAGADAVLLIAAI 141 (254)
T ss_dssp HHHHHHHHHHTT-SEEEEE---SCCCHHHHHHHHHHHHHSSS-EEEES------S----HHHHHHHHHTT-SEEEEEGGG
T ss_pred HHHHHHHHHhcCCCEEEEEC-CCCCCCCCHHHHHHHHHHhCCCcccccCCC---C----HHHHHHHHHcCCCEeehhHHh
Confidence 35566666778888888777 556667788888888777788777654443 1 23667778899999998853
Q ss_pred --hhhHHHHHHHHHhCCCCC
Q 003275 139 --PDTGLTIFSVAKSLGMTA 156 (834)
Q Consensus 139 --~~~~~~i~~~a~~~g~~~ 156 (834)
......++..|.++||..
T Consensus 142 L~~~~l~~l~~~a~~lGle~ 161 (254)
T PF00218_consen 142 LSDDQLEELLELAHSLGLEA 161 (254)
T ss_dssp SGHHHHHHHHHHHHHTT-EE
T ss_pred CCHHHHHHHHHHHHHcCCCe
Confidence 455588999999999854
No 486
>cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.
Probab=32.61 E-value=1.8e+02 Score=26.94 Aligned_cols=63 Identities=11% Similarity=0.075 Sum_probs=42.1
Q ss_pred EEEEEEEcCC--ccc---chHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhc-CCceEEEEEeC
Q 003275 74 EVIAIFVDDD--YGR---NGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANL-MESRVFVVHVN 138 (834)
Q Consensus 74 ~v~iI~~d~~--~g~---~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~-~~~~vivl~~~ 138 (834)
++++|...|+ .|+ .....+.+.+++.|.++.....++. +.+++.+.+++..+ +++|+||..+.
T Consensus 2 ~~~ii~~~~e~~~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~D--d~~~i~~~l~~~~~~~~~DlVittGG 70 (152)
T cd00886 2 RAAVLTVSDTRSAGEAEDRSGPALVELLEEAGHEVVAYEIVPD--DKDEIREALIEWADEDGVDLILTTGG 70 (152)
T ss_pred EEEEEEEcCcccCCCCccchHHHHHHHHHHcCCeeeeEEEcCC--CHHHHHHHHHHHHhcCCCCEEEECCC
Confidence 4666655442 222 2355788889999999888777773 33677777776644 36898888753
No 487
>cd08169 DHQ-like Dehydroquinate synthase-like which includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. Dehydroquinate synthase-like. This group contains dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. They exhibit the dehydroquinate synthase structural fold. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-Deoxystreptamine (DOS)-containing aminoglycoside antibiotics includes ne
Probab=32.48 E-value=4.1e+02 Score=28.56 Aligned_cols=101 Identities=11% Similarity=-0.019 Sum_probs=60.2
Q ss_pred HHHHHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhc-CCcEEEeeecCCCCCChHHHHHHHHHhhcC---CceEEEEE
Q 003275 61 HAVADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSK-KRAKISYKAPFSPGASRSAINSLLVGANLM---ESRVFVVH 136 (834)
Q Consensus 61 ~aia~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~-~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~---~~~vivl~ 136 (834)
..+.++++.++-+++.+|.....+. ...+.+.+.+++ .++.+..........+.+.+...+..+++. +.++||..
T Consensus 12 ~~l~~~~~~~~~~k~livtd~~v~~-~~~~~v~~~L~~~~~~~~~~~~~~e~~k~~~~v~~~~~~~~~~~~~r~d~IIai 90 (344)
T cd08169 12 ESVESYTTRDLFDQYFFISDSGVAD-LIAHYIAEYLSKILPVHILVIEGGEEYKTFETVTRILERAIALGANRRTAIVAV 90 (344)
T ss_pred HHHHHHHHhcCCCeEEEEECccHHH-HHHHHHHHHHHhhcCceEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEEE
Confidence 3355567777778888777544332 566778888876 566543322222333556777777777754 47888866
Q ss_pred eC--hhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 137 VN--PDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 137 ~~--~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
+. .-+...++......| ..++-|.|.
T Consensus 91 GGGsv~D~ak~vA~~~~rg---ip~i~VPTT 118 (344)
T cd08169 91 GGGATGDVAGFVASTLFRG---IAFIRVPTT 118 (344)
T ss_pred CCcHHHHHHHHHHHHhccC---CcEEEecCC
Confidence 54 456666655444334 355666664
No 488
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=32.46 E-value=37 Score=30.79 Aligned_cols=32 Identities=19% Similarity=0.371 Sum_probs=27.4
Q ss_pred cEEEECCCChhhHHHHHHhhccCCccEEeccc
Q 003275 5 VVAAIGPQSSGIAHVISHVVNELNVPLLSFGA 36 (834)
Q Consensus 5 V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~a 36 (834)
|+.++||.+|+=+..+..++...+.++|+...
T Consensus 1 lii~~G~pgsGKSt~a~~l~~~~~~~~i~~D~ 32 (143)
T PF13671_consen 1 LIILCGPPGSGKSTLAKRLAKRLGAVVISQDE 32 (143)
T ss_dssp EEEEEESTTSSHHHHHHHHHHHSTEEEEEHHH
T ss_pred CEEEECCCCCCHHHHHHHHHHHCCCEEEeHHH
Confidence 57899999999999999999888888887543
No 489
>cd03174 DRE_TIM_metallolyase DRE-TIM metallolyase superfamily. The DRE-TIM metallolyase superfamily includes 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 containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".
Probab=32.42 E-value=1.9e+02 Score=29.45 Aligned_cols=37 Identities=14% Similarity=0.128 Sum_probs=26.9
Q ss_pred CCCcEEEECCCChhhHHHHHHhhccCCccEEecccCC
Q 003275 2 ENEVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATD 38 (834)
Q Consensus 2 ~~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~ 38 (834)
+||-...-...+......++..+.+.+|+.|..+...
T Consensus 6 RDG~q~~~~~~s~e~~~~i~~~L~~~GV~~IEvg~~~ 42 (265)
T cd03174 6 RDGLQSEGATFSTEDKLEIAEALDEAGVDSIEVGSGA 42 (265)
T ss_pred CCcccCCCCCCCHHHHHHHHHHHHHcCCCEEEeccCc
Confidence 4444444455677788888899999999999876543
No 490
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=32.32 E-value=45 Score=30.02 Aligned_cols=27 Identities=37% Similarity=0.574 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 003275 743 GLFLICGIACFLALIFFFCRVCGQFRR 769 (834)
Q Consensus 743 g~f~il~~g~~lal~vf~~e~~~~~~~ 769 (834)
.+|+|++++++|.|+++++.--+++++
T Consensus 3 ~l~~iii~~i~l~~~~~~~~~rRR~r~ 29 (130)
T PF12273_consen 3 VLFAIIIVAILLFLFLFYCHNRRRRRR 29 (130)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 456666666666666666666666655
No 491
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=32.29 E-value=30 Score=24.97 Aligned_cols=30 Identities=23% Similarity=0.404 Sum_probs=0.0
Q ss_pred hhhHHHHHHHHHHHHhhhheeecccCCCCC
Q 003275 496 IPMWLVTGGFFLFVGAVVWILEHRFNNEFR 525 (834)
Q Consensus 496 ~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~ 525 (834)
...|.+++.+++++++++|.+..+..+.++
T Consensus 10 ~~~~~~v~~~~~F~gi~~w~~~~~~k~~~e 39 (49)
T PF05545_consen 10 ARSIGTVLFFVFFIGIVIWAYRPRNKKRFE 39 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcccchhhHH
No 492
>PRK00843 egsA NAD(P)-dependent glycerol-1-phosphate dehydrogenase; Reviewed
Probab=32.25 E-value=2.8e+02 Score=29.94 Aligned_cols=96 Identities=7% Similarity=0.025 Sum_probs=61.2
Q ss_pred HHHHHHHHHcCC-eEEEEEEEcCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-
Q 003275 61 HAVADLVEYYGW-REVIAIFVDDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN- 138 (834)
Q Consensus 61 ~aia~ll~~~~W-~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~- 138 (834)
..+.++++.++. +++.+|.....+. ...+.+.+.+++.| .+... +..+.+.+.+...+.++++.++++||-.+.
T Consensus 22 ~~l~~~l~~~~~~~~~livtd~~~~~-~~~~~l~~~l~~~~-~~~~~--~~~~~t~~~v~~~~~~~~~~~~d~IIaiGGG 97 (350)
T PRK00843 22 DDIGDVCSDLKLTGRALIVTGPTTKK-IAGDRVEENLEDAG-DVEVV--IVDEATMEEVEKVEEKAKDVNAGFLIGVGGG 97 (350)
T ss_pred HHHHHHHHHhCCCCeEEEEECCcHHH-HHHHHHHHHHHhcC-CeeEE--eCCCCCHHHHHHHHHHhhccCCCEEEEeCCc
Confidence 446667777775 7887777554443 24567888888777 44322 333456678888889998888999886654
Q ss_pred -hhhHHHHHHHHHhCCCCCCCeEEEEeC
Q 003275 139 -PDTGLTIFSVAKSLGMTAGSYVWIATD 165 (834)
Q Consensus 139 -~~~~~~i~~~a~~~g~~~~~~vwi~~~ 165 (834)
.-|+..++. ...| ..++-|.|.
T Consensus 98 sv~D~ak~vA--~~rg---ip~I~IPTT 120 (350)
T PRK00843 98 KVIDVAKLAA--YRLG---IPFISVPTA 120 (350)
T ss_pred hHHHHHHHHH--HhcC---CCEEEeCCC
Confidence 446666553 2233 345666655
No 493
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=32.11 E-value=74 Score=25.54 Aligned_cols=40 Identities=25% Similarity=0.274 Sum_probs=32.5
Q ss_pred HHHHHHcCCeEEEEEEEcCCcccchHHHHHHHHhcCCcEEE
Q 003275 64 ADLVEYYGWREVIAIFVDDDYGRNGISVLGDALSKKRAKIS 104 (834)
Q Consensus 64 a~ll~~~~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g~~I~ 104 (834)
.++++.+ -++|.+.+++|.-|......+.+.+.+.|..+.
T Consensus 36 ~~~L~~~-~~~vii~~D~D~aG~~a~~~~~~~l~~~g~~~~ 75 (79)
T cd03364 36 AELLKRL-AKEVILAFDGDEAGQKAALRALELLLKLGLNVR 75 (79)
T ss_pred HHHHHhc-CCeEEEEECCCHHHHHHHHHHHHHHHHCCCeEE
Confidence 4455555 588988888888999999999999999988764
No 494
>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=32.08 E-value=5.6e+02 Score=26.10 Aligned_cols=25 Identities=20% Similarity=0.218 Sum_probs=20.9
Q ss_pred CCChhhHHHHHHhhccCCccEEecc
Q 003275 11 PQSSGIAHVISHVVNELNVPLLSFG 35 (834)
Q Consensus 11 p~~S~~~~~~~~~~~~~~vP~Is~~ 35 (834)
+.+......+++...+.+|+.|-.+
T Consensus 16 ~~~~~~k~~i~~~L~~~Gv~~iE~g 40 (259)
T cd07939 16 AFSREEKLAIARALDEAGVDEIEVG 40 (259)
T ss_pred CCCHHHHHHHHHHHHHcCCCEEEEe
Confidence 4677788899999999999999764
No 495
>PRK12595 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed
Probab=31.87 E-value=6e+02 Score=27.52 Aligned_cols=70 Identities=19% Similarity=0.270 Sum_probs=43.7
Q ss_pred CcEEEECCC---ChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEccCChHHHHHHHHHHHHHcCCeEEEEEE
Q 003275 4 EVVAAIGPQ---SSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIF 79 (834)
Q Consensus 4 ~V~aiiGp~---~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~ 79 (834)
+...|+||. +-.....++..+...+++++--++..| ...||=||-.+. .....+.++.+.+|-..++-+.
T Consensus 118 ~~~~iaGpc~iE~~~~~~~~A~~lk~~g~~~~r~~~~kp----Rtsp~~f~g~~~--e~l~~L~~~~~~~Gl~~~t~v~ 190 (360)
T PRK12595 118 NQSFIFGPCSVESYEQVEAVAKALKAKGLKLLRGGAFKP----RTSPYDFQGLGV--EGLKILKQVADEYGLAVISEIV 190 (360)
T ss_pred CeeeEEecccccCHHHHHHHHHHHHHcCCcEEEccccCC----CCCCccccCCCH--HHHHHHHHHHHHcCCCEEEeeC
Confidence 355688996 345566777777788899886433332 233555665553 4456677777778866655444
No 496
>PRK00865 glutamate racemase; Provisional
Probab=31.83 E-value=2.6e+02 Score=28.67 Aligned_cols=31 Identities=10% Similarity=0.188 Sum_probs=21.6
Q ss_pred CCcEEEECCCChhhHHHHHHhhccCCccEEe
Q 003275 3 NEVVAAIGPQSSGIAHVISHVVNELNVPLLS 33 (834)
Q Consensus 3 ~~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is 33 (834)
.++.+|+=+..+..+.++..+-+..++|+|.
T Consensus 66 ~g~d~iVIaCNTa~~~~l~~lr~~~~iPvig 96 (261)
T PRK00865 66 YGVKMLVIACNTASAVALPDLRERYDIPVVG 96 (261)
T ss_pred CCCCEEEEeCchHHHHHHHHHHHhCCCCEEe
Confidence 4566676666666666666676777888886
No 497
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=31.76 E-value=6.2e+02 Score=26.44 Aligned_cols=91 Identities=13% Similarity=0.132 Sum_probs=59.5
Q ss_pred CcEEEECCCChhhHHHHHHhhccCCccEEecccCCCCCCCCCCCceEEcc-----CC---hHHHHHHHHHHHHHc-----
Q 003275 4 EVVAAIGPQSSGIAHVISHVVNELNVPLLSFGATDPTLTSLQYPYFLRTT-----QS---DYYQMHAVADLVEYY----- 70 (834)
Q Consensus 4 ~V~aiiGp~~S~~~~~~~~~~~~~~vP~Is~~at~~~ls~~~~p~~~r~~-----ps---~~~q~~aia~ll~~~----- 70 (834)
-++-++||-..+....++.++.+.++=++..+.... ...-.||.|+. +. ....-.++.++.+.+
T Consensus 10 ~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d---~~~~~ffm~i~~~~~~~~~~~~~~l~~~l~~l~~~l~l~~~ 86 (289)
T PRK13010 10 YVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDD---DESGRFFMRVSFHAQSAEAASVDTFRQEFQPVAEKFDMQWA 86 (289)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHCCCCEEecccccc---cccCcEEEEEEEEcCCCCCCCHHHHHHHHHHHHHHhCCeEE
Confidence 378899999999999999999999988887554321 12225676722 22 233445566666655
Q ss_pred -----CCeEEEEEEEcCCcccchHHHHHHHHhcCC
Q 003275 71 -----GWREVIAIFVDDDYGRNGISVLGDALSKKR 100 (834)
Q Consensus 71 -----~W~~v~iI~~d~~~g~~~~~~l~~~l~~~g 100 (834)
..++++++.+-. | ...+++.++.++..
T Consensus 87 i~~~~~~~kiavl~Sg~--g-~nl~al~~~~~~~~ 118 (289)
T PRK13010 87 IHPDGQRPKVVIMVSKF--D-HCLNDLLYRWRMGE 118 (289)
T ss_pred EecCCCCeEEEEEEeCC--C-ccHHHHHHHHHCCC
Confidence 356777777654 2 34666777766553
No 498
>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=31.61 E-value=2.2e+02 Score=28.89 Aligned_cols=77 Identities=8% Similarity=-0.071 Sum_probs=49.9
Q ss_pred EEEEEE--cCCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhh---HHHHHHH
Q 003275 75 VIAIFV--DDDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVN-PDT---GLTIFSV 148 (834)
Q Consensus 75 v~iI~~--d~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~-~~~---~~~i~~~ 148 (834)
|++|.. ++.|....+..+.+++++.|..+..... ..+.+.....++.+...++|.+++... ..+ ....+.+
T Consensus 2 Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~i~~ 78 (273)
T cd06292 2 VGLLVPELSNPIFPAFAEAIEAALAQYGYTVLLCNT---YRGGVSEADYVEDLLARGVRGVVFISSLHADTHADHSHYER 78 (273)
T ss_pred EEEEeCCCcCchHHHHHHHHHHHHHHCCCEEEEEeC---CCChHHHHHHHHHHHHcCCCEEEEeCCCCCcccchhHHHHH
Confidence 455554 4667788889999999999988764322 223345567788888888998887542 222 2234555
Q ss_pred HHhCCC
Q 003275 149 AKSLGM 154 (834)
Q Consensus 149 a~~~g~ 154 (834)
+.+.|+
T Consensus 79 ~~~~~i 84 (273)
T cd06292 79 LAERGL 84 (273)
T ss_pred HHhCCC
Confidence 665554
No 499
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=31.57 E-value=2.1e+02 Score=30.29 Aligned_cols=78 Identities=5% Similarity=-0.015 Sum_probs=50.9
Q ss_pred eEEEEEEEc--CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHH
Q 003275 73 REVIAIFVD--DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSLLVGANLMESRVFVVHVNPDTGLTIFSVAK 150 (834)
Q Consensus 73 ~~v~iI~~d--~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~i~~~a~ 150 (834)
+.|+++..+ +.|.....+.+.++++++|..+..... ..+.......+..+...+.|.||+.... .....++.+.
T Consensus 64 ~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~~~~~~vdgiI~~~~~-~~~~~~~~l~ 139 (331)
T PRK14987 64 RAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAHY---GYKPEMEQERLESMLSWNIDGLILTERT-HTPRTLKMIE 139 (331)
T ss_pred CEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEecC---CCCHHHHHHHHHHHHhcCCCEEEEcCCC-CCHHHHHHHH
Confidence 477877754 567778889999999999988765321 1122333456677777889998886422 1234556666
Q ss_pred hCCC
Q 003275 151 SLGM 154 (834)
Q Consensus 151 ~~g~ 154 (834)
+.|+
T Consensus 140 ~~~i 143 (331)
T PRK14987 140 VAGI 143 (331)
T ss_pred hCCC
Confidence 6664
No 500
>PLN02428 lipoic acid synthase
Probab=31.56 E-value=3.4e+02 Score=29.14 Aligned_cols=115 Identities=16% Similarity=0.131 Sum_probs=0.0
Q ss_pred CCceEEccCChHHHHHHHHHHHHHcCCeEEEEEEEc----CCcccchHHHHHHHHhcCCcEEEeeecCCCCCChHHHHHH
Q 003275 46 YPYFLRTTQSDYYQMHAVADLVEYYGWREVIAIFVD----DDYGRNGISVLGDALSKKRAKISYKAPFSPGASRSAINSL 121 (834)
Q Consensus 46 ~p~~~r~~ps~~~q~~aia~ll~~~~W~~v~iI~~d----~~~g~~~~~~l~~~l~~~g~~I~~~~~~~~~~~~~~~~~~ 121 (834)
.++..+..+.+......+++.+...|.+.+.++..| .|.|......+.+++++....+......+....+ ...
T Consensus 121 v~~~~~p~~~d~~Ep~~vA~~v~~~Glk~vvltSg~rddl~D~ga~~~~elir~Ir~~~P~i~Ie~L~pdf~~d---~el 197 (349)
T PLN02428 121 VKTSRTPPPPDPDEPENVAEAIASWGVDYVVLTSVDRDDLPDGGSGHFAETVRRLKQLKPEILVEALVPDFRGD---LGA 197 (349)
T ss_pred CCCCCCCCCCChhhHHHHHHHHHHcCCCEEEEEEcCCCCCCcccHHHHHHHHHHHHHhCCCcEEEEeCccccCC---HHH
Q ss_pred HHHhhcCCceEEEEEeCh---------------hhHHHHHHHHHhC--CCCCCCeEEEE
Q 003275 122 LVGANLMESRVFVVHVNP---------------DTGLTIFSVAKSL--GMTAGSYVWIA 163 (834)
Q Consensus 122 l~~l~~~~~~vivl~~~~---------------~~~~~i~~~a~~~--g~~~~~~vwi~ 163 (834)
|..|++++++++-..... +....+++.|++. |+...-+..++
T Consensus 198 L~~L~eAG~d~i~hnlETv~rL~~~Ir~~~~sye~~Le~L~~ak~~~pGi~tkSg~MvG 256 (349)
T PLN02428 198 VETVATSGLDVFAHNIETVERLQRIVRDPRAGYKQSLDVLKHAKESKPGLLTKTSIMLG 256 (349)
T ss_pred HHHHHHcCCCEEccCccCcHHHHHHhcCCCCCHHHHHHHHHHHHHhCCCCeEEEeEEEe
Done!